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Higher order thinking

The one thing you must read today is David Dobbs’ Die, Selfish Gene, Die. It’s good to see genetic accommodation getting more attention, but I’m already seeing pushback from people who don’t quite get the concept, and think it’s some kind of Lamarckian heresy.

It’s maybe a bit much to ask that the gene-centric view of evolution die; it’s still useful. By comparison, for instance, it’s a bit like Mendel and modern genetics (I’ll avoid the overworked comparison of Newton and Einstein.) You need to understand simple Mendelian genetics — it gives you a foundation in the logic of inheritance, and teaches you a few basic rules. But once you start looking at real patterns of inheritance of most traits, you discover that it doesn’t work. Very few traits work as Mendel described, and one serious concern is that we tend to select for genes to study that behave in comprehensible ways.

And every geneticist knows this. Mendel was shown to have got some things wrong within a decade of his rediscovery: Mendel’s Law of Independent Assortment, for instance, simply does not hold for linked genes, and further, linkage turns out to hold important evolutionary implications. But I still teach about independent assortment in my genetics course. Why? Because you need to understand how to interpret deviations from the simple rules; it’s an “a-ha!” moment when you comprehend how Morgan and Sturtevant saw the significance of departures from Mendel’s laws.

Most of genetics seems to be about laying a foundation, and then breaking it to take a step beyond. Teaching it is a kind of torture, where you keep pushing the students to master some basic idea, and then once they’ve got it, you test them by showing them all the exceptions, and then announcing, “But hey! Here’s this cool explanation that tells you what you know is wrong, but there’s some really great and powerful ideas beyond that.”

That’s what’s fun about genetics: compounding a series of revelations until the students’ brains break, usually right around the end of the term. Over the years I’ve learned, too. Undergraduate genetics students usually collapse in defeat once I introduce epistatic interactions — the idea that the phenotype produced by an allele at one locus is dependent on the alleles present at other loci — but it’s always great to see the few students who fully grasp the idea and see how powerful it is (future developmental biologists identified!).

And that’s how I see the gene-centric view: absolutely essential. You must understand Mendel, and Fisher, and Wright, and Hamilton, and Williams, and once you’ve mastered that toolkit, you can start looking at the real world and seeing all the cases where it’s deficient, and develop new tools that let you see deeper. The new idea that Dobb’s describes, and that is actually fairly popular with many developmental biologists, is that phenotype comes first: that organisms are fairly plastic in response to the environment in ways that can’t be simplified to pure genetic determinism, and that the genes lag behind, acting to consolidate and make more robust adaptive responses.

I’ve written about genetic assimilation/accommodation before, and have given one lovely example of phenotypic change occurring faster than the generation of new mutants can explain. It’s always baffled me about the response to those ideas: most people resist, and try to reduce them to good old familiar genes. It’s a bit like watching students wrestle with epistatic modulation of gene expression when all they understand is Mendel, and rather than try to grasp a different way of looking at the problem, they instead invent clouds of simple Mendelian factors that bring in multi-step discrete variations. They can make the evidence fit the theory — just add more epicycles!

I’m seeing the same responses to Dobbs’ article — it’s still all just genes at the bottom of it, ain’t it? Oh, sure, but the interesting parts are the interactions, not the subunits. We need to take the next step and build tools to study networks of genes, rather than reducing everything to the genes themselves.

Comments

  1. george gonzalez says

    It’s like that in Physics too, where you spend a semester learning about electric fields and waves and how well the math works. Then a semester or two later the prof says, well, no, it’s actually something far different having to do with quanta and probability and is much much weirder. You can use fields and waves for 88% of phenomena, but that breaks down completely once you get to photoelectric and two slit systems. Science can be like that.

  2. doublereed says

    I’ve heard it said that this is how we teach mathematics.

    “This is subtraction. You subtract a small number from a large number.”
    “But can you subtract a big number from a small number?”
    “No you can’t do that.”
    Next Year
    “We’re going to teach you about ‘negative numbers.'”

    “This is a ‘square root’. It’s the reverse operation for when you square something.”
    “But can you square root a negative number?”
    “No you can’t do that.”
    Next Year
    “We’re going to teach you about ‘imaginary numbers.'”

    “This is infinity! It’s bigger than everything!”
    “But what happens if you subtract infinity from infinity?”
    “No you can’t do that.”
    “GAHH!!”

    You know what the answer to “what’s infinity – infinity?” The answer is ‘it depends.’

  3. Max says

    I don’t see how any of this is inconsistent with the Selfish Gene model at all. So things are more complex than the simpliest of selfish gene analogies? So what? How does this dislodge the gene as the primary unit of selection? None of the criticisms ever made sense to me.

