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Jan 06 2014

One crank dies, another rises to take his place

The regulars here may recall John A. Davison, who died in 2012. He was notoriously persistent and repetitive, and rather clueless: he was the guy who started a blog with one article, never wrote another one, and just made new comments. He later announced that it was full, and so…he started a brand new blog, one article, and posted more comments to himself on it. It was rather sad.

Less well known is that he was actually a biologist, had a Ph.D. in zoology, and taught at the University of Vermont. He had a “scientific” theory, which was his, which he thought explained all that evolutionary change while refuting those silly scientists who believed that mutations occurred. No! Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species:

In 1940 Richard B. Goldschmidt [1940] presented the evidence that it is the chromosome, not the gene that is the unit of evolutionary change. While this was not then accepted by the evolutionary establishment, recent karyological studies fully support his perspective. The primary demonstrable differences that distinguish us from our closest primate relatives are revealed in the structure of our chromosomes. They consist of several reorganizations of homologous chromosome segments in the form of translocations, pericentric and paracentric inversions and a single fusion which result in the human complement of 46 chromosomes while the Chimpanzee, Gorilla and Orang each have 48 (Yunis and Prakash [1982]). The important point is that there is no evidence that such transformations involved in any way the introduction of species specific information into the genome. This is further reinforced by the demonstration that we are nearly identical at the DNA level with our close relatives. The simplest explanation is that the information was present in a latent state and simply revealed or derepressed when the chromosome segments were placed in a new configuration (Davison [1993]).

Yet when you read what he had to say about it, what was striking was the complete failure to read and understand the scientific literature — he had come up with his scientific theory, by God, and he didn’t have to address it critically, ever. All he had to do was go on blogs and internet forums and write the same pretentious catchphrases over and over again. And that was the saddest thing of all, that a mind could become so calcified and bitter and obsessed.

So he died, but you knew another had to emerge, and he has come. I was asked to look at a string of comments left on a science article by a fellow going by the pseudonym JVK, and all the Davison traits were there. Pretentious phrasing. Repetition: if the audience didn’t get it the first time, just say the same thing again, twice. A kind of sneering anger that people don’t understand how smart he is. An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong.

Behold James Vaughn Kohl.

Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species. The control of the differences in cell types occurs via the metabolism of the nutrients to chemical signals that control the physiology of reproduction.

These facts do not refute evolution; they simply refute the ridiculous theory of mutation-initiated natural selection that most people here were taught to believe is the theory of evolution.

That theory is far too ridiculous to be anything but a joke in the context of biological-based increasing organismal complexity. But here, we have lots of jokers, don’t we? The proof of ecological variation that appears to refute the theory of evolution, which actually refutes itself, is that ecological adaptations occur too fast for mutations to compete with them as a source of anything but diseases and disorders.

Basically what he’s saying in the first couple of sentences is that the environment induces variations in gene expression that are responsible for the differentiation of the various cell types. This is partly true; environmental influences certainly do contribute to cells developing in different directions. However, there are many examples of patterns that resist environmental influences, or in which maternal factors shelter the embryo from the environment. Fertilized human eggs, for instance, acquire polarity information when they implant in the uterus, but are largely insulated from temperature and nutrient stress.

Then there are other things that are just too narrow. Is alternative splicing the only mechanism to create variants in cells? No, of course not. External signals cause changes in the phosphorylation state of proteins in the cytoplasm, for example, that can affect metabolic activity; no alternative splicing involved. Signals can also switch on and switch off specific genes, again, no alternative splicing needed.

Then there are bits that are just plain weird. He gives the impression that what we eat dictates what signals we can generate. Do you get Sonic Hedgehog in your diet? No. It’s a protein synthesized by your cells.

The primary patterning elements in multicellular organisms are produced by networks of interacting genes; major body plan features might be initiated by environmental or maternal signals (which then begin a series of gene-regulated processes that produce the details), but the environment is primarily going to be an important modulator. Need I point out as well that what Kohl has described is a limited subset of the processes in development and that no one in their right mind thinks that development somehow refutes the contribution of other sources of variation to evolution? It was Van Valen who said in 1973 that “Evolution is the control of development by ecology…” That’s pretty much the mainstream view, so there’s nothing novel in what Kohl wrote.

Further, what he writes is a particularly pretentious, obfuscatory way of saying what he means — he’s trying to obscure rather than explain.

But then, that’s what he does. He crashes into a thread full of lay people and then lords it over them with his abuse of jargon. And he does it over and over again, and you can see the responses: most of the other commenters are more or less stunned, they don’t know how to deal with all the specific buzzwords he throws at them, and they have these doubts…maybe he’s saying something I should know about. No, he’s not. He’s babbling in scientese.

And he just keeps hammering away with his pseudo-scientific pronouncements.

Nutrient stress and social stress force organisms to adapt via seemingly futile cycles of protein biosynthesis and degradation that either result in amino acid substitutions that stabilize organism-level thermoregulation or the organism dies. It does not mutate into another species, which is why that cannot be explained to a high school freshman.

The point of this article was to show people that high school freshman have already been taught to believe in a ridiculous theory of mutation-initiated natural selection. Thus, they think everything that happens to DNA must be a mutation and there is plenty of extant literature that supports that idea. All of it is wrong in the context of ecological adaptations.

Based on Darwin’s ‘conditions of life’ ecological adaptations are nutrient-dependent and pheromone-controlled. The adaptations can be viewed as amino acid substitutions.

96 of them differentiate our cell types from those of most recent extinct ancestor.

He’s also obsessed with human pheromones. He has written a book, The Scent of Eros, about the physiological responses to pheromones — speaking of murky, difficult, ephemeral phenomena, I think the human dependence on pheromones is probably real, but only one tiny part of our behavioral repertoire, and almost certainly not a major influence on development. Kohl also sells a line of beauty products: for example, Scent of Eros With Musk Fragrance – Pheromones For Men To Attract Women.

Maybe he thinks belligerent pomposity is the way to attract the attention of investors from Axe.

822 comments

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  1. 1
    kevinalexander

    My theory, which is mine, is that life began in some yogourt that god had in the back of his fridge. At first he tried just scraping it off but we know that doesn’t work so he created more advanced green stuff (MAGS) to eat the less advanced green stuff (LAGS). Of course the MAGS tasted worse than the LAGS so he made EMAGS.
    And so on until he got to worms then republicans and I haven’t worked out the rest yet.

  2. 2
    raven

    I think the human dependence on pheromones is probably real,

    ?????

    Probably very minor.

    Humans have the same other olfactory system as other vertebrates. The vomeronasal system.

    It’s vestigal and apparently nonfunctional. The chemosensory receptors are mutationally wrecked and not connected to the brain by nerve tracts AFAIK.

  3. 3
    PZ Myers

    That’s why I continued with “but only one tiny part of our behavioral repertoire”, and linked to a site that gave a fuller explanation.

  4. 4
    twas brillig (stevem)

    Is he proposing “nano-evolution”, i.e. changes even smaller than micro-evolution, as the *real* mechanism for evolution? That “scientists” are distracted by micro-evolution, to see all the nano-details they are missing?

    Am I just over-simplifying him? I can’t keep track of his overuse of all those ‘big scientific words’ that he just keeps throwing around, over and over. <Monday morning>

  5. 5
    playonwords

    I’ve just looked at his biography – it’s errrrrr stunning
    He is certified with -
    American Society for Clinical Pathology (Medical laboratory scientist)
    American Medical Technologists (Medical technologist)

    and that’s it

    But wait! He has membership of
    American Society for Clinical Pathology
    American Society for Clinical Laboratory Science
    Society for Neuroscience
    Society for Behavioral Neuroendocrinology
    Association for Chemoreception Sciences
    Society for the Scientific Study of Sexuality
    International Society for Human Ethology

    But the killer is he is a member of a table – Mensa, the International high IQ society (and any organisation of intelligent people who make such a mistake in their acronym deserve all the ridicule they get)

    One more factor he sells pheremone sprays.

  6. 6
    dccarbene

    Um, what??
    Not clear how this “new” theory explains things like antibiotic resistance in bacteria, which can involve the appearance of novel proteins [enzymes] which can metabolize the drug – I don’t think that is epigenetic.
    And why bother with all that messy meiosis if it’s all epigenetic regulation?
    But wait – the proteins that run the epigenetics – are they not products of that stogy old genome? And don’t the proteins running the epigenetics change over time themselves? In what we might call – help me, I’m searching for the right word here – an evolutionary manner?
    Or am I completely misunderstanding the jargon?
    Probably not enough Monday morning pheromones. I don’t drink it, but is it possible that coffee is a pheromone for many humans?

  7. 7
    ttch

    I dunno. I think there may be something to this human pheromone business. I have an acquaintance, a guy in his late 60s, very overweight and frail and unkempt, and particularly negative when dealing with unwanted attention, and from time to time I’ve seen women just walk up to him and attempt to pick him up. (I have no reason to think they are prostitutes.)

    He is tall. Is that enough?

  8. 8
    raven

    wikipedia VMNO:

    Among studies that use microanatomical methods, there is no reported evidence that human beings have active sensory neurons like those in working vomeronasal systems of other animals.[21][43] Furthermore, there is no evidence to date that suggests there are nerve and axon connections between any existing sensory receptor cells that may be in the adult human VNO and the brain.[44] Likewise, there is no evidence for any accessory olfactory bulb in adult human beings,[45] and the key genes involved in VNO function in other mammals have pseudogeneized in human beings. Therefore while the presence of a structure in adult human beings is debated, a review of the scientific literature by Tristram Wyatt concluded, “most in the field… are sceptical about the likelihood of a functional VNO in adult human beings on current evidence.” [46]

    Referring to above, all mammals have a VNO system for detecting pheromones.

    It’s so important in humans that it is…vestigal, disconnected, and doesn’t seem to work any more.

  9. 9
    ekwhite

    Playonwords@5

    MENSA was originally founded as a “round table” for highly intelligent people to help solve the world’s problems. The table metaphor is intentional, and not a mistake. Of course, it has long since devolved into a society for egotistical libertarians who think they are never wrong because they scored well on an IQ test, but the original idea was good, if somewhat arrogant.

    PS: I admit the shameful secret that I used to be a member.

  10. 10
    Pteryxx

    dccarbene #6:

    Not clear how this “new” theory explains things like antibiotic resistance in bacteria, which can involve the appearance of novel proteins [enzymes] which can metabolize the drug – I don’t think that is epigenetic.

    It can’t, even if that mishmash of terms were coherent enough to present a theory. For one thing, most bacteria don’t even use alternative splicing or pre-mRNA – they just transcribe the gene directly from DNA to RNA and then to protein without tweaking.

    http://www.nature.com/scitable/topicpage/rna-splicing-introns-exons-and-spliceosome-12375

    For another, antibiotic resistance usually involves either mutations to an existing gene – which JVK seems to think can never be beneficial – or wholesale transfer of intact resistance genes from other bacteria, including genes from bacteria of different species that happened to die in the vicinity.

    http://www.tufts.edu/med/apua/about_issue/about_antibioticres.shtml

    And as far as ‘nutrient stress’ and mutations being only a source of diseases, when Lenski’s famous E. coli acquired the ability to metabolize citrate, they did it by means of a mutation potentiated by previous mutations.

    http://en.wikipedia.org/wiki/E._coli_long-term_evolution_experiment#Evolution_of_aerobic_citrate_usage_in_one_population

    Ecological adaptation occurs via the epigenetic effects of nutrients on alternative splicings of pre-mRNA which result in amino acid substitutions that differentiate all cell types of all individuals of all species.

    And that’s why feeding human babies on cow’s or goat’s milk causes them to grow horns and udders. Feeding them nothing but bamboo would make them grow up to be pandas.

    …What?

  11. 11
    ChasCPeterson

    The vomeronasal system. It’s vestigal and apparently nonfunctional.

    True, but some mammalian pheromones work through the olfactory system instead.

  12. 12
    Azuma Hazuki

    I do think epigenetics is an important and neglected (until recently) field of endeavour, but if anything, it’s a good thing epigenetic effects are so complex because they provide an explanation for much in the modern synthesis that has gone unexplained for far too long.

    Actually, I see the coming epigenetic revolution as the 21st century equivalent of discovering genetics in the first place. Darwin had only a lucky guess, but he had no mechanism to propose that would explain it; genetics was that mechanism. But biological reality is far too complex to be explained by “ein gene, ein protein, ein phenotype,” and while Lamarck was wrong about mechanism, he seems to have been right in that some acquired traits DO pass on to offspring.

    Nothing in plain genetics could explain this, but Lamarck failed to offer an explanation either. With epigenetics, we now understand that imprinting, silencing effects, gene expression, etc. can have sometimes drastic phenotypical effects even though the underlying DNA sequence is the same. In particular, this accounts for the ridiculous complexity of biological systems, which contain more information than the simple code itself and a laundry list of its resultant proteins, enzymes, etc. can account for.

    More and more, I am beginning to think that “human” is a verb, not a noun, and that all of us are a process connected to each other and all reality.

  13. 13
    unclefrogy

    I do not really know the details of the biology of pheromones in biology but I am aware that they are active even in some plants like African Acacia release chemicals to the atmosphere when they are attacked which they respond to. With many things about our biology it is difficult to study because our behavior is so influenced by our psychology, we seldom pay much attention to our body to such an extent that it can be said that we are completely disconnected from our body, nature.
    We do spend a tremendous amount of time and money of sent though so must be something there.
    I have to take PZ’s word on what this Genius is talking about because I do not have all day to work it out let alone to evaluate it.
    uncle frogy.

  14. 14
    unclefrogy

    spell check, scent
    uncle frogy

  15. 15
    James Kohl

    Thanks PZ. I was not aware that John A. Davison had also taken Dobzhansky’s (1964) approach, which first drew attention away from bird-watching and butterfly collecting in the context of morphological differences that were already known to be more closely associated with amino acid substitutions than with mutations and natural selection. Therefore, I am not surprised that you portray both of us as cranks, but wonder if you consider Dobzhansky to also be a crank.

    In case you do not consider Dobzhansky a crank, I suspect that would be because you actually read what he wrote in subsequent articles like: “Nothing in Biology Makes Any Sense Except in the Light of Evolution.” In fact, I’m willing to bet that you are still teaching that — like most uninformed biology teachers who have not yet realized that nothing about evolution makes sense in the absence of the conserved molecular mechanisms of amino acid substitutions.

    The conserved molecular mechanisms of ecological adaptations that result in amino acid substitutions are exemplified in my recent review — in case you would like to inform yourself and address the experimental evidence instead of providing only the personal insults that characterize the anonymous positions of fools everywhere.

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    See also: Physiology is rocking the foundations of evolutionary biology http://ep.physoc.org/content/early/2013/04/12/expphysiol.2012.071134.abstract

    You owe it to your “readership” to inform yourself

  16. 16
    Rich Woods

    Hmmm…

    like most uninformed biology teachers

    the anonymous positions of fools everywhere

    And:

    providing only the personal insults

    Oh dear.

  17. 17
    CaitieCat, getaway driver

    Yeah, if it talks like a crank and it cranks like a crank, I’ma go with provisionary classification as H. crankus, and head for the fridge for a beer.

    Thanks for the high-larity, though, PZed. And now with added bonus dollops of undiluted hokum*!

    * Hk, the ith element of the periodic table, in the Imaginides group. Atomic weight is i^3 x 10^4 kg/mol, making it among the densest bullshit ever.

  18. 18
    CaitieCat, getaway driver

    Aw, crap, borked my close tag on the em after i. :(

  19. 19
    gillt

    @#12: Azuma Hazuki:

    Actually, I see the coming epigenetic revolution as the 21st century equivalent of discovering genetics in the first place.

    I think the 21st century revolution you’re talking about is a technological one–from which epigenetics is benefiting–mainly in sequencing and driven by biomedicine. While epigenetcis is particularly suited to advances in sequencing the majority of the work and all of the innovation is in human disease etiology not evolution/ecology. Epigenetic inheritance isn’t something many evolutionary biologists have the tools or know-how to address, as evidenced by the lack of papers. We need to wait a few years or decades to see if epigenetics will cause some sort of paradigm shift in evolution, but I doubt it. I think it plays a role but likely something short of revolutionary.

  20. 20
    NitricAcid

    I once knew a brilliant chemist (taught at Waterloo, IIRC) who refused to shower because he thought natural pheremones would make him more attractive to women. He reeked like someone who had lived on the street all summer.

  21. 21
    Tony! The Queer Shoop

    Ooooh, the crank showed up!
    It’s popping popcorn time!

  22. 22
    Tony! The Queer Shoop

    NitricAcid:
    This is a derail, but I’m really curious: how long did the guy last without showering?

  23. 23
    Susannah

    ekwhite #9

    MENSA was originally founded as a “round table” for highly intelligent people to help solve the world’s problems. The table metaphor is intentional, and not a mistake.

    I think the original comment (playonwords #6) referred to another meaning of the word. In Spanish. I have often wondered why none of the smart people who came up with the acronym spoke such a common language.

    Mensa translates as “stupid female”.

  24. 24
    Inaji

    Susannah:

    Mensa translates as “stupid female”.

    :gigglesnort: Oh my. I had no idea. Now I’m extra glad I didn’t join when invited.

  25. 25
    Azuma Hazuki

    @15/James Kohl

    Why cannot evolution and molecular conservation co-exist? If anything, the epigenetic effects and amino conservations reinforce one another, since DNA itself is highly conserved.

    There is also still the endogenous retroviral record to contend with, the head-to-head fusion of ape chromosomes to create human chromosome 2, and so forth. And don’t forget that biology does not stand alone; the geological column and the fossil record also interact with it, and have their tales of eons to tell, as a backdrop to the zipping, zinging, nanosecond-scale interactions at the cellular level.

    Evolution via descent/mutation/selection is not falsified; all this means is that 1) much, much more information is stored in the environment — in Reality Itself — than in the strict sequence of DNA and the resultant proteins thereof, and 2) we now, finally, have an explanation for things that the older strictly-genes model couldn’t explain

  26. 26
    Tethys

    Oy. I read the provided links from Mr. Kohl, and now my brain hurts from reading a paper full of presupposational bullshit.

    Olfactory/pheromonal input is obviously important to the nutrient-dependent, hormone-organized and hormone-activated pheromone-controlled development of the invertebrate brain and behavior (Dickman, Kucharski, Maleszka, & Hurd, 2013; Lyko et al., 2010; Lyko & Maleszka, 2011). The claim that mammalian pheromones do not exist is an academically irresponsible misrepresentation. It is like saying that food odors do not exist for some species. If another species could think about such a claim, its answer to the question of whether food odors exist would probably be the same as its answer is to the question of whether pheromones exist. All organisms show us quite clearly that their survival is nutrient-dependent and that pheromones control their reproduction.

    Researchers, who deny the existence of pheromones in mammals, including the human pheromone-deniers, short-circuit interdisciplinary discussion of the nutrient-driven ecological epigenetics and the pheromone-controlled adaptive evolution of human behavior. For contrast, the honeybee has emerged as a model organism for understanding the epigenetic link from food odors and pheromones to neural networks of the mammalian brain, which ultimately determine human behavior (Kohl, 2012).

    How pitiful is it that he contradicts himself, and fail to provide any substantiation to his assertions.

    IANAB, but I do know that there is no such thing as pheromone controlled adaptive evolution of human behavior, and that you cannot extrapolate from invertebrates to humans.

    Unless we start to grow awesome antennae, Mr Kohl is telling us a just so story.

  27. 27
    Pteryxx

    Well, JK’s published material is just as much bodged word salad leavened with ego as his comments are.

    The epigenetic effects of nutrients on evolved differences in the diet and starch digestion of dogs and wolves (Axelsson et al., 2013) were detailed at the same time differences in the socialization of these subspecies were attributed to explorations involving only chemosensory input in 3 to 4-week-old wolf pups. For comparison, differences in starch digestion and exploration involving multisensory input in dogs begin a mere 2 weeks later (Lord, 2013). The differences in nutrient-dependent pheromone-controlled socialization, however, extend across a life-time of more aggressive behavior in wolves that have not been domesticated because less digested starch from their diet genetically predisposes infants to first respond to olfactory/pheromonal cues as they initially explore their postnatal environment.

    If only the differences between wolves and dogs were considered, it would be clear that mammalian pheromones exist, which may explain why they continue to be discussed in terms of olfactory/pheromonal control of adaptively evolved hormone-organized and hormone-activated behavior (Kohl, 2012). Indeed, mammalian pheromones are included in discussions that are essential in understanding the role of molecular epigenetics and the ecological epigenetics of nutrient-dependent pheromone-controlled reproduction in species from microbes to man. Furthermore, the concept of nutrient-dependent pheromone-controlled reproduction is important to neuroscientific progress. For example, it is essential for a better understanding of evolutionary endocrinology (Zafon, 2012) and its role in evolutionary medicine (Stearns, 2012).

    Take the first paragraph. Here’s what that first citation is actually about.

    Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves.

    And the second:

    The results suggest that wolves and dogs both develop olfaction by 2 wk, audition by 4 wk, and vision by 6 wk on average, despite the 2-wk shift in their ability to explore. This means that when wolves begin to explore at 2 wk, they are blind and deaf, and must rely primarily on their sense of smell. Thus, there is a significant alteration of how these subspecies experience their environment during the critical period of socialization. These findings lead to an alternative explanation for the difference in dogs’ and wolves’ abilities to form interspecies social attachments, such as those with humans.

    What’s missing is any connection between dogs’ ability to process starch and the timing of their explorations as pups. There’s a difference in their capacity to handle starch, there’s a difference in their early exploring behavior, therefore nutrients cause the behavior difference! Also epigenetics, because the nutrients had to cause the behavior by a mechanism! (No citation for the claim that dogs’ starch-processing even kicks in at the same time as their explorations as pups, unless it’s somewhere in the full-text cited articles. Did the pups in the behavior study even get exposed to any starch?)

  28. 28
    James Kohl

    Thanks for first reading the paper Tethys before commenting.

    You seem to have missed the fact that “From Fertilization to Adult Sexual Behavior” (1996) — with its details about the molecular epigenetics of cell type differences was extended to invertebrates in “Organizational and activational effects of hormones on insect behavior” (2000), and to their life history transitions in “Honey bees as a model for understanding mechanisms of life history transitions” (2005).

    Besides the honeybee, I gave several example from other model organisms that show the molecular mechanisms of cell type differentiation clearly extend across species via evidence of amino acid substitutions. Do you typically have difficulty comprehending what you read, or does the problem occur only when it refutes what you’ve been taught to believe about the differences between molecular mechanisms of ecological adaptation in invertebrates and vertebrates? What type of substantiation for my claims did you expect? Why aren’t examples across species acceptable as they would be if we were discussing experimental evidence that supports species mutating into other species?

    Why do you participate anonymously?

  29. 29
    Nerd of Redhead, Dances OM Trolls

    Why do you participate anonymously?

    Too many cranks out there who try personal revenge. Otherwise, your question is irrelevant.

  30. 30
    James Kohl

    Pteryxx, thanks. You seem unable to grasp the fact that the wolf – dog example was presented in the context of a model.

    Extracting it from the model may be tactical, or it may just indicate your inability to grasp the basic principles of biology and levels of biological organization required to link sensory cause to hormones and their affects on behavior.

    Are you familiar with the Society for Integrative and Comparative Biology that I mentioned at the beginning of the article? Or, like others, do you think that no integration is required, since you are comfortable with the idea of mutation-initiated natural selection?

  31. 31
    James Kohl

    @25 Azuma Hazuki

    Why not simple read my paper to see why it is titled: Nutrient-dependent pheromone-controlled adaptive evolution: a model.

    You asked: Why cannot evolution and molecular conservation co-exist?

    Thank you for your non-anonymous contribution, but I actually prefer the contributions of anonymous participants who have read the paper. At least others can then see they are not able to understand what is currently known no matter how it is presented.

  32. 32
    chigau (違う)

    Mensa?
    本当か?

  33. 33
    Tony! The Queer Shoop

    James Kohl:

    Why do you participate anonymously?

    That’s none of your business.
    The reasons people choose to remain anonymous are their own and no one has to answer to you.

    Here are some reasons people choose to remain anonymous online:

    Many people don’t want the things they say online to be connected with their offline identities. They may be concerned about political or economic retribution harassment or even threats to their lives. Whistleblowers report news that companies and governments would prefer to suppress; human rights workers struggle against repressive governments; parents try to create a safe way for children to explore; victims of domestic violence attempt to rebuild their lives where abusers cannot follow.

    Instead of using their true names to communicate these people choose to speak using pseudonyms (assumed names) or anonymously (no name at all). For these individuals and the organizations that support them secure anonymity is critical. It may literally save lives.

    https://www.eff.org/issues/anonymity

    Any other research you want others to do for you?

  34. 34
    chigau (違う)

    Tony!
    Never mind.
    James Kohl is posting here anonymously.
    The link in his nym, like the link in my nym, leads right back here.

  35. 35
    James Kohl

    @33 Tony! The Queer Shoop!

    Thanks. It’s always seemed to me to be a way to make ridiculous comments about works by others without being responsible for the consequences of making ridiculous comments. But, of course it would seem that way to me, since I do not participate anonymously. Perhaps I should be more concerned about offending anonymous others, and I might be — if I knew who they were. Indeed, some of them might actually be able to support their ridiculous opinions with experimentally established facts. But I’ve seen nothing that indicates that. Just more nonsense!

  36. 36
    Tony! The Queer Shoop

    James Kohl:

    Perhaps I should be more concerned about offending anonymous others, and I might be — if I knew who they were.

    That’s odd.
    Empathy and compassion are enough for me to make efforts to not offend others.

  37. 37
    Tony! The Queer Shoop

    James Kohl:

    Incidentally, when an individual makes an argument or expresses their opinion online, the strength of their position does not rest on whether or not they are posting anonymously.

  38. 38
    Inaji

    James Kohl:

    Perhaps I should be more concerned about offending anonymous others, and I might be — if I knew who they were.

    Well, there’s your problem, right there. You’re busy othering people on an absurd basis so you can ignore all the actual arguments they have made, which you obviously cannot refute. Tsk.

  39. 39
    ChasCPeterson

    I gave Mr. Kohl’s review paper in the journal Socioaffective Neuroscience & Psychology a quick read-through. (Background: I am a Ph.D. comparative physiologist and a 25+-year member of the Society for Integrative and Comparative Biology, since back when it was still the American Society of Zoologists). I found it almost entirely opaque.

    example sentence:

    Arguably, these newer and historically less well-defined terms help some researchers to cautiously avoid any connection from the stereotypical effects of insect pheromones on hormones and behavior to their adaptively evolved epigenetic effects on what appears to be hormone-organized neurogenetically controlled neurogenic niche construction in the human hypothalamus.

    oh, OK, just one more:

    Random mutations that somehow cause one or more amino acid substitutions are not likely to simultaneously cause adaptive evolution from the bottom up via the thermodynamics of chromatin remodeling and control of adaptive evolution from the top down via organism-level thermoregulation. However the nutrient-dependent substitution of alanine for valine appears to result in species-specific organism-level changes in skin, glands, and hair, through pheromone-controlled reproduction.

    wut

    The ‘model’ presented (illustrated by this impressively complex but unexplained flowchart) apparently aims to synthesize findings from honeybees and rodents and apply them to humans, but to the extent that I was able to discern any logical path at all, all or most of the important connections are simply asserted without support or supported solely by self-citation. The term ‘epigenetic’ is used at every perceived opportunity. Much is made of amino-acid substitutions without ever specifying what kind of protein we’re talking about. And what the nutrition-pheromone-hormone-reproduction business is supposed to have to do with ‘adaptive evolution’ in general is puzzling. (Mr. Kohl seems to think that Pavlovian clasical conditioning is an example of adaptive evolution, though, and he also seems to think that evolution by natural selection is a ridiculous story that nobody takes seriously any more, so I suspect the confusion is built in.) It’s a huge mess, and the journal (too new to even have an impact factor) ought to be thoroughly embarrassed about it.

    Some insight into Mr. Kohl’s thinking could probably be gleaned from his many posts at his dot-com chemical-sex-appeal-peddling website. I poked around for just a couple of minutes and learned that he has a Galileo complex and is actually some variety of creationist.

    In short, all indicators point to Crank.

    [By the way, some actual biologists are now questioning the existence of classical pheromones in mammals generally, let alone humans.]

  40. 40
    Inaji

    James Kohl! Please address every one of Mr. Peterson’s points in post #39, as he is a real person, as you can see, and not an anonymous non-person.

  41. 41
    Tethys

    Indeed, some of them might actually be able to support their ridiculous opinions with experimentally established facts

    Stop doing science wrong. Your paper is nothing but ridiculous opinion, and unsupported conclusions, as already noted by myself and Pteryxx.

    Pheromones in sex and reproduction: Do they have a role in humans?

    Pheromones are found throughout the living world and are a primal form of communication. These chemical messengers are transported outside the body and have a direct developmental effect on hormone levels and/or behaviour. This review article aims to highlight the role of human pheromones in sex and reproduction. A review of published articles was carried out, using PubMed, medical subject heading (MSH) databases and the Scopus engine. Key words used to assess exposure, outcome, and estimates for the concerned associations, were; olfaction; sex; pheromones; libido; behaviour; reproduction; humans; and smell. Although there are studies to support this phenomenon, they are weak because they were not controlled; others have proposed that human olfactory communication is able to perceive certain pheromones that may play a role in behavioural as well as reproductive biology. Unfolding the mysteries of smells and the way they are perceived requires more time and effort as humans are not systems that instinctively fall into a behaviour in response to an odour, they are thinking individuals that exercise judgment and subjected to different motivations.

    I do not deny that bees and many invertebrates use pheromones because it is well documented, AND they have body structures that are extremely specialized for the task. In contrast, some humans have no sense of smell at all yet they are quite capable of finding a mate. This simple fact tells me that humans rely much more on visual and social cues than they do on pheromones to find a mate.

    As far as posting anonymously, that question is only ever asked by bullies who have no factual basis for their opinions and whiny MRAs.

  42. 42
    James Kohl

    @10 Pteryxx

    Mutations cannot be beneficial because they perturb intercellular signaling and are eliminated if their effects are too deleterious. They can be maintained, but not fixed, in the organized genome of an organism only if they do not have deleterious effects on protein folding that is required for cell survival. They cannot be naturally selected because they are never permanently fixed in the organized genome.

    What are you unable to realize that antibiotic resistance is a function of nutrient-dependent thermodynamic changes that enable organism-level thermoregulation? Did you ever hear about anyone who died from an infection because the killer organism had learned to live with the heat that killed the patient?

    I always felt sorry for those who died from evolutionary theorist’s ideas about cause and effect. Unfortunately, I was not always able to correctly identify an organism and enable its treatment with an appropriate antibiotic. This was done based on the organism’s nutrient use in the context of antibiotics that might otherwise have killed all but a few of the organism’s conspecifics. As you may know, the survivors might kill the patient the next time around — not because they mutated into another species, but because nutrient-dependent amino acid substitutions enhanced their thermodynamic stability.

    It is the nutrient-dependent amino acid substitutions that could be blamed for patient deaths that occur because evolutionary theorists don’t understand anything about antibiotic resistance. Fortunately, theorists cannot be blamed for the deaths of others due to their ignorance or there would be no biology teachers left to teach their theories.

  43. 43
    Nerd of Redhead, Dances OM Trolls

    James Kohl! Please address every one of Mr. Peterson’s points in post #39, as he is a real person, as you can see, and not an anonymous non-person.

    Exactly JK. And citing work where you aren’t the author would be a plus, especially if it backs up your claims unlike the one source refuted above. Otherwise, you become nothing but self-referential, a sure sign of a Crank.

  44. 44
    CaitieCat, getaway driver

    But Nerd, Nerd, Galileo QED! All superbrilliant supervillains superscientists are completely underappreciated in their own time, that’s what makes them become supervillains.

    Oh, crap. Has anyone called Squidman and given him the high sign to watch this guy from his satellite base, the Mollusc of Inky Justice?

  45. 45
    James Kohl

    @39 ChasCPeterson,

    Thanks. The abstracts from this year’s SICB meeting include almost the same number of mentions of “mutations” and “amino acids” with a few that mention “natural selection.”

    Since last year, there have been 10-20 more papers published that clearly link amino acid substitutions to differences in cell types in individuals of different species, as I did in my review. However, in 395 pages of abstracts it appears that there is no common thread and no model of biologically-based cause and effect that explains how ecological variation results in species diversity.

    The common thread is obviously the organism level thermodynamic stability that is established by different amino acid substitutions with increasing organismal complexity in different ecological, social, neurogenic and socio-cognitive niches. For example, the substitution of achiral glycine in the GnRH molecule appears to have stabilized all other aspects of vertebrate species diversification during what appears to be the past 400 million years. That’s why GnRH is the central focus of my mammalian model.

    I hope you will comment on Kondrashov (2012) “One of the main duplicated gene families are the olfactory receptor proteins [18,117–119] so perhaps their duplication may lead to an increase in sensitivity to a particular odour may be adaptive under certain conditions.” http://rspb.royalsocietypublishing.org/content/early/2012/09/05/rspb.2012.1108.abstract

    Others can then compare your level of expertise to that of someone else who is more familiar with biologically based cause and effect across species from microbes to man. PZ Myers could also comment on the Black Queen vs the Red Queen discourse, but seems unlikely to do so. If there is some experimental evidence that you think supports the idea of mutation-driven evolution, we could compare it to what I have detailed in my model, and what is experimentally supported by across species evidence of epigenetic cause and effect via de novo creation of olfactory receptor genes.

  46. 46
    James Kohl

    The ‘model’ I detailed in the text of my published work is supported by what is known about
    “Signaling Crosstalk: Integrating Nutrient Availability and Sex”
    http://stke.sciencemag.org/cgi/content/abstract/sigtrans;6/291/pe28

    in unicellular yeasts and

    “Feedback loops link odor and pheromone signaling with reproduction”
    http://www.ncbi.nlm.nih.gov/pubmed/16290036

    in mammals.

    If ChasRPeterson is the cardiologist I found via a google search, he evidently does not realize that my model extends to the role of amino acid substitutions in the cell wall of atherosclerotic arteries. If he is not a cardiologist, that probably doesn’t matter to him because he has expertise in other areas of integrative and comparative biology.

  47. 47
    Nerd of Redhead, Dances OM Trolls

    If ChasRPeterson is the cardiologist I found via a google search,

    Why the fuck do you need to know who your critics are. It is up to you to provide the evidence to satisfy your critics. Not criticize them in any fashion. Where did you learn to do science? (speaking as a 35+ year practitioner of science).

  48. 48
    Nerd of Redhead, Dances OM Trolls

    Others can then compare your level of expertise to that of someone else who is more familiar with biologically based cause and effect across species from microbes to man.

    And your expertise *snicker* is shown where? NOT IN YOUR THEORY.

  49. 49
    James Kohl

    @48 Nerd of Redhead, Dances OM Trolls

    It’s a model, not a theory. For comparison, mutation-driven evolution is a theory with no model of biologically based cause and effect in any species.

    The ability to model cause and effect across species is evidence of my expertise.

    Those who are not cardiologists may be interested in extension of my model to cell types of different cancers and neurodegenerative diseases, if they are not concerned about atherosclerosis.

  50. 50
    dmgregory

    James Kohl wrote: (@42)

    Mutations cannot be beneficial because they perturb intercellular signaling and are eliminated if their effects are too deleterious. They can be maintained, but not fixed, in the organized genome of an organism only if they do not have deleterious effects on protein folding that is required for cell survival. They cannot be naturally selected because they are never permanently fixed in the organized genome

    In light of this revelation, please explain the results of the E. coli long-term evolution experiment led by Richard Lenski. (Credit to Pteryxx for noting the relevance of this result earlier in the thread @10)

    To summarize, one of the experimental strains developed an adaptation that allowed it to grow on citrate under oxygen-rich conditions. This is beneficial in the sense that it allowed this experimental strain to reach dramatically greater population sizes under the experimental conditions. Genome sequencing identified multiple genetic mutations responsible for this adaptation.

    If genetic mutations cannot be beneficial and cannot be naturally selected for, as you claim, how are we to account for this observation of multiple beneficial genetic mutations becoming dominant in a population?

  51. 51
    stripeycat

    Clear case for Proof by Contradiction:
    NOOoo!

    IOW, support your goddamn assertions, mister.

  52. 52
    Tony! The Queer Shoop

    Nerd:
    Thanks to Chas’ links @39:

    James Vaughn Kohl was the first to accurately conceptualize human pheromones, and he began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones.

    ****

    James Kohl:
    From the Table of Contents at Pheromones.com:

    The Scent of Eros product line is a product line that is supported by substantiated claims and research results, which are now being replicated through independent studies.

    Other commercial interests in the concept of human pheromones have led to blatantly inaccurate claims that have no scientific support, and thus must rely on links to mass media ‘news’ reports. The “sixth sense” and any indication that human pheromones activate the non-functional human vomeronasal organ (VNO) are red flags. Current scientific information has shown that the VNO/sixth sense approach to human pheromones is merely a marketing ploy.

    Need more information on pheromones and their effects? Please review the various articles below to learn more about the science behind of pheromones and to find quality human pheromone-enhanced products supported by a money back guarantee.

    Why are there no links to the substantiated claims and research that have been done? You make several claims about pheromones, but I cannot seem to find the evidence to support your claim.

    In and of itself, that would be bad enough.
    But no, you direct potential buyers to the “various articles below” to learn of the science behind pheromones. No mention of *which* article to read, and that would be incredibly helpful when trying to decide which of your many, many articles one should read (I gave up counting after 81; I’m sure there was 2-3 times more than that). In trying to figure out which of these links would provide the evidence to substantiate your claims, I decided to look for article titles with the word “pheromone”. One doesn’t find that until the 14th entry, pheromones and longevity in worms (and flies). I clicked the entry and found several links to a bunch of articles. I thought perhaps this might prove fruitful, but then I stopped.

    What was I looking for again?
    I had forgotten due to the sheer amount of links to articles. I’d gotten a bit daunted seeing hundreds of articles and having no clue where to start. You really should work on that. Other people might give up and just assume your claims are true and buy your product.

    Anyway, I had to remind myself of what you said:

    Human Pheromones enhance desire; they do not create it!

    Like adding spice to your favorite food, human pheromone-enhanced products increase your natural appeal. Marketing claims that guarantee you will get more sex are unscientific and unrealistic. If you are unappealing, human pheromones cannot magically make you appealing. However, human pheromones work because nearly everyone is somewhat appealing, and human pheromones enhance your natural appeal.

    Established in 1996, when human pheromone research was in its infancy, this site serves as a comprehensive information resource for general and for scientific knowledge. No other domain provides you with all the latest information about human pheromones.

    Since 2001, this site has also contained links to Scent of Eros pheromone-enhanced products as well as other similar products:
    http://pheromones.com/table-contents/

    (bolding mine)
    Ok, so now that I’ve refreshed my memory, back to work. I decided to go as far back as I could. In this case, an article dated 2/20/2010. There is no evidence to found here.
    Ah, the 2nd, 3rd, 4th, 5th, 8th and 9th articles all have “pheromones” in the title, so maybe one of those will have the evidence to support your claim.
    Perhaps you can help me. Which of these, if any, provides the substantiated claims and research results you mention?

  53. 53
    James Kohl

    @52 Tony! The Queer Shoop!
    Nutrient-dependent/pheromone-controlled adaptive evolution: a model
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

  54. 54
    Jimmy Carr

    Tethys @#41:

    “I do not deny that bees and many invertebrates use pheromones because it is well documented, AND they have body structures that are extremely specialized for the task. In contrast, some humans have no sense of smell at all yet they are quite capable of finding a mate. This simple fact tells me that humans rely much more on visual and social cues than they do on pheromones to find a mate.”

    Could your argument not also be written thusly:

    “Some humans have no sense of vision at all yet they are quite capable of finding a mate. This simple fact tells me that humans rely much more on audio and social cues than they do on vision to find a mate.”

    My point being, your extrapolation of the argument is flawed, as it changes one arm of the argument (sense of smell) and declares that this necessarily leads to a conclusion concerning another arm of the argument (sense of vision). Simply: why does the fact that a person (and a person merely conjured up by yourself, at that) with no sense of smell can find a mate infer that “humans rely much more on visual and social cues than they do on pheromones to find a mate”?

    You have much work ahead of you to bring your argument into line, I’m afraid.

  55. 55
    Tethys

    Tsk, tsk James Kohl. Your model is not proof of your model. Your model is a compleat mess of scientific gobbledegook and has a whopping lie in it where you claim no conflict of interest.

    You have as much scientific integrity as the Burzynski clinic.

  56. 56
    Tethys

    My link discussed anosmia at length, perhaps you should go back and reread it?

  57. 57
    Tony! The Queer Shoop

    James Kohl:

    Conclusion

    Nutrient-dependent pheromone-controlled reproduction underlies what is common (Locasale, 2012) to all models of natural selection, sexual selection, and species diversity (Frady, Palmer, & Kristan, 2012). Animal models are often used to model human physical and mental disorders. The honeybee already serves as a model organism for studying human immunity, disease resistance, allergic reaction, circadian rhythms, antibiotic resistance, the development of the brain and behavior, mental health, longevity, diseases of the X chromosome, learning and memory, as well as conditioned responses to sensory stimuli (Kohl, 2012).

    The mammalian model (Diamond et al., 1996) detailed here allows what we have learned from the study of invertebrates (Elekonich & Roberts, 2005; Elekonich & Robinson, 2000) to be used in attempts to understand the development of human behavior and in attempts to understand human physical disease. Those who adopted the position that mammalian pheromones do not exist, or who continue to insist that human pheromones do not exist, have for more than two decades made it seem that there was something ‘fishy’ or ‘funny’ about this model. For comparison to their claims, this model of systems biology exemplifies experimental results. For instance, ‘our experiments suggest that excitatory odor responses are transiently suppressed (in terms of overall firing rates), but more complex temporal shaping of responses may occur because of interplay of intrinsic properties, sensory drive, and the feedback activity’ (Markopoulos, Rokni, Gire, & Murthy, 2012, p. 1186). In context, this was suggested in ‘Feedback loops link odor and pheromone signaling with reproduction’ (Boehm, Zou, & Buck, 2005).

    If this genes-to-behavior-and-back model of systems biology is correct, it shows what has gone missing from cause and effect in the context of adaptive evolution of the human brain and behavior. What is missing is the complex interplay of intrinsic properties, sensory drive, and the feedback activity, which requires the acknowledgement that mammalian pheromones, including human pheromones, obviously exist. That fact should be as obvious as the fact that the ecological epigenetics of food odors exist.

    Assuming the conclusion is true, what does that have to do with the efficacy of the pheromone enhancement product you’re shilling for?
    My question wasn’t is there evidence that mammalian pheromones exist?.
    My question was where is the evidence to support the claims of the pheromone enhancing product?

  58. 58
    Jimmy Carr

    @#56, Tethys: who was this comment aimed at? Please read the rules:

    “VI. Courtesies:

    If you are replying to a specific comment, use the comment number and poster’s name.”

  59. 59
    chigau (違う)

    How close is the link between Jimmy Carr and James Kohl?
    both of them commenting anonymously?

  60. 60
    Nerd of Redhead, Dances OM Trolls

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    Self-referential. Obviously a paper from a CRANK. Cite people other than yourself, or shut the fuck up.

  61. 61
    Nerd of Redhead, Dances OM Trolls

    both of them commenting anonymously?

    Oh, an maybe sockpuppetly?

  62. 62
    Tony! The Queer Shoop

    Jimmy Carr:
    That’s a courtesy. Not a rule.
    I thought it was fairly obvious Tethys was replying to you.

  63. 63
    James Kohl

    @50 dmgregory

    Thanks for asking.

    For 25 years, Lenski has continued to provide experimental evidence of nutrient-dependent copy number variation of genes and nutrient dependent pheromone-controlled differentiation of cell types via amino acid substitutions. There is a model for that! But 25 years ago, Lenski decided the organisms were mutating, and his story hasn’t changed. Why would it? Most people believe it; tell it; and teach it to others. You’ve seen here what happens when someone challenges their nonsensical misrepresentation. If Lenski says they’re mutating, they’re mutating! He’s an expert, right?

    You get points for mentioning “…grow on citrate under oxygen-rich conditions…” since the oxygen-rich conditions tie into the 1181 hemoglobinopathies attributed to mutations in humans, which would be reported as adaptations in every other organism on the planet. The adaptations are why we calibrate blood gas analyzers with measurements of barometric pressure to account for altitude above sea level.

    Ecological adaptations enable survival in ecological niches that vary slightly, or with the major changes in parasite prevalence between Hemoglobin S and Hemoglobin A. What we see in the lab, however, with sickled cells is not mutated cells. We see cells that are not adapted. For comparison, what we see in sickle-cell trait and the thallasemias are cells that have adapted.

    Note: In my model, no mutated cells were harmed, or even mentioned in the context of ecological adaptations because mutations are not beneficial.

  64. 64
    Nerd of Redhead, Dances OM Trolls

    If Lenski says they’re mutating, they’re mutating! He’s an expert, right?

    And YOUR paper refuting his evidence with evidence, not just claims, of your own is found where? No evidence by you, Lenski’s claims stand. Welcome to real science, not your fiction of science.

  65. 65
    Tethys

    James Carr

    My 56 was aimed at you clearly. Did you read the link from my previous comment that you quoted from?

    Could your argument not also be written thusly:

    “Some humans have no sense of vision at all yet they are quite capable of finding a mate. This simple fact tells me that humans rely much more on audio and social cues than they do on vision to find a mate.”

    No, because the point is that insects have antennae (highly specialized structures) which detect pheromones.
    Human have no such structures, and the relevent anatomy used by other mammals is vestigial in humans, and does not connect to the brain, so on that basis alone it can be dismissed as having any major role in human mate selection and reproduction.

    Just because some humans are blind does not negate the fact that most people are first attracted to someone based on what they look like, not on how they smell.

  66. 66
    Nerd of Redhead, Dances OM Trolls

    Note: In my model, no mutated cells were harmed, or even mentioned in the context of ecological adaptations because mutations are not beneficial.

    Your model isn’t evidence. It is an inane hypothesis that must be backed by third party evidence, not your self-referential bullshit.

  67. 67
    James Kohl

    @ 60 Nerd of Redhead, Dances OM Trolls

    Control yourself, you idiot! I already provided links to papers that are not self-referential.

    1)“Signaling Crosstalk: Integrating Nutrient Availability and Sex”
    http://stke.sciencemag.org/cgi/content/abstract/sigtrans;6/291/pe28

    2) “Feedback loops link odor and pheromone signaling with reproduction”
    http://www.ncbi.nlm.nih.gov/pubmed/16290036

    Obviously, there is no point in my continued responses to fools. If PZ wants to address any of the real issues he has with my model, now is the time to do so. If others read the paper and ask questions I will try to answer them, but quite frankly there appears to be limited intelligence here, which makes mutation-driven evolution so appealing as to be accepted without any experimental evidence, makes the challenges presented to me simple-minded and ridiculous.

  68. 68
    chigau (違う)

    James Kohl (if that’s your real name)
    What do you ‘think’ about Medicine Wheels?

  69. 69
    dmgregory

    James Kohl @63

    For 25 years, Lenski has continued to provide experimental evidence of nutrient-dependent copy number variation of genes and nutrient dependent pheromone-controlled differentiation of cell types via amino acid substitutions.

    So, am I understanding your claim to be that the nutrient environment (prevalence of citrate and oxygen, or some other marker of the experimental conditions) triggered the observed change in the bacteria’s genotype in a non-random fashion, and that this change should not be considered a mutation?

    If this is the case, please explain why the other 11 experimental populations, raised on the same nutrient base, did not develop this novel genetic trait. It would appear that some causal factor other than nutrient environment is needed to account for this result.

  70. 70
    Tethys

    I read the latest links provided by James Kohl. #1 the model organism is yeast #2 mice

    Neither of them applies to humans.

    Poor James doesn’t like playing with us though, and he is going to take his ball and go home.

  71. 71
    Nerd of Redhead, Dances OM Trolls

    Poor James doesn’t like playing with us though, and he is going to take his ball and go home.

    Well he should. I was a young scientist during the

    http://en.wikipedia.org/wiki/Cold_fusion

    debacle. I expect the same from James as I expected from Pons and Fleischmann. Third party evidence corroborating their hypothesis, showing both the expected excess heat and neutrons in the right proportions. Conclusive experimental evidence. Never happened.
    James needs to stop citing himself, and go to third party evidence to show his ideas are even being considered by other scientists. I bet they are all laughing at his pathological ideas.

  72. 72
    Tony! The Queer Shoop

    Oh boy. A search for James Kohl turns up page after page of “buy this Eros product”. I did find some comments by Mr. Kohl over at Sandwalk.
    Here’s a response Mr. Kohl gave to a commenter implying that he was a snakeoil salesman:

    I get that a lot, too. Let’s compare it to selling a snake-centric approach to predation-driven evolution of the human brain.

    “Isbell calls these findings “the first neuroscientific support” for her snake-centric evolutionary theory.” excerpted from http://news.sciencemag.org/evolution/2013/10/did-snakes-help-build-primate-brain

    Q: What happens when thousands of imbecilic academics accept mutation-driven evolution, without questioning how it happens in moths via bird predation, or in any other species?
    A: The academic imbeciles must attack anyone who offers others an explanation of cause and effect that cannot be refuted, having already been supported by experimental evidence from every species on the planet.

    Do you think by any chance that you are an academic imbecile supported by government funding for non-exemplary work with no meaningful value to scientific pursuits whatsoever?

    this one is interesting (a response to John Harshman):

    Excerpted from “Mutation-Driven Evolution” (THE BOOK)
    “…natural selection is an evolutionary process initiated by mutation.” p 196.

    There has never been any experimental evidence to support that concept. Thus, every biologist you know may be incapable of thinking clearly and differentiating between theory and experimentally established scientific facts. But I am not accusing them of being stupid; just gullible.

    I’m not going to spend time explaining copy number variations and how alleles arise via experience dependent epigenetic effects, because you are gullible, rude, and have ignored the information in the links I have already provided that clearly states that natural selection is being removed from the theory of mutation-driven evolution because there has never been any evidence to suggest that natural selection occurs. But if you inform yourself by reading the article excerpted below and then ask pertinent questions, I may have time to waste on you in hopes that I will benefit others.

    Crank indeed.
    As is the case here, JVK has made various assertions but failed to supply the evidence in support of them.
    Oh, and I loved this response from Larry Moran.

  73. 73
    Tony! The Queer Shoop

    James Kohl:

    If others read the paper and ask questions I will try to answer them, but quite frankly there appears to be limited intelligence here, which makes mutation-driven evolution so appealing as to be accepted without any experimental evidence, makes the challenges presented to me simple-minded and ridiculous.

    ::sob, sob; wipes away tears::
    What will I do without your proclamations of intellectual superiority over everyone else?

  74. 74
    dWhisper

    See, now I read that part at the end as “Scent of Elon Musk” and was thinking that might be amazingly effective. I know I’d have to stop and think about it for a minute upon smelling…

  75. 75
    gillt

    James Kohl,

    What is pheromone-controlled adaptive evolution, and what makes you confident it supplants whatever you think it supplants (e.g., mutation-driven evolution, modern synthesis, molecular evolution, natural selection, genetic drift, the academic industrial complex etc.)?

    Be a good sport and describe this two part question in language 10 year olds would understand–10 year olds who throw tantrums when you don’t give us lots and lots of evidence.

    Remember, 10 year olds and evidence!

  76. 76
    James Kohl

    @69 dmgregory

    “It would appear that some causal factor other than nutrient environment is needed to account for this result.”

    The pheromone-controlled physiology of reproduction accounts for the result. That’s why in my model ecological adaptations are nutrient-dependent and pheromone-controlled.

    What has Lenski proposed is the alternative explanation of why mutations only sometimes occur? If they randomly occur, how are they selected. What is selected? Why doesn’t anyone else ask questions like those of Lenski? Why does it seem like PZ Myers is not aware of the Black Queen Hypothesis or is it simply too difficult to explain genes gained by mutations and genes lost by mutations in any context of evolution whatsoever?

    The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss
    http://mbio.asm.org/content/3/2/e00036-12.abstract

  77. 77
    James Kohl

    @75 Gilt

    “Remember, 10 year olds and evidence!”

    Thanks for asking:

    Remember that I linked to my published work and that the example in nematodes alone is enough evidence to inspire appropriate thoughts and intelligent questions.

    What happens when you feed one worm something different than another and it morphs into a worm species predator with teeth that eats your other worms? Do you claim it mutated into a monster worm with teeth, or do you ask yourself: Are similar changes nutrient-dependent and pheromone-controlled in every other species on the planet? If similar changes are nutrient-dependent and pheromone-controlled in every other species on the planet, are all species with teeth mutated monsters that arose from mutant worms?

    “Differences in the behavior of nematodes are determined by nutrient-dependent rewiring of their primitive nervous system (Bumbarger et al., 2013). Species incompatibilities in nematodes are associated with cysteine-to-alanine substitutions (Wilson et al., 2011), which may alter nutrient-dependent pheromone production.”

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

  78. 78
    James Kohl

    @72 Tony the queer

    “As is the case here, JVK has made various assertions but failed to supply the evidence in support of them.
    Oh, and I loved this response from Larry Moran.”
    ————————————————————————————————————————–
    Laurence A. Moran Saturday, November 16, 2013 1:16:00 PM

    Your claims are quite interesting. I had no idea that maple trees and E. coli responded to pheromones and food odors. In fact, I didn’t even know they had noses.
    ———————————————————————————————————————

    I suspect that anyone who does not know that the nutrient-dependent physiology of reproduction is chemically controlled in all species cannot recognize the nose on his face or see beyond it far enough to recognize the conserved molecular mechanisms that must be involved whether or not the species has a nose. Moran is obviously one of the morons Dobzhansky (1964) wrote about: “…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!”

    Birds don’t have a nose, so they have no sense of smell, right? What kind of idiot responds with a comment like that and then prevents me from posting to his blog? That was a rhetorical question. It will be answered again with a second example, when PZ Myers blocks me here.

    Pheromones in birds: myth or reality? http://www.ncbi.nlm.nih.gov/pubmed/20490809

  79. 79
    James Kohl

    Which cell type is the mutant and how are its offspring naturally selected?

    http://www.sciencedaily.com/releases/2014/01/140102142018.htm

    “…to stay alive, a bacterium must not hesitate to swim towards nutrients or away from toxins. This directional movement of microorganisms, spurred by the presence of a helpful or harmful substance, is known as chemotaxis. Different concentrations of c-di-GMP can have a profound influence on a cell’s behavior. For example, in the bacteria Pseudomonas aeruginosa, cells with high levels of c-di-GMP tend to remain still, adhere to surfaces and form colonies. Those with low levels [called hungry], on the other hand, tend to actively swim about by using a corkscrew-shaped propeller located at one end of the bacterium. In the latest study, the Miller and his colleagues worked out the molecular mechanism behind the difference in c-di-GMP concentrations seen between daughter cells.”

    My Summary: The hungry cell types swam because they were afraid they would starve to death and not produce viable offspring if they just sat on the couch watching TV all day. With E. coli, it’s more of a tumbling motion. It is definitely not a mutation that determines their survival, unless you’re Richard Lenski. In reality, however, I don’t think Lenski believes that. He probably just got tired of trying to tell people that mutation-initiated natural selection is a nonsensical theory, and started teaching the nonsense so he could be more popular.

  80. 80
    Timaahy

    I think I get it now. It’s like in The Very Hungry Caterpillar, where the caterpillar eats 1 apple, 2 pears, 3 plums, 4 strawberries, 5 oranges, 1 piece of chocolate cake, 1 ice cream cone, 1 pickle, 1 slice of Swiss cheese, 1 slice of salami, 1 lollipop, 1 piece of cherry pie, 1 sausage, 1 cupcake, and 1 slice of watermelon, but nothing happens. Then he eats 1 green leaf and BAM! he turns into a butterfly and sells pheromones.

  81. 81
    ChasCPeterson

    Crankier and crankier!

    The abstracts from this year’s SICB meeting include almost the same number of mentions of “mutations” and “amino acids” with a few that mention “natural selection.”

    Word-search counts? Srsly?
    SICB is a society of organismal biologists, not evolutionary biologists. We study the physiology, endocrinology, morphology, biochemistry, behavior, and ecology of extant organisms (mostly animals), and not so much their evolutionary origins. You know, bird-watching and butterfly-collecting *eyeroll*, So your cntrl-F study is a red herring.

    The common thread is obviously the organism level thermodynamic stability that is established by different amino acid substitutions with increasing organismal complexity in different ecological, social, neurogenic and socio-cognitive niches.

    word.
    salad.

    If ChasRPeterson is the cardiologist I found via a google search

    LOL. Did you think I was kidding about the middle initial?
    No, this is me, over here.

    my model extends to the role of amino acid substitutions in the cell wall of atherosclerotic arteries.

    ‘Cell wall’ means something in biology, and no animal cell has one.
    But please: in what specific protein(s) are these amino-acid substitutions occuring, and what is the biochemical mechanism by which they are substituted?

    What has Lenski proposed is the alternative explanation of why mutations only sometimes occur? If they randomly occur, how are they selected. What is selected? Why doesn’t anyone else ask questions like those of Lenski?

    Mostly because people in a position to ask such questions already have at least a rudimentary understanding of how evolution by natural selection occurs. By asking questions like “what is selected?” you, on the other hand, give away your utter ignorance.

    Tony the queer

    Say, there’s another tell: by changing the adjective to a noun, you give away your bigotry.

    Crank, ignoramus, creationist, con-man, and bigot. You’re a piece of work, Kohl.

  82. 82
    Menyambal

    I like how the Amazon ads for those amazing pheromones point out that the product has been on TV.

  83. 83
    James Kohl

    @80 Timaahy

    What the larvae eat is also important to the nutrient-dependent pheromone-controlled adaptations of invertebrates like butterflies and honeybees. The larvae of the fawn-to-peppered colored moths ate lead and manganese contaminated leaves, which cause their color change. The color change was attributed to mutations and natural selection via predation.

    See for example:
    Toxic Halitosis Protects Tobacco-Eating Caterpillar
    by Ed Yong http://phenomena.nationalgeographic.com/2013/12/30/toxic-halitosis-protects-tobacco-eating-caterpillar/

    Excerpt: In 2010, Kumar’s team, led by Ian Baldwin, raised tobacco hornworm caterpillars on genetically modified tobacco that doesn’t make much nicotine. They found that a gene called CYP6B46 was less active than usual in the guts of these insects, suggesting that it’s usually involved in resisting the effects of nicotine.

    My comment: Nutrient-dependent pheromone-controlled developmental staging and life history changes in a moth species: Manduca sexta, takes us from the ridiculous example of what some of us were taught to believe was mutation-initiated natural selection by bird predation in the peppered moth. We now have another accurate representation of ecological adaptations during the natural history of invertebrates, which is exemplified in all species.

    Kumar, Sagar, Pandit, Steppuhn & Baldwin. 2013. Natural history-driven, plant-mediated RNAi-based study reveals CYP6B46’s role in a nicotine-mediated antipredator herbivore defense.

    Pay attention as facts about natural history replace stories about natural selection. In this species, olfactory associations facilitate important life-history events, which are unrelated to the immediate foraging responses. Natural selection cannot enable these association as immature larvae and caterpillars become moths. Behavior is nutrient-dependent and pheromone-controlled during all stages of development as best exemplified in the honeybee model organism of ecological, social, neurogenic, and socio-cognitive niche construction.

    Do not get caught playing the fool, as others have been.

    Jay R. Feierman: I am absolutely certain that if you showed this statement to any professor of biology or genetics in any accredited university anywhere in the world that 100% of them would say that “Random mutations are the substrate upon which directional natural selection acts” is a correct and true statement.

    Jay R. Feierman: Variation is not nutrient availability and the something that is doing the selecting is not the individual organism. A feature of an educated person is to realize what they do not know. Sadly, you don’t know that you have an incorrect understanding Darwinian biological evolution.

  84. 84
    Nick Gotts

    In reality, however, I don’t think Lenski believes that. He probably just got tired of trying to tell people that mutation-initiated natural selection is a nonsensical theory, and started teaching the nonsense so he could be more popular. – James Kohl@79

    So you’re calling Lenski a liar, without a shred of evidence. What a little shit you are.

  85. 85
    James Kohl

    @81 ChasCPeterson

    Sorry about the middle initial. Thanks for the correction. Is the GnRH molecule conserved in turtles as it is in all other vertebrates?

    Evidently, we’re done discussing the content of my published work and I’m not interested in discussing turtles outside the context of conserved molecular mechanisms. Thus, I’ll return to the holy grail of evolutionary biology, which may interest people here — if not the SICB folks.

    The holy grail is de novo gene creation, of course, and it was placed into the context of nutrient-dependent copy number variation and nutrient-dependent differentiation of cell types in Nasvall et al (2012), who nevertheless, like Lenski, reported their findings in terms of mutations. Like you, they seem unable to distinguish between biologically based cause and effect across all species and a nonsensical theory of mutation-driven evolution.

    Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence
    http://www.sciencemag.org/content/338/6105/384.abstract

    Those of you who think that de novo creation of genes “just happens” via mutations, which means excluding nutrient uptake and amino acid substitutions, can now join Peterson in discussion of the “Turtles all the Way Down” theory of the cosmos.

  86. 86
    James Kohl

    @84 Nick Gotts

    I’m not calling Lenski a liar; I just think he would rather not discuss facts with people like you, or contradict what he’s been reporting for more than 25 years — even though others have learned virtually everything that’s known about the microRNA / messenger RNA balance and de novo gene creation in the past decade.

    Physiology is rocking the foundations of evolutionary biology (2013) discusses the problem. http://ep.physoc.org/content/early/2013/04/12/expphysiol.2012.071134.abstract

    “Perhaps the elegant mathematics and the extraordinary reputation of the scientists involved blinded us to what now seems obvious: the organism should never have been relegated to the role of mere carrier of its genes.”

  87. 87
    Nerd of Redhead, Dances OM Trolls

    Like you, they seem unable to distinguish between biologically based cause and effect across all species and a nonsensical theory of mutation-driven evolution. Citation needed from some source other than your lying and bullshitting writing, i.e. real scientists who demonstrate your inane and fuckwitted idea is correct. Until you have several of those, compared to thousands for mutations, you are full of shit and attitude.

  88. 88
    Nerd of Redhead, Dances OM Trolls

    Gack, borked the blockquote in #87. Should read:

    Like you, they seem unable to distinguish between biologically based cause and effect across all species and a nonsensical theory of mutation-driven evolution.

    Citation needed from some source other than your lying and bullshitting writing, i.e. real scientists who demonstrate your inane and fuckwitted idea is correct. Until you have several of those, compared to the (tens, hundreds of) thousands for mutations, you are full of shit and attitude.

  89. 89
    Nick Gotts

    I’m not calling Lenski a liar – James Kohl@86

    Yes you are, liar. You are claiming, without a shred of evidence, that he is deliberately misrepresenting his own beliefs, i.,e., lying, “so he could be more popular”.

  90. 90
    gillt

    Hi James Kohl,

    Thanks for responding…I guess, but you did not answered what is really a straightforward and simple question.

    1. How does your research program lift the veil from the conspiracy theory that is modern day evolutionary biology?
    2. Define all your terms in layman terms.

    Sidenote: the link in your comment disregards my request for brevity, clarity and simple language and contains at least one unsupported claim, such as ” The genetically predisposed embryonic migration of GnRH neurons to the hypothalamus is controlled by in utero nutrient stress and social stress.”

  91. 91
    John Doe

    I’ve been following Kohl for quite some time. There are a few conundrums he has yet to be able to explain:

    -regarding the peppered moth example, he quite commonly states that the presence of lead and manganese from the pollution were responsible for the melanism, while citing the peppered moth evolution wikipedia. However, there’s a section at the bottom of that article which refutes that claim.

    “Heslop Harrison (Harrison and Garrett 1926; Harrison 1928) suggested that the increase of melanic moths in industrialised regions was due to “mutation pressure”, not to selection by predators which he regarded as negligible. Salts of lead and manganese were present in the airborne pollutant particles, and he suggested that these caused the mutation of genes for melanin production but of no others. He used Selenia bilunaria and Tephrosia bistortata as material. The larvae were fed with leaves that had incorporated these salts and melanics subsequently appeared.

    Similar experiments by Hughes McKenney (1932) and Thomasen and Lemche (1933) failed to replicate these results. However, the statistician and geneticist Ronald Fisher, showed that Heslop Harrison’s controls were inadequate.[21] This hypothesis, however, appeared to be falsified by breeding experiments. Further evidence, if it were needed, is likely to come from research into the biochemistry of melanism.”

    -on a similar note, I have asked him if diet-induced color change really could explain the preponderance of white animals in the polar regions, sand-colored animals in deserts, green animals in forests, the various array of vivid insects demonstrating visual crypsis, etc, but have received no satisfactory answer. What a fantastic coincidence that their diet made all those animals perfectly match the color of their environment. I have yet to be told if those animals would have evolved the same way in a differently colored environment. Would arctic foxes and snowy owls still be white if they evolved eating their current prey in a more temperate climate? Doubt it.

    -He often cites James Shapiro and Denis Noble as directly refuting mutation and natural selection. I have pointed out to him before that “However, it is not a refutation of mutation and selection, it is merely the addition of other factors.

    From [Noble's] conclusion-

    “A central feature of the Integrative Synthesis is a radical revision of the concept of causality in biology. A priori there is no privileged level of causation. This is the principle that I have called the theory of biological relativity (Noble, 2008, 2012). As Werner puts it, ‘all levels have an equal contributing value’ (Werner, 2003). Control is therefore distributed, some of which is inherited independently of DNA sequences””

    In addition, he speaks as though induced genomic changes in his model are base-specific (and even worse, somehow made with a larger phenotypic goal in mind), but as I’ve pointed out to Kohl before, the mechanisms by which they happen are not as non-random as he thinks they are.

    http://shapiro.bsd.uchicago.edu/ExtraRefs.MolecularMechanismsNaturalGeneticEngineering.shtml

    Legion-bypass polymerases, for example, are not for making directed base sequence changes.

    http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.60.080805.142238

  92. 92
    Hekuni Cat, MQG

    Portia – I’ll gladly take one of your prescription hugs. It will greatly improve my day. I hope your day improves as well.

  93. 93
    ChasCPeterson

    Is the GnRH molecule conserved in turtles as it is in all other vertebrates?

    Of course (that is, they have a 10-residue peptide with the same amino acids at positions 1, 4, 9, and 10 as all other vertebrates).
    So what?
    The same could be said for any other small-peptide hormone.
    And what might be the mechanism responsible for such conservation across so many millions of generations of diverse animals with diverse diets, habitats, and life histories?
    SATAN????

  94. 94
    Hekuni Cat, MQG

    Sorry about #92. Wrong thread.

  95. 95
    James Kohl

    @91 John Doe

    At some point it would behoove someone to explain how random mutations arise and then are somehow selected to ensure that all morphological changes associated with all differences in all cell types in all species achieve species-wide distribution.

    “In 1927, J.B.S. Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect. This result, later generalized by M. Kimura, has since become the cornerstone of modern population genetics. There is no experimental test of Haldane’s insight…”
    http://www.nature.com/ncomms/2013/130913/ncomms3417/full/ncomms3417.html

    The fact that people here are still reasoning with an idea that became the cornerstone of modern population genetics before it was finally tested and — failed the test — attests to the fact that most people are living in the past and refuse to bring themselves current by reading the current literature and incorporating it into a model that makes sense of what we now know are the conserved molecular mechanisms of ecological adaptations.

    Noble concludes that ‘all levels have an equal contributing value.’ I have detailed the pathway via which the epigenetic landscape becomes the physical landscape of DNA. Gene activation in cells of tissues in the organs of all organ systems exemplifies increasing organismal complexity. The details demand that people do more than say “Nuh-uh” and proceed to then regurgitate the nonsense they were taught to accept, without question, as the CORNERSTONE OF MODERN POPULATION GENETICS.

    Indeed, the accusations of my arrogance and self-proclaimed intellectual superiority have never been the issue. It is the arrogance and self-proclaimed superiority of biology teachers like PZ Myers and researchers who should have known better than to accept the nonsense they were taught by people like him that is the problem.

    Look at the works or anonymous claims made by those who insist that I am the “crank” here, or that I have somehow misrepresented something. Where is the experimental evidence that indicates they have the right idea about mutation-driven evolution (or anything else), and I somehow got it all wrong during a career as a medical laboratory scientist / generalist with considerable expertise in diagnostic medicine, trouble-shooting, and quality control flow charts that eliminate the sources of error from test results?

    Then look at my model. If you can’t tell the difference between a model and a ridiculous theory, discuss your superiority with those who are like you. You’re not capable of discussion with those who understand the basic principles of biology and levels of biological organization that are required to link sensory cause to effects on organisms and affects on their species-specific behaviors.

  96. 96
    James Kohl

    @93 ChasCPeterson wrote: “The same could be said for any other small-peptide hormone.”

    Thanks; I needed someone like you to show how utterly ignorant you are when it comes to the importance of conserved molecular mechanisms that link differences in cell types in yeasts to differences in cell types in humans. If only the role of the GnRH molecule is considered, for example, we see that “Parenthetically it is interesting to note even the yeast Saccharomyces cerevisiae has a gene-based equivalent of sexual orientation (i.e., a-factor and alpha-factor physiologies). These differences arise from different epigenetic modifications of an otherwise identical MAT locus.” and that the concentrated alpha mating pheromone of S cerevisiae elicits an LH response from cultured rat pituitary cells.– from our 1996 Hormones and Behavior review.

    Intelligent researchers then note that one decapeptide molecule, among the GnRHs, was constructed perfectly at the beginning of what was supposedly 400 million years evolution and that it is not possible to improve its physiological potency using the any natural amino acid. They ask “What regulates GnRH secretion?” I’m asking you that question. If your answer is food and pheromones in species from microbes to man, you may help others to learn what you just learned.

    If you think that any other form of sensory input besides olfactory/pheromonal input directly regulates GnRH secretion, you might have the basis for another a model that refutes the ridiculous theory of mutation-driven evolution. But, if you are the typical uninformed researcher, you will now simply withdraw and hope that no one noticed what you wrote, or continue to criticize me and my published works without the ability to understand them.

    You asked: “And what might be the mechanism responsible for such conservation across so many millions of generations of diverse animals with diverse diets, habitats, and life histories?”

    I detailed the fact that it is nutrient uptake and the metabolism of nutrients to species-specific pheromones in the review article that you criticized: Nutrient-dependent pheromone-controlled adaptive evolution: a model.

  97. 97
    David Marjanović
    alternative splicings of pre-mRNA which result in amino acid substitutions

    What? That’s not how alternative splicing works. Do you, Mr. Kohl, know the meanings of the terms you use?

    that differentiate all cell types of all individuals of all species

    …Lots of species don’t have more than one cell type.

    that were already known to be more closely associated with amino acid substitutions than with mutations and natural selection. Therefore, I am not surprised that you portray both of us as cranks

    Um.

    Amino acid substitutions are mutations.

    If you so obviously don’t know highschool biology, but talk about it as if you were some kind of expert, do you know what that makes you?

    A crank perhaps?

    Researchers, who deny the existence of pheromones in mammals, including the human pheromone-deniers, short-circuit interdisciplinary discussion of the nutrient-driven ecological epigenetics and the pheromone-controlled adaptive evolution of human behavior. For contrast, the honeybee has emerged as a model organism for understanding the epigenetic link from food odors and pheromones to neural networks of the mammalian brain, which ultimately determine human behavior (Kohl, 2012).

    …Why honeybees and not mice?

    @25 Azuma Hazuki

    [...]

    Thank you for your non-anonymous contribution

    Even though it consists of two words, it’s a pseudonym. Why do you complain about pseudonyms? It’s not like you (or anyone but the NSA) had a reliable way of recognizing them.

    Mutations cannot be beneficial because they perturb intercellular signaling

    :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D

    Most genes have nothing to do with intercellular signaling! Consequently, when those genes mutate, in almost all cases nothing can possibly happen to intercellular signaling!

    And why do you think any change would immediately shut the whole thing down?

    and are eliminated if their effects are too deleterious.

    Yeah, if. BTW, that’s called natural selection.

    They can be maintained, but not fixed, in the organized genome of an organism

    “Fixed” is a term that applies to alleles in the gene pool of a population, not the genome of a single individual.

    only if they do not have deleterious effects on protein folding that is required for cell survival.

    …which is the case in the vast majority, as any amount of knowledge about molecular biology should make obvious.

    They cannot be naturally selected because they are never permanently fixed in the organized genome.

    What nonsense! :-D :-D :-D :-D :-D Clearly, you don’t know what “natural selection” means! Please explain it to us in your own words. That should be fun. :-)

    What[,] are you unable to realize that antibiotic resistance is a function of nutrient-dependent thermodynamic changes that enable organism-level thermoregulation? Did you ever hear about anyone who died from an infection because the killer organism had learned to live with the heat that killed the patient?

    Dude, did you seriously believe antibiotics cause fever, and only the fever kills “the killer organism”?!?

    That’s the only way I can make sense out of those two sentences. “Thermoregulation”, in case you didn’t know, means “regulation of body temperature”.

    Antibiotics are simply poisons. They kill bacteria by poisoning them. That’s why they’re useless against viruses, BTW.

    As you may know, the survivors might kill the patient the next time around — not because they mutated into another species, but because nutrient-dependent amino acid substitutions enhanced their thermodynamic stability.

    Species lie in the eye of the beholder. Everything after your comma is just technobabble.

    and no model of biologically-based cause and effect that explains how ecological variation results in species diversity.

    The ghost of competition past.

    I hope you will comment on Kondrashov (2012) “One of the main duplicated gene families are the olfactory receptor proteins [18,117–119] so perhaps their duplication may lead to an increase in sensitivity to a particular odour may be adaptive under certain conditions.” http://rspb.royalsocietypublishing.org/content/early/2012/09/05/rspb.2012.1108.abstract

    In humans, lots of genes for olfactory receptors have become pseudogenes. They don’t work anymore. They’re ex-genes. They’re pining for the fjords.

    my model extends to the role of amino acid substitutions in the cell wall of atherosclerotic arteries

    1) Atherosclerosis is not caused by mutations (including amino acid substitutions).
    2) Cell wall? Animals don’t have cell walls. Do you mean collagen in the extracellular matrix???

    For 25 years, Lenski has continued to provide experimental evidence of nutrient-dependent copy number variation of genes and nutrient dependent pheromone-controlled differentiation of cell types via amino acid substitutions.

    Escherichia coli has exactly one cell type, as you know full well. :-)

    What has Lenski proposed is the alternative explanation of why mutations only sometimes occur? If they randomly occur, how are they selected. What is selected? Why doesn’t anyone else ask questions like those of Lenski?

    Would it kill you to open a 101-level textbook!?!

    Mutations occur randomly. That’s an observed fact. If a mutation confers an advantage in a particular environment, the offspring of the individual that has this mutation will be overrepresented in the next generation; that’s called natural selection. If it confers a disadvantage in that environment, the offspring of the individual that has this mutation will be underrepresented in the next generation; that, too, is called natural selection.

    Why doesn’t anyone else ask questions like those of Lenski?

    Because the answers have been known for decades!!!

    or is it simply too difficult to explain genes gained by mutations and genes lost by mutations in any context of evolution whatsoever?

    Deletions and insertions of that exact size are rare. Genes don’t appear out of nothing, and they hardly ever disappear just so; they evolve from other genes by mutation, turn into pseudogenes by mutation, and occasionally evolve from junk DNA by mutation.

    What happens when you feed one worm something different than another and it morphs into a worm species predator with teeth that eats your other worms?

    :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D :-D

    Don’t you think the argument from ridiculous speculation is a logical fallacy?

    Finally, I love this part of your paper:

    Conflict of interest and funding

    The author has not received any funding or benefits from industry or elsewhere to conduct this study.

    How carefully worded it is. :-)

    and the something that is doing the selecting is not the individual organism.

    Indeed not. It’s the environment.

    What I just said about basic textbooks.

    A feature of an educated person is to realize what they do not know.

    Exactly.

  98. 98
    David Marjanović

    Oh. The <q> tag is automatically closed after one paragraph. I’ll try again:

    Conflict of interest and funding

    The author has not received any funding or benefits from industry or elsewhere to conduct this study.

    The quotation marks are automatically generated, I can’t do anything about them. Comic Sans is more important.

  99. 99
    David Marjanović

    Actually, I see the coming epigenetic revolution as the 21st century equivalent of discovering genetics in the first place. Darwin had only a lucky guess, but he had no mechanism to propose that would explain it; genetics was that mechanism. But biological reality is far too complex to be explained by “ein gene, ein protein, ein phenotype,” and while Lamarck was wrong about mechanism, he seems to have been right in that some acquired traits DO pass on to offspring.

    …Not only did you fulfill Godwin’s Law in comment 12 – seriously? –, you’ve built a really thin strawman. I’m not sure if anyone ever thought there’s such a 1:1:1 relationship. Unsurprisingly, things like gene regulation and alternative splicing have been discovered, never mind developmental plasticity.

    More and more, I am beginning to think that “human” is a verb, not a noun, and that all of us are a process connected to each other and all reality.

    I’m sorry, this is either banal or woo or both.

  100. 100
    dmgregory

    James Kohl @76

    The pheromone-controlled physiology of reproduction accounts for the result.

    You have not answered the question. Recall that all 12 experimental strains started out identical. That means their “pheromone-controlled physiology of reproduction,” if such a phrase can be applied to E. coli, would have started out in an identical state in all 12 populations, unless something occurred to change one population but not the other 11.

    It is this unique change in one population but not the other 11 for which you must account. It does not suffice to say “the black box did it” – if that black box is “pheromone-controlled physiology,” then what specific pheromones exerted what specific influence on the physiology, why did they only affect 1 of 12 populations this way, and what data do you have to demonstrate this actually occurs (in E. coli specifically)?

    What has Lenski proposed is the alternative explanation of why mutations only sometimes occur? If they randomly occur, how are they selected. What is selected?

    This is fairly elementary Bio 101, not specific to Lenski’s results. Here is a simplified version of the standard interpretation of the experiment:

    Mutations occur due to damage to DNA (eg. through radiation), errors in the process of repairing DNA, or errors in replication. These introduce permanent changes to DNA sequences or gene/chromosome counts. If these changes occur in germ-line cells and the organism survives and reproduces successfully, these changes may be inherited by its offspring.

    Mutational changes are undirected, in the sense that a stray bit of radiation that strikes and alters a segment of DNA doesn’t “know” which part of the DNA it should aim for. Various control & repair mechanisms make certain mutations less frequent than others, but overall mutation occurs randomly.

    This accounts for why the aerobic citrate metabolism trait Lenski’s team observed arose in only one of the 12 experimental populations: the required mutations are independent random events, with a small joint probability. They only occurred together in that one strain. This is the same reason why, after dealing 12 poker hands (from as many decks as you wish), you might discover that only one player holds a royal flush.

    Once an individual possessing the citrate-metabolizing trait (Cit+) arose, it had access to a greater supply of energy than its non-citrate-using (Cit-) peers. By using this greater energy source, bacteria with the Cit+ trait can out-survive and out-reproduce their Cit- peers.

    Because of this reproductive advantage, after a large number of generations have passed, we would expect to (and do!) find that a sample of the population contains more Cit+ bacteria than Cit-. The trait has proliferated through the population, a textbook example of selection in action.

    (Obviously it’s all a bit more complicated than this, what with horizontal gene transfer and the fact that Cit+ developed incrementally, through multiple duplication mutations increasing expression of the trait, but this gets the core idea across)

    As you can see, it’s very easy to account for these results using mutation and selection. This has not yet been demonstrated using James Kohl’s proposed model.

  101. 101
    Nerd of Redhead, Dances OM Trolls

    JK #96

    I detailed the fact that it is nutrient uptake and the metabolism of nutrients to species-specific pheromones in the review article that you criticized: Nutrient-dependent pheromone-controlled adaptive evolution: a model.

    I take your word as nothing but bullshit unless you can and do supply third party evidence that directly backs up your claims. And that level of evidence is sorely lacking. I would also suggest you kill your attitude you are the smartest person on this thread instead the least competent scientist who misunderstands very basic concepts. You haven’t earned your attitude. Which means you quit pretending you have evidenced something when you haven’t.

  102. 102
    dmgregory

    Oops, David Marjanović @97 beat me to it, and summarized mutation and selection more concisely. Thanks! :)

  103. 103
    ChasCPeterson

    Dude, you’re a nut.
    I’m happy to acknowledge that GnRH1 secretion is regulated by chemical signalling, that some of these chemical signals are linked to nutrition (e.g. via Neuropeptide Y) and that others, in some species, are linked to pheromones. That’s not controversial. There’s even evidence that olfactory control of reproduction is ancestral for vertebrates. Fine. (Of course, control of GnRH1 secretion is far more complex and diverse than that, with melatonin and sex-steroid feedback, among doubtless many other signals, also important in various species).

    But none of that has anything to do with this business of ‘nutrition- and pheromone- induced amino acid substitution’ making any sense as a mechanism of species divergence, let alone refuting the standard model of evolution by random mutation of DNA and environment-specific natural selection of variants.

    And yes, other peptide hormones are equally well conserved across vertebrates (e.g. the posterior pituitary hormones, oxytocin and arginine vassopressin in most mammals).

    But you’re right about one thing: I don’t understand your published work. Because it makes no sense. And that’s what I criticized about it: “opaque’, I wrote, the opposite of ‘clear’. Not because I’m stupid or uninformed, but because you write like shit and, all evidence suggests, think similarly.

    Have a nice life and good luck with the bogus con-game snake-oil business.

    [I'm done with this guy; wasted too much time already.]

  104. 104
    gillt

    James Kohl,

    The genetically predisposed embryonic migration of GnRH neurons to the hypothalamus is controlled by in utero nutrient stress and social stress.