  4. A Masked Avenger says

    The new idea that Dobb’s describes, and that is actually fairly popular with many developmental biologists, is that phenotype comes first: that organisms are fairly plastic in response to the environment in ways that can’t be simplified to pure genetic determinism, and that the genes lag behind, acting to consolidate and make more robust adaptive responses.

    Mind = blown.

    Thanks for this. I took exactly two semesters of chemistry in my life, on my way to a math degree, and passed by the skin of my teeth because I noticed that stoichiometry can be reduced to linear algebra. So the sum total of my knowledge of biochemistry comes from reading Dawkins, talk.origins, and your blog.

    Without understanding any of the underpinnings, the bit I just quoted from your post seems to have opened a window onto another world. It should be framed and posted somewhere.

  5. Sharon C says

    Agree with both the original article and your response. I had trouble getting through the Selfish Gene (never finished, actually) because I couldn’t get behind the central premise. This might be because I had already started grad school when I started it, and was neck-deep in a phenotypic plasticity project.

    Maybe it’s like watching classic children’s movies for the first time after you’ve grown up – I saw the Goonies for the first time when I was 22 and thought it wasn’t that great, to the horror of my peers.

    I did pick up a used copy of West-Eberhard’s textbook when I was studying for comps, and it might be the most useful book on evolution I ever read, I tell you what.

  6. stinkyj says

    My eldest son is pretty much settled on studying Biology / Genetics / Biochemistry for his degree. I think he’s actually looking forwards to having his brain broken on a regular basis!

  7. carlie says

    I’ve heard it said that this is how we teach mathematics.

    I still remember the thunderbolt that hit me when integrals were introduced, after we had spent weeks and weeks calculating the area under the curve the long way. I felt betrayed.

  8. Max says

    I still don’t see how this is inconsistent with genes as the primary units of selection.

    Is it just a matter of the word “selfish” because genes are cooperating or interacting? I don’t get it.

    Dawkins is completely write in the article. West-Eberhard’s arguing against a strawman of the Selfish Gene model.

    This is like arguing that “Darwinian Evolution is dead!” because you’ve found some things in Origin of the Species to be false. But the model’s been modified and updated over time. The same is true with the Selfish Gene.

    I see nothing here that is inconsistent with the gene-centric view. It’s just a lot more complex than Dawkins wrote about in 1976.

  9. Sharon C says

    The primary unit of selection isn’t the gene, it’s the phenotype. A phenotype is much more than the sum of its genes.

  10. Max says

    #6 @Sharon C

    I had a similar (though slightly different) experience as yours. I read Selfish Gene as an undergrad and had my mind blown. I was taking classes in evolution and learned all about phenotypic plasticity and epigenetics, etc. It fit very easily into Dawkins’ framework.

    Went to grad school and got a PhD in evolution and behavior. The problems people had with gene-centric models always baffled me because either (1) they weren’t problems or (2) the same problems existed for individual-centric models.

    Oh well!

  11. Max says

    #10 @Sharon C

    But phenotypes are still caused by genes, even if it isn’t a 1:1 relationship people thought it was 100 years ago. How does the fact that genes can have multiple effects in multiple environments eliminate genes as the units of selection? We already knew that selection ACTS on phenotypes, but it’s ultimately the genes that are selected. I’m not seeing anything to convince me otherwise.

  12. rq says

    I’m glad I can still read this article, and the links within, and understand what’s going on. This makes me happy.
    I have nothing brilliant to say on-topic, though. Carry on.

  13. Sharon C says

    #12 @Max

    It’s because when we’re talking about primary units, we’re talking about the smallest “unit” that selection is actually acting on. Selection is always acting on the expressed phenotype. Even the 1:1 genes we know about aren’t acting in total isolation – all of your developmental processes have to work to get you to that point, so selection is acting both on that large-effect gene and on all of the gene interactions that got you from embryo to the point where the large effect gene matters.

    So my (probably poorly articulated) argument is that genes are a component of selection, but not the primary unit.

  14. Antiochus Epiphanes says

    1. This isn’t a new idea. People have been kicking it around for more than sixty years. I doubt that it seems new to most developmental biologists.
     