    Random statement from James Kohl’s review article where the only evidence provided is his own flowchart.
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    For those interested there are *other* review articles that explains how GnRH neural migration works and they do it without ever mentioning social stress.
    Gonadotropin-releasing hormone (GnRH) neuron migration: initiation, maintenance and cessation as critical steps to ensure normal reproductive function

  105. 105
    John Doe

    @95

    You completely ignored the majority of my post.

    Address the refutation of the melanic gene being specifically changed by the metals, why diet supposedly caused such wonderfully coincidental color changes in the species I listed, and my quote from the conclusion of the Noble paper.

  106. 106
    David Marjanović

    Various control & repair mechanisms make certain mutations less frequent than others

    Importantly, these differences depend on chemical properties of the nucleotides, not on biological functions or lack thereof.

  107. 107
    James Kohl

    @97 David Marjanović
    “Would it kill you to open a 101-level textbook!?!”

    No, it would only make me more ignorant, when I’ve seen too much arrogant textbook ignorance come from people like you.

    @97 David Marjanović
    “Genes don’t appear out of nothing, and they hardly ever disappear just so; they evolve from other genes by mutation, turn into pseudogenes by mutation, and occasionally evolve from junk DNA by mutation.”

    I’ve already cited published work that details de novo gene creation. There are other examples of this with more detailed biophysics and examples where biophysical constraints are removed, which they must be to continue touting mutations theory. But, you will need to do your own homework.

    “…a slow epigenetic response coupled by a fast transcriptional response in our model is also applicable to other systems where monoallelic expression is desired, such as ….in the immune system…”

    No biophysical constraints and no conserved molecular mechanisms:
    “Each of these papers, in one way or another, consolidates the idea that there will probably be no fixed law, like gravity, to explain at the molecular level how endless forms most beautiful and most wonderful have been, and are being evolved. It rather seems that a wide variety of peculiar molecular mechanisms perform, together, the complex task of putting the genome in action, in each cell type of each animal species, at every moment in life and under every possible physiological and environmental circumstance.”

    @100 dmgregory
    “Mutations occur due to damage to DNA (eg. through radiation), errors in the process of repairing DNA, or errors in replication. These introduce permanent changes to DNA sequences or gene/chromosome counts. If these changes occur in germ-line cells and the organism survives and reproduces successfully, these changes may be inherited by its offspring.”

    De novo gene creation results when biophysically constrained nutrient-dependent duplication results in nutrient-dependent cell type differentiation via amino acid substitutions. http://www.sciencemag.org/content/338/6105/384.abstract
    “… we created, by duplication and divergence, a new gene that catalyzes a step in tryptophan synthesis. The original HisA and TrpF enzymes both catalyze isomerization of a phosphoribosyl compound, but each acts on different substrates in the biosynthesis of the amino acids histidine and tryptophan…”

    Ecological adaptations without natural selection are now being considered because biophysical constraints prevent beneficial mutations. “A mechanism of evolution that ensures adaptive changes without the obligatory role of natural selection is described.”

    “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”

    “Finally, and stunningly, evolution creates, without selection acting to do so, new “adjacent possible empty niches” which enable new possible directions of evolution.”

    I expected to see something better than more nonsense added to discussion here, especially after PZ’s derogatory comments. No one has turned the discussion back to him so that he can tell us what he knows that contradicts my representations. No one has offerred any experimental evidence to support what is rapidly becoming a non-existent theory of mutation-driven evolution, because natural selection is being removed along with all biophysical constraints so that mutations ‘just happen’ to somehow drive evolution, which takes us back to Haldane’s idea and the fact that most of you have been living in the past for more than 86 years.

  108. 108
    Nerd of Redhead, Dances OM Trolls

    Two quotes from Richard Feynman seem appropriate here:

    The first principle is that you must not fool yourself and you are the easiest person to fool.

    It doesn’t matter how beautiful your theory is, it doesn’t matter how smart you are. If it doesn’t agree with experiment, it’s wrong.

    James Kohl has fooled himself, and ignores solid and conclusive experimental evidence that refutes his inane idea.

  109. 109
    James Kohl

    @103 ChasCPeterson

    “I don’t understand your published work. Because it makes no sense.”

    Your inability to understand my published work does not make me a nut! It merely indicates how poorly informed you actually are.

    2001 Human pheromones: integrating neuroendocrinology and ethology (Zdenek Klein award)
    http://www.nel.edu/22_5/NEL220501R01_Review.htm

    2006/7 The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences (Ira and Harriet Reiss Theory Award) author’s copy of my book chapter: http://www.sexarchive.info/BIB/kohl.htm

  110. 110
    James Kohl

    @106 David Marjanović

    “…these differences depend on chemical properties of the nucleotides, not on biological functions…”

    Is it magic or biophysics that enables the flipping of bases that lead to the amino acid substitutions and morphological differences that include flagella in bacteria?

    You seem to have no idea, and are probably teaching others that people like me have no ideas (and no model) of biologically based cause and effect that can be compared to Haldane’s idea. You take all the information available, package it, and sell it to others as if it was relevant when it is nonsense. PZ should have criticized your works so we could discuss the real “cranks.”

    “…a consensus will not be reached soon, despite the increasing range of data and types of analysis that are used (morphological, molecular and combined phylogenetics, development biology, molecular divergence dating, paleontological supertree dating, combined dating, and calculation of confidence intervals on first appearances in the fossil record).” http://www.bioone.org/doi/abs/10.5252/g2013n1a8

  111. 111
    James Kohl

    @104 gillt “…the only evidence provided is his own flowchart.”

    You mean the only evidence besides the book, book chapter and series of other articles, right? Like this one:

    Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/17338/20758

    @105 John Doe:

    “You completely ignored the majority of my post.”

    Of course I did. You completely ignored the majority of my published works, like the one linked above.

  112. 112
    David Marjanović

    @97 David Marjanović
    “Would it kill you to open a 101-level textbook!?!”

    No, it would only make me more ignorant,

    …What, would it drain knowledge out of your head or something?

    when I’ve seen too much arrogant textbook ignorance come from people like you.

    I take it you’re not even trying to address my point.

    @97 David Marjanović
    “Genes don’t appear out of nothing, and they hardly ever disappear just so; they evolve from other genes by mutation, turn into pseudogenes by mutation, and occasionally evolve from junk DNA by mutation.”

    I’ve already cited published work that details de novo gene creation.

    Sorry, I missed that – please tell me in which comment.

    De novo gene creation results when biophysically constrained nutrient-dependent duplication results in nutrient-dependent cell type differentiation via amino acid substitutions.
    http://www.sciencemag.org/content/338/6105/384.abstract
    “… we created, by duplication and divergence, a new gene that catalyzes a step in tryptophan synthesis. The original HisA and TrpF enzymes both catalyze isomerization of a phosphoribosyl compound, but each acts on different substrates in the biosynthesis of the amino acids histidine and tryptophan…”

    Your claim does not follow from the quote you provide.

    “I don’t understand your published work. Because it makes no sense.”

    Your inability to understand my published work does not make me a nut! It merely indicates how poorly informed you actually are.

    No.

    When I started writing scientific papers, the very first thing my thesis supervisor told me was (paraphrased): “you will be misunderstood – by someone, at some point, for some reason –, so it’s your responsibility to minimize the opportunities for that”. If you haven’t expressed yourself clearly enough, that’s your fault, not that of your readers.

    “…these differences depend on chemical properties of the nucleotides, not on biological functions…”

    Is it magic or biophysics that enables the flipping of bases that lead to the amino acid substitutions and morphological differences that include flagella in bacteria?

    You seem to have no idea

    :-D :-D :-D :-D :-D :-D

    You still haven’t opened a textbook, I see. It’s neither magic nor biophysics, it’s quantum physics. It’s chemistry. DNA falls apart when stored in water (as organisms do), it reacts with water, and sometimes the repair enzymes fail to restore the original state correctly; bases can also rotate about their bonds to deoxyribose (this is directly Heisenberg’s uncertainty relation at work), leading to different hydrogen bonds that cause polymerases and repair enzymes to make mistakes. This is really elementary.

    and are probably teaching others

    Nope. I’ve never taught at the university level; I currently have a research-only postdoc position, and just applied for another research-only position yesterday.

    PZ should have criticized your works so we could discuss the real “cranks.”

    PZ’s time is limited. He teaches and does time-consuming lab work. Criticize my works yourself, preferably in this thread so we don’t derail the discussion here.

    http://www.bioone.org/doi/abs/10.5252/g2013n1a8

    Yep, that’s me. I don’t understand why you included a quote from that paper that is completely irrelevant to this discussion.

  113. 113
    David Marjanović

    @105 John Doe:

    “You completely ignored the majority of my post.”

    Of course I did. You completely ignored the majority of my published works, like the one linked above.

    The tu quoque argument is a logical fallacy.

  114. 114
    James Kohl

    @103 ChasCPeterson
    ‘I’m happy to acknowledge that GnRH1 secretion is regulated by chemical signalling, that some of these chemical signals are linked to nutrition (e.g. via Neuropeptide Y) and that others, in some species, are linked to pheromones. That’s not controversial. There’s even evidence that olfactory control of reproduction is ancestral for vertebrates. Fine.”

    http://www.bioone.org/doi/abs/10.1643/0045-8511%282006%296%5B216:LPASSI%5D2.0.CO%3B2
    Charles C. Peterson and Jerry F. Husak

    “The lack of sexual dimorphism in sprint speed may reflect trade-offs with other sexually selected traits (e.g., head size) and/or condition-dependence of running capability.”

    My comment: Evidently, in some species, sexual selection for head size and running capability has nothing to do with nutrient-dependent pheromone-controlled adaptations and the GnRH-modulated HPG and HPA axes regulation that I detailed in my model. Therefore, I am happy to acknowledge that Charles C. Peterson knows nothing about sexual selection for morphological traits associated with nutrition, pheromones, and amino acid substitutions because he believes in a ridiculous theory.

    He wrote: “But none of that has anything to do with this business of ‘nutrition- and pheromone- induced amino acid substitution’ making any sense as a mechanism of species divergence, let alone refuting the standard model of evolution by random mutation of DNA and environment-specific natural selection of variants.”

    My comment: Is this the type of teacher that you want telling your children and grand-children about evolution? When do we stop raising generation after generation of ignorant theorists?

  115. 115
    Tethys

    James Kohl

    Please use the blockquote tag. Thx

  116. 116
    Nerd of Redhead, Dances OM Trolls

    Reprised from the Soggy Ape Thread, but it also applies here:

    You are a crank/loon if……

    You know you are the brightest one out there, but nobody appreciates your genius

    If the idea you promote doesn’t have any real third party evidence

    If you take criticism as personal insults instead of criticism of the idea

    If asked what it would take to show your idea is wrong, you can’t/won’t supply an answer

    You promote your idea by infesting and threadjacking other peoples blogs, and not by the normal scientific methods of publishing in scientific journals and talking about your ideas at professional meetings

    You are a crank/loon if……

    You fail to consult with experts in the field, as they may refute your idea

    You think your opinion of the evidence means anything to those you are selling your idea to

    You think you must get the last word in for victory

    You don’t address solid evidence against your idea with third party scientific evidence, just your opinion of the evidence

    You avoid making any statements that you know can be refuted/falsified easily by people in the field

  117. 117
    James Kohl

    @112 David Marjanović
    “Yep, that’s me. I don’t understand why you included a quote from that paper that is completely irrelevant to this discussion.”

    I indicated why I included this quote.

    “…a consensus will not be reached soon, despite the increasing range of data and types of analysis that are used (morphological, molecular and combined phylogenetics, development biology, molecular divergence dating, paleontological supertree dating, combined dating, and calculation of confidence intervals on first appearances in the fossil record).” http://www.bioone.org/doi/abs/10.5252/g2013n1a8

    It was because you have not realized that no consensus is going to be reached, since the increasing range of data does not support the ridiculous theory of mutation-driven evolution. Nevertheless, when all else fails to provide any explanation of cause and effect, people like you can always fall back on the explanatory power of physics, since it has no explanatory power, either…. until you link it to the thermodynamics of intercellular signaling and organism-level thermoregulation like I have done via nutrient-dependent pheromone-controlled cycles of protein biosynthesis and degradation.

    David Marjanović “If you haven’t expressed yourself clearly enough, that’s your fault, not that of your readers.”

    I might be able to express myself more clearly, if I could think slower. Who taught you how to do that?

  118. 118
    Nerd of Redhead, Dances OM Trolls

    Oh, and JK, you are under Christopher Hitchens’ quote:

    That which is asserted without evidence can be dismissed without evidence.

    Which is your whole theory….

  119. 119
    Tony! The Queer Shoop

    James Kohl:
    First off, try getting ‘nyms right. It’s not hard to copy/paste if you cannot recall the nym.
    Secondly, your comment @78 is interesting. I provided a link to the full comment by Larry Moran. You copy/pasted (see, you can do that) *part* of his response. For the benefit of others, here is his full comment:

    Your claims are quite interesting. I had no idea that maple trees and E. coli responded to pheromones and food odors. In fact, I didn’t even know they had noses.

    James Vaughn Kohl, your posts are very much like spam because your profile links to for-profit websites where you have a vested interest and because you really don’t have anything to say about the subject of this post. You don’t seem to be very knowledgeable about biology and evolution.

    I’ve decided that you should take a little break from commenting here.

    As I read through that thread, and this one as well, all you seem to do is toss out your pheromone shit, and dismiss anyone who doesn’t believe you, even those that are clearly knowledgeable about biology and evolution.
    You’re a dishonest shit-shill.

  120. 120
    Tethys

    I might be able to express myself more clearly, if I could think slower.

    They have medications for that problem.

    ADD is not making you act like an arrogant asshole though, so you should just take your ball and go home like you said you were going to do last night.

  121. 121
    Nerd of Redhead, Dances OM Trolls

    I might be able to express myself more clearly, if I could think slower. Who taught you how to do that?

    Gee, thinking is beyond your capacity. It starts with concept you can be wrong. And then progresses to you are wrong, if there isn’t real evidence to back up your OPINION. OPINION that can and will be dismissed by the scientific community without evidence to back it up.

  122. 122
    John Doe

    @111

    Of course I did. You completely ignored the majority of my published works, like the one linked above

    I’ve read your papers numerous times. They address none of what I asked before.

    1. Pollutants causing color change in moths has been refuted.
    2. Coincidental coloration. Isn’t it odd that coloration supposedly stemming from diet so perfectly matches the environment?
    3. Quote from Noble’s paper where he SPECIFICALLY says he’s supplementing mutation and selection rather than replacing it.

  123. 123
    David Marjanović

    It was because you have not realized that no consensus is going to be reached, since the increasing range of data does not support the ridiculous theory of mutation-driven evolution.

    …What does the shape of the tetrapod tree have to do with the driving forces that created it?

    The consensus that won’t be reached soon would be about which Permian/Carboniferous animals are the closest relatives of today’s amphibians.

    until you link it to the thermodynamics of intercellular signaling and organism-level thermoregulation like I have done via nutrient-dependent pheromone-controlled cycles of protein biosynthesis and degradation.

    Do you know any example of a proteasome interacting with any pheromone in any organism?

    I might be able to express myself more clearly, if I could think slower.

    That does not make sense.

  124. 124
    dmgregory

    David Marjanović @106 Thanks for the clarification! I saw that my phrasing might be vulnerable to misinterpretation, but wasn’t sure how to improve it without overcomplicating.

    James Kohl @107

    @100 dmgregory
    “Mutations occur due to damage to DNA (eg. through radiation), errors in the process of repairing DNA, or errors in replication. These introduce permanent changes to DNA sequences or gene/chromosome counts. If these changes occur in germ-line cells and the organism survives and reproduces successfully, these changes may be inherited by its offspring.”

    De novo gene creation results when biophysically constrained nutrient-dependent duplication results in nutrient-dependent cell type differentiation via amino acid substitutions.
    http://www.sciencemag.org/content/338/6105/384.abstract

    Whether or not de novo gene creation can result from this “process” (ignoring for the moment the fact that E. coli do not have multiple cell types that undergo differentiation) has no bearing on the definition of genetic mutations, which is the subject of the paragraph from my post that you quoted. Even if we accept your statement as fact, it does not contradict the mutation-based interpretation of Lenski’s results.

    The link you cited is about new genes created involving gene duplication mutations (the same process at work in the standard, mutation-based interpretation of Lenski’s results), specifically supporting the IAD model, which is soundly within the paradigm of mutation & selection which you claim is invalid. As David Marjanović notes above, this paper does not support the claim you are making.

    More worrisome, you have once again failed to provide an explanation for how your model accounts for the development of the Cit+ trait in only one of the 12 experimental populations, despite identical initial conditions and nutrient environments.

    No one has turned the discussion back to him so that he can tell us what he knows that contradicts my representations. No one has offerred any experimental evidence to support what is rapidly becoming a non-existent theory of mutation-driven evolution

    This is dishonest on two counts. Speaking only for the subset of this thread about Lenski’s experiments…

    1. Even without PZ’s direct input, we already have at least one apparent contradiction of your representation: if adaptations are driven by nutrients and pheromones, why did identical colonies of bacteria (with identical physiology and “pheromones” if that word can be applied) in identical nutrient environments not develop the same Cit+ adaptation?

    You still have not described specifically how your model accounts for this, your model appears severely lacking. If we’re missing something here, you need to very clearly articulate what that is and how it resolves this apparent contradiction.

    2. Two of us have explained to you Lenski’s experimental evidence of mutation and selection in E. coli bacteria. It is false to claim that no evidence has been provided to you.

    If you claim that this explanation is incorrect, arguing from authority that “mutations cannot be beneficial” is especially unconvincing when you do so in the face of documented beneficial gene duplication mutations. In this case you will need to show how a gene duplication with a known beneficial effect (duplicating the citrate transport gene and promoter region to amplify citrate metabolism), is expressly forbidden from arising due to random mutation. Otherwise, mutation remains a viable candidate mechanism for initiating this genetic change.

  125. 125
    James Kohl

    @123 David Marjanović

    “Do you know any example of a proteasome interacting with any pheromone in any organism?”

    Thanks for asking, although the question either is phrased poorly, or perhaps I don’t understand it out of context. I am not a biophysicist but will try to place my answer to the question into the context of conserved molecular mechanisms.

    Nutrient-dependent pheromone-controlled amino acid substitutions establish differences in cell types via receptor-mediated intercellular signaling associated with immune system functions and the movement of flagella in microbes. That suggests there are epigenetic effects of pheromones on protein concentrations and protein folding mediated by proteosomes that may result in synthesis of new proteins that effect motion across chemical gradients as is required to find food.

    Do you know how mutations result in the synthesis of new proteins and de novo gene creation (the holy grail of evolutionary biology)? If so, it might help others to place mutated structures like microbial flagella into the context of mutation-driven evolution. But first you must indicate how a beneficial mutation somehow knew it would be beneficial, or how it was naturally selected outside the context of receptor-mediated beneficial movement across a chemical gradient that enabled one of the chemicals to induce the de novo creation of the receptor.

  126. 126
    gillt

    @James Kohl #111

    You made a wild claim in your review article here:

    The genetically predisposed embryonic migration of GnRH neurons to the hypothalamus is controlled by in utero nutrient stress and social stress.

    A series of experiments that tracks GnRH migration within developing brains differentially in response to exogenous stressors would be quite the feat. Instead you give us a flowchart. In response I linked a well-cited review article that does explain GnRH neuronal migration in the developing brain sans your pheromone theory. You ignored that piece of counter-evidence and instead chose to link to your copious writing here which, obliviously, has nothing to say about GnRH neuronal migration in the developing embryo, much less social or nutrient mediated migration. Here’s the only relevant section you believe makes your point.

    Brain development and behavior
    In mammals, the more broadly demonstrable and less stereotypical pheromone-driven behaviors are not limited by the tightly controlled social structure of insect colonies. A more developed mammalian brain probably also helps to ensure behavioral diversity. An evolutionary continuum ensures that, in well-nourished mammals that mature sexually, pheromones cause gene expression in hormone-secreting neurons of tissue in the brain. Changes in behavior are required in order for organisms to seek out food odors and pheromones that cause changes in gene expression in hormone-secreting neurons, and those changes in gene expression during an organism’s development are required in order for individuals and species to survive. This reciprocity between brain development and behavior in insects and in mammals better defines the term epigenetic, using all the links in a sequence of events from stimulus to gene activation and expression to neural activity to behavior and back out again (Alaux, Maisonnasse, & Le Conte, 2010; Bell & Robinson, 2011; Grozinger, Sharabash, Whitfield, & Robinson, 2003). The most sought-after sensory stimuli in any species that reproduces sexually are food odors and pheromones. Reciprocity can be represented as a sensory stimuli seeking organ system found in animal species from invertebrates to mammals that seek satiation via hormone-mediated affects on conditioned behaviors. The organ systems of all organisms seek satiation associated with sensory stimuli throughout life.

    And you still haven’t even attempted to address my original question from comment #75

    What is pheromone-controlled adaptive evolution, and what makes you confident it supplants whatever you think it supplants (e.g., mutation-driven evolution, modern synthesis, molecular evolution, natural selection, genetic drift, the academic industrial complex etc.)?

    If you’re an honest broker then show some clarity and brevity and make your case!

  127. 127
    dmgregory

    James Kohl @125

    Do you know how mutations result in the synthesis of new proteins and de novo gene creation (the holy grail of evolutionary biology)?

    Yes, many ways. And you’ve shown that you’re aware of at least one of them yourself, since you cited that IAD paper, outlining one of the possible routes of new gene creation via mutation and selection. You cited it favourably on the topic of de novo gene creation, so it seems that you agree that the authors indeed demonstrated a route to de novo gene creation.

    That route involved… wait for it… mutation!

    Quoting from the abstract, since this suffices to make the present point:

    Selection maintains the initial amplification and beneficial mutant alleles but is relaxed for other less improved gene copies, allowing their loss. This rapid process, completed in fewer than 3000 generations, shows the efficacy of the IAD model and allows the study of gene evolution in real time.

    I believe the technical term for this is an “own goal”

  128. 128
    James Kohl

    @124 dmgregory

    “Whether or not de novo gene creation can result from this “process”

    I cited the work that showed “De novo gene creation results when biophysically constrained nutrient-dependent duplication results in nutrient-dependent cell type differentiation via amino acid substitutions.
    http://www.sciencemag.org/content/338/6105/384.abstract

    There is no point to debate about whether or not de novo gene creation results from amino acid substitutions. You can waste time discussing amino acid substitutions as if they are mutations with someone else.

    What’s typical of many theorists is that when biological facts don’t fit their theories they resort to debate about definitions. Differences in cell types are common, and you insist that they don’t exist in Lenski’s experiments.

    “Organelle-based partitioning of cellular proteins could therefore be a broader mechanism by which bacteria generate cellular diversity within populations after cell division.” http://elife.elifesciences.org/content/2/e01402

  129. 129
    David Marjanović

    the question either is phrased poorly, or perhaps I don’t understand it out of context.

    The context is that you claimed there are “pheromone-controlled cycles of protein biosynthesis and degradation”. Protein degradation is done in proteasomes. In other words, you are saying that proteasome activity is controlled, at least in part, by pheromones. How does that happen?

    (…You do know what a proteasome is…?)

    Nutrient-dependent pheromone-controlled amino acid substitutions establish differences in cell types

    You’re just repeating your usual claim. I want you to support it instead.

    associated with immune system functions and the movement of flagella in microbes.

    What do you call “immune system” in microbes?

    That suggests there are epigenetic effects of pheromones on protein concentrations and protein folding

    What, why epigenetic? What does heritable gene regulation have to do with it?

    And what is “suggest” about? The causes of flagella movement in E. coli are understood in excruciating detail. Every protein in the cascade is known, and so is what they all do. I once had to learn the whole pathway; forgot it long ago, but I’m sure it’s in textbooks like the Alberts.

    mediated by proteosomes

    1) Proteasomes. Protease-o-somes.
    2) Proteasomes don’t mediate effects on protein folding. They shred proteins so there’s nothing left to fold.

    de novo gene creation (the holy grail of evolutionary biology)

    What do you even mean by “de novo”? Genes aren’t created ex nihilo. As several people (myself included) have already mentioned in this thread, new genes are usually mutated versions (often mutated copies) of older genes, and when they’re not, they’re usually mutated junk DNA that has acquired a start and a stop codon by random mutation. The rest is lateral transfer of genes that are only new for the receiving organism.

    how a beneficial mutation somehow knew it would be beneficial

    You’re as clueless as a creationist. You have no idea what you’re talking about. I’m sorry, it’s true, there’s no point in trying to sugar-coat it. :-|

    A mutation is beneficial in a particular environment if it causes the organism that has it to have a larger number of surviving fertile offspring. Any more questions?

    or how it was naturally selected outside the context of receptor-mediated beneficial movement across a chemical gradient that enabled one of the chemicals to induce the de novo creation of the receptor.

    …Not every protein is a soluble signaling factor that binds to a receptor. o_O And no receptor is 100 % specific. For “de novo”, see above.

  130. 130
    David Marjanović

    You can waste time discussing amino acid substitutions as if they are mutations with someone else.

    Dude.

    Seriously.

    Do you believe something comes along, takes an amino acid out of an existing protein and puts another one in? Or what are you imagining???

  131. 131
    CaitieCat, getaway driver

    DM @130: goddidit?

  132. 132
    jste

    This exchange is fascinating.

    But first you must indicate how a beneficial mutation somehow knew it would be beneficial…

    I don’t even… Why must a mutation (that hasn’t happened yet) have magical pre-cog powers about whether it will be a good mutation or a bad mutation? How does a mutation in something as un-self-aware as a gene know (or even need to know) anything at all??

  133. 133
    Nerd of Redhead, Dances OM Trolls

    DM @130: goddidit?

    Since JK has no evidenced method for mutations, it must come about by an external force. Goddidit is close enough. A creationist hiding behind word salad would explain the crank….

  134. 134
    sawells

    I think this is one of those guys who have become physically incapable of understanding how wrong they are – because if they allow a single crack in their wall of denial, their whole world will come crashing down.

    Amino acid substitutions typically occur when genome copying errors lead to a SNP – single nucleotide polymorphism ( http://ghr.nlm.nih.gov/handbook/genomicresearch/snp ) – and a codon changes. They are the single most common form of mutation that exists. If this guy honestly thinks they are not mutations then he isn’t even writing in English, just gibberish.

  135. 135
    Tony! The Queer Shoop

    I wonder if James Kohl has heard of this logical fallacy:

    Argument by assertion is the logical fallacy where someone tries to argue a point by merely asserting that it is true, regardless of contradiction

    http://rationalwiki.org/wiki/Argument_by_assertion

  136. 136
    dmgregory

    James Kohl @128

    Note that in my post to which you replied, I said that even if we grant your claim that nutrients can trigger gene creation, this still in no way contradicts the mutation-based interpretation of Lenski’s results. (To do that, you would need to show, not merely assert, that mutations CANNOT create the observed changes)

    You then proceeded to attempt to defend the claim anyway, and a side note about cell types in E. coli, despite their irrelevance to the questions asked of you.

    You can waste time discussing amino acid substitutions as if they are mutations with someone else.

    The very paper you are citing as evidence for your claim attributes this gene creation to mutation-based processes, not to nutrient-dependent processes via amino acid substitutions. (See my reply @127) Did you read the paper, or simply conclude “this study involved nutrients and new genes, therefore nutrient-dependent amino acid substitutions created the new genes.”? And you continue citing it, despite it being pointed out to you twice already that it does not support the claim that you are making.

    Meanwhile, you have continued to ignore the two specific problems I laid out:

    1. You have not explained how your model accounts for development of the Cit+ adaptation in only one of twelve experimental populations, despite identical nutrient conditions and physiology of the initial populations.

    2. You have not demonstrated anything that prevents mutations from causing the genetic changes observed in Cit+ bacteria.

    Until you address these points, the mutation-based model continues to account for Lenski’s results better than the model you have described thus far.

    If you cannot address these points to show how your model offers a superior explanation of this simple test case, you have a very long uphill battle ahead in trying to overturn all of modern biology.

  137. 137
    Rey Fox

    I might be able to express myself more clearly, if I could think slower.

    SUPER GENIUS!

    (I promised myself I wouldn’t sit on the sidelines and snark here because I don’t really have the expertise to argue on the Marjanović level, but really…)

  138. 138
    Tony! The Queer Shoop

    Rey Fox:
    Even Wile E. Coyote didn’t repeat himself this much…

  139. 139
    Colin J

    James Kohl, @107:

    …and the fact that most of you have been living in the past for more than 86 years.

    I have to confess that I’ve spent my whole life living in the past. But I’m only in my 40s.

    I never realised that the average age of the readership here was so high!

  140. 140
    James Kohl

    A Lapse in Watchfulness: New York Times Admits Neo-Darwinism Faces a “Paradigm Shift” Over “Failure” to Explain Body Plans http://www.evolutionnews.org/2013/11/a_lapse_in_watc078601.html

    “The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether.”

    The body plans are nutrient-dependent and pheromone-controlled via amino acid substitutions. Whether you like it or not, this will soon be the accepted paradigm.
    ————————————
    Chemical ecology drives adaptations via niche construction. Nutrients metabolize to pheromones that epigenetically effect hormones that affect behavior. The epigenetic effects of olfactory/pheromonal input on invertebrate behavior and vertebrate behavior are hormone-organized and hormone-activated. For example: glucose and pheromones alter the secretion of hormones that affect behavior.

    Systems biology: This model represents the conservation of bottom-up organization and top-down activation via the 1) thermodynamics of nutrient stress-induced and social stress-induced intercellular changes in the microRNA / messenger RNA (miRNA/mRNA) balance; 2) intramolecular changes in DNA via alternative splicings; 3) non-random experience-dependent stochastic de novo gene creation exemplified by the biosynthesis of receptors; 4) the required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the ecologically adapted mammalian brain; and 5) the reciprocity that links the thermodynamics of gene expression to behavior and altered organism-level thermoregulation in species from microbes to man.

    Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intercellular and intramolecular interactions, which result in de novo creation of olfactory receptor genes. Thermodynamically controlled cycles of RNA transcription and protein degradation are responsible for organism-level changes in pheromone production, which enable accelerated changes in the nutrient-dependent miRNA/mRNA balance and thermoregulation of ecological adaptations controlled by the physiology of reproduction.
    —————————————-
    The fact that no one here is currently willing to accept the biological facts, which are already generally known to serious scientists, simply shows how ridiculous theorists can continue to be if only because they were taught by other theorists to believe in a ridiculous theory. I need not explain anything further or demonstrate anything. The examples I’ve provided in my published works attest to the facts and refute evolutionary theory — albeit after the fact since it has already refuted itself via its lack of explanatory power. Natural selection is gone and therefore all that’s left of mutation-driven evolution is a joke played on YOU. Ecological variation has always led to adaptations via amino acid substitutions or extinction.

    Our most recent extinct ancestor varied from us by only 96 amino acid substitutions, but most people here seem to have survived just fine without the substitutions that led to higher intelligence. See for example: MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates http://dx.doi.org/10.1371%2Fjournal.pbio.1001214

    When you look in the mirror, do you see a human or some other primate? If you’re not sure, you must surely be an evolutionary theorist.

  141. 141
    CaitieCat, getaway driver

    I’ll admit, I don’t have the knowledge that Chas and David and you others do to challenge this more clearly, but it honestly sounds to me like basically a Gish Gallop, isn’t it?

  142. 142
    Menyambal

    James Kohl, everyone else has been comparing you to the cranks we get here. I am going to compare you to the teenage driver I spent the day with. The kid couldn’t drive for shit, really, but kept screaming at all the other drivers and explaining to me exactly why they were stupid. Snarlingly impatient, contemptuous of the rules, foul-mouthed, incompetent, hateful, ranting and cranky. And, oddly, addicted to some smelly crap that affected behavior.

  143. 143
    Rey Fox

    When you look in the mirror, do you see a human or some other primate? If you’re not sure, you must surely be an evolutionary theorist.

    Ah, so it’s the usual “my dad ain’t no monkey” dismissal. Creationist.

  144. 144
    ChasCPeterson

    The body plans are nutrient-dependent and pheromone-controlled via amino acid substitutions. Whether you like it or not, this will soon be the accepted paradigm.

    dream on, crank.
    When you cite Casey Luskin, you’ve scraped the barrel-bottom.

  145. 145
    Nerd of Redhead, Dances OM Trolls

    Again, claims without scientific evidence to back them up. That is creationism to a tee. Nothing but religious bullshit. What a CRANK.

  146. 146
    Tethys

    Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intercellular and intramolecular interactions, which result in de novo creation of olfactory receptor genes.

    I keep reading this sentence. It makes as much sense as “Goats On Fire!”.

    The microRNA link is very interesting, technically dense, and the authors were clear that it didn’t really provide more than a good basis for further research. It doesn’t support the proposed model where pheromones are somehow driving human evolution. Or is it thermodynamics?

    In any case the paper was quite clear about it’s limitations.

    Meanwhile, our work has a number of limitations. First, as our main analysis is based on human microarrays, we exclude any probes that do not match each of the three species’ genomes perfectly and uniquely (Materials and Methods). Thus, we ignore regions that show copy number variation among species, or are species-specific. Likewise, our analysis is restricted to regulators conserved across the three species. This is important, because fast evolving or human-specific genes, TFs [36], or miRNAs [37] may have significant contributions to the evolution of primate brain development and species divergence [38]. Second, when analyzing the effects of cis-regulation on expression divergence, we are constrained by the limited annotation of cis-regulatory regions, and it is conceivable that mutations in a yet unidentified class of neural enhancers drive a substantial portion of developmental pattern divergence in humans. Third, our study is restricted to species differences in postnatal development……

    Possible mutations , but nowhere are pheromones listed as possible controls on the process.

  147. 147
    Colin J

    @140:

    The fact that no one here is currently willing to accept the biological facts, which are already generally known to serious scientists, simply shows how ridiculous theorists can continue to be if only because they were taught by other theorists to believe in a ridiculous theory. I need not explain anything further (FTFY) or demonstrate anything. The examples I’ve provided in my published works attest to the facts and refute evolutionary theory — albeit after the fact since it has already refuted itself via its lack of explanatory power. Natural selection is gone and therefore all that’s left of mutation-driven evolution is a joke played on YOU.

    Well, I’m convinced. The fact that all serious scientists accept James Kohl’s genius is good enough for me. It’s just a pity that they are so quiet – bullied by that small clique of cool scientists, no doubt, just like Lenski. Thank goodness we have someone of James Kohl’s calibre (and business acumen) who can stand up to the bullies. Someone who can stand up for the hidden truth that is absolutely obvious to anyone with a brain. Someone who can take on the monolith of evolutionary theory that has already crumbled into ruin. Someone who can stand up so the silent majority can cheer him on. Silently.

    Say, where can I get me some of those pheromones?

  148. 148
    stripeycat

    I’ve met a lot of people incapable of logic and proud of it, as if being able to parse and follow your own train of thought is a bad thing, and jumping around like the proverbial pea on a drumskin is good. I think that’s what this is about:

    I might be able to express myself more clearly, if I could think slower.

    I babble and free-associate when I’m drunk or sleep-deprived. Neither’s conducive to fine thinking.

  149. 149
  150. 150
    Rey Fox

    Read a little more of the comment that I replied to earlier, and I guess it’s not the “monkey’s uncle” denial, it’s some sort of attempted insult that those of us not brilliant enough to grok the Kohl “you are what you eat” theory of evolution must not have evolved enough beyond our primate ancestors. So teleology then.

  151. 151
    djr1

    @ 140.

    James Kohl quotes from and article that he referenced. Here is the quote -

    “The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether.”

    Here is the quote with the last sentence included.

    “The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether. Namely intelligent design.”

    Interesting omission.

  152. 152
    Nick Gotts

    djr1@151,

    How about we apply Kohl’s own technique of truncated quotation to his own vapourings?

    I might be able to express myself more clearly, if I could think – James Kohl

    Yup, seems to work fine!

  153. 153
    James Kohl

    @144 ChasCPeterson

    “When you cite Casey Luskin, you’ve scraped the barrel-bottom.”

    The following quotes are note from Casey Luskin. What difference does it make who they’re from unless you are saying they are wrong? Tell me which of the quotes below is wrong, and I’ll provide the source. My point is that Luskin is not the only one saying that “natural selection” is gone from any further consideration whatsoever. If you would still like to believe in it, tell me which of these three quotes should not be given consideration and what is naturally selected.

    “A mechanism of evolution that ensures adaptive changes without the obligatory role of natural selection is described.”

    “Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.”

    “Finally, and stunningly, evolution creates, without selection acting to do so, new “adjacent possible empty niches” which enable new possible directions of evolution.”

  154. 154
    James Kohl

    @146 Tethys

    “The microRNA link is very interesting”

    That’s like saying, of course you just explained everything about the differentiation of every cell type in every individual of every species. But, what difference does that make when we have a theory of mutation-initiated natural selection we believe in, even when no serious scientists believe in it?

    ————————————For comparison to that ridiculous theory———————————–

    Ingested plant microRNAs influence gene expression across kingdoms. In mammals, this epigenetically links what mammals eat to changes in gene expression and to new genes required for the evolutionary development of the mammalian placenta and the human brain.

    A gene that codes for the mammalian olfactory receptor, OR7D4, links food odors to human hunger, dietary restraint, and adiposity. OR7D4 exemplifies a direct link from human social odors to their perception and to unconscious affects on human behavior associated with human olfactory-visual integration; human brain activation associated with sexual preferences, human learned odor hedonics; and motor function.

    Insect species exemplify one starting point along an evolutionary continuum from microbes to humans that epigenetically links food odors and social odors to multisensory integration and behavior.
    ————————————-
    And hopefully, for the last time — since everyone loves to criticize Creationists and whatever they think exemplifies Creationism, Dobzhansky (1973) “Nothing in Biology Makes Any Sense Except in the Light of Evolution” wrote: “I am a creationist and an evolutionist. Evolution is God’s, or Nature’s, method of Creation.”

    When your “god” of evolutionary biology 1) tells you he’s a creationist; 2) when natural selection is removed from consideration, and when 3) in the same article Dobzahansky noted that “hemoglobin S differs from A in the substitution of just a single amino acid” and 4) also noted that alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but 5) they differ in a single amino acid (out of 141) in the gorilla — how can you not realize that you are the cranks here because you are too ignorant to be anything but cranks?

    Or, is the problem that you clearly recognize that you are the cranks and are desperately trying to substitute me for your nonsensical selves rather than acknowledge that the facts about amino acid substitutions are what make you the cranks?

  155. 155
    Lofty

    Do I smell word salad or boiled head of cabbage? Hard to tell.

  156. 156
    pentatomid

    But first you must indicate how a beneficial mutation somehow knew it would be beneficial

    Uhm… What?

  157. 157
    Nick Gotts

    But first you must indicate how a beneficial mutation somehow knew it would be beneficial – James Kohl@125

    And James Kohl confirms that he, literally, doesn’t know the first thing about the theory he pretends to overturn.

  158. 158
    James Kohl

    @155, 156, and 157

    The undereducated simply must stop commenting here lest it appear that only the undereducated participate.

    I am
    1) not pretending to overturn anything;
    2) not using terms unknown to scientists;
    and
    3) not saying anything different than what can be found in the extant literature.

    The most that can be said of what is happening here is that I am being attacked for integrating information and offering it to fools who don’t want to know about it. We know how that communications problem arose via Dobzhansky’s proclamation in 1964 that “…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!” http://icb.oxfordjournals.org/content/4/4/443.citation

    There were not enough ignorant fools at the time to attack Dobzhansky, but 50 years makes a difference in how much collective ignorance can be put to no good purpose and used to further delay scientiific progress (e.g., by serious scientists). For example Bird watchers and butterfly collectors now report:: “Recent studies show that interactions with pests may promote local plant diversity, accelerate plant evolution, and enhance the proliferation of species over evolutionary time.” http://www.sciencemag.org/content/343/6166/35.short

    This takes claims by the late Lynn Margulis that were finally accepted by virtually everyone who has any common sense, and extends her claims globally to all interactions among all species. However, it does not support the “… Red Queen hypothesis (13), which states that antagonistic interactions between hosts and their pests lead to natural selection for beneficial adaptations and counteradaptations in both groups.

    Natural selection has already been dismissed as a ridiculous idea because it was never supported by experimental evidence. In addition, we now see that mutation-driven evolution has refuted itself, since beneficial mutations cannot result in beneficial adaptations without natural selection — and there is no such thing as natural selection. Instead, there is symbiosis. The idea of natural selection (e.g., via predation) reached its epitome of ridiculousness in the report on snake-centric evolution of the human brain. http://news.sciencemag.org/evolution/2013/10/did-snakes-help-build-primate-brain

    Not even the least intelligent students are going to accept that nonsense, which only goes to show how much nonsense it takes to finally reach the tipping point, when any more nonsense is simply dismissed — as it has been everywhere else except here.

  159. 159
    sawells

    James, you need to know what natural selection means before you can argue about it, and you don’t know what it means. Learn. If you think you do know what it means, describe it – this can be done in a couple of short sentences – and then we can talk. At the moment you don’t seem to know the meanings of the words you are trying to use.