    2. I think this passage explains genetic assimilation/accommodation a little better:

    This scenario of phenotypic evolution posits that (1) a mutation or environmental change triggers the expression of a novel, heritable phenotypic variant, (2) the initially rare variant phenotype starts to spread (in the case of an environmentally induced change, due to the consistent recurrence of the environmental factor), creating a subpopulation expressing the novel trait, and (3) selection on existing genetic variation for the regulation or formof the trait causes it to become (a) genetically fixed or to remain (b) phenotypically plastic.(10)
     
    Braedle, C. and T. Flatt. 2006. A role for genetic accommodation in evolution. Bioessays 28:868-873

    3. Genetic determinism may thrive in pop-science writing, but isn’t a common position for those who study population genetics. I mean, FFS, Fisher, Wright, and Haldane introduced probabilistic modeling to science in response to the hokey just-so story telling of the Mendelians and Biometricians who preceded them.
     
    4. Along those lines, people should understand that testing evolutionary hypotheses by modeling allele frequency is hardly some kind of dogmatic assertion of genetic determinism. Allele frequency is something that can be measured and is expected to change in response to some fairly model-able violations of HWE. Of course population geneticists understand that phenotypic plasticity must be accounted for*, and that epistatic interactions take place, and that no gene is an island–if you want to test a hypothesis of genetic assimilation, clearly you would have to incorporate plasticity as one or more parameters in your model.

     
    5. Why not always incorporate these parameters? These factors would make models more realistic, but also greatly expand the number of free parameters that must be estimated; this has the effect of rendering model predictions so diffuse as to be useless. As statistician George Box wrote, “Remember that all models are wrong; the practical question is how wrong do they have to be to not be useful.” To be useful, a model must simply provide a test; it doesn’t need to account for all potential sources of variation.
     
    6.

    It is saying the gene is not the primary unit of selection.

    There is no “primary unit of selection”. The unit of selection is whatever you have decided to measure as input in a selection model: quantitative phenotypic characters, allele frequencies, substitution rates, etc. Ability to use any of this information to test hypotheses of selection are only as good as the model used to test them.
     
    *We have a term for it, even.

  15. grahamjones says

    Anyone seriously interested in this subject should read this article:
    How learning can guide evolution, Hinton and Nowlan, 1987.
    According to Google scholar it has been cited about 1000 times. West-Eberhard’s big 2003 book does not cite it though. Sometimes the barriers to meme flow are high.

    I’m sure West-Eberhard will triumph over Dawkins eventually: she has mathematicians on her side!

  16. Antiochus Epiphanes says

    We need to take the next step and build tools to study networks of genes, rather than reducing everything to the genes themselves.

    In process. This paper offers an explanation of one such tool, and offers an elegant explanation of the inferential difficulties inherent in such models:

    As the field moves toward whole genome association mapping, the problem of scale that pervades all interaction tests becomes intense. The total number of tests required suggests that very stringent significance thresholds will be needed to control against false positives, but this in turn means that the only epistatic effects that will be detected will have to be really gigantic and/or sample sizes will need to be very large.

  17. says

    @2 beat me to it. Teaching, in many, many subjects, is a process of, as PTerry puts it, “Lying To Children” (where “Children” can include undergrads and even grad students). Starting with simple explanations, then introducing some rule-breaking exceptions, which give way to a higher-order synthesis, which is broken in its turn. Lather, rinse, repeat.

  18. ChasCPeterson says

    As a poor benighted phenotype-obsessed physiologist these arguments always bewilder me. Any phenotypic character that evolves has genetic determinants, by freakin definition. These determinants vary in complexity, depending on the character in question. Some few are textbook Mendelian, others variously pleiotrpic or epistatic, many to the point of nightmarishly networky, others highly plastic and environmentally dependent. So what? To frame it as West-Eberhard vs. Dawkins is just weird. Polyphenisms and apparently altruistic behaviors probably have different sorts of genetic determinants and probably ought to be analyzed and explained differently. Pluralism ftw.
    [That said I haven’t read Dobbs’s OP and do not have the time atm.]

  19. Amphiox says

    re Max, Sharon, etc, etc

    My feeling on this is that in many ways it boils down to how we define “primary” as opposed to “secondary”.

    This seems to be a recurring pattern in the history of science. First we see A, and then we determine that A is a result of X. For a while we think that X is the primary cause of A. Then we find out that there are other steps before X and between X and A, and reality is more like Y->X->B->A. The X->A relationship turns out to be secondary, and the effects of Y and B produce the exceptions we observe that refuted our earlier simplistic X->A model and twigged us onto the fact that something more complicated was going on.

    I do recall from reading Dawkins that I’m pretty sure he did state somewhere in his writing, perhaps not The Selfish Gene itself, but in later books, that selection first acts of phenotype, and so the effect of selection on specific genes is in fact indirect.

  20. Amphiox says

    One thing to remember is that genes do not produce traits. Genes produce SOME of the components of chemical reactions, and some of the components of these chemical reactions are not produced by genes.