  160. 160
    Tony! The Queer Shoop

    You know, I do believe our resident crank is going to hang out until he’s banned by PZ.

  161. 161
    Tony! The Queer Shoop

    djr1:
    Interesting omission indeed.

    ****

    James Kohl:
    Trying to hide creationist beliefs behind your pseudoscience.
    Can you *get* more dishonest?

  162. 162
    Nerd of Redhead, Dances OM Trolls

    Not even the least intelligent students are going to accept that nonsense, which only goes to show how much nonsense it takes to finally reach the tipping point, when any more nonsense is simply dismissed — as it has been everywhere else except here.

    Sorry non-scientific crank, either provide several citations where YOUR ideas are being accepted by real working scientists, or shut the fuck up about there being a revolution with you as the leader. That is call evidence, plus honesty and integrity. Three things you so sorely lack, but necessary for any successful scientist. Which is why you are a crank.

  163. 163
    pentatomid

    I am
    1) not pretending to overturn anything;

    Oh really? Then what’s all the ranting against mutations and natural selection about. As far as I can tell those are still very much part of the scientific consensus about how evolution works.

    2) not using terms unknown to scientists;

    Well, the terms you’re using sound like terms routinely used by scientists. The definitions you use for those words are… somewhat off (now there’s an understatement!).

    3) not saying anything different than what can be found in the extant literature.

    Uhm… Perhaps if you squint really hard while reading the literature or if you suffer from a severe lack of reading comprehension, then maybe I can see how you might think that.

  164. 164
    Ogvorbis: Still failing at being human.

    Has anyone else noticed the intersection of science crank, libertarian and Christian fundamentalist? All three are (1) sure that they have the only possible correct answer, (2) are notoriously resistant to evidence — either examining evidence contrary to his or her position or actually supplying evidence to support his or her position, and (3) convinced that the only reason people do not flock to their paradigm is that they don’t understand what AAT, or Jesus, or the Magic Hand of the Free Market, or fill-in-the-blank really means. They never seem to grok that we know what they are selling and still think it is bullshit.

  165. 165
    pentatomid

    The undereducated simply must stop commenting here lest it appear that only the undereducated participate.

    Arrogant shit.

  166. 166
    sawells

    I’m amused by the bit about there being no such thing as natural selection. That means he believes that all creatures pass on their genes at the same frequency regardless of whether they reproduce or not. That’s novel.

  167. 167
    pentatomid

    Ogvorbis (@164)

    I was just thinking the same thing myself.

  168. 168
    Ogvorbis: Still failing at being human.

    And add an “are” to my (3) in 164.

    All hail Grammatika.

  169. 169
    John Doe

    I’ll do these people a favor and tell them what you think natural selection is, James. No need to thank me.

    He seems to think that natural selection means “the selection of nutrients by an organism”.

    This is not the first time he has blatantly changed the definition of an established term to suit his needs. He did the same thing with Darwin’s term “conditions of life”, which if you have read On the Origin of Species, clearly refers to the environmental conditions that an organism is exposed to and must adapt, aka, its habitat. He’s been known to say “the conditions of life are nutrient-dependent and pheromone-controlled”, which makes absolutely no sense. Those do not apply at all as descriptors of the physical environment.

  170. 170
    David Marjanović

    A Lapse in Watchfulness: New York Times Admits

    A Lapse in Basic Knowledge of the World: Noted Kook Uncritically Citing Noted Kooks Who Don’t Even Know That Almost No Science Journalists Ever Understand What They’ve Been Told to Write About

    Also, evolutionnews.org isn’t the NYT. It’s a creationist website, written by people who don’t understand what they read. No wonder they try to use a newspaper article as evidence in a discussion about science.

    Is it really possible that you didn’t notice this?

    thermodynamics of nutrient stress-induced and social stress-induced intercellular changes in the microRNA / messenger RNA (miRNA/mRNA) balance

    This is just technobabble. I know what the words mean; they don’t go together.

    Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intercellular and intramolecular interactions, which result in de novo creation of olfactory receptor genes.

    Explain.

    The fact that no one here is currently willing to accept the biological facts, which are already generally known to serious scientists,

    Did you follow the link to ChasCPeterson’s Google Scholar profile? If not, now would be a good time.

    Our most recent extinct ancestor varied from us by only 96 amino acid substitutions, but most people here seem to have survived just fine without the substitutions that led to higher intelligence. See for example: MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates http://dx.doi.org/10.1371%2Fjournal.pbio.1001214

    Being RNA, miRNA doesn’t contain any amino acids. :-| I have no idea what, if anything, your point is.

    Being RNA, miRNA aren’t pheromones either, and they’re not made from food any more directly than any other RNA (there are nucleases in the gut).

    I’ll admit, I don’t have the knowledge that Chas and David and you others do to challenge this more clearly, but it honestly sounds to me like basically a Gish Gallop, isn’t it?

    Sort of. It’s a prepared script consisting of word salad, regurgitated again and again and again.

    Take “the ecologically adapted mammalian brain”. Uh, of course the mammalian brain is adapted, and adaptation means adaptation to an environment, so you can call any adaptation “ecological”… the whole phrase is a heap of tautologies that means nothing more than look how many technical terms I know, I must be totally smart.

    James Kohl quotes from and article that he referenced. Here is the quote -

    Wow. He quote-mines creationists. He’s the meta-creationist.

    I sit in awe.

    Who quote-mines the quote-miners? James Kohl!

    Ingested plant microRNAs influence gene expression across kingdoms. In mammals, this epigenetically links what mammals eat to changes in gene expression and to new genes required for the evolutionary development of the mammalian placenta and the human brain.

    Wow.

    No. miRNAs bind to specific sites with specific nucleotide sequences. A mammal is exceedingly unlikely to have a site where any miRNA from any plant species could bind. And how exactly do you even get a miRNA into a cell?!? The cells of a plant are all connected to each other, but animal cells lack even plasmodesmata. I’m not aware of any transport system that could get RNA across a cell membrane, or what in the fuck it could be good for. And as I just said, the gut secretes nucleases.

    Genetic manipulation of animal cells requires pretty brutal methods: two methods that come to mind are strong electric pulses that flip patches of cell membrane around, and industrial-grade detergents that partially destroy the cell membrane till it leaks.

    You’re making shit up!

    A gene that codes for the mammalian olfactory receptor, OR7D4, links food odors to human hunger, dietary restraint, and adiposity. OR7D4 exemplifies a direct link from human social odors to their perception and to unconscious affects on human behavior associated with human olfactory-visual integration; human brain activation associated with sexual preferences, human learned odor hedonics; and motor function.

    No idea what your point is. Is it that smells can affect the expression of certain genes? That hasn’t been news since Jacques Monod.

    When your “god” of evolutionary biology

    No.

    Science isn’t hero-worship, and hero-worship isn’t science.

    Worship isn’t science. Science is doubt. You have a lot to learn, young padawan.

    when natural selection is removed from consideration

    It isn’t, and it can’t be. But then, you don’t even understand what the term means.

    and when 3) in the same article Dobzahansky noted that “hemoglobin S differs from A in the substitution of just a single amino acid” and 4) also noted that alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but 5) they differ in a single amino acid (out of 141) in the gorilla — how can you not realize that you are the cranks here because you are too ignorant to be anything but cranks?

    Huh? The chimps are more closely related to us than to the gorillas, so where’s the surprise?

    Seriously, what do you imagine how evolution works?

    Or, is the problem that you clearly recognize that you are the cranks and are desperately trying to substitute me for your nonsensical selves rather than acknowledge that the facts about amino acid substitutions are what make you the cranks?

    Explain to us in your own words what “mutation” means and how amino acid substitutions happen. In particular, explain what problems you have with comment 134.

    Do I smell word salad or boiled head of cabbage?

    “Cabbage”, incidentally, is what Kohl means.

    The undereducated simply must stop commenting here lest it appear that only the undereducated participate.

    Do tell what your education in this subject is. Did you ever study molecular biology at a university? It really doesn’t look like you did. Even what’s highschool knowledge over here has passed you by.

    I am
    [...]
    2) not using terms unknown to scientists;

    You are, however, putting them together into tautological and nonsensical sentences. The sentence “colorless green ideas sleep furiously” is perfectly, impeccably grammatical English, and it consists exclusively of fairly to extremely common English words; and yet it’s meaningless.

    And that’s before we get to those terms you use but clearly don’t understand.

    Because you can’t dazzle us with brilliance, you’re trying to baffle us with bullshit. Be ashamed.

    and
    3) not saying anything different than what can be found in the extant literature.

    Yeah, if we count your papers as part of the literature. *snort*

    “Recent studies show that interactions with pests may promote local plant diversity, accelerate plant evolution, and enhance the proliferation of species over evolutionary time.”

    Uh, how is that surprising? It has long been predicted. Parasites prevent the best competitors from reproducing quickly enough to blanket the landscape, so more diversity remains; parasites exert selection pressure, changing stabilizing to directional selection, resulting in visible changes over generations; and because there are different heritable ways to adapt to parasites, diversification results – just like how you often get ambush predators and pursuit predators for the same prey.

    I’m not saying it wasn’t worth publishing. Every hypothesis needs to be tested. I’m just saying the outcomes of the tests weren’t surprising.

    and there is no such thing as natural selection.

    Oh, do explain. Read comment 166 before you try.

    The idea of natural selection (e.g., via predation) reached its epitome of ridiculousness in the report on snake-centric evolution of the human brain.

    You’ve committed a logical fallacy. Yes, that particular idea was ridiculous; however, your claim that this somehow makes the theory of natural selection itself ridiculous simply doesn’t follow.

  171. 171
    John Doe

    Even worse, here he is mincing the conditions of life definition while also stating his definition means that Darwin was a creationist-

    Click “show message history” on my post at the top.
    http://groups.yahoo.com/neo/groups/evolutionary-psychology/conversations/topics/151760

    james kohl wrote:

    Darwin’s ‘conditions of life’ are obviously nutrient-dependent and pheromone-controlled, which suggests that Darwin was a creationist

  172. 172
    gillt

    James Kohl: comment 158

    1) not pretending to overturn anything;

    [...]

    Natural selection has already been dismissed as a ridiculous idea because it was never supported by experimental evidence. In addition, we now see that mutation-driven evolution has refuted itself, since beneficial mutations cannot result in beneficial adaptations without natural selection — and there is no such thing as natural selection.

  173. 173
    ChasCPeterson

    there is no such thing as natural selection

    lol
    meine Kohlköpfe!!

  174. 174
    CaitieCat, getaway driver

    meine Kohlköpfe!!

    *grabs and raises Chas’ fist in the air*

    The winner, by TKO, fight stopped in the first round when the challenger merely ran around in circles flapping his arms and shouting “PHEROMONES! NUTRITION!” over and over.

  175. 175
    James Kohl

    No need to shout or repeat anything — as if I were a theorist touting mutations. If you scan my most recently published review and find evidence that mutations are naturally selected, we can discuss it — since we’re obviously not going to be discussing the rest of the content.

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    Conclusion: “Unconscious affects that are manifested during the development of diversified life and human behavior are, by their very nature, part of life that few people think about (Kohl et al., 2001). Therefore, the largest contributor to the development of our personal preferences may be the unconscious epigenetic effects of food odors and pheromones on hormones that organize and activate behavior. If so, the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”

    Addendum: My model could also be compared to the theory of mutation-initiated natural selection — if any experimental evidence supported that theory had ever been detailed in the context of how the theory was exemplified in model organisms or via the conserved molecular mechanisms of ecological adaptations that are nutrient-dependent and pheromone-controlled in every species on this planet that has not mutated into another species or emigrated to another planet or is incapable of placing their thoughts into the context of what is known about life on this planet, but has nevertheless survived — as if it did not matter what the conspecifics of that species thought about anything.

  176. 176
    sawells

    ” If you scan my most recently published review and find evidence that mutations are naturally selected, we can discuss it”

    Hang on, you’re saying that the only place we’re allowed to look for evidence for evolutionary theory is in things that you wrote? Fuck off.

    Start here: http://en.wikipedia.org/wiki/Natural_selection and educate yourself until you can talk to other people without embarrassing yourself and others.

  177. 177
    Nerd of Redhead, Dances OM Trolls

    My model

    You haven’t evidenced that you have a working model. I’m not taking your word for anything other than bullshit.

    If you scan my most recently published review and find evidence that mutations are naturally selected, we can discuss it

    Sorry fuckwit, that isn’t how science is done. Your review is bullshit until you show otherwise with experimental evidence. I will read the scientific literature found in libraries at institutions of higher learning world-wide (places you appear to be unfamiliar with.), and that is what will be discussed. If you refute it, you will do so with something other than your mere opinion, with links to third party scientists who back you up. Your word is bullshit.

  178. 178
    Thumper: Who Presents Boxes Which Are Not Opened

    “Pretentious phrasing.” Check

    “Repetition: if the audience didn’t get it the first time, just say the same thing again, twice.” Check

    “A kind of sneering anger that people don’t understand how smart he is.” Check

    “An obsession with one narrow idea, which is his, which explains all of evolution and proves that everyone else is wrong” Check

    Add in a slew of fallacies such as Failure to Elucidate, Argument by Prestigious Jargon and a kind of round-about Appeal to Accomplishment, and you have Mr. James Kohl.

  179. 179
    Ogvorbis: Still failing at being human.

    I think Mr. Kohl’s performance here is worth of The Order of the Brassica, Second Class.

  180. 180
    Rey Fox

    Well, at least the cranks have moved on from their Darwin obsession and onto Dobzhansky obsession. So about a hundred years, there’s a nice leap.

  181. 181
    Inaji

    Chas @ 173:

    meine Kohlköpfe!!

    Pure win. +8

  182. 182
    James Kohl

    @134

    “Amino acid substitutions typically occur when genome copying errors lead to a SNP – single nucleotide polymorphism ( http://ghr.nlm.nih.gov/handbook/genomicresearch/snp ) – and a codon changes. They are the single most common form of mutation that exists. If this guy honestly thinks they are not mutations then he isn’t even writing in English, just gibberish.”

    ———————————-
    Anyone who thinks that the automagical occurrence of mutations that lead to the amino acid substitutions in the above example of someone who is incapable of thinking their way out of the wet paper bag of evolutionary theory should attempt to explain what caused the mutations and how the mutations lead to amino acid substitutions in differentiated cell types that benefit an organism or species by enabling its ecological adaptation or whatever else you think was beneficial.

    You will get bonus points for explaining how the mutations led to amino acid substitutions that were naturally selected. As theorists, however, you will never be penalized for not knowing anything that other theorists do not know. You will be automatically accepted into the “evolution for dummies” club and can chat with other theorists about anything except what has been learned about molecular epigenetics during the past few decades. You can even make up your own theories about cause and effect — except for the one that suggests the human brain evolved for purposes of snake detection. That new theory was proposed last year. But lion, tiger, and bear detection theories are still waiting to be proposed in the context of human brain evolution. Lions and Tigers and Bears. Oh my!

    How does a theorist choose what to theorize about? There are unlimited choices and no biological facts need be considered.

  183. 183
    James Kohl

    @ 25 Azuma Hazuki

    I apologize for dismissing your question and comments. A friend reminded me to address you respectfully — since you are the only one here who has done that to me.

    Why cannot evolution and molecular conservation co-exist?

    I detailed the conserved molecular mechanisms that coexist in Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/17338/20758

    1) You are correct: “If anything, the epigenetic effects and amino [acid substitutions are] conservations reinforce one another, since DNA itself is highly conserved.”

    2) You are correct that “There is also still the endogenous retroviral record to contend with, the head-to-head fusion of ape chromosomes to create human chromosome 2, and so forth. And don’t forget that biology does not stand alone; the geological column and the fossil record also interact with it, and have their tales of eons to tell, as a backdrop to the zipping, zinging, nanosecond-scale interactions at the cellular level.”

    All these considerations are removed from consideration in the theory of mutation-initiated natural selection.

    3) You may also be correct that “Evolution via descent/mutation/selection is not falsified; all this means is that 1) much, much more information is stored in the environment — in Reality Itself — than in the strict sequence of DNA and the resultant proteins thereof, and 2) we now, finally, have an explanation for things that the older strictly-genes model couldn’t explain.

    The only thing that is currently known with absolute certainty is that there is no such thing as mutation-driven evolution, and that may explain why it can’t be falsified. It’s like a ghost in an academic machine that keeps coming back to haunt those who have never seen it because ghosts don’t exist. Evolutionary theorists actually believe they have seen that ghost and it scares them to think it wasn’t real. I think the ghost scares ChasCPeterson and David Marjanović more that most others. They appear to have a vested interest in the ghost’s reappearances, so they see it…. everywhere.

  184. 184
    pentatomid

    Chas, @173,

    That was a thing of beauty.

  185. 185
    James Kohl

    @ 25 Azuma Hazuki

    You may also be interested in the award-winning book chapter that I wrote, which used the same model to explain sexual orientation in yeasts and human male sexual orientation, before the experimental evidence subsequently extended the model to human females.

    The Mind’s Eyes: Human pheromones, neuroscience, and male sexual preferences
    http://www.sexarchive.info/BIB/kohl.htm

    I have the powerpoint slides from my Society for the Scientific Study of Sexuality plenary session that I can provide, if you are interested in a shorter version of the biological facts.

  186. 186
    John Doe

    @182

    Automagical mutations? Replicative enzymes are not perfect. Every once in a while, they add in the wrong base. This can be seen even outside of an organism if you isolate the enzymes and run the replication process in vitro. There’s nothing automagical about that.

    What causes mutations?

    -the imperfection of the replicative systems to begin with
    -radiation
    -mutagen molecules that interfere with replication
    -etc.

    How the mutations lead to amino acid substitutions?

    If a DNA base is altered, an amino acid-coding codon may be altered. If you change the DNA, you change the mRNA, and ultimately, the primary structure of the protein. Depending on the protein, the domain in which the substitution took place, and the nature of the substitution itself (how it affects protein folding), the effect of the mutation may be inconsequential or drastic.

  187. 187
    ChasCPeterson

    dude, have you ever published a single datum in your life?
    (no? hint: that makes you a “theorist”)

  188. 188
    James Kohl

    http://tech.groups.yahoo.com/group/human-ethology/message/48152

    Natural selection http://evolution.berkeley.edu/evolibrary/article/evo_25

    “If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that.”

    My comment: “The [ecological] variation is nutrient availability and nutrients metabolize to species-specific pheromones that control reproduction and heredity. Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

    If it is not that simple, someone needs to explain why they believe in a theory of mutation-driven evolution and detail how mutation-driven evolution occurs.”

  189. 189
    James Kohl

    @187 ChasCPeterson

    As you must know by now, I did not have the luxury of any theoretical approach that still needed experimental evidence to support it. Like many who do not teach biology, my profession forced me to incorporate biological facts. I also had the advantage of being forced to produce results of diagnostic testing that were accurate, not guesses based on theories of biologically-based cause and effect.

    Thus, we have reached an age of science where epigenetic effects on the microRNA/messenger RNA balance have become predictable and the epigenetic effects extend across species via conserved molecular mechanisms that enable us to discern what roles specific microRNAs play.

    Meanwhile, you’ve been watching turtles, haven’t you? Do you think what you have observed will have any significance at all to the future of scientific progress? I think that you already know it won’t and are simply angry at me for calling attention to that fact. If I were a theorist, patient deaths would have accumulated like you think mutations do and I would have mutated into a turtle-watching researcher who believes in ghosts.

  190. 190
    Nerd of Redhead, Dances OM Trolls

    . Evolution by natural selection cannot be the outcome if something is not first selected. Selection is always for nutrients. It is as simple as that.

    Bwahahahahahaha. So fuckwit, selection can’t be for better hair (like polar bears versus their close relative the grizzly) for Artic regions, for a layer of fat for insulation for a colder climate, or losing said layer of fat if the climate gets warmer. Tsk, basic biological facts sail over your head.

  191. 191
    Nerd of Redhead, Dances OM Trolls

    As you must know by now, I did not have the luxury of any theoretical approach that still needed experimental evidence to support it.

    Gee, a repeat of a prior quote from a Nobel prize winner.

    It doesn’t matter how beautiful your theory is, it doesn’t matter how smart you are. If it doesn’t agree with experiment, it’s wrong.
    Richard P. Feynman

    Learn how to do science. Experimental evidence wins every time.

  192. 192
    Azuma Hazuki

    @185/James Kohl

    Now that sounds interesting. I am a lesbian, and would be interested in knowing what the “cause” was, since apparently the signs were there from very early childhood (giant girl-crushes on media/cartoon characters like Sailor Jupiter or Celes from Final Fantasy 6 for example). My parents, bless them, went “Well, duhhhh!” when I came out at age 16.

    It would also be interesting to see how this squares with the various twin studies done on the subject; if I recall correctly, identical twins raised apart all their lives were much more likely to share the same sexual orientation than same-gender fraternal twins raised together, which suggests a pre-natal hormonal influence if not a genetic one.

    And I can provide two data points against “abuse makes girls gay,” as well. My sister took much worse and much more frequent abuse from our father than I did and she is exclusively heterosexual, whereas he mostly ignored me due to my staying out of his way.

    And still, I don’t think you’re seeing the entire picture here. For a long time (and bear in mind I’m a geologist, not a biologist) I’ve felt dissatisfied with the strictly-genes model, but that doesn’t mean it’s wrong, just incomplete. Epigenetics needs something to operate on, and it seems to me you’re sawing off the limb of the tree you’re sitting on in order to make these statements at all.

  193. 193
    ChasCPeterson

    “If you have variation, differential reproduction, and heredity, you will have evolution by natural selection as an outcome. It is as simple as that.”

    This is absolutely true, if you know what the words mean.

    The [ecological] variation is nutrient availability and nutrients metabolize to species-specific pheromones that control reproduction and heredity. Evolution by natural selection cannot be the outcome if something is not first selected.

    You, however, are very, very confused about what the words mean.

    ‘Selection’ is defined as environment-specific differential reproduction of phenotypically variant individual organisms (not environments).
    If the phenotypic variation is heritable (i.e. DNA-coded), such nonrandom differential reproduction results in evolution of populations over generations.
    The most common source of variation in DNA is mutation.
    Do those three sentences make sense to you?
    It really is that simple.
    What’s your problem?

  194. 194
    gillt

    James Kohl @ 189

    Seriously James Kohl, where can we find any original data you have gathered in support of your speculative, hypothetical theory-model?

    Because all I’ve ever seen is you cherry-picking papers and re-interpreting the results to fit some poorly communicated ideas. Time to put up or shut up.

  195. 195
    ChasCPeterson

    Do you think what you have observed will have any significance at all to the future of scientific progress? I think that you already know it won’t and are simply angry at me for calling attention to that fact.

    Naw, man, I’m not angry about that. Want to know why? Because I know that the publication list I linked above represents actual scientific progress. Sure, it’s not Big Science, it’s not human-medical bioscience; it’s little, esoteric niche science that not many people care much about, and I’m fine with that. I have been fortunate enough to be able to pursue my own interests–I’ve had to teach for a living to do that–but I have published observations, measurements, and conclusions that nobody else ever had before. That’s what scientific progress is. Not buzzword-salad data-free Grand Models.
    As for the future of scientific progress, it’s going to be made by people like me who test hypotheses, record observations, and measure aspects of the real world. Not by clowns with a pet hobby-horse Theory Model who just waste time misinterpreting the work of real scientists.

    I’ll tell you what I am angry about, though. I’m a little bit angry that clowns like you can get away with publishing unintelligible crap like the paper of yours I read. And I’m really angry that you are taking advantage of lonely and predatory people by selling them bullshit faux “pheromones”.

  196. 196
    ChasCPeterson

    I should have written ‘lonely and/or predatory people’.

    and now I shall stick me flounce.

  197. 197
    zenlike

    185, James Kohl

    You may also be interested in the award-winning book chapter that I wrote

    You seem to be very focused on the fact that your stuff has ‘won awards’ without specifying those awards. You claim the same thing for your papers at your website. So, which awards did your books and papers win by any chance?

  198. 198
    sawells

    Okay, I’ll bite on the questions in 182 – the conference is over for today and there’s nothing good on telly. Plus somebody smarter than little Jamey might learn something.

    Let’s see:
    “Anyone who thinks that the automagical occurrence of mutations that lead to the amino acid substitutions in the above example of someone who is incapable of thinking their way out of the wet paper bag of evolutionary theory should attempt to explain what caused the mutations and how the mutations lead to amino acid substitutions in differentiated cell types that benefit an organism or species by enabling its ecological adaptation or whatever else you think was beneficial.

    You will get bonus points for explaining how the mutations led to amino acid substitutions that were naturally selected.”

    Ooh, you’re challenging me with questions. Hyakunenhayaii, laddy…

    “What caused the mutations?” Mutations are physical, chemical changes in the DNA structure. Typical causes include ionizing radiation and hydrolysis, both of which can alter the structure of DNA bases. The real biggy, however, is just the imperfection of DNA replication. The fidelity of DNA copying in the cell is excellent but not 100%, so sometimes the new copy of the DNA differs from the original. Such copying errors can take multiple forms:
    SNPs, where a single base is changed. If this occurs in a coding region then it can change a codon (see here : http://en.wikipedia.org/wiki/DNA_codon_table because I don’t believe Jamey knows what a codon is). That in turn means that the protein formed when the gene is transcribed will have a different amino acid at some point in the sequence… which is the amino acid substitution that Jamey has been failing to understand for so long.
    Frame shifts, where a base is simply not copied – that will shift the reading of all the codons downstream and this can change a lot of a protein’s sequence all at once when the new sequence is transcribed.
    Duplications: entire stretches of DNA can be copied twice instead of once, when the transcription machinery stutters. This is a fruitful source of new genes – if now there are two copies of a gene where only one existed before, then in future the two copies can evolve independently and acquire different functions.
    Okay, done that with no problems. Maybe Jamey should have learned more before asking dumb questions, hey?

    “how the mutations lead to amino acid substitutions?” – see above for SNPs, change the coding sequence of the gene and you change the amino acid sequence of the transcribed protein, trivial, bored now.

    “in differentiated cell types” – trivial, since every organism grows from _one_ cell, every cell in the body will end up with a copy of the DNA from that one cell. Maybe you don’t know what you meant by the question? Statistically, my daughter is carrying a copy of 50% of my alleles, and she’ll have around 150 SNPs – places where her inherited copy of my DNA differs from my copy at a single base- and every cell in her body gets a copy! (Yes, I know erythrocytes lose their nuclei, but I’m trying not to scare little Jamey with too much science in one go.)

    “that benefit an organism or species” – For organisms, you must surely know that the vast majority of mutations are _neutral_ with respect to fitness, while of the remainder some will be harmful (typically loss of function) and others beneficial (improved function – unless you believe that every protein is utterly perfect and can’t be improved?). For species – no idea what you think you’re on about, it is individuals that reproduce.

    “You will get bonus points for explaining how the mutations led to amino acid substitutions that were naturally selected.”
    I’ve already explained how changes in the coding sequence of a gene lead to a different amino acid sequence in the protein transcribed from that gene.
    I don’t think you know what “natural selection” actually is. Let’s revise! Evolution is driven by the combination of mutations – which generate random variation – and natural selection – where that random variation is non-randomly pared down.

    What do we mean by natural selection? Well, you’ve probably noticed that organisms reproduce – yes? Also, organisms are not identical to each other, there is variation – yes? And some of those variations are heritable – yes?

    In agriculture, pigeon-fancying, horse-racing etc., it has long been the habit of the discerning animal-breeder to exert _artificial selection_ over the breeding stock. Only those specimens with traits desirable to the breeder – a particularly swift horse, a particularly productive cow, a particularly stupid-looking pigeon – are bred, while others are not and are typically castrated, eaten etc. Thus the heritable variation passed on to the next generation is a _selected subset_ of the variation present in the previous generation, and the traits considered desirable are present at a higher frequency in the next generation than in the previous. Thus much for artificial selection.

    Now, it is also the case for organisms in the wild that they do not all get an equal opportunity to reproduce and pass on their heritable variation. Some – indeed the vast majority – do not leave offspring at all, falling victim to one of life’s innumerable fatal challenges without having successfully reproduced. Thus all the heritable variation in the next generation is again a subset of that present in the previous generation.

    And it must also be obvious to the meanest intellect – even yours, Jamey, even yours if you try really hard – that any variation which unfits a creature for reproduction in any way – making it infertile, or unable to attract a mate, or less resistant to cold or heat or damp or dry, or less able to find food, or less able to avoid predation – will tend to put that creature into the category of those that fail to reproduce. And thus that variation is less likely to be present in the next generation.

    Whereas any variation which makes a creature more capable of reproduction, more able to meet any of the challenges I rehearsed above, is likely to be passed on to the many, many offspring of this reproductively successful bird, beast, bush, bug, or bacterium, and thus will be present at a higher frequency in the next generation.

    And thus process of differential reproductive success is known, by analogy to the artificial selection of stock-breeders, as “natural selection”. There was a terribly nice gentleman by the name of Charles who wrote a little book on the subject, you should really have a look at it.

    Now go get your milk and cookie and go to bed, that’s enough for one day.

  199. 199
    Rey Fox

    dude, have you ever published a single datum in your life?

    Doesn’t need it. He’s got MODELS!

    And I’m really angry that you are taking advantage of lonely and predatory people by selling them bullshit faux “pheromones”.

    True that. Maybe it’s an ad hominem, but I don’t expect much honesty from a snake oil salesman.

  200. 200
    dean

    He may be playing the “I’m a deadly serious scientist with revolutionary ideas” here, but it seems James the self-promoting lab tech is simply using this to further his “lone candle in the wind science” scheme as an aid in selling his snake oil at his his pheromone site.
    Methinks he knows his ideas are crap but needs the controversy as an advertising tool.

  201. 201
    Tethys

    I find it particularly appalling that people like Mr. Kohl actually have advanced scientific degrees and use them to spout utter bullshit in an attempt to undermine science.

    Studying the effect of pheromones on mate selection and pair bonding in humans is actually useful and could tell us something about how we percieve different signals of genetic compatibility*. I would expect to find that the normal physical contacts between humans is the vector by which various endocrine responses are activated, with a smaller input from inhalation.

    If I understand the miRNA paper and the reading I did on epigenetics correctly, it is entirely possible that the environmental variable of ingesting another persons DNA could have a behavioral effect through the mechanism of subtle differences in miRNA processes. Sort of like how grasshoppers can turn into locusts if population and environmental factors are just right? (I’m sorry for using an insect example as I’m sure it will encourage more waggling and fanning from our visitor)

    I am old enough to remember all the mood rings, pheromone sprays, and musk perfumes of the 70′s. Who could forget such classic commercials as Brut – for MEN!, with the bonus “Over The Top” sweepstakes starring Sylvester Stallone in manly combat and giant trucks bursting through paper walls.

    *IIRC, some studies were done which support mate preference for individuals with the greatest degree of genetic variation from their own genome.

  202. 202
    gillt

    what’s with the unsolicited lab tech jab? Is it because you’re a first year grad student?

  203. 203
    David Marjanović

    James the self-promoting lab tech

    Lab tech? What lab? He’s completely unqualified to work in a molecular-biology lab. O_o

    Methinks he knows his ideas are crap but needs the controversy as an advertising tool.

    Methinks he knows nothing, especially not that he knows nothing. He believes he’s above learning the meanings of technical terms!

  204. 204
    John Doe

    @201

    I find it particularly appalling that people like Mr. Kohl actually have advanced scientific degrees

    James holds no degree.

  205. 205
    David Marjanović

    If I understand the miRNA paper and the reading I did on epigenetics correctly, it is entirely possible that the environmental variable of ingesting another persons DNA could have a behavioral effect through the mechanism of subtle differences in miRNA processes.</blockquote<

    Again: How do you get miRNA, let alone DNA, into a cell?

    I think the ghost scares ChasCPeterson and David Marjanović more that most others. They appear to have a vested interest in the ghost’s reappearances, so they see it…. everywhere.

    You’re projecting. :-)

  206. 206
    James Kohl

    @198 sawells

    Thanks for taking the time to detail the theory of mutation-initiated natural selection that has refuted itself in the context of ecological adaptations. It sounds like you may be attending the SICB conference. If so, did anyone present experimental evidence that you think supports what you just tried to teach me about mutation-driven evolution? I noticed in the abstracts that there were indications several other people still believe in the nonsense you just regurgitated.

    Their abstract info would allow me to compare what is currently known about ecological adaptations to any representations that are still based on a ridiculous theory. Just let me know if any of those representations appealed to your understanding about how mutation-initiated natural selection works, or how mutation-driven evolution works without natural selection.

    Did you happen to attend SICB in 2012, or look at the reports from the Ecological Epigenetics Symposium that prompted me to quickly complete my submission last February?

    “In this review, we first highlight the advances that have been made toward understanding molecular epigenetic mechanisms underlying behavioral variation, and their potential role in ecological and evolutionary processes.” http://beheco.oxfordjournals.org/content/early/2013/01/28/beheco.ars145 by Ledón-Rettig, Cris C.; Richards, Christina L.; and Martin, Lynn B.

    Do these folks openly laugh at you when you pass by, or simply laugh at you behind your back? Did you ever read about the advent of sexual reproduction in yeasts of different cell types. Like it is in all species that sexually reproduce, the physiology of reproduction is nutrient-dependent and pheromone-controlled. How does what you think about mutations enable what actually happens in yeasts or any other organisms that sexually reproduce?

  207. 207
    Tethys

    Again: How do you get miRNA, let alone DNA, into a cell?

    I thought that not altering or being coded for in DNA is what is meant by miRNA?
    I didn’t mean to imply that others peoples DNA gets into your cells somehow. I mean it effects the native miRNA by subtle difference in processing.

    One of the links in this thread was to a study on differences in age of sexual maturity for mammals when they were raised separately, with females who were exposed to males during childhood becoming sexually mature at a younger age.

  208. 208
    Nerd of Redhead, Dances OM Trolls

    http://beheco.oxfordjournals.org/content/early/2013/01/28/beheco.ars145 by Ledón-Rettig, Cris C.; Richards, Christina L.; and Martin, Lynn B.

    And they admit there is no change in the DNA coding, therefore it is of limited scope. Just like any sources you cite. They don’t quite say what you claim except by your quote-mining. Which is de rigueur for creobots/IDiots.

  209. 209
    David Marjanović

    It sounds like you may be attending the SICB conference. If so, did anyone present experimental evidence that you think supports what you just tried to teach me about mutation-driven evolution? I noticed in the abstracts that there were indications several other people still believe in the nonsense you just regurgitated.

    …What a deeply bizarre thing to say!

    I thought that not altering or being coded for in DNA is what is meant by miRNA?

    Uh, no. miRNAs are small RNA molecules, coded for in DNA and transcribed from it like every other kind of RNA. They attach to regulatory regions (with complementary sequences) of mRNA, and then the recognition system for double-stranded RNA (mostly an enzyme named Dicer) comes and shreds the whole complex.* It’s one of several ways (perhaps the most wasteful one) of gene regulation after transcription.

    Only eukaryotes have miRNAs. miRNA genes are, however, very easily gained and not easily lost, so there tend to be lots of them in any eukaryotic genome.

    * When double-stranded RNA appears in a cell, it usually comes from a virus, so shredding it on sight is a very useful thing to do.

  210. 210
    dean

    Is it because you’re a first year grad student?

    I’m past the grad student status, but if your comment indicates that I made a slight to lab techs, I apologize. If you trying to support him, I ignore you.

    I made the comment because of the descriptions of his “work history” found online.

  211. 211
    Tony! The Queer Shoop

    john doe @204:
    I wondered about that.

    ****

    James Kohl:
    So, Mr. Creationist, why haven’t you dazzled us with your credentials? We’ve heard all about your award winning books (though as mentioned earlier, we’ve no idea what those awards are), we know you peddle pseudoscienfitc bullshit to people…shouldn’t your creds have come first?

    Oh, and where’s your evidence that there’s any deity, let alone the one you picked?

  212. 212
    gillt

    Hi dean,
    If you say your intention wasn’t to make spurious comparisons between Kohl’s delusions of being a”serious scientist” and his status as a lab tech I’ll take you at your word.

  213. 213
    dean

    If you say your intention wasn’t to make spurious comparisons between Kohl’s delusions of being a”serious scientist” and his status as a lab tech I’ll take you at your word.

    My intention was to make a shot at his self-presentation as a serious scientist when he isn’t. It was not a “shot” at all lab techs.

  214. 214
    sawells

    So Jamey can’t understand a single word of the answers to his stupid, ignorant questions. Quelle surprise!

    I wonder if Jamey would favor us with his definition of “mutation-driven natural selection?” I ask because it’s obviously nothing to do with actual natural selection as understood by real scientists.

  215. 215
    sawells

    And I wonder which bit Jamey thinks is wrong – does he think that living things do not reproduce? Does he think that they are all identical? Does he think there is no inheritance? He’s making a really stupid mistake _somewhere_, but who can guess what specific form his idiocy takes?

  216. 216
    Inaji

    Chas:

    And I’m really angry that you are taking advantage of lonely and/or predatory people by selling them bullshit faux “pheromones”.

    And this is all there is to Herr Cabbage, too. All the rest of it is bafflegab to make the snake oil more palatable. Also, as Tethys says:

    I am old enough to remember all the mood rings, pheromone sprays, and musk perfumes of the 70′s. Who could forget such classic commercials as Brut – for MEN!,

    I’m old enough to remember, too. Hai Karate, anyone? All of which makes what Herr Cabbage is doing much worse, because people would dearly like to believe that there is some way to bypass the messiness of relationships, casual or otherwise, some sort of miraculous shortcut. This is about yet another unethical, unscrupulous asshole who wants to make money off those who can ill afford it (on many levels), and thinks attempting to wrap it up in science terms makes it all okay.

  217. 217
    James Kohl

    @192 Azuma Hazuki

    “Epigenetics needs something to operate on, and it seems to me you’re sawing off the limb of the tree you’re sitting on in order to make these statements at all.”

    The entirety of the concept of molecular epigenetics is gene-environment interactions.

    Epigenetics: An essential mechanism for pruning down the wide range of possible behaviors permitted by genes, selecting those that fit an individual’s environment (Berreby, 2011).

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

  218. 218
    sawells

    Oh, for amusement: googling for “mutation-driven natural selection”, in quotes, brings up… only its use by Jamey. Absolutely nobody else uses the phrase. Now, some people might take that as an itty-bitty hint that this “mutation-driven natural selection” thing is not, in fact, a thing.

    Just to be sure I’ve also put the phrase into Google Scholar and … no hits!

    So, Jamey, just to be clear, whatever you think “mutation-driven natural selection” is, it is nothing to do with anything in science. It is your own personal private wrongness.

    You were also wrong about what conference I’m at, by the way, so you’re batting .000 on everything at the moment.

    Since you couldn’t respond to or refute anything I posted, I’ll take it that you concede your utter rout. No need to thank me for the biology lesson either, it was a pleasure schooling you.

  219. 219
    PZ Myers

    This has been quite nice. Mr Kohl has been thoroughly eviscerated, and right now everyone’s just stirring the viscera.

  220. 220
    chigau (違う)

    Back at #78 James Kohl indicated that he expects to be banned (he called it blocked).
    He’s here for his MeritBadge.

  221. 221
    sawells

    @220: it’s understandable. He can’t make an actual argument in science, but he can be so obnoxious that he gets banned, and then he gets that lovely warm glow of feeling like Galileo. It’s ego-validation.

  222. 222
    PZ Myers

    Why would I ban him? So far, this has been an exercise in humiliation of and by Kohl.

    Well, I suppose banning him would be an act of mercy, and if I were kind…but you know, I’m not a nice person.

  223. 223
    Nerd of Redhead, Dances OM Trolls

    The entirety of the concept of molecular epigenetics is gene-environment interactions.

    Depending on the definition of “environment”. Which usually means age-related turning off of genes due to development.

    Epigenetics: An essential mechanism for pruning down the wide range of possible behaviors permitted by genes, selecting those that fit an individual’s environment (Berreby, 2011).

    For some unbizaire reason, I don’t accept your definition. Might have to due with the fact you are nothing but a liar and bullshitter. Your quote-mining is becoming legendary.

  224. 224
    chigau (違う)

    I think “Stirring the Viscera” might be a good name for a band but I can’t quite figure what genre.

  225. 225
    James Kohl

    @218

    “googling for “mutation-driven natural selection”, in quotes, brings up… only its use by Jamey.

    My name is James V. Kohl, and I had no idea that folks like you are so ignorant as to think that I simply made that phrase up — or that it does not accurately reflect your ridiculous belief.

    Mutation-Driven Evolution http://www.amazon.com/books/dp/0199661731

    “…natural selection is an evolutionary process initiated by mutation.”

    Quote mining at its best! Obviously, however, you do not want others to know what you believe in. You had the chance to tell us that it was not mutation-initiated natural selection. Is it …natural selection: an evolutionary process initiated by mutation, or is it mutation-driven evolution? If so, what is the difference between the phrases and beliefs that accompany them? Aren’t the phrases and the beliefs examples of nonsense?

  226. 226
    chigau (違う)

    I’m pretty sure that St. Heinlein covered that whole mutation thing
    http://en.wikipedia.org/wiki/Orphans_of_the_Sky

  227. 227
    Nerd of Redhead, Dances OM Trolls

    My name is James V. Kohl, and I had no idea that folks like you are so ignorant as to think that I simply made that phrase up — or that it does not accurately reflect your ridiculous belief.

    I had no idea you were so stupid until you opened your mouth and proved otherwise with solid evidence, arrogance, and continuing level of evidenceless assertion and bullshit.

    natural selection is an evolutionary process initiated by mutation.”

    Now, you prove, with third party scientific evidence, this statement is WRONG. Or shut the fuck up arroagant evidenceless fool.

  228. 228
    James Kohl

    @222 PZ Myers,

    I can’t thank you enough for enabling this debate. It attests to the belief of most participants in what has been dismissed as utter nonsense by nearly every serious scientist I know. Even among intelligent evolutionary theorists, the nonsense here is unacceptable. Obviously, that’s why no intelligent evolutionary theorists are here.

    Besides, like me, they would not care if a biology teacher called them a “crank.” Intelligent scientists have learned that biology teachers and theorists have not learned anything new in the past 50 years, but have somehow managed to keep their positions — as scientific progress moves forward and leaves them further and further behind.

    Your blog exemplifies everything that’s wrong with biology teachers today. Keep up the good work, so today’s students have proof of what they were taught, when they finally learn that ecological variation causes nutrient-dependent pheromone-controlled adaptations sans mutations.

    Thanks again.

  229. 229
    Nerd of Redhead, Dances OM Trolls

    It attests to the belief of most participants in what has been dismissed as utter nonsense by nearly every serious scientist I know.

    Assertion without evidence, dismissed as fuckwittery.

    Obviously, that’s why no intelligent evolutionary theorists are here.

    Obviously you have nothing intelligent to say, and only have arrogance to pretend you are right. NOT ONE WHIT OF SOLID EXPERIMENTAL EVIDENCE TO BACK UP YOUR CLAIMS.

    Intelligent scientists

    You aren’t one. You aren’t even a scientist. Just a loudmouthed CRANK.

    Your blog exemplifies everything that’s wrong with biology teachers today.

    No, it exeplifies how real science is done. Question everything. Which you don’t do. If you did, your inane model would be in the dumpster where the experimental evidence says it belongs. But your arrogance and ignorance won’t allow you to see the truth.

  230. 230
    chigau (違う)

    James V. Kohl
    You are a very funny person.

    Since you like it here, try this

    <blockquote>paste copied text here</blockquote>

    it will offset your pasted quotations, thus

    paste copied text here

    It will make it easier for us to read your comments.

  231. 231
    chigau (違う)

    It’s difficult to determine to which people James V. Kohl is responding so if my #230 doesn’t fix things,
    someone with a real name, pass it on, eh?

  232. 232
    James Kohl

    Ecological variation leads to adaptations via nutrient-dependent pheromone-controlled amino acid substitutions that differentiate cell types. That is the only model of species diversity that is supported by experimental evidence.

    I think that fact is why people like this “Nerd of Redhead, Dances OM Trolls” are so hostile and foul-mouthed. The quote from Nei’s book: Mutation-driven evolution did not even register as anything more than something I am supposed to prove is wrong: “natural selection is an evolutionary process initiated by mutation.” It’s not enough to say there is no experimental evidence that supports that statement, I must PROVE that there is no experimental evidence. Has anyone else ever tried to prove there was no evidence for anything?

  233. 233
    James Kohl

    @205

    If I understand the miRNA paper and the reading I did on epigenetics correctly, it is entirely possible that the environmental variable of ingesting another persons DNA could have a behavioral effect through the mechanism of subtle differences in miRNA processes.

    If you are just now reading about epigenetics, you are more than a decade behind. What’s worse is your criticisms of me in the context of mutations theory after I co-authored a Hormones and Behavior review article in 1996 that had a section on molecular epigenetics with details on alternative splicings and sex differences in cell types. Didn’t I mention this before?

    From Fertilization to Adult Sexual Behavior http://www.hawaii.edu/PCSS/biblio/articles/1961to1999/1996-from-fertilization.html

    “Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans (Adler and Hajduk, 1994; de Bono, Zarkower, and Hodgkin, 1995; Ge, Zuo, and Manley, 1991; Green, 1991; Parkhurst and Meneely, 1994; Wilkins, 1995; Wolfner, 1988). That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes.”

    Others extended our mammalian model of hormone-organized and hormone-activated behavior to invertebrates in 2000 and to their life history transitions in 2005. It has since come back around to what we wrote about yeasts, which is represented in James A. Shapiro’s book along with many other aspects of what is currently known by serious scientists.

    I’m beginning to wonder if biology teachers and theorists know anything at all about science. But perhaps they just missed out on 17 years of progress.

  234. 234
    Nerd of Redhead, Dances OM Trolls

    Ecological variation leads to adaptations via nutrient-dependent pheromone-controlled amino acid substitutions that differentiate cell types. That is the only model of species diversity that is supported by experimental evidence.

    Unevidenced claim, dismissed as fuckwittery.

    I think that fact is why people like this “Nerd of Redhead, Dances OM Trolls” are so hostile and foul-mouthed.

    No, I’m a 35+ year practinioner of real science, know real science when I see it, and am a 30+ year skeptic. You are nothing but a loudmouthed arrogant bullshitter of the worst sort. YOU CAN’T/WON’T EVIDENCE YOUR CLAIMS WITH EXPERIMENTAL EVIDENCE. NOTHING BUT YOUR OPINION.

  235. 235
    chigau (違う)

    Has anyone else ever tried to prove there was no evidence for anything?

    T-SHIRT!

  236. 236
    chigau (違う)

    woohoo

  237. 237
    Nerd of Redhead, Dances OM Trolls

    I’m beginning to wonder if biology teachers and theorists know anything at all about science. But perhaps they just missed out on 17 years of progress.

    Perhaps they follow the real evidence, and not blowhards like you. Your model is dumpster feed. Put it where it belongs.
    If you were a real scientist, you could answer the one question you haven’t. What experimental evidence would it take for you to acknowledge your model is bullshit? If the answer is none, you are a crank and will be dismissed as such.

  238. 238
    Colin J

    All you people demanding evidence must be blind, or just not reading the thread carefully enough. Are you forgetting that way back at #77, James Kohl gave us this:

    What happens when you feed one worm something different than another and it morphs into a worm species predator with teeth that eats your other worms? Do you claim it mutated into a monster worm with teeth, or do you ask yourself: Are similar changes nutrient-dependent and pheromone-controlled in every other species on the planet? If similar changes are nutrient-dependent and pheromone-controlled in every other species on the planet, are all species with teeth mutated monsters that arose from mutant worms?

    James Kohl’s worm-based studied are absolutely conclusive. What more evidence can you ask for?

    If you feed human flesh to worms, they immediately evolve into man-eating worms. That’s obvious. Do you think that happens by chance, by random mutation? Do you think it’s a coincidence that they happen to become man-eaters at exactly the same time you give them man to eat? No! It’s absolute proof positive of nutrient-dependent pheromone-controlled adaptation.

    Of course, if you gave them dog food they’d evolve into dogs and if you gave them baby food they’d evolve into babies. Don’t forget, “human” is just an adjective. Incidentally, this also proves that all those stories of pensioners eating dog food are just urban myths. You only get to evolve into a pensioner by eating pensioner food.

    My attention is flagging. I’m off to evolve into something that drinks coffee.

  239. 239
    Inaji

    Hmmmm, pheromone-controlled. I prefer leeched poltroon norm. Or perhaps comprehend loner tool. Maybe clomped northern oleo or cloned hormone petrol. Anagrams go so well with cabbage salad.

  240. 240
    Tony! The Queer Shoop

    @232:

    I think that fact is why people like this “Nerd of Redhead, Dances OM Trolls” are so hostile and foul-mouthed

    Nerd is just as ‘hostile’ to all creationists and pseudoscience shills like yourself. Stop trying to feel special.

  241. 241
    theophontes (恶六六六缓步动物)

    @ Caine

    Anagrams go so well with cabbage salad.

    Kohl’s Law.

  242. 242
    Inaji

    Theophontes:

    Kohl’s Law.

    I like it.

  243. 243
    chigau (違う)

    teamwork!
    thread won!

  244. 244
    James Kohl

    It’s the “Kohlian model” you idiots!

    http://en.wikipedia.org/wiki/Idiot
    An idiot, dolt, or dullard is an intellectually disabled person, or someone who acts in a self-defeating or significantly counterproductive way.

    INVERTEBRATES
    J. Kohl et al (2013) A Bidirectional Circuit Switch Reroutes Pheromone Signals in Male and Female Brains http://www.sciencedirect.com/science/article/pii/S0092867413014761

    VERTEBRATES
    K. Kohl (2012) Diversity and function of the avian gut microbiota [manifested in pheromone-controlled reproduction] http://dx.doi.org/10.1007/s00360-012-0645-z

    ALL ANIMALS
    J. Kohl (in prep): Nutrient-dependent pheromone-controlled ecological adaptations
    Chemical ecology drives adaptations via niche construction. Nutrients metabolize to pheromones that epigenetically effect hormones that affect behavior. The epigenetic effects of olfactory/pheromonal input on invertebrate behavior and vertebrate behavior are hormone-organized and hormone-activated. For example: glucose and pheromones alter the secretion of hormones that affect behavior. Systems biology: This model represents the conservation of bottom-up organization and top-down activation via the 1) thermodynamics of nutrient stress-induced and social stress-induced intercellular changes in the microRNA / messenger RNA (miRNA/mRNA) balance; 2) intramolecular changes in DNA via alternative splicings; 3) non-random experience-dependent stochastic de novo gene creation exemplified by the biosynthesis of receptors; 4) the required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the ecologically adapted mammalian brain; and 5) the reciprocity that links the thermodynamics of gene expression to behavior and altered organism-level thermoregulation in species from microbes to man. Examples of nutrient-dependent amino acid substitutions clarify the involvement of seemingly futile thermodynamic control of intercellular and intramolecular interactions, which result in de novo creation of olfactory receptor genes. Thermodynamically controlled cycles of RNA transcription and protein degradation are responsible for organism-level changes in pheromone production, which enable accelerated changes in the nutrient-dependent miRNA/mRNA balance and thermoregulation of ecological adaptations controlled by the physiology of reproduction.

  245. 245
    ChasCPeterson

    kohlslaw

  246. 246
    James Kohl

    @238

    James Kohl’s worm-based studied are absolutely conclusive. What more evidence can you ask for?

    Cori Bargmann’s worm studies are absolutely conclusive.
    High-content behavioral analysis of Caenorhabditis elegans in precise spatiotemporal chemical environments http://dx.doi.org/10.1038/nmeth.1630

    High-throughput imaging of neuronal activity in Caenorhabditis elegans
    http://www.pnas.org/content/early/2013/10/16/1318325110.abstract

    She may have help from her husband, 2004 Nobel Laureate Richard Axel who shared the prize with Linda Buck (see A novel multigene family may encode odorant receptors: a molecular basis for odor recognition http://www.ncbi.nlm.nih.gov/pubmed/1840504)

    Would the person who asked others to SEND IN THE CLOWNS please rescind their request? They are overwhelming PZ Myers blog. But wait, maybe it’s not a biology teacher’s blog after all. Finally, it dawns on Kohl. This is a blog for biology teachers and clowns! That’s why they’re all here.

  247. 247
    James Kohl

    @245 ChasCPeterson

    kohlslaw

    This comes from the turtle guy who has not yet realized that glucose and pheromones are the two things that impact vertebrate GnRH secretion and link the epigenetic landscape to the physical landscape of DNA in the organized genome of all vertebrates, which links their glucose-dependent brain development to the control of human brain development by the epigenetic effects of pheromones.

    @93 He asked

    And what might be the mechanism responsible for such conservation across so many millions of generations of diverse animals with diverse diets, habitats, and life histories?

    Let me try to make this perfectly clear. The mechanism in the Kohlian model is GnRH pulse frequency.

    Did you not see that fact represented in the diagram? Please link it again, so that others can see how difficult it is for you to grasp the obvious.

  248. 248
    ChasCPeterson

    more kohlslaw

  249. 249
    theophontes (恶六六六缓步动物)

    an intellectually disabled person

    Why the overt ableism?

  250. 250
    pentatomid

    James Kohl, @244

    PLease provide some literature that:
    1)Clearly and unambiguously supports your model while being in clear contradiction to evolution by natural selection.
    2)Was not written by you.

  251. 251
    pentatomid

    Oh and I mean serious, peer-reviewed stuff.

  252. 252
    Weedless Monkey

    theophontes

    Kohl’s Law.

  253. 253
    Thumper: Who Presents Boxes Which Are Not Opened

    I am only a lay person and am frankly confused by all the jargon. How exactly does Mr. Kohl suppose that evolution occurrs without mutations? I understand that nutrients and pheremones are involved somehow, but that’s about it.

    Presuming that Mr. Kohl accepts that DNA provides the “instructions” for our bodies development, then surely he accepts that DNA must change in order for evolution to occurr. What does he call these changes if not mutations?

    @James Kohl

    intellectually disabled

    Dude, not cool.

    @Chas C Petersen

    kohlslaw

    Hah!

  254. 254
    Nerd of Redhead, Dances OM Trolls

    Please link it again, so that others can see how difficult it is for you to grasp the obvious.

    Why bother. If you wrote it, it is nothing but bullshit from start to finish. Just like your prose here. Authoritarian bullshit, full of buzzwords linked in impossible ways, meaning nothing at the end of the day.

  255. 255
    Lofty

    As relevant as anything posted here by Herr Kohl I’ve been reading up on the cabbage looper. Fascinating which way evolution takes a humble cabbage and its foe.

  256. 256
    Nerd of Redhead, Dances OM Trolls

    The mechanism in the Kohlian fuckwitted model is GnRH pulse frequency.

    Don’t know what the words mean….

  257. 257
    pentatomid

    Thumper,

    Trust me, I think you’re not half as ‘confused by all the jargon as James Kohl is. He uses all these words (natural selection, mutation,… ) but I don’t think they mean what he thinks they mean. Reminds me of that other nut, the one with all the gyres. Can’t remember his name.

  258. 258
    Nerd of Redhead, Dances OM Trolls

    Reminds me of that other nut, the one with all the gyres. Can’t remember his name.

    Remove the stars, as that nut Googles his name: V*inc*ent Fl*eur*y.

  259. 259
    Anri

    James kohl waaaay back @ 125:

    But first you must indicate how a beneficial mutation somehow knew it would be beneficial, or how it was naturally selected outside the context of receptor-mediated beneficial movement across a chemical gradient that enabled one of the chemicals to induce the de novo creation of the receptor.

    Well, I might give it a shot – but first, I have to qualify what you mean by a beneficial mutation knowing it is beneficial.

    For example, a mutation causing an organism to be born without eyes – would that be a beneficial or a harmful mutation?

  260. 260
    Ogvorbis: Still failing at being human.

    James Kohl:

    Have you considered, within your model, the influence of lunar gyres on the expression of pheromone emission within the concept of receptor-mediated gene mutational nutrition? If not, why not?

  261. 261
    James Kohl

    What is missing from all the nonsense and the criticisms of what seems unlikely to ever be understood by pissy little schoolboys and their biology teachers is consideration of biological facts like this:

    “…because phenotypic variation decreases through geologic time, because microRNAs (miRNAs) increase genic precision, by turning an imprecise number of mRNA transcripts into a more precise number of protein molecules, and because miRNAs are continuously being added to metazoan genomes through geologic time, miRNAs might be instrumental in the canalization of development. Further, miRNAs ultimately allow for natural selection [of food] to elaborate morphological complexity, because by reducing gene expression variability [and deleterious but not neutral mutations], miRNAs increase heritability, allowing selection to change characters more effectively.” http://dx.doi.org/10.1002/bies.200900033

    There is now clear evidence that the nutrient-dependent pheromone-controlled microRNA/messenger RNA balance is responsible for amino acid substitutions and the ecological adaptations that result in different “body plans” with comparable physical features like teeth in nematodes, beaks of birds, and variations in the structure of teeth in all primates. There has never been any experimental evidence that supports mutation-initiated natural selection (or mutation-driven evolution). The only natural selection that is required for species diversity is the natural selection of nutrients which is receptor-mediated in species from microbes to man.

    Because the details of the body plan have been placed into a context that does not require either mutations or natural selection for physical features, the inability of theorists to tether their theories to any biologically-based discipline whatsoever spells the end of evolutionary theory and its replacement with a model of ecological adaptations, which are obviously nutrient-dependent and pheromone-controlled. The fact that molecular biologists saw this replacement coming 50 years ago, and told bird-watchers and butterfly collectors to watch for the change (not watch birds) attests to the ignorance of virtually ever participant or lurker who has visited this blog. Nevertheless, if there is but one intelligent potential discussant here, I will cite the latest research — reported last month, and on Jan 7 and on Jan 8 so that discussion of biological facts instead ridiculous beliefs may follow.

    We know who the idiots are. Thus, the question is: are there any intelligent potential discussants here?

    Alternatively, you can find the latest research in contributions on my blog, in my published works and in the in prep article I will complete as soon as I am completely fed up with the nonsense here.

  262. 262
    Thumper: Who Presents Boxes Which Are Not Opened

    @pentatomid

    Seeing as, back at #125 as quoted by Anri, he appears to be saying that a) mutations are capable of knowing something and b) are capable of telling the future, and if mutations didn’t know in advance that they were beneficial then natural selection is debunked, somehow; then I am inclined to agree with you.

    His main tactic seems to be Argument by Prestigious Jargon, to put it politely.

  263. 263
    Rey Fox

    Front-loading?

  264. 264
    Nerd of Redhead, Dances OM Trolls

    Because the details of the body plan have been placed into a context that does not require either mutations or natural selection for physical features, the inability of theorists to tether their theories to any biologically-based discipline whatsoever spells the end of evolutionary theory and its replacement with a model of ecological adaptations, which are obviously nutrient-dependent and pheromone-controlled.

    Meaningless word salad by a supreme egotist. Show me, from legitimate sources outside of yourself, how an adaptation is known to be beneficial, when there is no imaginary deity to make that decision, or you for that matter.

  265. 265
    ChasCPeterson

    miRNAs ultimately allow for natural selection [of food] to elaborate morphological complexity

    That is the single most dishonest piece of citation I have ever seen.
    Not content with good ol’-fashioned quote minig, this guy has to deliberately alter the mined quote so that it means something entirely different from what its authors intended.

    Kohl, you and your slaw are beneath contempt.
    Good luck storming the castle, asshole.

  266. 266
    James Kohl

    @255

    I’ve been reading up on the cabbage looper. Fascinating which way evolution takes a humble cabbage and its foe.

    What fascinates me is the inability of theorists to think in terms of biologically based cause and effect — even when they read the literature. For example, you read EVOLUTION “into” the story of the cabbage looper, when natural history-driven cause and effect eliminates mutations and evolution by placing cause and effect into the context of ecological adaptations based on natural selection for

    1) what the larvae eat,
    2) what the caterpillars eat, and
    3) how the male moth finds a female mate based on what she ate during her multi-stage morphogenesis, which results in the production of species-specific pheromones that control the physiology of reproduction in species from microbes to man.

    See for example: Natural history-driven, plant-mediated RNAi-based study reveals CYP6B46’s role in a nicotine-mediated antipredator herbivore defense http://www.pnas.org/content/early/2013/12/27/1314848111.abstract

    Even if you cannot comprehend anything in the article linked above, the title alone “Natural history driven…” tells you that this is not about mutation-driven evolution. Thus, an intelligent evolutionary theorist would acquire a copy of the article and ask “Why is there no mention of MUTATION in the context of what is obviously natural history-driven?”

    If the theorist had been taught by PZ Myers, they would ask: Is PZ Myers a “crank” for continuing to teach a ridiculous theory to unsuspecting students, or is he merely so incredibly stupid that he has never learned anything about biologically based cause and effect because he believes in a ridiculous theory?

    Thanks again, PZ, for facilitating this discussion. I apologize for merely inferring you are the “crank” here.

    Let me be perfectly clear: PZ is one of a long line of “cranks” who think that people who understand the basic principles of biology and levels of biological organization required to link sensory cause to ecological adaptations manifested in the human brain are “cranks.”

    “Accepting that the brain is a highly plastic, modularly dimorphic, developmentally biased organ of learning, one which is organized and activated by both hormones and experiences across the lifespan, is essential for doing ‘‘good science’’ well. Interactionist theories of psychosexual development provide an empirically sound, strong, yet modifiable foundation for testable hypotheses exploring biologically biased sexual learning.” — James C. Woodson (2012)

  267. 267
    Nerd of Redhead, Dances OM Trolls

    If the theorist had been taught by PZ Myers, they would ask: Is PZ Myers a “crank” for continuing to teach a ridiculous theory to unsuspecting students, or is he merely so incredibly stupid that he has never learned anything about biologically based cause and effect because he believes in a ridiculous theory?

    You are the one with the ridiculous theory, not PZ. PZ is a realist, unlike you. Your attitude won’t win you this argument. It requires a level of experimental evidence you have failed to provide.
    Lose the arrogant attitude. It marks you as a crank, not a legitimate scientist.

  268. 268
    chigau (違う)

    They laughed at me at the Academy!
    Laughed!
    I’ll show them!

  269. 269
    gillt

    Who is Kevin D. Kohl?

  270. 270
    gillt

    Kohl

    [My model] is the only model of species diversity that is supported by experimental evidence.

    Where can I find a concise description then application of this model across taxa and ecologies?

  271. 271
    John Doe

    Further, miRNAs ultimately allow for natural selection [of food] to elaborate morphological complexity, because by reducing gene expression variability [and deleterious but not neutral mutations], miRNAs increase heritability, allowing selection to change characters more effectively.

    Wow. Are we going to have to have another Fink/Chelo situation here? Should I pass this blatant misrepresentation along like the others and get a response straight from the source that you’re wrong?

    Your second addition doesn’t even make sense. It’s concerning expression variability, not sequence variability.

    For the record, I have, on two occasions, successfully contacted authors of papers that Kohl has seemingly drawn fallacious conclusions from. Lo and behold, they both told me that he did indeed draw conclusions that did not logically follow from the premise of the papers.

    The most important part, however, is that one person that I contacted was a coauthor of a paper Kohl contributed to! Not even his colleagues agree with him.

  272. 272
    Nerd of Redhead, Dances OM Trolls

    Gillt#270

    Where can I find a concise description then application of this model across taxa and ecologies?

    From legitimate sources outside of yourself. Cite your own unexperimental work, and tacitly acknowledge your crankdom.

  273. 273
    Nerd of Redhead, Dances OM Trolls

    My #272 is aimed at JK, using Gillt’s request.

  274. 274
    Tony! The Queer Shoop

    pentatomid:

    Oh and I mean serious, peer-reviewed stuff.

    James Kohl reviewed his own papers. Isn’t that enough?

  275. 275
    Tony! The Queer Shoop

    Chas:
    Seriously?
    Kohl…slaw?
    That’s aaaaaaaawful :)

  276. 276
    pentatomid

    Nerd of Redhead, @258

    Yeah, that’s the one!

  277. 277
    pentatomid

    Tony, @274

    James Kohl reviewed his own papers. Isn’t that enough?

    I guess maybe it is, since he’s a SERIOUS SCIENTIST…

  278. 278
    zenlike

    Yep, if you are refuted by the entirety of the scientific field you claim to be part of, just call every other scientist except yourself a crank. Keep digging that hole boyo.

  279. 279
    gillt

    Kohl:

    See for example: Natural history-driven, plant-mediated RNAi-based study reveals CYP6B46’s role in a nicotine-mediated antipredator herbivore defense. Even if you cannot comprehend anything in the article linked above…

    It’s you, James Kohl, who failed to comprehend the article. The paper attempted to link the expression of a single gene to a particular anti-predatory defense under controlled experimental conditions. It’s almost as if you all you saw and comprehended was the first half of the title of the paper.

    The authors artificially silenced a naturally occurring and evolved gene to determine its function. They made a transgenic plant that silenced larval gene expression when ingested (the engineered plant made an insect gene specific silencer), thus reducing its DNA sequence dependent evolved function to metabolize or transport nicotine.

    The interpretation of the results is a little dodgy in my opinion since a functioning cyp gene is thought to break-down nicotine, but the whole molecule is needed to deter spiders. Nonetheless larva with cyp transcripts in their midgut were differentially avoided by predators, suggesting that cyp does not completely metabolize nicotine or only transiently metabolizes is so it can be exported out of the gut…or something. The reason the paper doesn’t say anything about mutation-driven evolution is because this isn’t a paper about the evolution of the CYP family genes; it’s about artificially silencing expression of cyp to see if it plays a role in anti-predator defense.

  280. 280
    John Doe

    The reason the paper doesn’t say anything about mutation-driven evolution is because this isn’t a paper about the evolution of the CYP family genes; it’s about artificially silencing expression of cyp to see if it plays a role in anti-predator defense.

    That’s another thing he does a lot. If a paper doesn’t specifically mention mutation and natural selection, he takes that as a sign that the authors don’t believe in it, which is obviously fallacious. Of course, this is another thing I have previously pointed out to him and yet that leap in logic still persists.

  281. 281
    John Doe

    @274

    I once tried to contact the chief editor of Socioaffective Neuroscience & Psychology, Harold Mouras, urging him to reevaluate Kohl’s paper and pointing out some of the flaws that were also noted here, but I never got a response.

  282. 282
    Rev. BigDumbChimp

    I think the overall message I am getting here is:

    Words mean things

  283. 283
    chigau (違う)

    and
    ‘When I use a word,’ Humpty Dumpty said, in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’

  284. 284
    Inaji

    Chigau:

    and
    ‘When I use a word,’ Humpty Dumpty said, in rather a scornful tone, ‘it means just what I choose it to mean — neither more nor less.’

    That quote has been running through my brain since Herr Cabbage first showed.

  285. 285
    Rich Woods

    Fuck. Well, that was a thread I could have left out of my life. Maybe there’s something to this ‘internet addiction’ concept after all…

  286. 286
    David Marjanović

    Is it …natural selection: an evolutionary process initiated by mutation, or is it mutation-driven evolution?

    Those are not the same thing. That’s why Nei bothered writing his book, you dolt.

    The usual idea is that enough mutations happen for everything, so selection is the important step. Nei says that, no, you have to wait for the right mutations to happen.

    So, his idea is mutation-driven instead of selection-driven. That’s why he used this distinction as the title of his book.

    Once again you misunderstand technical terms but use them anyway.

    Instead of noticing the obvious, you only read to quote-mine. Instead of reading scientific works for understanding, you perform exegesis on them. Shame on you!

    I can’t thank you enough for enabling this debate. It attests to the belief of most participants in what has been dismissed as utter nonsense by nearly every serious scientist I know.

    Then get to know more scientists – preferably serious ones!

    Besides, like me, they would not care if a biology teacher called them a “crank.”

    Oh, look! An argumentum ad hominem!

    Plus, it contains a dishonest omission! University professors don’t only teach; they also do research. The whole idea behind a university is that the teaching is done by people who actually do the stuff they teach. Ask Google Scholar for PZ, and you shall find.

    teamwork!
    thread won!

    Quite!

    It’s the “Kohlian model”[,] you idiots!

    :-D :-D :-D :-D :-D

    Hint: the missing comma isn’t what I’m laughing at. :-)

    INVERTEBRATES
    [...]

    VERTEBRATES
    [...]

    ALL ANIMALS

    “Invertebrates” is a thoroughly misleading term. Vertebrata is just one branch of the chordate deuterostome bilaterian animals. “Invertebrates” just means “all animals except Vertebrata”.

    You’re 100 years out of date and berate people for being 17 years out of date?

    J. Kohl (in prep):

    Seriously? You cite an “in prep.” manuscript?

    because phenotypic variation decreases through geologic time

    Does it? Has anybody quantified that?

    You see, I’m a paleontologist, and to me it doesn’t at all seem like phenotypic variation… varies much, definitely not like it decreases. You’ll forgive me for not being convinced by a mere assertion.

    and because miRNAs are continuously being added to metazoan genomes through geologic time

    It’s not like they’re never lost!

    Further, miRNAs ultimately allow for natural selection [of food]

    Several people have already explained to you that that’s not what natural selection means! It means that the environment, not any organism, metaphorically “selects” those organisms whose offspring will be overrepresented in the next generations!

    Did you fail highschool, or did highschool fail you?

    by reducing gene expression variability [and deleterious but not neutral mutations], miRNAs

    miRNAs cannot reduce mutations. They can’t do anything about mutations. They do not and cannot modify DNA, which is what “mutation” means.

    FFS.

    There is now clear evidence that the nutrient-dependent pheromone-controlled microRNA/messenger RNA balance is responsible for amino acid substitutions

    Please explain in your own words how amino acid substitutions happen. Go into as much molecular detail as you need, I have a bachelor degree in that stuff, I can take it.

    1) what the larvae eat,
    2) what the caterpillars eat,

    …You know what a caterpillar is, right…?

    Even if you cannot comprehend anything in the article linked above, the title alone “Natural history driven…” tells you that this is not about mutation-driven evolution. Thus, an intelligent evolutionary theorist would acquire a copy of the article and ask “Why is there no mention of MUTATION in the context of what is obviously natural history-driven?”

    The article is not about evolution in the first place. It explains what is, not how it came to be.

    Did you really not notice?

    Seriously?

    The most important part, however, is that one person that I contacted was a coauthor of a paper Kohl contributed to! Not even his colleagues agree with him.

    Wow.

  287. 287
    Colin J

    James Kohl @261:

    We know who the idiots are. Thus, the question is: are there any intelligent potential discussants here?

    If that’s the question then why do you say “we” in the first sentence? Are you using the royal “we”?

    I’ve suspected for a while now – we’re dealing with Old King Kohl.

    Thumper: Token Breeder @262:

    Seeing as, back at #125 as quoted by Anri, he appears to be saying that a) mutations are capable of knowing something and b) are capable of telling the future, and if mutations didn’t know in advance that they were beneficial then natural selection is debunked, somehow; then I am inclined to agree with you.

    Clearly it’s not selection if the mutations aren’t working towards a goal.

    John Doe @271:

    Not even his colleagues agree with him.

    It’s easy for them to disagree. They don’t have pheromones to sell.

  288. 288
    chigau (違う)

    So.
    Are we done here?

  289. 289
    John Doe

    @288

    Of course not. James will reply with another copy+pasted diatribe that doesn’t directly address any comment here and expect that we will be swayed by it.

  290. 290
    ChasCPeterson

    I’ll take over here.
    Ecological adaptation occurs by nutrient-regulated pheromone-controlled amino acid substitutions in species from microbe to man.
    Any questions?

  291. 291
    chigau (違う)

    ChasCPeterson #290
    so that includes Brassicas?

  292. 292
    theophontes (恶六六六缓步动物)

    @ ChasCPeterson #290

    Tardigrades?

  293. 293
    ChasCPeterson

    The utter ignorance of these questions proves that there are no serious scientists here, only biology teachers. Nutrient-dependent mRNA/miRNA balance drives species diversification from microbes to man, as Dobzhansky knew in 1964. Pheromone-controlled GnRH pulse frequency affects effects of affective reproduction effects due to affective nutrient selection. Every serious scientists has known this for 37 years.

  294. 294
    theophontes (恶六六六缓步动物)

    X’D

  295. 295
    chigau (違う)

    I’m an archaeologist…
    I’m …
    I …
    *you big meany*
    *runs away*

  296. 296
    Anri

    …I guess my question was a bit too hard.

    Sorry ’bout that.

  297. 297
    Ogvorbis: Still failing at being human.

    Chas @290:

    Any questions?

    Yes.

    How do the lunar gyres influence the regulation of nutrient-regulated pheromone-controlled amino acid substitutions in species from microbes to man? Additionally, how would pheremones and microbes interact?

  298. 298
    James Kohl

    @293 ChasCPeterson

    Nutrient-dependent mRNA/miRNA balance drives species diversification from microbes to man, as Dobzhansky knew in 1964. Pheromone-controlled GnRH pulse frequency affects effects of affective reproduction effects due to affective nutrient selection.

    I hope that others immediately see the overwhelming fear that Peterson expressed in his deliberate misrepresentation of my works and my comments here. Misrepresentation of facts is one of the “last-ditch” efforts that I commonly see come from the ranks of ignorant theorists, and Peterson’s ignorance is exemplified in a NY Times article about “fish-faced” attraction.

    “…a neuron called TN-GnRH3 became active in the females when they saw the familiar male, releasing peptides into the brain that made the female more receptive to mating.”
    http://www.nytimes.com/2014/01/07/science/these-females-prefer-a-familiar-fish-face.html?emc=eta1

    If you ask someone like Peterson to explain how GnRH is involved in sexual attraction in other fish or in turtles or birds, you might get something similarly stupid. He is unable to differentiate between sensory EFFECTS on hormones like GnRH and the AFFECTS of hormones on behaviors. Therefore, he is one of many fools incapable of understanding the conserved molecular mechanisms that I have modeled.

    In moths, for example, juvenile hormone (JH) is similar to GnRH, and JH is involved in the development of the sexual preferences of males for adult females that have developed from single celled (eggs) larvae to multicellular (caterpillars) larvae to finally become reproductively mature females that control the physiology of reproduction in males via their nutrient-dependent secretion of species-specific pheromones.

    Peterson and also Marjanović and PZ Myers would, no doubt tell you that bird predation controls reproduction in moths — as shown in the peppered moth example of accumulated mutations and mutation-initiated natural selection. That explains their belief that the faces of vertebrates, such as male fish are attractive to females; that male turtles choose females who are, anthropomorphically, not just another pretty face; and that female birds chose for plumage color and vocalization of males. (It does not explain non-heterosexual attraction in any species, but who cares about that).

    Their ridiculous beliefs will never change. We know this because experimental evidence has established the role of nutrient-dependent pheromone-controlled amino acid substitutions in 1) eye regression in cave fish; 2) plumage color in birds; and 3) in all morphological characteristics that exemplify the differences in species that bird watchers and butterfly collectors observe. Thus, no matter how much evidence continues to accumulate, if Peterson decides to determine what causes sexual attraction in turtles, he will design an experiment to show that male or female faces (or colors) are obviously the cause, because that fits with his belief in a ridiculous theory. And now, it fits what was reported in the NY Times about “fish-faced” attraction.

    See, for comparison, my comments on the advice for increased dietary choline, “fish odor” syndrome, and brain development in mammals in my recent review. Start thinking about how to make fish faces more attractive to increase the world-wide decline in populations of fish, or start making sense of conserved molecular mechanisms in species from microbes to man.

    Remember, no one is forcing you to be an ignorant theorist; you must do that to yourself.

  299. 299
    sawells

    Jamie, you’re going to have explain what _you_ think the words “amino acid substitution” mean, because the meaning of that phrase as used by real scientists is clearly not the meaning in your head. In scientific usage it means a change in the peptide sequence of a protein, with one amino acid in the sequence being replaced by a different one, caused by a single nucleotide polymorphism in the DNA sequence coding for that protein. See for example http://cancerres.aacrjournals.org/content/58/4/604.short

    Explain what _you_ think you mean. I don’t think you actually can. I also think that you are persistently misreading the scientific literature because you mistakenly believe that you know what the words mean, and you clearly don’t.

  300. 300
    Nerd of Redhead, Dances OM Trolls

    Remember, no one is forcing you to be an ignorant theorist; you must do that to yourself.

    And you do a mighty fine job of being an ignorant and evidenceless theorist JK, with a word salad inane “model” without any hope of being recognized as anything other than crank bullshit by the scientific community.

    Stop with the attitude. You can’t force your idea on us. We must accept it, but we will only do so if your word salads made scientific sense, and you presented the copious third party evidence that actually backs up your theory. Which means you have to read and understand the FULL papers, not just the titles and abstracts. And you have to use those words with their commonly used definitions. Which you consistently fail to do. Failure all around, and the problem is yourself, not us.

  301. 301
    James Kohl

    “I think it is interesting that the nervous system is so well preserved, from an evolutionary point of view, that you can observe a nerve-cell-specific expression of a pig gene in a zebrafish. It is impressive that something that works in a pig also works in a fish,” says Knud Larsen. (in a news report on this open access article: http://www.sciencedirect.com/science/article/pii/S2211546313000594)

    I think it is interesting that some evolutionary theorists believe mutation-initiated natural selection in moths extends to a snake-centric theory of evolution of the human brain based on our adaptively evolved visual acuity and ability to detect snakes. http://news.sciencemag.org/evolution/2013/10/did-snakes-help-build-primate-brain.

    But, after nearly 300 posts here, I may have said that before. And, we shall certainly see theorists repeat what they’ve been saying about evolution for the past several decades, despite what is now known about the basic principles of biology and levels of biological organization that links sensory cause to effects on hormones that affect behavior.

  302. 302
    sawells

    So, you can’t explain what you mean by “amino acid substitution”, then? Thought not. I’ve told you what scientists understand by the phrase; what do _you_ mean?

  303. 303
    chigau (違う)

    OMFG
    Chas, you are actually speaking Kohl’s language.

  304. 304
    Tony! The Queer Shoop

    James Kohl:
    You still have not produced evidence to support the claims of your pheromone enhancing products.
    Put up or for your own sake, shut up.

  305. 305
    Ogvorbis: Still failing at being human.

    James Kohl:

    You have a model that overturns the dominant paradigm of evolution via natural selection. You claim to have evidence that this model is destined to be the new dominant paradigm. You claim your antithesis will become the new thesis for evolutionary biology.

    Fine.

    Why are you pissing away your time here rather than applying for grants which would allow you to gather more evidence for your model? Why are you spending your time and energy here rather than preparing your earth-shattering paper which will overturn all that we think we know about evolution?

    When Alvarez et al published their evidence for an end-Cretaceous bolide impact, they created a brand new antithesis — the new synthesis is still being argued out the way that science always gets argued out — lots of vituperative letters, articles, papers, and books. Eventually, palaeontologists will arrive at something that will become the new synthesis. The point is, Alvarez et al actually published the paper that they thought would overturn the dominant paradigm of the time. They found the evidence and they published. Had they taken your route, they would have traveled the country giving talks to random groups of people and, no matter how good their evidence, they could/would have been dismissed as cranks (well, the senior Alvarez already had a Nobel Prize, so ….).

    So, put up. Stop arguing in circles (really, dude, I’m an historian and even I know that you can’t really use the model in your unpublished paper as evidence for the existence of your new model). Get the grants. Find the evidence. Win a fucking Nobel Prize for showing that 99.999% of evolutionary biologists are completely wrong. Do it. Stop mucking about on a blog comment thread and fucking do it!

  306. 306
    ChasCPeterson

    Darn it. I got it wrong?
    Sorry, man; you weren’t here and so I thought I’d try to supply the boilerplate. Did my best.

    He is unable to differentiate between sensory EFFECTS on hormones like GnRH and the AFFECTS of hormones on behaviors.

    It’s true! *sob* That makes no sense to me! I am SO embarrassed.

    bird predation controls reproduction in moths

    uh

  307. 307
    Rey Fox

    So basically Kohl is saying “pheromones control such-and-such genetic/chemical reactions in organisms, therefore pheromones are EVERYTHING and oh by the way buy my pheromones”? I want to make sure I’m not missing anything.

  308. 308
    Thumper: Who Presents Boxes Which Are Not Opened

    @James Kohl #298

    …the faces of vertebrates, such as male fish are attractive to females…

    Wait… you think fish are attracted to each other by facial appearance?

    That seems like bollcoks, but for the life of me I can’t think of a logical reason why. Fish of a certain species may all look the same to me, but…

  309. 309
    Thumper: Who Presents Boxes Which Are Not Opened

    @Rey Fox

    It’s all wrapped up in incomprehensible jargon which, according to those better educated in biology and genetics than I, doesn’t mean anything even when you know what the individual words mean; but that’s about the strength of it, yeah.

  310. 310
    ChasCPeterson

    you think fish are attracted to each other by facial appearance?

    I think he’s ridiculing the idea (despite the DATA).
    All is pheromone-controlled and nutrient-dependent. All.

  311. 311
    PZ Myers

    That explains their belief that the faces of vertebrates, such as male fish are attractive to females

    Uh, zebrafish are sexually dimorphic. They live in a sea of signals — tanks can be conditioned by the presence of breeding fish to encourage horniness in new fish, and there are also fear pheromones that can change the behavior of a whole school, so there really is something to this idea of an exchange of chemical signals — but they don’t seem to color responses to individuals. Zebrafish provoke mating by responding to the rising of the sun, by poking at potential mates, by ‘flirting’ with acrobatics. They target females visually: a large belly, bold dark stripes (they respond to environmental stresses by going pale), and size are very, very important. I don’t know about specific responses to faces, but there are distinct whole body patterns that influence mating.

    Do I need to mention the hyperstimulus experiments on swordtails, where female fish were highly responsive to larger sword prostheses? No pheromones involved, just a more prominent visual target.

    It looks like Kohl fails at basic ethology, as well as at understanding the molecular biology of evolutionary change.