    Traits are the emergent results of many chemical reactions interacting. When selection acts on a trait, what it actually acts on is a pattern of chemical reaction interactions, to which genes contribute only one portion.

    However, the gene is one of the few of the contributors to this pattern that is heritable, and evolution can only act on things that are heritable.

  21. ChasCPeterson says

    OK, I’ve had the chance to read Dobbs’s piece, and I am still bewildered. It reads to me like journalistic gee-whiz Darwin Dawkins-was Wrong overspin. West-Eberhard has some interesting ideas (I have read some of her tome), and there seems little doubt that processes like genetic accomodation can be important in the evolution of specific phenomena like castes, polyphenisms, and particularly striking cases of phenotypic plasticity. But it’s not a one-size-fits all revolution in evolutionary theory or anything like that. The us-vs.-them tone of the article is unfortunate, in my view.

    ‘The gene does not lead,’ [West-Eberhard] says. ‘It follows.’

    except, you know, when it doesn’t. Or does. *shrug*
    I hope that kind of absolutist statement was quoted out of context.

    Dobbs’ thumbnail summary of genetic accomodation:

    First, an organism (or a bunch of organisms, a population) changes its functional form — its phenotype — by making broad changes in gene expression.

    Hold it. The unfortunate teleological phrasing notwithstanding, where is this kind of plasticity supposed to have come from in the first place? Certainly not all traits of all species are imbued with this kind of “broad changability” due to environment or nurture. There are, in fact, more genes and probably selection at the bottom of this capability, where present.

    Second, a gene emerges that happens to help lock in that change in phenotype. Third, the gene spreads through the population.

    Straightforward Darwinism.

    This isn’t the gene-centric world in which genotype creates phenotype. It’s a phenotype accommodating a new genotype by making it relevant.

    uh, sort of. Except that steps 2 and 3 are genotype–>phenotype. Every new mutation is selected in the context of its environment, and as Dawkins was explicit about in TSG, that environment includes abiotic, biotic, and cogenetic aspects.

    ‘evolution is not about single genes,’ [West-Eberhard] says. ‘It’s about genes working together.’

    it’s still all just genes at the bottom of it, ain’t it? Oh, sure, [sez PZ], but the interesting parts are the interactions, not the subunits.

    In some cases yeah, in other cases not so much. You can’t extrapolate from social wasps or hopper-to-locust transitions to all of biology. Case by case. Pluralism.

    We need to take the next step and build tools to study networks of genes, rather than reducing everything to the genes themselves.

    uh, because networks of genes don’t reduce at some level of analysis to the genes that are themselves networked? More power to you and good luck with that project.

  22. Ichthyic says

    Read it again. It is saying the gene is not the primary unit of selection.

    FWIW, there isn’t a publishing evolutionary biologist alive, and that goes back to even when I was in grad school, that ever accepted the idea that selection acts on genes.

    the model is, and always was, for decades and decades now, that selection acts on the individual. even the group selectionists have failed to produce any significant evidence to discount this as the primary mode of selection.

    so… I keep wondering what the point of blog articles such as this one even is?

  23. Ichthyic says

    phenotype comes first: that organisms are fairly plastic in response to the environment in ways that can’t be simplified to pure genetic determinism, and that the genes lag behind, acting to consolidate and make more robust adaptive responses.

    ok, now go back and tie this to heritability and selection.

    you’ve left a bit out.

  24. erik333 says

    So, at the end of this road lies “highest order thinking” where we account for the entire “cone”* of space-time as bounded by the speed of light and the big bang. ;-)

    *pretend spacetime is 3-dimensional for easier visualisation

  25. zenlike says

    Maybe it’s because I’m a total layman in these subjects, but I’m a bit baffled by the commentary:

    On one hand there are commenters arguing that this blogpost is totally superfluous because ‘everybody knows this already’, on the other hand there are commenters arguing that the blogpost is incorrect or not at least not entirely correct.

    Something doesn’t square here.

  26. Antiochus Epiphanes says

    zenlike: can’t both of those be true? And can’t some parts of the OP be on point?

  27. sharkjack says

    Selection takes place on gene level as well, just like it does on cell level. Cancer can be seen as cell level selection, where a cell has managed to random walk it’s way through the neutral mutation space until it stumbled upon a mutation that lets it divide unconstrained by the very safety mechanisms that were selected for on the individual level. Since we as humans are on the individual level, we tend to look that level as the norm, but cells and genetic material are both capable of reproduction with heridity and as such undergo evolution of their own on their own timescales. Our single celled ancestors underwent selection at the cell level, at what point did the individual cells in the ancestral aggregate stop being individuals and start being part of an individual? Whatever the criterium, it can be applied to eusocial nests. They’re dominant level of selection is the nest. So should we stop calling bees individuals and start calling the nest as a whole an individual? Of course biology doesn’t care about what we call individuals. It’ll just throw a slime mold in your face.

  28. unclefrogy says

    so it is not the genes themselves as discrete units of heredity that is determinate but the interaction of the whole.
    From what I can see without all the in depth information that is becoming a more common insight into other phenomena in the natural world. To see things in their interaction like the mind as an emergent property resulting from the interaction of all the parts of the nervous system and the body
    uncle frogy

  29. says

    Argh! Such a good article, but why didn’t they mention genetic DRIFT? It’s also such a huge contributing factor to evolution, speciation, etc. You can’t bring up Hardy and Weiberg like that and then not mention one of the other bits of the modern synthesis that flies in the face of selfish gene based intuitions!

  30. ChasCPeterson says

    Random chance fixes traits in a population, and that force is stronger than most selection pressures.

    You sound pretty certain. It should be no problem for you to supply a couple of well-documented examples of such traits.

  31. says

    Bringing in some empirical evidence from my field (stickleback):

    Sticklebacks have undergone a massive adaptive radiation following the last ice age, with ancestral marine fish colonizing freshwater lakes and streams along the coast following the last ice age. These freshwater populations have undergone parallel evolution, with many of the same phenotypes appearing across multiple geographically isolated freshwater populations.

    One particular trait (the loss of the pelvic spine) is almost entirely explained by the loss of an enhancer of the Pitx1 gene. This loss was independently derived across multiple populations.

    Another trait (the loss of the bony armor plates) is almost entirely able to be explained by an ancient haplotype of the morphogen Eda. This haplotype appears in very low frequency in the marine ancestors, but in very high frequencies in the derived freshwater populations. Again, one locus is able to explain the majority of an evolved trait.

    These are two examples of changes in single genes that are able to give rise to massive changes in morphology. Note that these are not derived changes studied in a lab, but real phenotypes and genotypes that evolution has previously selected for.

    Dobbs has a interesting hypothesis, but there is not data to support it within the stickleback system, and a large amount of data on the selection of a phenotype from standing genetic variants. Evolution has seemed to act on genes, not full networks.

  32. Suido says

    I’m not a biologist, but I stopped short at this sentence:

    This means that we are human, rather than wormlike … or excessively simian

    My understanding of the word simian is that it includes humans. Was this likely an imprecise usage of the term simian by the author, and he really meant we’re not excessively non-human ape-like, or am i wrong in my understanding of the word?

  33. gillt says

    @James Hart.

    I don’t study sticklebacks but I know someone who does and what you’re saying seems to me a bit selective, trenchant and premature.

    Are you familiar with the work of Caty Peichel at UW? She wrote a review in Integrative and Comparative Biology: Perspective on the Genetic Architecture of Divergence of Body Shape in Sticklebacks.

    However a recent study demonstrated that independent mutations at the same locus underlie the repeated evolution of pelvic reduction in three-spine stickleback populations [Chan et al., 2009], strongly suggesting a role for genetic constraint. However, in other stickleback species different genes are responsible for pelvic reduction [Shapiro et al., 2009]. Therefore, we do not yet have a comprehensive view of the role of genetic constraint in the evolution of sticklebacks….There are relatively few data on the genetic basis of parallel divergence in body shape.

    She’s talking about the only study as of 2010 that has done the necessary QTL mapping to link genomic regions with body shape among stickleback populations. The conclusion being that body shape is genetically additive and polygenic in sticklebacks. So how do you parse that with

    Evolution has seemed to act on genes, not full networks.

  34. Stacy says

    @ChasCPeterson #20

    As a poor benighted phenotype-obsessed physiologist these arguments always bewilder me….So what? To frame it as West-Eberhard vs. Dawkins is just weird.

    and

    @Ichthyic #26

    there isn’t a publishing evolutionary biologist alive, and that goes back to even when I was in grad school, that ever accepted the idea that selection acts on genes….

    so… I keep wondering what the point of blog articles such as this one even is?

    The article is about how the public understands genetics and evolution. It’s not about how professional scientists (you) understand it. The argument is that “The Selfish Gene” metaphor, while useful, is too simplistic and needs to give way to a more nuanced model.

    From the article:

    This matters like hell to people like West-Eberhard and Wray. Need it concern the rest of us?

    In other words, the gene-centric model survives because simplicity is a hugely advantageous trait for an idea to possess. People will select a simple idea over a complex idea almost every time. This holds especially in a hostile environment, like, say, a sceptical crowd….