  312. 312
    gillt

    I, for one, want to extend a tiny bit of gratitude to James Kohl for serendipitously highlighting some useful papers for which I was previously unaware. Granted, Kohl is a bullshit artist with no understanding of the papers he cites or the words he types and I hope his snake oil business never sells another bottle of shitty water.

  313. 313
    PZ Myers

    sawells, #299:

    Jamie, you’re going to have explain what _you_ think the words “amino acid substitution” mean,

    I second that. It’s really unclear what mechanism he’s talking about: the way you get amino acid substitutions is by changes in the nucleotide sequence of DNA, which is the mechanism of mutation that he seems to deny exists. Unless he’s talking about RNA editing, which would be really weird and specific, and not at all a likely mechanism.

    Kohl is not only bad at science, he’s bad at communicating.

  314. 314
    James Kohl

    @297

    how would pheremones and microbes interact?

    1) Nutrient-dependent production of pheromones controls reproduction in species from microbes to man.

    @305

    you can’t really use the model in your unpublished paper as evidence

    2) I’ve published a series of papers,a book, and a book chapter with and without co-authors that detailed my model of cause and effect before it was extended to insects from mammals and then back to yeasts (and bacteria) in my mammalian model.

    @305

    Why are you pissing away your time here rather than applying for grants which would allow you to gather more evidence for your model?

    3) Post publication and after 2 decades of increasingly detailed experimental support that links nutrient-dependent pheromone-controlled ecological adaptations to differences in cell types of individuals in all species, I am pissing away my time here because evolutionary theorists are still touting the nonsense that is killing people. Theorists want nutrient-dependent pheromone-controlled ecological adaptation via amino acid substitutions to only be considered in the context of mutations and attraction to fish faces as you have seen here.

    As I probably said before, I’m here because this is where the ignorance is, and because PZ Myers invited me to comment on the ignorance. How could I refuse his invitation?

    How could I not add — for the “fish faced” attraction folks — that the conserved role of GnRH has been detailed across all vertebrates?

    Why would I go looking for a Nobel Prize after being banned from commenting to Science, Nature, and even to Nobel Laureate Sheckman’s eLife?

    I wrote: In my model, the bottom-up epigenetic effects on stochastic gene expression are largely dependent on adaptively evolved glucose uptake and the top-down epigenetic effects on stochastic gene expression come from the metabolism of nutrient chemicals to species specific pheromones. The honeybee model organism best exemplifies this epigenetic tweaking of immense gene networks and how the epigenetic effects of food odors and pheromones on the glucose-dependent secretion of mammalian gonadotropin releasing hormone also links genes to behavior and back. The additional information about the histone core and fine-tuning of the required plasticity appear to attest to the control of chromatin remodeling by the microRNA / messenger RNA balance. It would interest me to learn if others agree with that proposal given the extreme technicalities of the issues addressed by Santoro and Dulac.

    My first comment on http://elife.elifesciences.org/content/1/e00326 was then removed.

    ME: Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?

    The response from that comment by Lomvardas was also removed:

    LOMVARDAS “The article elucidates how the environment can broadly influence gene expression through an epigenetic effect chromatin – the way DNA is package and organized. This allows the environment to influence sensory function, to tune the olfactory sense to better suit the surrounding environment, because these environmentally regulated chromatin changes are coupled to cell longevity. This results in a change in the distribution of cells in the tissue that have made particular stochastic choices, where the stochastic choice is which olfactory receptor to express, without affecting the mechanism of stochastic gene expression.”
    ———————————-
    Lomvardas simply regurgitated part of what I wrote, and dismissed the part about pheromone-controlled reproduction.

    As a historian you must be aware that no amount of experimental evidence can overcome the ridiculous beliefs of theorists until those who are continuing to teach those ridiculous beliefs die.

    Where else should I be pissing away my time until that happens?

    New experimental evidence that supports my model is reported almost daily.

    I’ve presented my model to very intelligent audiences of scientists since 1992 — at different conferences for different disciplines. It’s long past time for the experimental evidence to have trickled down to the ignorant theorists.

    Let me know if, in the future, you report on when exactly the paradigm shift happened that forced evolutionary theorists to start making sense.

  315. 315
    Weedless Monkey

    Kook. I’ll give you points for believing in your shit, though.

  316. 316
    gillt

    There is such a thing as olfactory kin recognition in zebrafish.

    Mate choice in zebrafish, a simple study, has more to do with females but not males showing preference for body size.

    Which somewhat contradicts the observation that assortative mating is not correlated to male rank/dominance.

  317. 317
    chigau (違う)

    Kohl
    you must close each blockqoute with a /
    </blockquote>

  318. 318
    James Kohl

    @313 PZ Myers

    I second that. It’s really unclear what mechanism he’s talking about: the way you get amino acid substitutions is by changes in the nucleotide sequence of DNA, which is the mechanism of mutation that he seems to deny exists. Unless he’s talking about RNA editing, which would be really weird and specific, and not at all a likely mechanism.

    Kohl is not only bad at science, he’s bad at communicating.

    Re: Nutrient-dependent/pheromone-controlled adaptive evolution: a model
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    I exemplified the fact that the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED. If the details with examples indicate to anyone that I am bad at science and bad at communicating, they should simply detail with examples how mutations cause adaptive evolution (and diseases and disorders) via amino acid substitutions.

    Here’s the 6 minute video from my poster presentation at the International Society for Human Ethology Summer Institute (2013) http://youtu.be/DbH_Rj9U524
    I have power point slides from an oral presentation a few years ago, and our award-winning review: Human pheromones: integrating neuroendocrinology and ethology is available here:
    http://www.nel.edu/22_5/NEL220501R01_Review.htm

    Again, thanks to PZ, especially for saying that

    It looks like Kohl fails at basic ethology, as well as at understanding the molecular biology of evolutionary change.

    He just exemplified the problem I’m having here with attempt to explain the molecular biology of ecological adaptations to those who have been taught “evolution for dummies.” It’s not my understanding of molecular biology that’s the problem; the dummies –like their teachers– are the problem.

  319. 319
    ChasCPeterson

    the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.

    That’s not a mechanism, you doofus. Even in all caps it’s not a MECHANISM.

  320. 320
    James Kohl

    @312

    I, for one, want to extend a tiny bit of gratitude to James Kohl for serendipitously highlighting some useful papers for which I was previously unaware.

    You’re welcome. Have you ever considered what review articles do? They highlight the papers that many people do not know are the most significant to be published during the time-frame covered by the review.

    Prior to 1996 Our Hormones and Behavior review
    Prior to 2001 Our Neuroendocrinology Letters review
    Prior to 2007 My book chapter
    Prior to 2012 Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors

    Between 2012 and 2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model

  321. 321
    Nerd of Redhead, Dances OM Trolls

    I exemplified the fact that the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.

    So you assert. You haven’t shown conclusive experimental evidence to back up that assertion. Therefore, the assertion is DISMISSED WITHOUT EVIDENCE.

  322. 322
    James Kohl

    @319

    That’s not a mechanism, you doofus. Even in all caps it’s not a MECHANISM.

    Thanks. It seems that mutation-driven amino acid substitutions are being offered in the context of a MECHANISM for evolution, but nutrient-dependent pheromone-controlled amino acid substitutions are not a comparable MECHANISM in the context of ecological adaptations. I can accept that — since it’s typical of your nonsense.

    However, we can proceed to discuss the thermodynamics and organism-level thermoregulation of mutations compared to ecological adaptations — if you would like me to further detail how ignorant you are with examples of seemingly futile cycles of protein biosynthesis and degradation. Honestly, I had no idea that anyone was even close to understanding those MECHANISMS, especially since PZ commented on

    RNA editing, which would be really weird and specific, and not at all a likely mechanism.

  323. 323
    ChasCPeterson

    Are you really this dense?
    The mechanism of amino-acid substitution via mutation, transcription, and translation is highschool-level molecular biology.
    You are being asked to supply a different mechanism–step-by-step cause and effect–for amino-acid substitution that is somehow instead nutrient-dependent and pheromone-controlled.
    OK?
    Not a mechanism of evolution (yet), not a mechanism for ecological adaptation.
    Just a mechanism for amino-acid substitution. Are there enzymes involved? Which ones? Ribosomes? What is the specific causal role of the miRNA you keep mentioning? Understand?

    What is your proposed mechanism for how amino acids are substituted?
    That’s the single, simple question before you now. Please demonstrate that you can understand that question and focus for 5 minutes on answering just that limited question. Please.

    (later on we can try to suss out what you mean by “organism-level thermoregulation”, a subject I happen to know something about, at least in the conventional meanings of those words.)

    I will repeat, because you are a big fan of repetition:

    What is your proposed mechanism for how amino acids get substituted?

  324. 324
    James Kohl

    @298

    “…a neuron called TN-GnRH3 became active in the females when they saw the familiar male, releasing peptides into the brain that made the female more receptive to mating.”
    http://www.nytimes.com/2014/01/07/science/these-females-prefer-a-familiar-fish-face.html?emc=eta1

    http://www.sciencemag.org/content/343/6166/91.abstract
    Social familiarization—the process of becoming familiar with an individual through visual or odor contact—affects mate preference in various species (1, 2).

    The idea that social familiarization is due to visual input has not been supported by experimental evidence in any species. For contrast, social familiarization in all species is known to be nutrient-dependent and pheromone-controlled via conserved molecular mechanisms.

    That makes anything that PZ Myers or anyone else has taught about social familiarization in fish a ridiculous misrepresentation of biological facts.

    @318

    …there really is something to this idea of an exchange of chemical signals — but they don’t seem to color responses to individuals. Zebrafish provoke mating by responding to the rising of the sun, by poking at potential mates, by ‘flirting’ with acrobatics. They target females visually: a large belly, bold dark stripes (they respond to environmental stresses by going pale), and size are very, very important. I don’t know about specific responses to faces, but there are distinct whole body patterns that influence mating.

    Russ Fernald could not have said that better or been more wrong than he has been for his entire career. Now that his student Karen Maruska is out from under his control, she can continue to refute the nonsense you’ve been teaching. Russ, for example, once told me that the color change was probably due to differences in the motion of the water, and that it had nothing to do with pheromones.

    http://www.ncbi.nlm.nih.gov/pubmed/22958303
    “This rapid endocrine and transcriptional response suggests that the SBN is involved in the integration of social inputs with internal hormonal state to facilitate the transition to dominant status, which ultimately leads to improved fitness for the previously reproductively-suppressed individual.”

  325. 325
    Nerd of Redhead, Dances OM Trolls

    The idea that social familiarization is due to visual input has not been supported by experimental evidence in any species. For contrast, social familiarization in all species is known to be nutrient-dependent and pheromone-controlled via conserved molecular mechanisms.

    Assertion dismissed without evidence. SHOW YOUR EVIDENCE.

  326. 326
    James Kohl

    @323

    The mechanism of amino-acid substitution via mutation, transcription, and translation is highschool-level molecular biology.

    You mean it automagically happens, don’t you? If not, where are your details?

    My molecular mechanisms start with the nutrient-dependent flipping of base pairs, but I refuse to take this any further since you refuse to acknowledge your ignorance and continue to attribute your ignorance to me. You’re obviously one of many people who receive all the details of what caused the paradigm shift and then claim “I knew that all along” when — as we can see here that you’ve known nothing about anything.

    When people like you are cornered they can only attack from fear. If you continue to do that, you will end any further attempts I might otherwise have made to detail anything because the details might scare you to death. Minimally, you will be left to think, how could I ever have thought I knew anything at all?

  327. 327
    ChasCPeterson

    unbelievable.

    where are your details?

    Where are my details?
    ffs.
    here, for one place. Crank.

    I mean it this time; I’m done with this guy.
    Yes, I retreat in abject fear.

  328. 328
    sawells

    James, you claimed that you “exemplified the fact that the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.”

    This is false.

    Firstly, you did not exemplify anything, you merely emphasised.

    Secondly, what you emphasised is not a fact, but an unsubstantiated claim.

    Words have meanings. Learn them and use them properly.

    Also, I note that you are incapable of providing any details of your proposed mechanism, instead producing a laughable cloud of bluster and bombast @326. You have no model or theory and are lying when you claim that you do. Prove me wrong or shut the fuck up.

  329. 329
    James Kohl

    @323

    “organism-level thermoregulation”, a subject I happen to know something about, at least in the conventional meanings of those words.)

    You mean you know something about sex determination in turtle eggs, right? My model addresses organism level thermoregulation the begins with an amino acid substitution in the human influenza virus.

    Do you known why chicken eggs are used in production of new influenza vaccines instead of turtle eggs? If so, which came first, the virus, the chicken or turtle, or the chicken or turtle egg? When did the first ecological adaptation occur? How did the first mutation occur that led to our evolution?

    Dumb ass!

  330. 330
    ChasCPeterson

    Dumb ass!

    stop scaring me

  331. 331
    Nerd of Redhead, Dances OM Trolls

    You mean it automagically happens, don’t you? If not, where are your details?

    Try reading this if you can understand basic biology. I understand it totally, and have for forty years. What is your excuse?

  332. 332
    sawells

    I bet his dad can beat up your dad, Chas. And he totally has a really hot girlfriend who lives in Canada.

  333. 333
    Nerd of Redhead, Dances OM Trolls

    My model addresses organism level thermoregulation the begins with an amino acid substitution in the human influenza virus.

    Technobabble from an ignorant asshat.

  334. 334
    Inaji

    Chas:

    Are you really this dense?

    I think that’s been proved beyond all doubt.

  335. 335
    Rey Fox

    are still touting the nonsense that is killing people.

    This ought to be good. How is it killing people?

  336. 336
    zenlike

    (I know it’s pretty much poking a dead body at this point but:)

    James Kohl, can you answer my question at 197?

  337. 337
    Inaji

    Rey:

    How is it killing people?

    Oh their gods, Rey! If people aren’t protected by the scimagic pheromone spray, well…bad things will happen. Oh yes.

  338. 338
    gillt

    Kohl:

    The idea that social familiarization is due to visual input has not been supported by experimental evidence in any species.

    Processing visual input and receptors and signaling pathways aren’t mutually exclusive, especially when social dominance is correlated to size. Follow the links in comment 316 which will take you to primary research that stands in opposition to your walled-off mind or simply google mate preference and zebrafish.

  339. 339
    James Kohl

    @327

    Where are my details?
    ffs.
    here, for one place. Crank.

    Dumb ass!

    Please join me in the second decade of the 21st century. You obviously missed everything that’s been learned in the first decade of this century.

    Evolution: A View from the 21st Century
    http://www.audible.com/pd/Science-Technology/Evolution-Audiobook/B0062CHLSY/ref=sr_1_7?qid=1384027525&sr=1-7

    We can begin our meeting of the minds with the nutrient-dependent pheromone-controlled physiology of reproduction in yeasts (in Shapiro’s first chapter, as I recall) or end it with your withdrawal from the reality of chirality and continued nonsensical claims about mutations.

    James A. Shapiro’s Evolution: A View from the 21st Century proposes an important new paradigm for understanding biological evolution. Shapiro demonstrates why traditional views of evolution are inadequate to explain the latest evidence, and presents a compelling alternative. His information- and systems-based approach integrates advances in symbiogenesis, epigenetics, and mobile genetic elements, and points toward an emerging synthesis of physical, information, and biological sciences.

    “Shapiro has written a stimulating, innovative manuscript that surely Darwin would have liked.”
    —Sidney Altman, Yale University; Nobel Laureate in Chemistry, 1989

    “Based on a long and highly competent personal experience in science and his novel insights into biological functions, the author has reached views of biological evolution that can reveal to a wide, interested readership how the living world co-evolves with the environment through its intrinsic powers.” —Werner Arber, Professor Emeritus, University of Basel, Switzerland; Nobel Laureate in Physiology/Medicine, 1978

    “Professor Shapiro’s offering is the best book on basic modern biology I have ever seen. As far as I can tell, the book is a game changer.” —Carl Woese, University of Illinois; discoverer of Archaea, the third realm of life; National Medal of Science 2000

    “‘[N]atural genetic engineering’ explains evolutionary processes that preceded people by at least 3,000 million years. Shapiro’s detailed account of ubiquitous genetic dynamism, DNA machination, repair, and recombination in real life, bacterial to mammalian, destroys myths…. Shapiro’s careful, authoritative narrative is entirely scientific and should interest all of us who care about the evolution of genetic systems.” —Lynn Margulis, University of Massachusetts, Amherst; National Academy of Sciences, National Medal of Science 1999

    “[T]his book is a magnificent analysis of the key questions of the origin of variation…. Jim Shapiro has new insights on all the central issues of evolutionary theory. The genome becomes a read-write storage system rather than the sole determinant of heredity. After reading this book, you will find it imperative to see biology as the 21st century is coming to see it.” —Denis Noble, CBE FRS, Balliol College, Oxford; author of The Music of Life

    “This book highlights…dynamic systems biology and engineering between the evolving genome, cell, and environmental stresses…affecting the…read-write memory system underlying life’s evolution.”
    —Eviatar Nevo, University of Haifa, U.S. National Academy of Sciences; explorer of Evolution Canyon

    “Shapiro’s new evolutionary synthesis reveals life to possess an immense subtlety of integration and embedded sentience. No evolutionary biologist can afford to ignore Shapiro’s message.”
    —Simon Conway Morris, FRS, Cambridge University; paleontologist and expert on the Cambrian Explosion; author of Life’s Solution

    I reiterate No evolutionary biologist can afford to ignore Shapiro’s message.
    ————————————-
    This is not true for evolutionary theorists. They can continue to ignore Shapiro’s message because no one has ever considered an evolutionary theorist to exemplify an ecologically adapted intelligent creature.

  340. 340
    James Kohl

    http://www.amazon.com/Scent-Eros-Mysteries-Human-Sexuality/dp/0826406777/ref=tmm_hrd_swatch_0?_encoding=UTF8&sr=1-1&qid=1368493382

    The Scent of Eros is an excellent source for easy-to-read, yet scientifically supported, information about human pheromones and their influence on behavior. It has been professionally reviewed by respected authors from various scientific disciplines, and by non-scientists as well. Here a a few examples of these reviews:

    “This is science at its best, with adventure, ideas, and lots of facts… You will never look at your lover or your family the same way again.” –Helen Fisher, Ph.D., author of “The Anatomy of Love”

    “This book examines odors and subliminal scents (termed sex attractants or pheromones), and how they influence numerous aspects of our sexuality and sexual behavior. While presenting important and complex research, the book is accessible to the general reader and makes science applicable to daily life.” –(1996) SIECUS Report 24:3

    “Kohl and Francoeur lead us on a treasure hunt through history, literature, and scientific data – providing clues to what today’s human mating patterns have in common with moths, marmosets, minotaurs, and even the serpent in the Garden of Eden.” –Gina Ogden, Ph.D., author of Women Who Love Sex”

    “A challenging and original work at the cutting edge of sexual science – innovative, quirky, speculative, and solid thinking all at once. Kohl and Francoeur’s thesis, that odor plays a far larger role in human sexuality than hitherto imagined, will give both lay and professional readers much to ponder about. It’s also fascinating for showing how science is actually done, not by oracular statements from on high, but by leaps of imagination about topics we thought we had completely comprehended.” –Timothy Perper, Ph.D., author of “Sex Signals: the Biology of Love”

  341. 341
    gillt

    Kohl

    My molecular mechanisms start with the nutrient-dependent flipping of base pairs

    hold your horses, base pairs are complimentary nucleotides (A-T,G-C), but those don’t mutate according to you, and you alone, so how can they flip?

  342. 342
    Tethys

    You mean it automagically happens, don’t you?

    No fool, there is nothing magical about transcription errors. We know they happen because in many cases we have isolated the exact mutations that cause the observed genetic disorder

    I’ve been attempting to fact check Mr Slaw’s link in #233. At least it’s on humans, though in light of John Does remarks I wonder if Milton Diamond is aware that he is a co-author. The first section isn’t terrible but later sections have a lot of self citation and sheer speculation;

    The vomeronasal organ (VNO). Despite years of controversy, there now seems to be evidence enough to confirm the presence of a paired VNO, not only in nonhuman species (Vandenbergh, 1994) but in humans as well. Moran and colleagues have presented clinical, ultrastructural, electrophysiological, and neuroanatomical evidence which suggests the presence of paired VNO in most, if not all, humans (Moran, Monti-Block, Stensaas, and Berliner, 1995).

    A quick check of wiki states that most researchers do not believe in a human VNO. I tried to locate the Moran et al reference online without much luck, but I did come across this interesting detail in a review of literature on the subject.

    None of the speculations about vomeronasal chemosensory neurons would be worth much consideration if there were not some positive evidence for a non-olfactory, non-trigeminal chemosensory function located in the region of the human VNO. This evidence comes almost exclusively from the work of Monti-Bloch and colleagues. They report an electrophysiological response to application of small amounts of steroid chemicals confined to the VNO region. Because these studies are supported in part by corporations with a commercial interest in exploiting the findings, the results are widely discounted by the academic community. However, they should be evaluated on their merits.

    After evaluating the merits, the review comes to this conclusion;

    The hormonal changes elicited by steroid chemicals in these studies are not evidence for a physiological connection between the VNO region and the brain and provide no evidence for VNO function.

    Human Vomeronasal Organ Function: A Critical Review of Best and Worst Cases

    I’m glad he doesn’t actually hold any degrees. I would be in process of moving to a different country if universities gave this idiot a passing grade much less a degree. My 80′s bio education may be partly outdated, but I’m certain I am a much better scientist than JK.

  343. 343
    Rey Fox

    So now we’re down to just out-and-out spamming. Delightful.

  344. 344
    ChasCPeterson

    re #339: cranks love a crank

  345. 345
    Nerd of Redhead, Dances OM Trolls

    I reiterate No evolutionary biologist can afford to ignore Shapiro’s message.

    Any message without evidence can and will be ignored by science. Your OPINION is bullshit. just like your evidence. You can’t put up, you can’t shut up. No honesty, intelligence, integrity, and scientific knowledge to be seen.

  346. 346
    James Kohl

    @342:

    The vomeronasal organ (VNO). Despite years of controversy, there now seems to be evidence enough to confirm the presence of a paired VNO

    Re: seems to be evidence

    There is now some evidence that appears to at least partially confirm the possible fact that mammals may process pheromones via the main olfactory system, and that the de novo creation of insect and mammalian olfactory receptor neurons links food odors and pheromones to the human GnRH-modulated response and the conserved molecular mechanisms of epigenetically-effected experience-dependent receptor-mediated pheromone-controlled physiology of reproduction in species from microbes to man.

    I apologize if anyone was led astray by what we (i.e., what I) said about the likelihood of a human VNO in our 1996 review. As sometimes occurs, we (i.e., I was) were wrong. But, so far, it seems we were right about everything else that evolutionary theorists continue to be wrong about (e.g., everything)!

    If you look at anything that is now known about the importance of alternative splicings (that lead to the amino acid substitutions) you can track it back to what we wrote in our section on molecular epigenetics and about the sexual orientation of yeasts.

    However, it is nice to known that at least one person here seems to know who Milton Diamond is. (He exposed the horrific misrepresentations of the textbook nature vs nurture example in the John/Joan case).

    Have you ever heard of Karl Grammer, who is senior author of our 2001 review? Do you have any idea of who you are insulting with your ongoing opinions about my published works. Well, do ya, punk?

    And, what kind of idiot continues to say I’ve provided no evidence to support my claims? That was a rhetorical question.

  347. 347
    alwayscurious

    @324:
    I’m late to all of this, but interested in the answer: Which comment had the link to the paper explaining the specific nutrient deficiencies & the resulting base pair swapping? How many species has this been analyzed in? Is this tissue specific and/or heritable? Thanks!

    In followup, you cite Grossman,et al 2013 (http://www.sciencedirect.com/science/article/pii/S009286741300087) as evidence in humans for your hypothesis (in Nutrient-dependent/pheromone-controlled adaptive evolution: a model). However, in the discussion they clearly state that the majority of the changes they found are in in regulatory sequences, not in coding sequences. Neither Grossman et al. 2013 nor Kamberov et al.2013 (http://www.sciencedirect.com/science/article/pii/S0092867413000676) mention nutrient status or pheromones. But these are the only two human papers you cite under the heading “An epigenetic continuum of nutrient-dependent / pheromone-controlled adaptive evolution” Could you please provide a corrected reference or direct me to the passage I overlooked?

  348. 348
    James Kohl

    @341

    base pairs are complimentary nucleotides (A-T,G-C), but those don’t mutate according to you, and you alone, so how can they flip?

    Thanks for the sign of somewhat intelligent life. I could tell you how they flip and may do so if you tell me where I said anything to infer that mutations don’t effect base pairs. You seem very confused about what I am actually saying, or perhaps I am.

    Let’s try to determine who’s the most confused about what I am saying, and why. Is it because of their belief in a ridiculous theory for example, or because of a belief in biological facts that are not biological facts in species from microbes to man?

  349. 349
    James Kohl

    @ 347

    But these are the only two human papers you cite under the heading “An epigenetic continuum of nutrient-dependent / pheromone-controlled adaptive evolution” Could you please provide a corrected reference or direct me to the passage I overlooked?

    No! Sorry, I did not have the time to detail what had been shown in every species on the planet before linking it to humans. In the context of ecological adaptations you can either believe that the same molecular mechanisms enable them in all species (as in the other examples I offered) or you can try to support mutation-driven evolution with experimental evidence from one species, like Chelo et al (2013) did.

    Instead, what you will do is tell me that Chelo et al (2013) did not rule out the possible involvement of mutations that are not fixed in the genome of nematodes, after I provided evidence that the morphological changes in two different are due to nutrient-dependent and pheromone-controlled amino acid substitutions.

    But obviously, you are showing some exemplary intelligence merely for asking the right questions instead of berating me for telling you something you don’t want to hear.

    Do you think it is unusual that I am just now seeing signs of intelligent life in #341 and #347? Now that intelligent life is beginning to be found here, do you think it could be found on other blogs that are not hosted by biology teachers?

  350. 350
    James Kohl

    @343

    So now we’re down to just out-and-out spamming. Delightful.

    PZ compared me to

    …John A. Davison, who died in 2012. He was notoriously persistent and repetitive, and rather clueless: he was the guy who started a blog with one article, never wrote another one, and just made new comments. He later announced that it was full, and so…he started a brand new blog, one article, and posted more comments to himself on it. It was rather sad.

    PZ forgot to mention the differences between me and John A. Davison that include my various publications beginning with my book in 1995. If I were spamming, I would link to my own blog posts on the domain I founded in 1996 (more than 800 of them in the past 4 years) that include citations to current research that evolutionary theorists have ignored.

    When my colleague Dick Doty wrote a book and told everyone there is no such thing as mammalian pheromones, I decided “enough is enough”. But there will never be enough experimental evidence to convince any ignorant evolutionary theorist of anything. That’s why they’re called ignorant theorists. Doty, for comparison, is not ignorant — he’s simply wrong. Obviously, he knows that since he is familiar with my works, but failed to acknowledge any of them.

    Rarely do you see anyone so bold as to completely ignore the seminal writings on an issue they attack. But Dick totally missed out on everything about what’s been learned about the conserved molecular mechanisms of olfactory/pheromonal input that link it to the development of behavior in every species via the nutrient-dependent physiology of reproduction. I don’t remember what he said about mutation-driven evolution for comparison. Does anyone remember if he suggested anything that could be compared to my model of ecological adaptations?

  351. 351
    Arawhon, a Strawberry Margarita

    Wow. James Kohl, you are one of the smarmiest and arrogant cranks. Several of the telltale signs of crankness I have encountered online is a hyperfocus on the credentials of their opponents, a shifting of the burden to explain how their their “theory” works, the constant calling of their opponents dumb or idiotic for any criticisms of their “theory”.

  352. 352
    Nerd of Redhead, Dances OM Trolls

    But there will never be enough experimental evidence to convince any ignorant evolutionary theorist of anything.

    What you mean is that they won’t accept your fuckwitted spin on non-sequitur evidence, that actually supports standard evolutionary theory.
    Your word, and any works you present, are dismissed as evidenceless fuckwittery. Your word is shown to be nothing but lies, bullshit and arrogance unsupported by the scientific facts. Nothing but hot smell air.

  353. 353
    Tethys

    I read an entire chapter of Doty, complete with MRI’s, that dealt with nasal-cranial pathology, one of which was Kallman’s syndrome. It only included a “basic” five paragraph description of the relevant human anatomy involved from scent molecule to nasal vault to brain. It’s true, he did not mention the VNO at all.

    I second PZ,

    It looks like Kohl fails at basic ethology

    At least he has learned to blockquote correctly.

  354. 354
    James Kohl

    @351
    Doty did not oppose anything I’ve detailed. He simply ignored it; redefined the term “pheromones” to suit his purpose of selling “sniff tests” that did not include any putative human pheromones, and then managed to convince a few other psychologists to become human pheromone-deniers. http://www.firstnerve.com/2011/07/family-feud-gilbert-vs-vosshall-on.html

    So far as I know, he never convinced anyone who is familiar with nutrient-dependent hormone regulation or pheromone-controlled physiology of nutrient-dependent reproduction to deny everything known about the conserved molecular mechanisms of biologically based cause and effect in species from microbes to man. If you can find the entire video of the debate, you’ll see how incredulous Leslie Vosshall found Avery’s comments to be.

    See also: http://www.ncbi.nlm.nih.gov/pubmed/17873857 Genetic variation in a human odorant receptor alters odour perception — and ask yourself why Doty ignored all aspects of molecular biology in his book as if he were pretending to be an ignorant evolutionary theorist. I think he knew who his target audience was, and pretended to be like them.

  355. 355
    Nerd of Redhead, Dances OM Trolls

    Yawn, more non-sequitur evidence from the liar and bullshiter, JK.

  356. 356
    Nerd of Redhead, Dances OM Trolls

    It appears JK doesn’t do anything other than read the title of the paper. He doesn’t even read the full abstract. Just presumes with certain keywords it backs his fuckwitted idea. It doesn’t.

  357. 357
    Tethys

    Here is a citation in support of my #353. It’s the Doty textbook chapter on radiologic anatomy in Handbook of Olfaction and Gustation.
    Evaluation of Olfactory Deficits by Structural Medical lmaging PDF

  358. 358
    Nerd of Redhead, Dances OM Trolls

    A new logical fallacy, argument by keywords….

  359. 359
    Inaji

    Oh, I just have to. Really. Couldn’t help myself.

  360. 360
    John Doe

    @342 Tethys

    though in light of John Does remarks I wonder if Milton Diamond is aware that he is a co-author

    I have indeed also tried to contact Dr. Diamond. I got no response.

    As for the recent mechanism discussion, the first link that I posted back in @91 covers that (it took quite a long time for me to get that out of Kohl). Despite how much he implies that the mechanisms somehow know what DNA bases to alter to create the required phenotypic change, none of them have such specificity. The legion bypass polymerases, for example, are merely more error-prone versions of the normal DNA polymerases. They don’t make specific changes, they just allow more mutations to occur in hopes that one will make a beneficial modification.

  361. 361
    James Kohl

    How is it killing people?

    Thanks for asking.

    The John/Joan case that my 1996 co-author Milton Diamond exposed in published works led to the book: As Nature Made Him: The Boy Who Was Raised as a Girl http://www.amazon.com/As-Nature-Made-Him-Raised/dp/0061120561 It exemplified one way that evolutionary theory has killed people. In college textbooks, homosexual males did not fit within John Money’s characterizations of how it was nurture, not nature, that determined sexual orientation. Some homosexual males who were unable to find help with the issues that Money’s dictates caused, killed themselves. So it wasn’t necessarily evolutionary theory that killed them, it was the belief in evolutionary theory by evolutionary theorists who convinced others to believe that homosexual orientation was a choice that killed the homosexuals who believed in the theory. And, in the end, both the twins whose case was exposed by Diamond, also committed suicide.

    Today, however, we have patients dying from sepsis due to the evolutionary theory of mutation-driven antibiotic resistance. Evolutionary theorists haven’t learned anything new, so they attribute the thermodyamics of organism-level thermoregulation to mutations instead of nutrient-dependent pheromone-controlled ecological adaptations. Thus, antibiotics are over-prescribed by physicians who don’t realize that one prescription that’s helpful now may contribute to the antibiotic resistance that later in life kills the patient. Typically, the medical profession and family members of the grand parents that are killed, comment on how — at least their loved ones had a “good long life.” But sepsis is not a good way to die. The thermodynamic stability of the organism that kills the patient gradually causes ever organ of every organ system to shut down.

    Again, however, I can’t really say that evolutionary theory is killing via sepsis. As with the John/Joan case it is the ignorance of the theorists that gets passed on to the masses in terms of experimentally unsubstantiated ridiculous beliefs. That’s what kills people. Perhaps I should simple say it’s their own stupidity, but it’s hard for me to imagine people being that stupid. If they were told about biologically based cause and effect and decided not to believe in a ridiculous theory, some people might make better decisions.

  362. 362
    Nerd of Redhead, Dances OM Trolls

    It exemplified one way that evolutionary theory has killed people.

    More non-sequitur evidence. No refutation of the mutation/natural selection. No support for his fuckwitted and demented theory. Just non-squitur with commentary from a known liar and bullshitter. *snicker*
    Try again.

  363. 363
    Tethys

    Sorry, I did not have the time to detail what had been shown in every species on the planet before linking it to humans.

    Except birds, adult catarrhine monkeys, and apes, all animals who do not have a functional VNO.

  364. 364
    Nerd of Redhead, Dances OM Trolls

    Evolutionary theorists haven’t learned anything new, so they attribute the thermodyamics of organism-level thermoregulation to mutations instead of nutrient-dependent pheromone-controlled ecological adaptations.

    More non-sequitur evidence. Evolution gives the results seen. You present no experimental evidence, just your fuckwitted OPINION to refute the claim. You lose each and every time on the burden of evidence.

  365. 365
    chigau (違う)

    James Kohl #361
    The John/Joan case is about homosexuality‽
    Does this thread have a demented fuckwit tag?

  366. 366
    Nerd of Redhead, Dances OM Trolls

    Does this thread have a demented fuckwit tag?

    I keep getting the feeling JK is an IDiot, trying to hide behind keyword jargon. But exposes his real ignorance to those who know the science, but can’t/won’t accept that fact.

  367. 367
    gillt

    Kohl says

    I could tell you how they flip and may do so if you tell me where I said anything to infer that mutations don’t effect base pairs.

    You’ve been denying it entire time!

    Every time someone says mutations and DNA in the same sentence you respond with…

    I exemplified the fact that the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.

    You are a very confused man and it shows in your writing.

  368. 368
    James Kohl

    @ 359 Oh, I just have to. Really. Couldn’t help myself.

    Thank you; the skit was hillarious! As they did, you demonstrate the complete lack of regard for anyone who does not fit within the confines of what was taught to students about the nature / nurture controversy until after Milton Diamond exposed the nonsense of that theory, the year after we published our Hormones and Behavior review article with the section on molecular epigenetics.

    Diamond, Milton, and HK Sigmundson. 1997. Sex Reassignment at Birth: A Long Term Review and Clinical Implications. Archives of Pediatric and Adolescent Medicine 150:298-304. Available on http://www.hawaii.edu/PCSS/online_artcls/intersex/mdfnl.html.

  369. 369
    James Kohl

    @367

    Every time someone says mutations and DNA in the same sentence you respond with…

    “…the amino acid substitutions [in my model] are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.”

    You may continue to take what I’ve repeatedly stated out of its context as is typical of all fools. However, I’ve also asked how mutations in DNA benefit organisms and are somehow selected at the same time I have asked for experimental evidence to support that ridiculous idea so that it could be compared to the nutrient-dependent pheromone-controlled ecological adaptations that I have modeled.

  370. 370
    Nerd of Redhead, Dances OM Trolls

    the year after we published our Hormones and Behavior review article with the section on molecular epigenetics.

    Oh, the year after you lied and bullshat?

  371. 371
    Nerd of Redhead, Dances OM Trolls

    . However, I’ve also asked how mutations in DNA benefit organisms

    Showing with prima facie evidence. your lack of understanding of the science. The organism/animal has no idea. But he amount of viable offspring it leaves behind is the benefit, it it exists (mutations can also be neural or detrimental). Whereas your fuckwited idea explains nothing, having no mechanism you have elucidated and evidenced, meaning you have nothing….

  372. 372
    Nerd of Redhead, Dances OM Trolls

    JK, until you provide the experimental evidence to support your ideas, you are like the cold fusion cranks of the late eighties. All talk, no evidence to convince serious scientists.

  373. 373
    gillt

    Kohl:

    However, I’ve also asked how mutations in DNA benefit organisms and are somehow selected at the same time

    So you don’t think mutations in nucleotide base pairs, especially at the third triplet, lead to changes in amino acids?

  374. 374
    Tethys

    chigau

    The John/Joan case is about homosexuality‽

    Mr Kohl’s paper at #233 actually has three sections. The third purports to show endocrine factors involved in transgender and homosexual orientation through intrauterine hormones etc…..

    I have zero confidence in his science, and it seems likely to cause a massive derail. Oh well, I guess its a good time for popcorn.

  375. 375
    James Kohl

    @363

    Except birds, adult catarrhine monkeys, and apes, all animals who do not have a functional VNO.

    [SARCASM] Sorry, I forgot to mention that those species mutated into existence from accumulated mutations in other species. Dinosaurs mutated into birds over millions of years, and only recently did different species of birds decide to become different species due to amino acid substitutions. Evidently, they learned to fear the slow rate of mutation-initiated natural selection and learned about how Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
    http://www.sciencemag.org/content/342/6164/1367.abstract

    See also: Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence http://www.biomedcentral.com/1471-2164/14/95

    But seriously folks, if I don’t see any more signs of intelligent life here, I’m going to quit toying with the dumb asses. Ignorance always triumphs, doesn’t it?

  376. 376
    Nerd of Redhead, Dances OM Trolls

    I have zero confidence in his science, and it seems likely to cause a massive derail. Oh well, I guess its a good time for popcorn.

    We’re past the derail point. *sharpens titanium fang*. The Pullet Patrol is making a huge batch of Popcornz, and the Pharyngula Saloon and Spanking Parlor management has decreed drinks are on the house *sets out a selection of grog an swill*.

  377. 377
    chigau (違う)

    Tethys
    Since this thread is about James Kohl, anything about James Kohl isn’t derailing.
    However, I am out of popcorn, so if you have any extra…
    grog sounds good, too

  378. 378
    Tethys

    I had a comment that quoted some objectionable parts of the third section get swallowed by the spam filters.

    I am completely out of my depth on the science of transgender endocrinology, perhaps someone else could offer an informed opinion? I just don’t want any derailing at the expense of trans hordlings.

  379. 379
    alwayscurious

    @349

    No! Sorry, I did not have the time to detail what had been shown in every species on the planet before linking it to humans. In the context of ecological adaptations you can either believe that the same molecular mechanisms enable them in all species (as in the other examples I offered) or you can try to support mutation-driven evolution with experimental evidence from one species, like Chelo et al (2013) did.

    What I’m getting from this is that you entirely misrepresented the contents & conclusion of two papers in a key part of yours. You ostensibly did this because you didn’t have time to find the correct papers or do the research yourself. Which makes me believe that there really isn’t any research out there that supports this idea. {Chelo et al didn’t have anything enlightening to say about nutritionally-driven base-pair substitutions or pheromones}.

    I have every reason NOT to believe that mechanisms functioning in other animals are not preserved in us:

    Birds & bees lay eggs & fly (therefore humans do too?)
    Fish & flatworms can breathe underwater (therefore humans can too?)
    Monkeys & rats use their tails for balance (therefore humans do too?)

    Bees & mice use pheromones to communicate (do you see why I hesitate to believe the hand waving?)

    I could be convinced that some kind of external chemical (pheromone or otherwise) is capable of changing the genetic sequence in a predictable fashion. But you’ve utterly failed to presented evidence supporting that claim–or even the mundane claim that humans respond to pheromones in the first place. I am not dead set against the possibility of human pheromones, but you’ve not presented any evidence for it. Despite all your talk of nutrition deficits and base-pair substitution, not a single paper mentioned so far describes this. Sorry, but the science isn’t on your side on this one. And pointing out the shortcomings of its practitioners doesn’t make your crackpot idea any stronger.

  380. 380
    alwayscurious

    edit: I have every reason NOT to believe that mechanisms functioning in other animals are not preserved in us:

  381. 381
    James Kohl

    I’m not sure this link to a recent comment on my 2012 review will work, so I am including the text:
    http://www.linkedin.com/groups/Human-pheromones-food-odors-epigenetic-3821392.S.101285441?view=&srchtype=discussedNews&gid=3821392&item=101285441&type=member&trk=eml-anet_dig-b_pd-ttl-cn&fromEmail=&ut=3ovJs1hlPAlS41

    ‘Makes me wonder whether certain environmental metal ion exposures might be related to acquired behavioral dysfunctions. Also, it’s a bit off topic, but how does the TOFT (tissue organization field theory) fare at this discussion group? Or are you still advocates of the central dogma of molecular biology? I’m referring to the chapter by Sonnenschein and Soto in the book Genetic Explanations: Sense and Nonsense (2013).”
    —————————————————————————-
    RMD,

    The biophysics of how metal ion exposure results in amino acid substitutions and differences in cell types is beyond my ability to comprehend. You are the first person I know besides me to find the possible connection to behavior to be interesting.