    ‘Dawkins understands very well that gene expression is powerful,’ she says. ‘He sees things are more complex than a selfish gene. He could turn on its head the whole language.’

    Yet Dawkins, and with him much of pop science, sticks to the selfish gene.

  35. Stacy says

    I wonder, if this new phenotype-centric model took hold, would it rout those who argue for the social status-quo on the basis of genetic determinism (including all the simplistic evo-psych promoters?)

  36. Antiochus Epiphanes says

    The argument is that “The Selfish Gene” metaphor, while useful, is too simplistic and needs to give way to a more nuanced model.

    Like this?

    “The gene does not lead,” [West-Eberhard] says. “It follows.”

  37. chrislawson says

    Perhaps I’m feeling churlish at having my hard-thought ideas described as epicycles, but despite all the interesting things that genetic accommodation has to say, I’m still bothered by…

    (1) Its insistence that the phenotype comes first, then the genotype follows. Did humans really evolve red hair as a phenotype before there were genes for it? Did sickle-cell phenotype exist before the HbS mutation?

    (2) The existence of phenomena that, to me, only make sense with a selfish gene explanation, such as LINES and SINES, cytoplasmic male sterility in angiosperms, the amazing homozygote-queen-killing worker ants of the Solenopsis invicta species, or the equally amazing transmissible mammalian cancer in Tasmanian devils. If someone can provide convincing genetic accommodation explanations for these observations I’d be interested to hear them…but they have to explain why selfish gene theory is the epicycle and not genetic accommodation.

    I think it’s fair to say that selfish gene theory can’t explain everything about evolution — but neither can any single evolutionary concept. And if I was to point to evolutionary ideas that explain important evidence that selfish gene theory doesn’t really address, I’d turn to genetic drift, epigenetics, and endosymbiosis first.

  38. davidwhitlock says

    The problem is with the “centric” view. There is no “center”.

    Everything is coupled, and coupled at the level of noise. That is the definition of “noise” in a physiological sense, where “signals” are “interfered with” by physiological and non-physiological things that are not “signals”.

    Genomes don’t specify phenotypes. A genome specifies the genomic response of an individual cell to “signals” at the cell surface or inside the cell.

    The phenotype is the emergent property of the zillions of cells working together “in sync” based on local “signaling” between cells.

    All “signaling” is local because there is no ‘action at a distance’. There is no “center” that “central signals” can come from.

    It isn’t “genes all the way down” because it doesn’t go “all the way down”.

  39. erik333 says

    Since I barely know the first thing about biology, I have this question:

    Does the plasticity of gene expression talked about in the article really have the same (or reasonably similar) degrees of freedom in phenotype space as mutations do?

    From my novice perspective it seems likely that some type of changes would be easier with one or the other, and some would be outright impossible without mutations preceding change. Take the example in the article with the forest predators becoming faster by practice, where later mutations would “follow” and lock in “faster”. Cat e.g. could get “faster” by changing upper to lower limb length ratios instead of more fast twitch muscle fibre?

    How do you get from gene expression being more malleable to the evironment than the genome to “gene expression leads and genes follow” without it being a potential deepity?

  40. davidwhitlock says

    erik333, the degrees of freedom from epigenetic programming are larger than the degrees of freedom from gene mutations and deletions.

    Somatic cell nuclear transfer clones, in mice are ~1-2% viable. These are organisms with identical DNA, coding and non-coding. The only difference is in the epigenetic programming of the genomic DNA.

    SCNT clones have larger phenotypes than the donor and unrelated conspecifics. Naturally bred conspecifics have very high viability. In mice, ~43% of single gene deletions are non-viable compared to ~98% of SCNT clones. In other words, the phenotype of 98% of SCNT clones are outside the viability range! That is with identical DNA sequences, coding and non-coding.

  41. chrislawson says

    david whitlock:

    Genomes don’t specify phenotypes.

    That would make GMO technology impossible.

  42. Antiochus Epiphanes says

    erik333, the degrees of freedom from epigenetic programming are larger than the degrees of freedom from gene mutations and deletions.

    I think this statement is far too general, and really almost beyond being testable. Some epigenetic changes have much greater phenotypic effect than others–and this applies to genetic/genomic changes as well–you’d have to be able to scale these effects equally across different types of change to even begin to quantify correlations with phenotypic variability. Within populations and lineages over short periods of evolutionary time, epigentic effects may be used to explain quite a bit of variation, but over longer periods and among higher order taxa, genetic/genomic change would appear to be the main correlate (as is recognized even in genetic accommodation).

  43. says

    I’ve heard it said that this is how we teach mathematics.