    However, it is becoming clearer from what some people know about the requirements for the growth of microbes (such as Neisseria species) in nutrient-enriched media containing horse blood, sheep blood (chocolate agar) et al,, and from what is known about iron and copper present in cell culture media, either added as part of the media formulation or appearing fortuitously, that metal ions are likely to help nutrients pass through the cell membrane, since they are required for normal cell growth and function.

    This tentatively links metal ions to the thermodynamics of intercellular signaling and to amino acid substitutions that differentiate cell types in individuals of different species, which links nutrient-dependent pheromone-controlled ecological adaptations to species diversification via organism-level thermoregulation (the subject of my 2013 review in this journal).

    For some reason, researchers have not made the connection to the hot-spots associated with vitamins and glucose uptake in malignant tissues. That may be due to the theory of mutation-driven evolution in which beneficial mutations somehow also contribute to malignancies.
    —————————

    I’ve always suspected there would be serious scientists who are interested in the link from my model to cancer. For comparison, evolutionary theorists seem likely to continue contributing indirectly to cancer deaths and other deaths by suicide and sepsis. Taken together, the ridiculous belief that the molecular mechanisms, which are conserved across all species, are not preserved in us, because we don’t have wings, tails, breath under water et al is more nonsense than I can deal with intellectually, humorously, or sarcastically. Participants here may be among the dumbest evolutionary theorists to ever come together on a blog and claim that I am a crank. But those claims are as unimportant to scientific progress as the claims made by evolutionary theorists who can’t think their way out of the ridiculous theory of mutation-driven evolution.

  382. 382
    zenlike

    So no answer on my comment 197? I feel sad :(

  383. 383
    Nerd of Redhead, Dances OM Trolls

    I’m not sure this link to a recent comment on my 2012 review will work,

    Since it is a review by YOU, your OPINION is dismissed, and any Evidence you present is dismissed until it has been review by skeptics. And you lose loser. Your ideas are BULLSHIT until YOU provide the evidence what we, not you, consider conclusive. And you present nothing but OPINION and FUCKWITTERY.

  384. 384
    zenlike

    Nerd of Redhead

    I keep getting the feeling JK is an IDiot

    Since he already linked to evolutionnews.org (an ID website), even worse, to an article of Casey Luskin, I think this is pretty much a given.

  385. 385
    Al Dente

    James Kohl reminds me very much of Anne Elk (Miss) and her theory (which is hers) on brontosauruses.

  386. 386
    alwayscurious

    #381,
    No primary data? Tell me before I waste my time reading this mess, are all of your references misrepresenting the original authors’ work, or just the ones about humans? And did you just extrapolate honeybees to humans without stopping anywhere in-between? (bees see in the near UV, so therefore humans can too) Or have I presumed too much and this is not related to my question about how your imaginary mechanism works: nutrient dependent/pheromone mediated selective base-pair changes in protein coding stretches of our genes? I think it would be a great start for a fiction book. Have you considered the additional income available in that line of work?

  387. 387
    Tethys

    alwayscurious

    did you just extrapolate honeybees to humans without stopping anywhere in-between?

    Oh c’mon, do you seriously think a mere drone is capable of answering that question? We raise them for one reason and one reason only, whichever one of them flies highest will sacrifice himself to the Queen while sating her sexual and reproductive needs.

    Seriously, he thinks yeast and humans are analogues too.

  388. 388
    James Kohl

    Birds & bees lay eggs & fly (therefore humans do too?)
    Fish & flatworms can breathe underwater (therefore humans can too?)
    Monkeys & rats use their tails for balance (therefore humans do too?)

    And did you just extrapolate honeybees to humans without stopping anywhere in-between?

    What I did was show that the molecular mechanisms of nutrient-dependent pheromone-controlled cell type differentiation are conserved in species from microbes to man. I did this during the past 20 years in a series of published works that integrated the available experimental evidence from different disciplines.

    What you did was make the most ignorant statement about observed differences in morphology that has ever been made in the context of what is currently known, or what was known by any serious scientists since Dobzhansky 1972/3.

    The “extrapolation” from yeasts to honeybees and humans is one that is commonly used in every aspect of modern medicine and I have detailed the connection with examples of amino acid substitutions in different species, while citing the works of others in the process of integration.

    I am amazed that people as stupid as you are know how to use a computer and formulate sentences in attempts to discuss things they know nothing about. Thanks for taking participation here to a new level of ignorant babble.

    If no one else takes the time to correct you, and perhaps even if they do, you are destined to remain one of the most ignorant people in the known world, and perhaps in the cosmos –if unintelligent life exists elsewhere.

  389. 389
    Nerd of Redhead, Dances OM Trolls

    What I did was show that the molecular mechanisms of nutrient-dependent pheromone-controlled cell type differentiation are conserved in species from microbes to man.

    NO YOU DIDN’T. You fallaciously claim you did liar and bullshitter. Nobody believes a word you say, not supported by direct( not your imagined) third party evidence. So, shut the fuck up, as you are exposed for the crank you are. Nothing but hot air, noise, and flatulence smell….

  390. 390
    chigau (違う)

    James Kohl
    be ashamed

  391. 391
    Tony! The Queer Shoop

    James Kohl:

    And, what kind of idiot continues to say I’ve provided no evidence to support my claims? That was a rhetorical question.

    ::points at self::
    Fine. I’m an idiot. You really should work on insulting people with better flair.

    Still waiting for the evidence that your Pheromone product is effective at enhancing the appeal of the user.

    Also, your #339 was really pathetic. You copied the “From the Publisher” comments on your book from Amazon (did you forget how to blockquote?). Those comments-and all the wonderful anecdotes -are totally evidence of…something.

  392. 392
    James Kohl

    @391 Tony! The Queer!

    Still waiting for the evidence that your Pheromone product is effective at enhancing the appeal of the user.

    Thanks for asking.

    http://f1000.com/posters/browse/summary/1387

  393. 393
    Tony! The Queer Shoop

    James Kohl:
    Thanks for the link.
    I saw something curious there:

    Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed

    Has your work been peer reviewed or is it still preliminary in nature?

  394. 394
    Nerd of Redhead, Dances OM Trolls

    Has your work been peer reviewed or is it still preliminary in nature?

    It isn’t even preliminary, it is nothing but a pipe dream. If it is peer reviewed, the editor sent it to follow cranks, not serious working scientists who would point out the obvious flaws and recommend against publishing such tripe.

  395. 395
    PZ Myers

    So far, Kohl has left 73 comments in this thread. I’ve read them all. I still have no idea what the mechanism behind his “theory” is — my experience is that even the worst communicators among scientists can usually get across the core ideas behind their work, but never have I encountered a scientist as opaque and evasive as this Kohl fellow.

    How can you leave that many comments with so many people specifically asking for a summary of his mechanisms and not even touch any kind of explanation?

  396. 396
    James Kohl

    Thanks PZ Myers,

    THE SUMMARY OF MY MECHANISMS IS: Nutrient-dependent pheromone-controlled alternative splicings of pre-mRNA cause the amino acid substitutions that differentiate cell types in individuals of species.

    THE EXPLANATION IN MY MODEL IS: Alternative splicings enable the ecological adaptations that are responsible for species diversity that I exemplified after detailing cause and effect.

    Like everyone else here, you keep asking for an explanation when I provided it in:

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    You also insist on inferring that the model is a theory.

    Simply put, you want an explanation of a biologically based explanation. Instead, you should be asking yourself by now: “Why don’t I understand what Kohl is saying? Is it because he doesn’t know what he has detailed, or because I am a biology teacher?

    You can answer that question by reading something that was not written by a biology teacher, an evolutionary theorist, or any other idiot who doesn’t understand the molecular mechanisms of alternative splicings. So, let’s start with Jon Lief’s article on alternative splicings, shall we?

    Alternative RNA Splicing in Evolution http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

  397. 397
    djr1

    I think I understand it now – thanks to many for the thread. Across the world – millions of scientists are engaged in the fun – of figuring out how stuff works. It is a community process – because of course the body of human knowledge is vast – and it takes decades to gain the training and knowledge needed to do research in any specialty. Fairly frequently – one individual comes along and says ‘hey dummies – you are all wrong – and I understand the way things really are.’ They fall back on examples like Galileo to show that sometimes one individual does turn science on its head. Of course 1600 was a very different time for science than 2014.

    The interesting thing is how these people can take up so much bandwidth with their word salad. We seem to have a need to engage them – because we are offended by them calling scientists stupid. I guess at some point – it is important to limit the energy we put into this kind of weirdness – and just learn from the experience ourselves.

  398. 398
    Nerd of Redhead, Dances OM Trolls

    THE EXPLANATION IN MY MODEL IS: Alternative splicings enable the ecological adaptations that are responsible for species diversity that I exemplified after detailing cause and effect.

    Where the fuck is your THIRD PARTY evidence.
    Since you are proven liar and bullshitter, self-referencing is just more imagufactured nonsense like your inane and incomprehensible whacky-baccy pipe dream.

    Show your work from places like this: Science Library.

  399. 399
    James Kohl

    @397

    I think I understand it now – thanks to many for the thread.

    What is it you understand, and who are you thanking for enabling that understanding?

    Do you understand the biological fact that “…alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes.” http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

    Do you understand that fact is what I exemplified in my model?
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    Who do you think was being called stupid? Was it Kohl (the crank) or the evolutionary theorists who continued to call Kohl a crank despite all his efforts to educate them in published works and presentations during the past two decades.

    Please make yourself clear. What do you think was a community process here? What do you think is different now compared to in 1600. I think that today’s evolutionary theorists come from a long line of idiots who have ignored Darwin’s ‘conditions of life’.

  400. 400
    James Kohl

    @398 Nerd of Redhead, Dances OM Trolls

    Where the fuck is your THIRD PARTY evidence.

    Thanks for asking again, you foul-mouthed dumb ass. How did you become scientifically illiterate?

    The third party evidence is cited and integrated into the model, just like it has been in all my published works:

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model
    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

  401. 401
    zenlike

    Strange, still no answer on my very simple, easy to answer question which I posed three times already.

    Could it be that claiming that his book and papers won awards was merely dishonest bluster to falsely claim a sort of appeal to authority (which is a fallacy anyway)?

    A kook being dishonest? Can it truly be?

  402. 402
    Tony! The Queer Shoop

    James:
    Repeating yourself does not enhance your argument.
    Citing your own work repeatedly does not count as third party evidence.

    Now, once again, where is the evidence to support the claims of the pheromone product you sell?

  403. 403
    Tony! The Queer Shoop

    Zenlike:
    I’m over in the corner holding my breath waiting on an answer to my question. There is room for two.

  404. 404
    Nerd of Redhead, Dances OM Trolls

    The third party evidence is cited and integrated into the model, just like it has been in all my published works:

    Nutrient-dependent/pheromone-controlled adaptive evolution: a model

    Sorry, your imagufactured bullshit won’t be read by any serious scientists except for a laugh. You claim references, YOU POST THEM HERE OR THEY DON’T EXIST.

  405. 405
    Nerd of Redhead, Dances OM Trolls

    I suspect there are no third party references. It is all self-referential.

  406. 406
    djr1

    @399 “What is it you understand, and who are you thanking for enabling that understanding?”

    I am thanking the community on Pharyngula – for an extensive thread – that has helped me sort out the issue of one individual – who claims to know truth – and asserts that the whole body of science is wrong.

    “Who do you think was being called stupid?” I will reference your own words to answer that question. “I think that today’s evolutionary theorists come from a long line of idiots”

    “What do you think is different now compared to in 1600. ” I think that the majority of people in 1600 were illiterate – and that science and academia were very exclusive practices – controlled very heavily by superstitious religionists – who were very threatened by any knowledge that may jeopardize their power base (the church). I am in no way a historian – but it intrigues me that you are not aware of the difference in science today vs 400 years ago.

    “Please make yourself clear.” I think my post was written in very accessibly language – and that it would be reasonable to think that I was fairly clear with what I was saying.

  407. 407
    djr1

    @399 “Please make yourself clear.” I think my post was written in very accessibly language – and that it would be reasonable to think that I was fairly clear with what I was saying.

    “What is it you understand, and who are you thanking for enabling that understanding?”

    I am thanking the community on Pharyngula – for an extensive thread – that has helped me sort out the issue of one individual – who claims to know truth – and asserts that the whole body of science is wrong.

    “Who do you think was being called stupid?” I will reference your own words to answer that question. “I think that today’s evolutionary theorists come from a long line of idiots”

    “What do you think is different now compared to in 1600. ” I think that the majority of people in 1600 were illiterate – and that science and academia were very exclusive practices – controlled very heavily by superstitious religionists – who were very threatened by any knowledge that may jeopardize their power base (the church). I am in no way a historian – but it intrigues me that you are not aware of the difference in science today vs 400 years ago.

  408. 408
    James Kohl

    @140 djr1

    “The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether. Namely intelligent design.”

    Interesting omission.

    Let’s put that omission back into perspective. The nutrient-dependent pheromone-controlled de novo creation of olfactory receptor genes via alternative splicings in insects and mammals is the holy grail of evolutionary biology. It links ecological variation to receptor-mediated adaptations in species from microbes to man. Thus, the acceptance of a different paradigm altogether is not “intelligent design.” Is it?

    The acceptance of the “different paradigm” is acceptance of the basic principles of biology and levels of biological organization that link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. Acceptance of biological facts eliminates any further consideration of mutation-initiated natural selection or mutation-driven evolution.

    The theory that you were taught to believe in has been repeatedly refuted with experimental evidence since 1996. Crying about it, or calling anyone a ‘crank’ is not the best way to deal with a different paradigm. And, resistance is futile! As we’ve seen here, resistance makes people look like fools.

  409. 409
    Nerd of Redhead, Dances OM Trolls

    Djr1, please use <blockquote>Material to be quoted for a response</blockquote> for this:

    Material to be quoted for response

    Quote marks make it difficult to determine who you are responding to.

  410. 410
    Nerd of Redhead, Dances OM Trolls

    The theory that you were taught to believe in has been repeatedly refuted with experimental evidence since 1996.

    Evidenceless assertion, dismissed as fuckwittery by a crank.

  411. 411
    James Kohl

    @407 djr!

    I think that the majority of people in 1600 were illiterate – and that science and academia were very exclusive practices – controlled very heavily by superstitious religionists – who were very threatened by any knowledge that may jeopardize their power base (the church).

    Thanks for answering my questions.

    I think what you’re saying is that academia took over the role of the church, and that academics have refused to acknowledge biological facts that jeopardize their power base.

    What I’ve been saying is that the whole body of science is right and the evolutionary theorists do not understand enough about science to separate biological facts from their ridiculous theories and focus on the biological facts. Thus, I can quote Dobzhansky, the Creationist who best described evolutionary theorists in his 1964 Presidential address “Biology, molecular and organismic”

    He said: “…the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!” http://icb.oxfordjournals.org/content/4/4/443.citation

  412. 412
    James Kohl

    @404

    Sorry, your imagufactured bullshit won’t be read by any serious scientists except for a laugh. You claim references, YOU POST THEM HERE OR THEY DON’T EXIST.

    That is the most ridiculous assertion I have ever seen anyone make. Thanks.

    http://www.amazon.com/Gay-Straight-Reason-Why-Orientation/dp/0199737673/ref=sr_1_1?s=books&ie=UTF8&qid=1305424382&sr=1-1#reader_0199737673
    p. 210 “This model is attractive in that it solves the “binding problem” of sexual attraction. By that I mean the problem of why all the different features of men or women (visual appearance and feel of face, body, and genitals; voice quality, smell; personality and behavior, etc.) attract people as a more or less coherent package representing one sex, rather than as an arbitrary collage of male and female characteristics. If all these characteristics come to be attractive because they were experienced in association with a male- or female-specific pheromone, then they will naturally go together even in the absence of complex genetically coded instructions.”

  413. 413
    pentatomid

    Captain Cabbage still at it, I see. Very well then.

    James Kohl, @411

    Please cite some third party evidence. Do not just refer to your own work and the references therein, because it’s already been established you have no problem with misrepresenting the work of others in your work (or you’re just completely unable to understand their work, that remains a possibility). Please refer to the scientific literature which specifically supports your ideas and specifically contradicts evolution by natural selection.

    And frankly, drop the gorram attitude. If it is indeed the case that it is us who are misunderstanding you (and I seriousy doubt that. I think you’re just a babbling crank, but hey), than that is your fault for failing to communicate your ideas. If you are a scientist of any kind, you should be deeply ashamed.

    I think what you’re saying is that academia took over the role of the church, and that academics have refused to acknowledge biological facts that jeopardize their power base.

    You… You have no idea at all what actual scientists actually do, do you?

  414. 414
    Prof Weird

    @140 djr1

    “The rejection of natural selection is the beginning of a process that will ultimately lead to the acceptance of a different kind of paradigm altogether. Namely intelligent design.”

    Interesting omission.

    Let’s put that omission back into perspective. The nutrient-dependent pheromone-controlled de novo creation of olfactory receptor genes via alternative splicings in insects and mammals is the holy grail of evolutionary biology.

    Nope – understanding how evolution happens is the goal of evolutionary biology; getting reality to conform to your ‘model’ is your holy grail.

    You seem to have the ridiculous idea that receptor genes are poofed into existence at need – the EVIDENCE (other than your misquoted and cherry-picked articles) is what again ?

    Alternative splicing isn’t used to generate single amino acid substitutions – DECADES of real world experimentation showed that they are generated via mutation. It is also incapable of generating a novel molecule – alternative splicing can only use sequences that are already present.

    IF genes worked the way you hallucinate they do, all genes should have dozens of alternative exons for every part of the protein.

    Reality kicks your model in the crotch about 19995 times, since most genes don’t show much alternative splicing, and do NOT show what would be required for your ‘model’ to work.

    Whether a mutation is beneficial, neutral or deleterious depends on environmental context – so parts of your hallucinatory ‘model’ are already included in reality-based evolution.

    You seem to have the rather stupid idea that pheromones are magical and all-powerful. That they can induce new genes to poof into existence from nowhere with PRECISELY the properties needed.

    Decades of real world biology show you are wrong – mutations arise in genomes because replication is never perfect. Some of these variants are more effective at keeping the organism alive long enough to reproduce successfully. Over time, that variant will become more common.

    Slack-witted, posturing monomaniacs will notice that, then delude themselves into ‘thinking’ that the environment somehow induced the changes directly

    It links ecological variation to receptor-mediated adaptations in species from microbes to man. Thus, the acceptance of a different paradigm altogether is not “intelligent design.” Is it?

    No need to invoke a magic-based model of genes (with PRECISELY the needed changes) poofing into existence at need, given the FACT that reality-based evolution explains things quite well already.

    It has been known for decades that variation in populations exist. It has also been known that some variants fare better than others over many generations. It has also been known that those variations tend to become more common. Thus, it is known that evolution works despite the fact that it is too complicated for you to understand.

    Cells use inter- and intra-cellular signaling; only a gibbering poseur would jump to the conclusion that pheromones rule everything. The FACT of alternative splicing doesn’t harm the theory of evolution one little bit – in fact, it HELPS, because it increases variation (which is what selection works on).

    And here is where you jump the rails and fall (howling and screaming) into the Abyss :

    The acceptance of the “different paradigm” is acceptance of the basic principles of biology and levels of biological organization that link the epigenetic landscape to the physical landscape of DNA in the organized genome of species from microbes to man. Acceptance of biological facts eliminates any further consideration of mutation-initiated natural selection or mutation-driven evolution.

    Too bad for you that natural selection happens, and mutation-driven evolution has decades of EVIDENCE backing it up; all you’ve got is your egomaniacal rantings and misunderstandings of real world biology.

    Again, poser : variations arise. Some variants are more successful at living long enough to reproduce than others. Those variants tend to become more common in the population.

    Again, twit : whether a given MUTATION is beneficial, neutral, or deleterious is context dependent. The context is the environment (both where the organism lives and what other genes are present).

    So OF COURSE altering nutrient availability will have an effect – it will select from the variants present in the population that can best handle current conditions.

    What does not happen is the formation of a new gene (with PRECISELY the needed changes) appearing in the genome.

    BTW – alternative splicing is for mRNA, not DNA. So ‘thinking’ that alternative splicing will cause a gene to appear in the DNA is just simply wrong.

    Unless, of course, you have EVIDENCE that such an event actually happens often enough to be of use ….

    More of the usual screaming of one’s greatness :

    The theory that you were taught to believe in has been repeatedly refuted with experimental evidence since 1996.

    Nope – that evidence helps SUPPORT evolution. That you are too ignorant and too arrogant to accept it will not change it or make it go away.

    For instance, a human gene I work on has a silent mutation in the 2nd exon (the first exon ends ‘AG’, and the second exon starts with either an ‘A’ or a ‘G’. When linked, this will form either an ‘AGA’ or an ‘AGG; codon – both of which code for arginine.

    Funny thing – if the 2nd exon starts with ‘A’, the protein splices normally; if it starts with a ‘G’, it uses a different splice site which ends up adding 17 new amino acids to the protein.

    BUT YET THE PEOPLE WITH THIS MUTATION ARE STILL HUMAN !

    This finding doesn’t harm the ToE in any way, shape, or form (in utter defiance of your many assertions that even a single amino acid substitution can be enough to change a species).

    A gene I isolated from MDCK cells has two amino acid changes from the GenBank entry – mainly because MDCK cells are derived from cocker spaniel kidney, while the sequence in GenBank is derived from a bulldog.

    Yet cocker spaniels are NOT considered a different species from bulldogs.

    More vainglorious posturing :

    Crying about it, or calling anyone a ‘crank’ is not the best way to deal with a different paradigm. And, resistance is futile! As we’ve seen here, resistance makes people look like fools.

    Well, your continued resistance to accept REALITY certainly makes you look like a fool.

    You don’t have a different paradigm – all you’ve got is a mishmash of ideas you barely understand cobbled together into an incoherent, vomitous mass that you insist on spewing all over the place.

    Nothing discovered in the last few decades has been a threat to the theory of evolution – all they do is explain HOW it works, not overthrow it. Generating complexity is easy; getting it under control is kinda what natural selection does.

  415. 415
    James Kohl

    @413

    After quoting what neuroanatomist Simon LeVay concisely said in his book about my model, we see

    that is your fault for failing to communicate your ideas.

    That means it is my fault for failing to communicate my ideas to idiots who cannot understand my ideas, and I am not willing to take responsibility for their ignorance. Also, I am not willing to take responsibility for the examples of that ignorance that we have been offered here by anonymous fools.

  416. 416
    Rey Fox

    You seem to have the rather stupid idea that pheromones are magical and all-powerful. That they can induce new genes to poof into existence from nowhere with PRECISELY the properties needed.

    Which is why I was wondering about front-loading before. Without mutations, where does all our present genetic information come from? How do nutrients and pheromones create it?

  417. 417
    Nerd of Redhead, Dances OM Trolls

    That means it is my fault for failing to communicate my ideas to idiots who cannot understand my ideas, and I am not willing to take responsibility for their ignorance. Also, I am not willing to take responsibility for the examples of that ignorance that we have been offered here by anonymous fools.

    JK, who the fuck are you to say the trouble is us, when the trouble is you. You present no data. You present no solid mechanism in detail. You present nothing but a bit of word salad meaning nothing scientifically, and repeat yourself ad nauseum, instead of doing what real scientists and teacher do, which is find a way to communicate the idea and provide scientific evidence to back it up.

    Your problem is that once you and your opinion is removed, your ideas is unsupported by anybody or any scientific evidence. Just your massive ego holds your idea together.

  418. 418
    Inaji

    djr1, your posts will be clearer if you use quotes. To quote someone, use <blockquote>Place Text Here</blockquote> to get:

    Place Text Here

    For emphasis, <i>Text Here</i> gives you italics, and <b>Text Here</b> gives you bold.

  419. 419
    John Doe

    @369

    THE SUMMARY OF MY MECHANISMS IS: Nutrient-dependent pheromone-controlled alternative splicings of pre-mRNA cause the amino acid substitutions that differentiate cell types in individuals of species.

    He didn’t ask for a summary. He asked for specifics regarding the enzymatic pathways involved- something I have asked you many times and not received a proper answer.

    @408

    The nutrient-dependent pheromone-controlled de novo creation of olfactory receptor genes via alternative splicings

    How does splicing mRNA make new genes? That has yet to be explained. Splicing is merely a way to alter transcription products. What is the MECHANISM?

    Example: The process of splicing is moderated by the spliceosome enzymatic complex.

    Now, what enzymes are used in your model to make novel genes following splicing?

  420. 420
    Amphiox

    De novo creation of genes by alternative splicing requires the action of a reverse transcriptase. This should be easily testable.

  421. 421
    John Doe

    @369

    THE SUMMARY OF MY MECHANISMS IS: Nutrient-dependent pheromone-controlled alternative splicings of pre-mRNA cause the amino acid substitutions that differentiate cell types in individuals of species.

    He didn’t ask for a summary. He asked for specifics regarding the enzymatic pathways involved- something I have asked you many times and not received a proper answer.

    @408

    The nutrient-dependent pheromone-controlled de novo creation of olfactory receptor genes via alternative splicings

    How does splicing mRNA make new genes? That has yet to be explained. Splicing is merely a way to alter transcription products. What is the MECHANISM?

    Example: The process of splicing is moderated by the spliceosome enzymatic complex.

    Now, what pathway is used in your model to go from splicing to making novel genes?

  422. 422
    John Doe

    Computer froze. Double post.

  423. 423
    gillt

    Kohl:

    Do you understand the biological fact that “…alternative splicing may be the critical source of evolutionary changes

    That’s not how facts work. Facts aren’t may be’s. You are speculating, ignorantly it turns out, without evidence and no original data. That is your entire schtick repeated across this thread.

    And stop linking lying to some one else’s published work (we all know you don’t have any of your own to to reference). This thread is riddled with your attempts to reappropriate other scientist’s data to support your absurd models. I would say quit while you’re ahead James Kohl, but it’s far too late for that.

  424. 424
    pentatomid

    James Kohl,
    Brian Blessed’s Beard, you are dense!

  425. 425
    Inaji

    Perhaps Captain Cabbage saw the movie Splice one too many times. And took it seriously.

  426. 426
    PZ Myers

    #396, Kohl:

    THE SUMMARY OF MY MECHANISMS IS: Nutrient-dependent pheromone-controlled alternative splicings of pre-mRNA cause the amino acid substitutions that differentiate cell types in individuals of species.

    THE EXPLANATION IN MY MODEL IS: Alternative splicings enable the ecological adaptations that are responsible for species diversity that I exemplified after detailing cause and effect.

    Repeating yourself doesn’t help. Your mechanism is nonsense. Just focus on one little piece: “alternative splicings” causing “amino acid substitutions”. Try explaining that in different words, because as it stands, that is word salad. I’m a biologist, and I do know what alternative splicing is, and what amino acid substitutions are, but together…those make no sense.

    I’ve also read that paper you keep citing. It also makes no sense. You string together sciencey words into an incoherent glop that is only going to make you look intelligent to people who know nothing about the subject you’re discussing.

  427. 427
    ChasCPeterson

    Followers of this trainwreck of a biology thread have doubtless noticed that our Mr. Kohl is fond of repeating a quote he attributes to Dobzhansky 1964, to wit (as quoted in his #78, #158, AND #411):

    …the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!

    Now this has bothered me all along, because it just doesn’t ring true. Dobzhansky himself was no molecular biologist, and it seemed strange that someone who started out as a classical entomologist would disparage butterfly collectors.
    But it wasn’t until the requote in #411 with reference to a presidential address that I followed the link, because my memory was jogged. Sure enough, the quote was mined from Dobzhansky’s presidential address to the American Society of Zoologists, a group that then, as now (since renamed SICB), includes quite a number of scientific bird watchers and butterfly collectors.
    Dobzhansky’s address is available in full here (pdf), and is well worth reading–for everyone, not just biologists–these 50 years later. In stark contrast to Mr. Kohl’s slaw, the writing is crisp and clear throughout. And–surprise!–the clear message is exactly the opposite of Kohl’s claims.
    Here is the full sentence from which he has mined his quote, complete with surrounding context (my ellipses are intended for conciseness, not a change of meaning, as can readily be verified at the link provided):

    Molecular biology has become a glamor field….Glamor and brilliance generate enthusiasm and optimism; they may also dazzle and blinfold. The notion has gained some currency that the only worthwhile biology is molecular biology. All else is “bird watching” or “butterfly collecting.” Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!…Such pronouncements can be dismissed as merely ridiculous. They are, however, caricatures of opinions entertained by some intelligent and reasonable people, whose views deserve an honest and careful consideration and analysis.

    Dobzhansky then proceeds to 9 cogent and eloquent pages of such “honest and careful consideration and analysis”, reaching these conclusions:

    organismic biology will always occupy a leading place in the enterprise of science.

    surely no solution ignoring either the organismic or the molecular biology can be right or reasonable.

    In short, Mr. Kohl has quotemined Dobzhansky extremely dishonestly, attributing to him opinions that are exactly opposite from those he explicitly actually held. Needless to say, this kind of shit is beneath contempt.

    James V. Kohl: Crank, ignoramus, creationist, con-man, bigot, and liar.
    Fuck you.

  428. 428
    John Doe

    Wow! Fantastic catch, Chas. That really is the complete opposite of what Kohl was trying to pass off as the meaning of that excerpt.

  429. 429
    Rey Fox

    Spam, spam, crank, and spam.

  430. 430
    djr1

    @ 409, 418

    Djr1, please use
    Material to be quoted for a response

    for this:

    Thanks for the help – it is new for me – but I guess even old dogs have to change. (hopefully it worked!!)

  431. 431
    chigau (違う)

    Bravo, Chas.
    Thank you.

  432. 432
    myeck waters

    Beautiful, Chas.
     
    Kohl, you are done. A well-executed disappearing would be the best move for you.

  433. 433
    djr1

    @ 411 JK

    “I think what you’re saying is that academia took over the role of the church, and that academics have refused to acknowledge biological facts that jeopardize their power base.”

    No – that is not what I was saying at all. I was trying to make the point that 400 years ago our world was very different – and science and academia were at a totally different place. The chances of a Galileo, or a Newton developing a radical new explanation for some phenomena were pretty good. Today – science and academia are much more of a community process. I am not a scientist – but in the research class I took in college – the importance of documenting your research in intense detail was stressed. That way – the science community could fully understand what you had done – and begin the process of validating your work, or shredding your work. Academics are a part of a global community. Science is not done on a blog – it is done by highly specialized researchers. Go talk to them about your new theory – that invalidates the currently held understanding of evolution by mutation, and selection.

  434. 434
    Tethys

    James Kohl the crank was over here getting his model (which is not a theory) ridiculed before PZ started this thread. His most telling comment;

    It’s more likely that Carl Zimmer is becoming a Creationist, like the more famous Creationist: T. Dobzhansky, based on biological facts currently presented in this article from Science.

    Please feel free to address the data or Carl Zimmer’s comments on it, and skip your opinions.

    Read more at: http://phys.org/news/2014-01-americans-dont-evolution.html#jCp

    The link discusses species diversity in the rainforest. Why our cabbagey friend thinks that either of these scientists is a creationist is perhaps just another aspect of his break with reality.

  435. 435
    Lofty

    PZ @426

    I’ve also read that paper you keep citing. It also makes no sense. You string together sciencey words into an incoherent glop that is only going to make you look intelligent to people who know nothing about the subject you’re discussing.

    I think this is standard operating procedure for woo sellers. He knows his target audience. And I’m sure Mr Cabbage will busily quote mine this thread to make him look more like a genius to the rubes.
    .
    Does Cabbage go well with Ham?
    .
    Ignorant rubes happily consume colored woo poo.

  436. 436
    zenlike

    Thanks for that Chas, James totally misrepresented that bit. A whopper of a lie.

    James Kohl, please answer this very simple rhetorical question: if you are truly right, why do you have to lie so much?

  437. 437
    zenlike

    Tony! I’ honoured to stand in your corner while we wait. The contents of my bag of popcorn are getting pretty damn low though.

  438. 438
    Nerd of Redhead, Dances OM Trolls

    Tony! I’ honoured to stand in your corner while we wait. The contents of my bag of popcorn are getting pretty damn low though.

    Have no fear, free popcornz, and gr*g or swill will be provided, until JK posts he is wrong, the banhammer falls, or JK actually gives a straight answer.

  439. 439
    James Kohl

    @436

    James Kohl, please answer this very simple rhetorical question: if you are truly right, why do you have to lie so much?

    There is no question about whether or not I am right. Dobzhansky (1973) noted the amino acid substitution that differentiates chimps, gorillas, and humans.

    “…alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”

    Then, suddenly, only 4 days ago we see this reported (why did they lie?):

    “In humans and chimps, the higher proportion of amino acid changes suggests that some of those genes are under the influence of “positive selection,” meaning that the altered proteins give the primates some evolutionary advantage, Johnson said.”
    http://phys.org/news/2014-01-lice-men-chimps-tracks-pace.html

    If evolutionary theorists had ever tried to explain how the evolutionary advantage arose via amino acid substitutions in different species, they might have realized that mutation-driven evolution was a simple-minded and meaningless/ridiculous theory. The fact that it is so utterly ridiculous and that every bit of experimental evidence since Dobzhansky (1964) has attested to conserved molecular mechanisms, which refute the ridiculous theory is why I need not lie about anything here. I need only provide the biological facts for every one of you to show how ridiculous your beliefs have become.

    Your beliefs have no explanatory power and yet you all criticize me for explaining that the conserved molecular mechanisms exemplify nutrient-dependent pheromone-controlled adaptations to ecological variation in species from microbes to man. How can you not realize that all serious scientists simply laugh at you. They’re not going to debate nonsense; they dismiss it — as I did with publication of my book, my reviews, and my book chapter (and in every presentation to every scientific forum since 1992).

  440. 440
    ChasCPeterson

    zenlike: We’ve seen that Kohl has no problem with outright lying, and that deliberate misrepresentation is simply his SOP (hey, there he goes again in #439). However, he does not seem to be lying about having won a couple of awards:
    something called the Ira and Harriet Reiss Theory Award (presumably they meant ‘model’)
    and (with 3 coauthors) something called the Zdenek Klein Award for Human Ethology.

  441. 441
    Nerd of Redhead, Dances OM Trolls

    There is no question about whether or not I am right. Dobzhansky (1973) noted the amino acid substitution that differentiates chimps, gorillas, and humans.

    Which is explained by mutations, and not your fuckwitted and terminally inane idea

    If evolutionary theorists had ever tried to explain how the evolutionary advantage arose via amino acid substitutions in different species,

    They have. It’s called genetic drift, since most of those mutations are neutral. And you haven’t shown otherwise with real scientific evidence, and your unevidenced claims are and always will be dismissed as crank fuckwittery.

    Your beliefs have no explanatory power

    Your beliefs, which means accepting something without evidence, is your fuckwitted crank model. Whereas evolution has a million or so scientific papers to back it up. You, ZERO, ZILCH NOTHING. NADA.

  442. 442
    John Doe

    Another Kohl post, another opportunity to quickly answer the questions that need elucidation, another failure to do so.

    I’ll try again.

    What mechanism (enzymes/pathway) is responsible for making changes to the genome in your model?

    The spliceosome is to splicing, as __________ is to nutrient-dependent, pheromone-controlled, specifically directed base substitutions.

    Fill in the blank, James. It’s that easy.

  443. 443
    Nerd of Redhead, Dances OM Trolls

    *snicker* Why do creobots/IDiots/cranks always think that mutations only occur in protein making genes. Some are going to occur in regulatory genes, and JK’s model explains nothing if that happens. But Evolution says now we have different patterns in feline coats, antelope horns, etc. and it is all explained by mutation/natural selection. JK loses again, as he was never, ever in the game. Ego can’t win in science. Evidence that JK lacks is so important to those pesky things like acceptance and scientific prizes.

  444. 444
    James Kohl

    @443

    “…we have different patterns in feline coats, antelope horns, etc. and it is all explained by mutation/natural selection.

    How can this dumb ass not realize that mutation/natural selection has no explanatory power, which is why serious scientists consider it to be such a ridiculous theory?

    “The application of the Avy [Agouti] mouse model as an epigenetic biosensor for environmental effects on the fetal epigenome has identified several important nutritional factors affecting epigenetic gene regulation. The determination of other key chemical and physical environmental factors affecting the fetal epigenome will allow for better health intervention and preventive strategies for protecting individuals from environmentally induced changes in the fetal epigenome.”
    http://www.sciencedirect.com/science/article/pii/S0890623806001973

  445. 445
    Nerd of Redhead, Dances OM Trolls

    How can this dumb ass not realize that mutation/natural selection has no explanatory power, which is why serious scientists consider it to be such a ridiculous theory?

    This, like all your inane babble JK, is evidencless assertion.

    I’ll help you with what is real evidence to make us think you are right JK. Cite real working scientists, say 100, why find your theory explains life better than and Standard Model with mutation/natural selection.
    This is put up or shut the fuck up loser time for you JK. Do you have those scientists? PZ can check with them to see if you aren’t blowing smoke.

  446. 446
    zenlike

    Thanks Chas, with the lie I was indeed referring to the quote mining, not specifically to the awards.

    The reason I asked about the awards was that I have become very suspicious about anyone claiming that online without specifying the award. Most of the time it is just bluster and bullshit.

    I do find it very funny however, that Kohl has won an award for a ‘theory’, when he seems to be very allergic to that particular term :)

  447. 447
    James Kohl

    @427

    But it wasn’t until the requote in #411 with reference to a presidential address that I followed the link, because my memory was jogged. Sure enough, the quote was mined from Dobzhansky’s presidential address to the American Society of Zoologists, a group that then, as now (since renamed SICB), includes quite a number of scientific bird watchers and butterfly collectors.

    How many more posts will he make before this turtle watcher realizes that the introduction to my last review starts with:

    “Members of the Society for Integrative and Comparative Biology (SICB) recently organized and held an ecological epigenetics symposium (January, 2013). Clearly, a new generation is familiar with the concept of ecologically driven epigenetic effects, which can be caused by sensory input that effects hormones, which affect behavior.”

    Peterson finally goes back to the paper I have repeatedly cited in a specific context and adds back everything Dobzahansky said 50 years ago that was wrong. He claims to be a member of SICB, but I didn’t find his name on the membership list. Maybe he’s an anonymous member. Even so, why isn’t he citing and addressing “Epigenetics for behavioral ecologists.” http://beheco.oxfordjournals.org/content/early/2013/01/28/beheco.ars145

    If he did address the SICB conference reports we would be discussing ecological adaptations, wouldn’t we? Is it dishonest to cite and quote one SICB source from 50 years ago to derail the topic and make others question my honesty, but to ignore the report of the 2012 conference?

    Could the problem be that he’s a turtle watcher and cannot possibly take the time to learn anything new because the turtles move so fast and are leading the race towards scientiific progress? Or, could it be merely that he’s a dumb ass?

  448. 448
    Nerd of Redhead, Dances OM Trolls

    Or, could it be merely that he’s a dumb ass?

    No fuckwit, you are the dumb ass. Where is your 100 working biological scientists who acknowledge your genius, and renounce the Standard Model with mutation/natural selection. Preferably from this list to show you have some heavyweights backing your demented claims.

  449. 449
    James Kohl

    @445

    Cite real working scientists, say 100, why find your theory explains life better than and Standard Model with mutation/natural selection.

    Are you alluding to the fact that I cited approximately 100 published works in my most recent review?
    see: http://scholar.google.com/scholar?q=related:8awUFujdfNIJ:scholar.google.com/&hl=en&as_sdt=0,43

    Is this dumb ass, or anyone else here familiar with the works of Ryzsard Maleszka, like his works that I cited in these three extracts?

    “In the honey bee, the outputs of gene regulatory networks stemming from near identical genomes are altered by differing nutritional intakes which can be considered to be alternate trajectories along an epigenetic landscape. Differential nutrition results in different morphologies, different physiologies, different nervous systems and very different behaviors, all arising from different developmental trajectories that end in queen and worker. (Gabor Miklos & Maleszka, 2011, p. 403)”

    “Olfactory/pheromonal input is obviously important to the nutrient-dependent, hormone-organized and hormone-activated pheromone-controlled development of the invertebrate brain and behavior (Dickman, Kucharski, Maleszka, & Hurd, 2013; Lyko et al., 2010; Lyko & Maleszka, 2011).”

    “For contrast, the epigenetic tweaking of immense gene networks by nutrient intake (e.g. glucose uptake in cells) exemplifies a vastly more complex synergy. Glucose causes changes in GnRH pulse frequency and amplitude in mammals (Roland & Moenter, 2011). The GnRH pulse controls nutrient-dependent and sex steroid hormone-dependent body odor production in a manner similar to the nutrient-dependent and hormone-dependent production of pheromones in the honeybee model organism and nutrient-dependent pheromone production in microbes. For example, the diet of the honeybee queen determines her pheromone production, which controls interactions among colony members (Gabor Miklos & Maleszka, 2011; Kohl, 2012).”