    I bought a book a while back “The Calculus Direct by John Weiss”, since I never got into Calculus in school, in the hopes it would help me deal with some of the crazy shit you get with 3D math. Never did get around to following it all through, to understand it, but the starting premise in the book was (not quoting exactly), “First thing, lets throw out this stupid idea that numbers are concrete things. They are place holders. Kind of like buckets, or bits of stick. Everything you do with them is just stacking the bloody things end to end, or cutting them into pieces, and counting how many of the things you have after you are done, and, as a consequence, you can name the things anything you like, such as say.. X, and then, just count how many of some other known sized thingy you have “in” the section that X occupies.” So, “variables” are a core principle, not something tacked on years later, and “negative numbers”, in that context, is a natural extension of whether or not the arbitrary things you are counting all have to be one “one side” of “edge”, i.e. zero, or not. In fact, even zero is just a placeholder itself. Means.. nothing more or less than, “This is where I am starting to count the bits from, so, since its where I started, I will call it zero.”

    The whole book is like a few hundred pages, and, while its probably the case that someone too young wouldn’t “get” all of it, it goes from basic math, all the way up to basic calculus (well differential equations anyway), while skipping years, and years, of people telling you, “things can’t happen, or don’t work that way, except… this year they do.” lol

    It was an interesting read, and one of these days I really need to go back and read the later parts with pen and paper handy, instead of over breaks at work.

  44. thewhollynone says

    Although I have the delusion that I understand almost everything that’s been written in this blog piece and in the comments, I don’t know too much about biology, but I do know something about teaching, particularly about teaching critical thinking, and PZ, you, sir, are a great teacher. I hope that your students appreciate you, and I bet most of them do. Do you have anything to do with training teachers of high school science?

  45. says

    @37 “You sound pretty certain.”

    Yes. Because the math is good, and population data matches the models.

    “It should be no problem for you to supply a couple of well-documented examples of such traits.”

    Sure. After you show me an example of an optimal trait that fixed without the influence of drift. If you’re going to argue against basic principles of population genetics, it’s not my job to educate you.

  46. davidwhitlock says

    Antiochus Epiphanes, you do appreciate that the only difference between a liver cell, a heart cell, a neuron and a fat cell is that they have differential epigenetic programming.

    You can’t change a skin cell into a nerve cell by changing genes. You can do it by epigenetically reprogramming it.

    The signaling between cells that differentially regulates the epigenetic programming of cells in embryogenesis and organogenesis is more robust than the signaling inside of cells which regulates gene expression.

    Mosaic sheep-goat chimera are easy to produce.

    http://www.ncbi.nlm.nih.gov/pubmed/4020767

    Sheep-goat hybrids are very difficult to produce, even in sheep-goat chimera with mosaic uterus.

    http://www.ncbi.nlm.nih.gov/pubmed/7506792

    Differential epigenetic programming of sheep and goat cells has sufficient degrees of freedom to instantiate whole, mosaic, sheep-goat chimera.

    In other words, sheep cells have the epigenetic flexibility to instantiate goat-compatible organs and goat cells have the epigenetic flexibility to instantiate sheep-compatible organs.

  47. Antiochus Epiphanes says

    Antiochus Epiphanes, you do appreciate that the only difference between a liver cell, a heart cell, a neuron and a fat cell is that they have differential epigenetic programming.

    Of course. But it is quite another* thing to say that the difference between a sheep cell and a goat cell is epigenetic. And it is even more implausible to attribute the difference between a sheep and a termite cell to epigentic effects. I think we both know that, but for some reason you are thinking only of development within an organism, while the erik333 was discussing the kind of phenotypic variation on which evolution may act…variation that is both heritable and distributed across a population. Applied to erik333’s question, your answer far too general.

    *”Quite another” meaning false.

  48. ChasCPeterson says

    If you’re going to argue against basic principles of population genetics, it’s not my job to educate you.

    indeed not. But I wasn’t arguing against basic principles of population genetics so much as confirming that that’s what you were talking about; i.e., when you say “trait” you really mean a hypothetical allele parameterized in a mathematical model. Not that there’s anything wrong with that. But as far as I know, the actual importance of drift in the evolution of actual phenotypes of actual organisms in actual environments is still a wide-open question. I take your inability to cite examples as confirmation.

  49. Antiochus Epiphanes says

    Chas: I like this paper because it presents drift and selection as interacting forces.
     

    But as far as I know, the actual importance of drift in the evolution of actual phenotypes of actual organisms in actual environments is still a wide-open question.

    It may be that people are not generally interested in drift as an explanation for something that appears to be adaptive. And people are also generally not interested in studying traits that are likely to be neutral and hence drifty.