    The problem with this dumb ass: Nerd of Redhead, Dances OM Trolls, is repeated requests for THIRD PARTY evidence that supports my model, when I have included it in the published article as support for the model. The problem with everyone else is that they are not providing any experimental evidence that supports their ridiculous belief in mutation-driven evolution. Has anyone else noticed that theorists can do nothing more than repeatedly reassert the ridiculous?

  450. 450
    Nerd of Redhead, Dances OM Trolls

    re you alluding to the fact that I cited approximately 100 published works in my most recent review?

    No, your reviews, like your word, are bullshit. I’m talking about 100 scientists who acknowledge in writing your genius, while denouncing the Standard Model. You have nothing but bullshit, and we both know that. Loser writ large over your ego driven crankdom.

  451. 451
    Nerd of Redhead, Dances OM Trolls

    when I have included it in the published article as support for the model.

    Sorry, your word or your writing is bullshit until you provide the evidence here. In public, where the ridicule from those who you pretend support your fuckwitted idea will be deafening.
    Why can’t you name names? Afraid to do so? Why?

  452. 452
    Tethys

    make others question my honesty

    You don’t have any honesty to question. You continue to post reworded quote mines of links that in no way support your model. The most recent example is #444 where your quote

    environmentally induced changes in the fetal epigenome.”

    is not found in the abstract.

    Traditional studies on the combined effects of genetics and the environment on individual variation in disease susceptibility primarily focus on single nucleotide polymorphisms that influence toxicant uptake and metabolism. A growing body of evidence, however, suggests that epigenetic mechanisms of gene regulation, such as DNA methylation and chromatin modification, are also influenced by the environment, and play an important role in the fetal basis of adult disease susceptibility. Studying the influence of early environmental exposures on metastable epialleles and imprinted genes offers insight into the mechanisms affecting the fetal epigenome and subsequent adult disease susceptibility. In this review, we introduce the reader to the field of environmental epigenomics, provide information on the important epigenetic control mechanisms and epigenetic phenomena in mammals, and summarize the current body of literature on nutritional and environmental influences affecting the epigenome.

    It is clear that JK is lying about the bit I have helpfully bolded for clarity. I didn’t need Chas to confirm that JK is completely lacking in both integrity and reading comprehension.

    The environmental influences are proper maternal nutrition and the observed results pertain to adult disease incidence, not “environmentally induced changes in the fetal epigenome.” as JK claims.

  453. 453
    James Kohl

    @450

    I’m talking about 100 scientists who acknowledge in writing your genius, while denouncing the Standard Model.

    What is the “Standard Model?”. I think you may be inferring that the ridiculous theory of mutation-initiated natural selection is the “Standard Model” when there are no model organisms that exemplify anything except the nutrient-dependent pheromone-controlled ecological adaptations in my model.

    That makes my model the “Standard Model” on which all other models must be based. But I think you may mean there is some other “Standard Model.” Or, at least you may think that there is, since you are such a dumb ass.

    In any case, I guarantee you cannot find 100 serious scientists who still think in terms of mutation-driven evolution. Serious scientists are not dumb asses. They may not acknowledge my genius because, like Dobzhansky, they were able to see how the role of alternative splicings and amino acid substitutions was going to play out. Unlike me, however, they did not want to excite the theorists who never had a clue about how that role was going to play out — and still don’t realize that it has played out exactly as I have detailed it.

    For more than a year, I’ve asked evolutionary theorists who tout mutation-driven evolution: “Is there a model for that?” Well, is there, dumb ass?

  454. 454
    Nerd of Redhead, Dances OM Trolls

    What is the “Standard Model?”. I

    I meant modern synthesis, but otherwise the argument holds. You are a liar and bullshitter until you provide the names of biologists, preferable from the NAS, who think your model overturns Modern Synthesis. Real, solid and conclusive evidence if you are right, and your failure to provide those names solid and conclusive evidence you are an egotistical liar and bullshitter without honesty and integrity,.

  455. 455
    Rey Fox

    Peterson finally goes back to the paper I have repeatedly cited in a specific context and adds back everything Dobzahansky said 50 years ago that was wrong.

    Wow. Quoting doesn’t work that way, you know. If you want to say that Saint Dobzhansky said such-and-such, then you have to actually be able to back up that he said such-and-such. Now, if YOU want to say such-and-such and have it be your own words, then go right ahead, it would be no less inane than anything else you’ve said here. But you can’t claim to be standing on the shoulders of any giants when you do.

    They may not acknowledge my genius

    But soon they will see…they will ALL SEE! MUWAHAHAHAHAHAHAAAA!

  456. 456
    vaiyt

    How can this dumb ass not realize that mutation/natural selection has no explanatory power, which is why serious scientists consider it to be such a ridiculous theory?

    How are things going over there on Bizarro Earth?

  457. 457
    James Kohl

    @454 Nerd of Redhead, Dances OM Trolls

    I meant modern synthesis, but otherwise the argument holds.

    No,the argument does not hold. It’s not even an argument. It’s never been anything but a nonsensical theory that is of no use to anyone who understands biologically based cause and effect (like the hundreds of members of the International Society for Physiological Sciences).

    Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?
    http://jp.physoc.org/content/589/5/1007.abstract

    “If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based.”

    If you do not become more aware, people will think you are a dumb ass, because you are a dumb ass. Thank you for setting an example of how ignorant a dumb ass can be.

  458. 458
    zenlike

    They may not acknowledge my genius because

    Bwahahahaha. Seriously dude, you are a fucking joke.

  459. 459
    Nerd of Redhead, Dances OM Trolls

    If you do not become more aware, people will think you are a dumb ass, because you are a dumb ass. Thank you for setting an example of how ignorant a dumb ass can be.

    Sorry fuckwit, you set the example for a dumb ass whereever you post. After all, I present evidence, you present demented and unevidenced OPINION. Which is properly dismissed by any cogent person.

    It’s never been anything but a nonsensical theory that is of no use to anyone who understands biologically based cause and effect (like the hundreds of members of the International Society for Physiological Sciences).

    Then Name NAMES of those who renounce Modern Synthesis for your demented and unevidenced model. PUT UP OR SHUT THE FUCK UP AS THE LOSER YOU WILL SHOW YOURSELF TO BE WITHOUT NAMES THAT ARE CONFIRMED AS AGREEING WITH YOU.

  460. 460
    zenlike

    Yes, evolutionary biology and genetics have ‘moved on’ in the last decade. Moved on as in ‘progressed considerably’, not as in ‘found to be in error and replaced by the pet theory of a single kook’.

  461. 461
    James Kohl

    @455

    If you want to say that Saint Dobzhansky said such-and-such, then you have to actually be able to back up that he said such-and-such.

    Dobzhansky (1972) “Reproductive isolation evidently can arise with little or no morphological differentiation.” http://www.sciencemag.org/content/177/4050/664.short

    Do you remember what he said about natural selection for mutatations? Is there a model for that? Dumb ass!

    The role of ecological variation in driving divergence of sexual and non-sexual traits in the red-backed fairy-wren (Malurus melanocephalus) http://www.biomedcentral.com/1471-2148/13/75

  462. 462
    Nerd of Redhead, Dances OM Trolls

    Do you remember what he said about natural selection for mutatations? Is there a model for that? Dumb ass!

    You are the dumbass. Dobzhansky was a leader for the Modern Synthesis, for which there is no evidence it is wrong. You just don’t understand science. You are a loser with an ego the size of Montana, an intellect the size of Rhode Island, and honesty and integrity at the Planck constant.

  463. 463
    Nerd of Redhead, Dances OM Trolls

    Do you remember what he said about natural selection for mutatations? Is there a model for that? Dumb ass!

    Dumbass, name names of those who back your inane and demented model. Or they don’t exist. And we both know they don’t exist. Without your ego and subintellect, the model will be ignored, as it is now, and as it should be in the future.

  464. 464
    Ogvorbis: Still failing at being human.

    James Kohl:

    Do you have a contract with We Are Igors? Do you have an Igor working for you? ” They may not acknowledge my genius because, hahahaha. Haha. Ha hahaha ha! Hahaha. HAHAHA HAHA!!!!

  465. 465
    David Marjanović

    Hello again, Mr Kohl. I asked you a bunch of questions. Then I went away for a day. Now I’m back, and I see that you haven’t even tried to answer a single one of those questions – even though you remembered me well enough to mention me.

    What’s the problem?

    If you can’t answer them, why don’t you just say so?

    Peterson and also Marjanović and PZ Myers would, no doubt tell you that bird predation controls reproduction in moths — as shown in the peppered moth example of accumulated mutations and mutation-initiated natural selection. That explains their belief that the faces of vertebrates, such as male fish are attractive to females; that male turtles choose females who are, anthropomorphically, not just another pretty face; and that female birds chose for plumage color and vocalization of males. (It does not explain non-heterosexual attraction in any species, but who cares about that).

    Wow. I’ve never seen anybody put quite so many words into my mouth.

    For starters, bird predation doesn’t control reproduction in moths. It controls survival in moths. That should have been obvious.

    Start thinking about how to make fish faces more attractive to increase the world-wide decline in populations of fish

    Ever encountered the word overfishing?

    conserved molecular mechanisms in species from microbes to man

    You’re really fond of that phrase, hm?

    “I think it is interesting that the nervous system is so well preserved, from an evolutionary point of view, that you can observe a nerve-cell-specific expression of a pig gene in a zebrafish. It is impressive that something that works in a pig also works in a fish,” says Knud Larsen.

    I don’t find it surprising at all. The nervous systems of vertebrates (and indeed beyond) are all quite similar, apart from quirks like the thickened cerebral hemispheres of mammals.

    Nothing in evolution makes sense except in the light of evolution. Without evolution, everything seems surprising.

    It’s really unclear what mechanism he’s talking about: the way you get amino acid substitutions is by changes in the nucleotide sequence of DNA, which is the mechanism of mutation that he seems to deny exists. Unless he’s talking about RNA editing

    As far as I understand him, he’s talking about protein editing – which doesn’t even exist, but not only does he not know that, he doesn’t know that anyone else knows it.

    @297

    how would pheremones and microbes interact?

    1) Nutrient-dependent production of pheromones controls reproduction in species from microbes to man.

    That doesn’t answer the question. It doesn’t even try.

    (I closed the blockquote tag for you.)

    Why would I go looking for a Nobel Prize after being banned from commenting to Science, Nature, and even to Nobel Laureate Sheckman’s eLife?

    …This just makes no sense whatsoever.

    You think Nature and Science would automatically reject your manuscript? Fine, why don’t you submit to PNAS? To Cell? To the Journal of Evolutionary Biology? To Evolutionary Biology? To another widely read journal that publishes papers on how evolution works?

    Why “even” some Nobel laureate’s site that I’ve never heard of? The Nobel committee does not consist of former award winners, in case you didn’t know. ~:-| Even if *scrolls up* Sheckman hates your guts, he can’t prevent you from winning a Nobel prize.

    As a historian you must be aware that no amount of experimental evidence can overcome the ridiculous beliefs of theorists until those who are continuing to teach those ridiculous beliefs die.

    That’s not always the case. It took about five years till every geologist in the world accepted plate tectonics.

    People basically just said “oh, OK” and moved on to arguing about details.

    I exemplified the fact that the amino acid substitutions are NUTRIENT-DEPENDENT and PHEROMONE-CONTROLLED.

    You exemplified it? That means you are an amino acid substitution.

    For fuck’s sake, learn what words mean before you use them! You’re not two years old anymore!

    That makes anything that PZ Myers or anyone else has taught about social familiarization in fish a ridiculous misrepresentation of biological facts.

    Did you just seriously extrapolate from one species of vertebrate to twenty-five thousand just because they all happen not to be tetrapods?

    My molecular mechanisms start with the nutrient-dependent flipping of base pairs

    How does that work? Do you mean “mutagens” by “nutrients”? If so, what do we eat that causes mutations to specific sites and not to others? And what exactly do you mean by “flipping”?

    That’s what we mean by “mechanism”!

    When did the first ecological adaptation occur?

    Isn’t every adaptation an adaptation to the environment and can therefore be called “ecological”?

    How did the first mutation occur that led to our evolution?

    By any of the usual causes – radiation, mutagens, or (most likely) a partial failure of replication. :-| Four billion years after the fact it’s impossible to tell which.

    Let’s try to determine who’s the most confused about what I am saying, and why. Is it because of their belief in a ridiculous theory for example, or because of a belief in biological facts that are not biological facts in species from microbes to man?

    …It couldn’t possibly be because you’re bad at explaining, or because you’re confused yourself (especially about the meanings of technical terms). Riiiiight?

    If I were spamming, I would link to my own blog posts on the domain I founded in 1996 (more than 800 of them in the past 4 years) that include citations to current research that evolutionary theorists have ignored.

    Spam appears to be another vocable you don’t understand.

    It refers to advertisements that are dumped on people unsolicited. When you peddle the stuff you sell, you’re spamming. When you link to a blog post, you can only metaphorically be spamming.

    The thermodynamic stability of the organism that kills the patient gradually causes ever organ of every organ system to shut down.

    What? How does thermodynamics play into this?

    So you don’t think mutations in nucleotide base pairs, especially at the third triplet, lead to changes in amino acids?

    The second base pair is the one that differs most between codons for different amino acids. Your use of “triplet” is an error, too.

    and only recently did different species of birds decide to become different species due to amino acid substitutions. Evidently, they learned to fear the slow rate of mutation-initiated natural selection

    1) There’s no decision involved, no consciousness at all.
    2) Slow rate???

    Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
    http://www.sciencemag.org/content/342/6164/1367.abstract

    Has nothing to do with nutrients or pheromones. Do you know what kind of molecule those transcription factors are?

    They’re proteins made by the organism in question, and coded in its genome.

    What I did was show that the molecular mechanisms of nutrient-dependent pheromone-controlled cell type differentiation are conserved in species from microbes to man.

    The fuck you did. You just repeated your assertion once again!

    Nutrient-dependent pheromone-controlled alternative splicings of pre-mRNA cause the amino acid substitutions that differentiate cell types in individuals of species.

    Oh, good. What do bacteria do, then? As has been mentioned in this thread, bacteria don’t do alternative splicing.

    And how short do you imagine any exon is?!?

    The nutrient-dependent pheromone-controlled de novo creation of olfactory receptor genes via alternative splicings in insects and mammals is the holy grail of evolutionary biology.

    If you say so… *eyeroll*

    Hey, remember when I asked you what you mean by “de novo”? You still haven’t replied.

    I’m waiting.

    That means it is my fault for failing to communicate my ideas to idiots who cannot understand my ideas, and I am not willing to take responsibility for their ignorance. Also, I am not willing to take responsibility for the examples of that ignorance that we have been offered here by anonymous fools.

    I burp in your general direction!

    De novo creation of genes by alternative splicing requires the action of a reverse transcriptase. This should be easily testable.

    Indeed. Is there any genome that encodes reverse transcriptase and doesn’t belong to a retrovirus?

    James V. Kohl: Crank, ignoramus, creationist, con-man, bigot, and liar.

    Actually, I don’t think he lies. I think his reading comprehension is so catastrophically bad that he really believes his extreme misinterpretations. Watch him utterly failing to understand what “natural selection” means! Or watch this:

    Dobzhansky (1973) noted the amino acid substitution that differentiates chimps, gorillas, and humans.

    “…alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla.”

    Jimmy, dear, the gene for the alpha chain of hemoglobin is not the whole genome, you incredible dumbass. Dobzhansky (1973) noted one amino acid substitution that distinguishes chimps + humans from gorillas, not all that distinguish these five species*. He noted one out of a whole lot!

    * Chimps proper, bonobos, humans, eastern gorillas, western gorillas.

    Then, suddenly, only 4 days ago we see this reported (why did they lie?):

    “In humans and chimps, the higher proportion of amino acid changes suggests that some of those genes are under the influence of “positive selection,” meaning that the altered proteins give the primates some evolutionary advantage, Johnson said.”
    http://phys.org/news/2014-01-lice-men-chimps-tracks-pace.html

    The study reported there looked at a thousand five hundred thirty-four genes, not at one gene like Dobzhansky did.

  466. 466
    David Marjanović

    “Reproductive isolation evidently can arise with little or no morphological differentiation.”

    Things like sperm membrane proteins don’t count as morphology, you know.

    Do you remember what he said about natural selection for mutatations? Is there a model for that?

    It’s called population biology. Look it up.

  467. 467
    ChasCPeterson

    Do you remember what he said about natural selection for mutatations?

    Genes reproduce themselves
    generally with an astonishing accuracy; the
    sequences of the four “letters,” the nucleotide
    bases, are usually identical in hundreds
    of billions of cells of the bodies of the
    parents and of their progeny. Occasionally,
    there occur, however, changes, “misprints,”
    mutations. Self-reproduction plus mutation
    make possible natural selection. Natural
    selection makes possible evolution. Evolution
    is not always, and not necessarily, but
    sometimes, progressive.

    - Dobzhansky, 1964 (op. cit.)

  468. 468
    James Kohl

    @465 David Marjanović

    I see that you haven’t even tried to answer a single one of those questions – even though you remembered me well enough to mention me.

    What’s the problem?

    The problem is that — like everyone else here — you are still going to believe in a ridiculous theory and ask me questions about what my model does not explain in the context of that theory when it explains how ecological variation results in adaptations in species from microbes to man.

    @ 466

    It’s called population biology. Look it up.

    Population biology explains nothing. That’s why “Physiology is rocking the foundations of evolutionary biology” http://ep.physoc.org/content/early/2013/04/12/expphysiol.2012.071134.abstract

    Finally, someone who is not a dumb ass told the dumb asses that the nutrient-dependent physiology of reproduction must control species diversity. That meant the end of mutation-initiated natural selection or the Modern Synthesis or Neo-Darwinism and all other nonsense that the folks here have been touting for decades beyond the time when serious scientists started looking at conserved molecular mechanisms. Shapiro’s book exposes the ridiculous mess that evolutionary theorists have left us with, and others are quickly following his lead.

    A post-genomic view of behavioral development and adaptation to the environment
    http://www.sciencedirect.com/science/article/pii/S0273229713000038

    Darwin’s passionate environmentalism or the dangerous fallacy of the ‘All-sufficiency of natural selection’ theory
    http://nah.sagepub.com/content/21/1/76.abstract

    Evolutionary Epigenetics
    http://www.davidmarsh.org.uk/?Articles:Evolutionary_Epigenetics

    The fact that you have not even realized after more than 450 posts here that your ridiculous theory is no longer accepted by anyone with even the slightest knowledge of biologically based cause and effect should have been the first indicator that you should do more than dismiss me as a crank. Instead, the unbearable ignorance of this entire group of participants and lurkers has now been exposed.

    Anyone who thinks they have told me a thing or two will be happy if they did so anonymously. People like you and Peterson and PZ Myers will from now on be ridiculed for being the fools that you are. Yet, nothing will change for you.

    As others accept the reality of nutrient-dependent pheromone-controlled ecological adaptations, you’ll all be stuck here with your ridiculous theory since there is no where else in the world you can tout it. You can only keep telling yourselves “it’s random mutations that are responsible for natural selection and evolution” — just look at that bird over there, it’s obvious. Oh look, there’s another one — a whole population that mutated into existence. Isn’t evolution wonderful?

  469. 469
    Nerd of Redhead, Dances OM Trolls

    you are still going to believe in a ridiculous theory and ask me questions about what my model does not explain in the context of that theory when it explains how ecological variation results in adaptations in species from microbes to man.

    No it doesn’t. You haven’t shown a mechanism and showed the biochemical steps in it. All you have done is made inane and unevidence assertions. You have no theory, model, or anything else but your inane and overblown ego.
    Still not one name to back up your assertions. Meaning you are nothing but liar and bullshitter. Nobody supports your fuckwittery but you. All alone against a world who follows standard evidential science, which is the modern synthesis with random mutation/natural selection.

  470. 470
    James Kohl

    @467

    Self-reproduction plus mutation make possible natural selection. Natural selection makes possible evolution.

    Self-reproduction is nutrient-dependent. It is made possible by selection of nutrients. Ecological variation in the availability of nutrients results in the metabolism of nutrients to specie-specific blends of pheromones that control physiology of reproduction.

    Ecological adaptations thus may result in species diversification sans mutations.

    Dobzhansky and everyone else has been wrong about the role of mutations because they could not grasp the fact that self-reproduction requires food, and organisms that out-reproduce their food supply result in population-wide extinctions.

  471. 471
    Nerd of Redhead, Dances OM Trolls

    Self-reproduction is nutrient-dependent. It is made possible by selection of nutrients. Ecological variation in the availability of nutrients results in the metabolism of nutrients to specie-specific blends of pheromones that control physiology of reproduction.

    Meaningless word salad, shown your inability to define your own ideas to present to the scientific community. Which doesn’t like word salad for any meal. Your model is dismissed as evidenceless fuckwittery, and you can’t show ANYBODY who agrees with you, and renounces modern synthesis with random mutations/natural selection. Poor, poor, egotist. All alone with your delusions, and nobody comes to play. Since you make no sense.

  472. 472
    ChasCPeterson

    they could not grasp the fact that self-reproduction requires food

    Let me get this straight.
    You are now claiming that Theodosius Dobzhansky–the guy whose scientific reputation was founded on extensive experiments raising flies in population cages–could not grasp the fact that animals require food for reproduction?
    That’s your claim?

  473. 473
    James Kohl

    Idiots!

    http://pheromones.com/interdisciplinary-integration-replaces-mutation-driven-evolution/

    Epigenomics and the concept of degeneracy in biological systems “A multi-level regulatory network consisting of such mechanisms as modular utilization of protein domains, alternative splicing and epigenomic modifications of DNA has been the driving force behind the wide radiation, rapid evolution and evolutionary success of eukaryotic organisms.”
    Read more: http://pheromones.com/#ixzz2q9ZGC6pI

    http://pheromones.com/aerobic-glycolysis-and-amino-acid-substitutions-in-the-brain-sans-mutations/

    The complexity of how conserved molecular mechanisms enable ecological adaptations via nutrient-dependent amino acid substitutions that differentiate cell types in individuals of all animal species remains beyond the grasp of evolutionary theorists.
    Read more: http://pheromones.com/#ixzz2q9Z7ijks

  474. 474
    Rey Fox

    Are you a Lamarckist?

  475. 475
    Nerd of Redhead, Dances OM Trolls

    Idiots!

    That’s you demented fool. I see no evidence for your idea being supported, nor ONE scientist supporting your idea while denouncing Modern Synthesis. I wonder why? It might be they are smarter and more in tune with the real science than you are, with your big ego and lack of knowledge.

  476. 476
    Ogvorbis: Still failing at being human.

    Rey:

    More of an olfactory Lamarckist.

  477. 477
    ChasCPeterson

    yay, blog-pimping.
    (btw, serious scientists high-school sophomores know that “aerobic glycolysis” is an oxymoron.)

  478. 478
    Tethys

    Gee whiz, aerobic glycolysis and amino substitutions in the brain sure sounds sciencey. However since glycolysis both aerobic and anerobic actually takes place in the cell, any discussion about the brain is utter nonsense.

    I am not going to click any of those pheremone links. Spam from known liars is best avoided.

  479. 479
  480. 480
    John Doe

    As I pointed out before, Denis Noble is not rejecting Modern Synthesis, he’s merely supplementing it.

    A central feature of the Integrative Synthesis is a radical revision of the concept of causality in biology. A priori there is no privileged level of causation. This is the principle that I have called the theory of biological relativity (Noble, 2008, 2012). As Werner puts it, ‘all levels have an equal contributing value’ (Werner, 2003). Control is therefore distributed, some of which is inherited independently of DNA sequences

    For emphasis:

    some of which is inherited independently of DNA sequences

    I’ll also quote myself again and give you another chance:

    Another Kohl post, another opportunity to quickly answer the questions that need elucidation, another failure to do so.

    I’ll try again.

    What mechanism (enzymes/pathway) is responsible for making changes to the genome in your model?

    The spliceosome is to splicing, as __________ is to nutrient-dependent, pheromone-controlled, specifically directed base substitutions.

    Fill in the blank, James. It’s that easy.

    As I’ve told you before, I’ve read your papers. You make mention of exactly 0 enzymes that fit in that blank.

  481. 481
    Nerd of Redhead, Dances OM Trolls

    Still no evidence for the 100 working biologists backing your fuckwitted model JK. Nothing but noise, bullshit, lying, evading, and ego.

  482. 482
    Arawhon, a Strawberry Margarita

    Is this what Dunning Kruger looks like when taken to an extreme? Its like he had an epiphany while learning about a part of the science and has subsequently been trying to massage and twist all the facts he keeps encountering into his pet model which he is utterly certain is correct. Mr. Kohl, utter certainty is a bad thing, it prevents you from being able to reevaluate an idea when new data is encountered.

  483. 483
    Tony! The Queer Shoop

    James Kohl:
    I really hope your link to a book on Amazon.com @412 was not an example of providing third party evidence…

  484. 484
    Tony! The Queer Shoop

    James Kohl:

    Also, I am not willing to take responsibility for the examples of that ignorance that we have been offered here by anonymous fools.

    ::lightbulb moment::
    After reading all your comments in this thread (what a task, btw. And without a single drink…), I’ve come to the conclusion that you exemplify (please don’t be mad that I used your third favorite word) smugnorance (for those uncertain, that’s smug+ignorance)

    Hmmm, need to add ‘Smugnoramus’ or ‘Smugnorance’ to the Pharyngula Wiki, with a pic of James Kohl and any random nutrient/pheromone BS comment he’s infected this thread with.

  485. 485
    Menyambal

    Tony! I love “smugnorance”. The word, I mean, not the state of mind.

    Heh. The ad at the top of the page has picked-up on “pheromones”, and I tapped on it. They were adverting a comparison of the best pheromone products, and I tapped that. Kohl’s product did not make the list. None of the products rated as very effective, really.

    Kohl, I am not enough of a biologist to have any stake in defending the status quo, and I even wondered for a while if pheromones were what got me dates with some women and not others. But I think you are a crank for many reasons. I’m not detailing them on this touchpad, mostly because you won’t comprehend.

    You are a crank, James Kohl, for advancing a “model” that requires that many people are gullible, stupid, deluded and close-minded, while showing every sign of being so yourself, and while bringing up the problem yourself, as your prime argument.

    Me, personally, I am annoyed by your habit of using phrases as if they were facts, over and over. Dude, if you again write “microbes to man”, I am going to go find a keyboard and cut loose.

  486. 486
    Azuma Hazuki

    I would like to know how epigenetics and nutrition relate to those massive chunks of LINE and SINE repeats scattered all over the genome, or the occasional telomere slippage, or the fact that pseudogenes for gulonolactone oxidase appear in humans and high apes, or the very idea of a “molecular clock” at all…

    Really, I think Kohl’s mechanisms are real, but I also think he’s way overplayed his hand. Epigenetics is important, sure, and I’d even be willing to grant them a primary role over the direct genes–>protein code if evidence showed it, but his model doesn’t account for the above. He’s got just a hammer and damn it, everything looks like a nail.

  487. 487
    pentatomid

    Chas, @427

    Great catch! And thanks for the link.

    James Kohl,

    Frankly it was bad enough when I thought you were just being dense. You’ve now been shown to be completely dishonest, to the point where you attribute views to people which are the exact oppoosite of the views they actually hold. There is no excuse for this. You are a lier and a bullshitter. You should be very very ashamed of yourself.

  488. 488
    blf

    What I am starting to wonder is what other delusions cabbage-for-brains holds: AGW denial? Birther? HIV/AIDS denial? Holocaust denial? Moon landing hoaxer? …?

    He is appears to be sufficiently disconnected from reality, with no obvious ability to either present or comprehend either evidence or truth/facts, then I assume he’s a polycrank.

  489. 489
    Ogvorbis: Still failing at being human.

    blf @488:

    What I am starting to wonder is what other delusions cabbage-for-brains holds

    Do you really want to go down that road?

    I did a quick check on polycranking and asked how lunar gyres are involved but got no answer. Not definitive as there was nothing there to cherry pick so Kohlslaw may have just ignored it.

    I am impressed with the circular reasoning, though. I know my model is true because I have published papers (and a chapter in a book) about it and the scientific literature backs me up because there are papers that agree with me which I have published. If I had tried that in a high school science class I would have gotten a well deserved D double minus.

  490. 490
    EnlightenmentLiberal

    Wow. This is rather impressive. Even after all of this, I don’t think we really understand what the hell he actually thinks.

    @James Kohl

    I am not a trained biologist. My training is in mathematical, computer science, with a small amount of theoretical physics. My formal biology training is at the high school level, although I have supplants this with guided self learning. To avoid any confusion, I shall try to avoid technical words and stick with laymen terms.

    In order to help me understand your position, please read carefully the following, and state immediately where you disagree. It’s vital that you pick out the first thing which you disagree with.

    Let’s consider single celled creatures like E. coli. They have a genome. A genome consists of DNA. Each individual E. coli cell has a very similar set of DNA. During everyday, normal cell function, proteins create RNA from the DNA, and then create proteins from the RNA. I’m sure I’m skipping over a lot of important steps, but this should be good enough for now. Are you with me thus far?

    It is a well observed fact that some kinds of radiation alter DNA strands in living cells like E. coli. For example, a stray cosmic ray or whatever can alter one base pair of DNA to another base pair. This process, this mechanism, is entirely random. Specifically, it has basically absolutely nothing to do with nutrient availability, and has absolutely nothing to do with pheromones, and has absolutely nothing to do with any environmental factors except the closeness to a radiation source. All of this is also overwhelmingly supported by evidence. This alteration of the DNA strand in the living cells of E. coli is an example of what we call a “mutation”. A mutation is a change to the DNA of a living organism.

    When E. coli cells reproduce, a copy of the genome, the DNA, is made. This copy process usually produces an exact copy. However, sometimes this copy process makes an inexact copy – a copy with errors. So, after replication, two E. coli cells usually have the exact same DNA, but sometimes they will have slightly different genomes. They will have slightly different DNA strands. The DNA strands will have almost the same base pairs in the same order, but some base pairs will be different, or some sections will be repeated in one and not the other, or some sections will be missing in one and not the other. This process is entirely unguided. It is random which sections of the DNA are altered, copied, or dropped. Specifically, it has basically absolutely nothing to do with nutrient availability, and has absolutely nothing to do with pheromones, and has absolutely nothing to do with any environmental factors. This changing of base pairs, and introduction of copies into the genome, and dropping of sections of the genome, are also examples of “mutation”. A mutation is a change to the DNA of a living organism.

    Are you with me thus far? Mutations are changes to the DNA of a living organism, and I’ve provided two very common mechanisms which change – aka mutate – the DNA of living organisms in a completely random way. When it happens is very random. What sections of the DNA it affects is random. What kind of change – an addition, deletion, or substitution – is also random. It has nothing to do with nutrients, pheromones, nor environment.

    Let’s talk about the Michigan State E. coli experiment. If I recall correctly, the 12 lines of the experiment started with E. coli from the same population. We can talk about the total distribution of genomes in each of the 12 lines, and each of the 12 lines contained the same set of genomes.

    At some point in the future, this changed. It was observed, measured, and documented that one of the lines of E. coli had individual E. coli cells with a distinct and unique and new genome which allowed it to “eat” a nutrient that E. coli normally could not “eat”. This particular genome was not present in the other 11 lines.

    No one observed how this new genome came about. However, it came about in only one of those lines, and thus it’s probably safe to say that it had nothing to do with nutrients, pheromones, nor environment. In fact, I would say that the evidence is good that the new genome came about from a random mutation, such as from the copying errors mentioned above or the radiation-mutations mentioned above.

    I can only assume you disagree with me thus far, and so I’ll stop for now. What I am desperately curious about is exactly where you disagree.

  491. 491
    James Kohl

    @490 EnlightenmentLiberal

    What I am desperately curious about is exactly where you disagree.

    Thanks for your detailed attempt to determine the difference between the theory of mutation-initiated natural selection and my model of ecological variation, adaptations, and species diversification. I especially appreciate that lack of name-calling. Also, after more than 480 posts, it is great that you make no attempt to bully me into admission of any belief in nonsense or force me to waste time discussing it. You simply state your case, and it is easy to see that our disagreement begins with the start of paragraph 5 (above):

    You wrote:

    When E. coli cells reproduce…

    In my model, the physiology of reproduction is nutrient-dependent and pheromone-controlled. Thus, any disagreement can be framed in the context of whether reproduction is a function of conserved molecular mechanisms in species from microbes to man.

    If the physiology of reproduction is not nutrient-dependent, species diversification might occur via mutations — as it appeared to do in Lenski’s experiments. If there is a model for mutation-driven evolution of the differences in cell types of E. coli that explains their survival, that model could be compared to my model of: Nutrient-dependent/pheromone-controlled adaptations, which is why I wrote:

    “…the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.”

    http://www.socioaffectiveneuroscipsychol.net/index.php/snp/article/view/20553/27989

    Another approach to the differences between my model and the theory of mutation-driven evolution would be an experiment that might yield sufficient experimental evidence to support the findings of Chelo et al (2013) who reported that mutations are not fixed in the genome of C. elegans. To determine whether conserved molecular mechanisms are responsible for ecological adaptations to variations in the availability of nutrients that metabolize to species-specific pheromones, which control the physiology of reproduction in species from microbes to man, Lenski could quit “feeding” the E. coli, and Chelo et al (2013) could approach the testing of the null hypothesis in the same manner.

    If the E. coli mutated into another species, or if the C. elegans model organism mutated and became the predator with teeth (P. pacificus), the idea of mutation-driven evolution would be supported by experimental evidence. If the two different model organisms, E. coli and C. elegans starved to death, my model would be supported by the experimental evidence that has made it obvious that mutation-driven evolution is not something that researchers who understand the basic principles of biology and levels of biological organization should discuss with theorists who do not. Tempers flare; facts are dismissed, name-calling is facilitated, I begin to laugh hysterically… at “When E. coli cells reproduce…”

    I’m not laughing at you, however, since you are not a trained biologist. But since you also appear to understand the theory of evolution, please let me know if it still makes sense to you that evolution is mutation-driven. If it does, we can make some additional comparisons with my model in which ecological variations result in nutrient-dependent pheromone-controlled adaptations and species diversity via ecological, social, neurogenic, and socio-cognitive niche construction sans mutations.

    Thanks again.

  492. 492
    Nerd of Redhead, Dances OM Trolls

    please let me know if it still makes sense to you that evolution is mutation-driven.

    Since you present no conclusive evidence that any real scientist, and not a monomaniacal crank finds conclusive, yes evolution is mutation driven. You and your interpretations of the data are bullshit from a crank, and you haven’ shown otherwise. In fact, all, your evidence doesn’t say what you claim it says when examined by scientists. Until you stop with the bullshit, your idea will remain where it belongs. In the dumpster.

  493. 493
    PZ Myers

    Dear god.

    Thanks for your detailed attempt to determine the difference between the theory of mutation-initiated natural selection and my model of ecological variation, adaptations, and species diversification. I especially appreciate that lack of name-calling. Also, after more than 480 posts, it is great that you make no attempt to bully me into admission of any belief in nonsense or force me to waste time discussing it.

    I’ve been asking you to explain this difference. Chas has been asking you to explain this difference. After more than 480 posts, a remarkably evasive 92 of them yours, I am convinced that you cannot explain the difference.

  494. 494
    James Kohl

    @492 Nerd of Redhead, Dances OM Trolls

    Since you present no conclusive evidence…

    @473 See:

    Epigenomics and the concept of degeneracy in biological systems
    http://bfg.oxfordjournals.org/content/early/2013/12/12/bfgp.elt050.abstract

    “The reiterations of living systems are developmentally constructed and come into being through internal interactions within organisms, interactions between organisms, and interactions between organisms and their surroundings. Novelty and variation arise from these interactions.”

  495. 495
    ChasCPeterson

    To determine whether conserved molecular mechanisms are responsible for ecological adaptations to variations in the availability of nutrients that metabolize to species-specific pheromones, which control the physiology of reproduction in species from microbes to man, Lenski could quit “feeding” the E. coli, and Chelo et al (2013) could approach the testing of the null hypothesis in the same manner. …If the two different model organisms, E. coli and C. elegans starved to death, my model would be supported by the experimental evidence

    Damn. If there’s a flaw in that logic, I can’t find it.

  496. 496
    Nerd of Redhead, Dances OM Trolls

    Epigenomics and the concept of degeneracy in biological systems
    http://bfg.oxfordjournals.org/content/early/2013/12/12/bfgp.elt050.abstract

    I read it. It doesn’t support your ideas at all, it just has your buzzwords. They acknowledge the genes, but will argue different ways to turn on the genes. You claims aren’t that. Your claims are bullshit. You can’t explain why your idea works, and random mutation/natural selection doesn’t. When there are millions of papers without your name on them that say otherwise. In fact, only those with your name on them support you. Prima facie evidence of a crank.

  497. 497
    Ogvorbis: Still failing at being human.

    “The reiterations of living systems are developmentally constructed and come into being through internal interactions within organisms, interactions between organisms, and interactions between organisms and their surroundings. Novelty and variation arise from these interactions.”

    Now, I know that I am just a lowly historian, but reading this quote you have provided sounds just like the current synthesis of evolution through mutation and natural selection.

    Interactions within organisms — if a mutation stops something important happening, that organism dies before it can reproduce. If a mutation enhances something important, that organism may be more likely to produce offspring which may, or may not, carry the beneficial mutation.

    Interactions between organisms — if a mutation makes it more likely that an organism will be eaten — slower, really bad birthmark — or less likely to breed — wrong smell/pheromone, no tail feathers, small antlers — that organism is less likely to reproduce and those deleterious mutations are not passed on. Conversely, if a mutation makes it less likely to be eaten — more speed, bigger muscles, thicker shell –or more likely to breed — better colour, better smell, bigger antlers — that organism will be more likely to pass on the beneficial mutations into future generations.

    Interactions between organisms and their surroundings — If an organism, through a deleterious mutation, is less able to tolerate cold, heat, dehydration, too much moisture, different foods in a low-food time, whatever, it will be less likely to breed. Conversely, if an organism can better tolerate extremes in the environment, or different foods, it will be more likely to survive and thus more likely to add those beneficial mutations to the gene pool.

    Novelty and variation arise from these interactions — NO SHIT! This is called variability with a population and, in times of stress, that variability may allow some to survive while others die. Do this long enough and you get new subspecies, species and genus. This is evolution through mutation and natural selection. The interactions you quote are the vehicles of natural selection.

  498. 498
    Rey Fox

    No, his model is totally different because it’s got like pheromones and stuff.

  499. 499
    Ogvorbis: Still failing at being human.

    Well, I did mention pheromones as something that could be affected by a deleterious or beneficial mutation as regards an organisms likelihood of mating, but he will, most likely, ignore that and continue to claim that environmental affects have nothing to do with natural selection.

  500. 500
    James Kohl

    @493: PZ Meyers who repeatedly assured others that I am a just another “crank” wrote:

    I am convinced that you cannot explain the difference.

    @495 ChasCPeterson wrote:

    Damn. If there’s a flaw in that logic, I can’t find it.

    Biology is logical. Models — like my model — take advantage of that logic. Theories take advantage of ignorance. The difference between PZ Myers and ChasCPeterson is that most ignorant evolutionary theorists cannot be convinced that their theories are ridiculously illogical nonsense.

    But, as we can deduce from the comments of ChasCPeterson, he probably will not starve to death any turtles to help prove that nutrient-dependent pheromone-controlled ecological adaptations are responsible for species diversity in species from microbes to man. And, as we can deduce from the comments of PZ Myers, he will not perform any experiments and not accept any experimental evidence from others, or accept models or explanations of cause and effect from others.

    He has now inferred, as most of you have, that my co-authors, like Milton Diamond and Karl Grammer, are also “cranks” for helping me to detail my model in published reviews. PZ Myers also infers that Ryszard Maleszka and his co-authors (for example Gene E. Robinson in http://www.pnas.org/content/early/2012/03/12/1202392109.abstract and in http://www.ncbi.nlm.nih.gov/pubmed/10980296, which extended our mammalian model to insects) are “cranks.”

    After 500 posts here, we can now see that people like PZ Myers are those most likely to be so ignorant as to assume that anyone who does not agree with them is a “crank.” They will then continue to assert that anyone who does not agree with them is a crank, and hope that others will join in an attest to the same things for the same reasons.

    But the only reason that others will join in is that they are as ignorant as PZ Myers is. They are the “cranks” who like to associated with “cranks” who think everyone who doesn’t agree with them is a “crank.”

    @496 we see an example of a crank: Nerd of Redhead, Dances OM Trolls, who may be out there starving organisms to death in an attempt to prove that mutation-driven evolution is possible and compare it to my model of ecological variations and nutrient-dependent pheromone-controlled adaptations. How many more organisms must die before the ridiculous theory dies and is not simply resurrected in some other nonsensical form of experimentally unsupported nonsense?

    Each of you can make a difference in the needless deaths of other organisms and your loved ones. Start by telling others who the “cranks” are, and