  50. ChasCPeterson says

    AE, thanks for the herpy link.

    Jerry Coyne often makes me crazy (and it’s mutual; he’s banned me, twice), but he does a very nice job of explaining some of what’s wrong with Dobbs’s piece here, and it’s just part 1 of 2.

    Dobbs backfills here, but it’s (imo) ineffectual and self-serving. In particular, the claim (made also by Stacy in the comments here) that he wasn’t criticizing the actual science, just the popular memey representation of it, is imo belied by the tone and emphasis of his writing. And he suggests that all of the really good and charitable discussion is on twitter. *shrug*

  51. Antiochus Epiphanes says

    Along those lines, there are several tests of the neutral model that are used all the time (Tajima’s D, Fu and Li’s test, and ds/dn tests spring to mind)…rejection of the null is almost always interpreted as natural selection (population expansion is often an interpretation as well). However, every time the model is not rejected could be taken as support for the importance of drift in evolution.
     
    I kind of wish Joe Felsenstein would pop in and holler more about this. Is there some kind of like, bat signal we could throw up? No offense to Aron Ra, but JF is the real Ace of Clades.

  52. gillt says

    @#58 Antiochus Epiphanes
    Joe Felsenstein is at comment 12 doing his usual historical trivia schtick.

    @57 Chas: Agreed! I’d like to post over at Coyne’s *website* sometimes but he’s banned me twice now as well. First time for mistakenly thinking I called Lawrence Krauss a pedophile in the comments section, and the second time for suggesting that Stephen Pinker doesn’t know enough about epigenetics to say anything interesting about it. Or at least I think so..my comments have been held up indefinitely ever since he reprimanded me for that. I’ve learned that even perceiving to criticize his friends is bad form.

  53. alwayscurious says

    @Kagehi

    I was thinking something similar: Genetics need a script that lays the groundwork out fresh across the board–reaching well beyond Mendel. The rewritten/overwritten system that we use to teach math & science leaves some people in the sandboxes unnecessarily. Teach the basics early & correctly: then teachers can build continuously rather than tear down, fix, or reshape the mis-taught groundwork.

  54. nohellbelowus says

    I’m seeing the same responses to Dobbs’ article — it’s still all just genes at the bottom of it, ain’t it? Oh, sure, but the interesting parts are the interactions, not the subunits.

    The interesting parts are the molecules, not the atoms.

    The interesting parts are the interactions between people, not personalities.

    The interesting parts are the equations, not the variables.

    Hmm… I dunno PZ.

  55. Vilém Saptar says

    AE @ 15, Chas @ 20, 25 put everything I was thinking, and a little bit more, in biologese.

    Dobbs’ article does look like he just wants to do some Dawkins bashing and pushback against what he considers an unjustified entrenchment of the “Selfish Gene” metaphor in pop science and a perceived coupling of that metaphor with genetic determinism.

    IMO it all boils down to names. Whether you want to call it,

    conversations that define the organism and drive the evolution of new traits and species

    or more simply “gene”(okay, simplistically even), the idea is the same. A gene (or more precisely a genome) is a record of that conversation. More to the point, evolution being messy, random, blind, imprecise (“Evolution is like a drunk reeling back and forth between the gutter and the Bar Room door”) and non-teleological, driven by natural selection on multiple traits concurrently, phenotypic plasticity is something you’d expect, even if you adopted the hated gene-centered view. In fact, whatever plasticity the phenotypes exhibit must by definition be encoded in the genome, if not in the genotype, because there is nowhere else to put it.

    Maybe the fact that most environmental change occurs gradually confounds this clarity as it may create the illusion that phenotypic plasticity is midwifing genetic change, while it could just be an artifact(of the impreciseness of evolution). To make this more apparent, imagine there was no phenotypic plasticity and just when accumulated environmental factors had driven a species to the brink of extinction, miraculously, a species saving mutation arose that did everything that was needed. It would still spread and halt the extinction and get fixed in the genome, given of course that there’s enough time.

    Alternatively and more realistically imagine that the environmental factors that caused phenotypic plasticity to manifest were to disappear before there was an opportunity for a gene to come along and fix the phenotypic changes in the genome. Then, suppose that the environmental factors recurred suddenly after the genome had drifted away drastically from the kind of traits the environmental factors favored (say, due to other environmental factors that came into play and stayed long enough to have an impact on the genome in the interim), then these traits would be forever beyond the reach of plasticity alone, and only the gene centered view could explain the non-reappearance of the traits with the return of the original environment.

    Random mutations are random. They occur all the time. Unless a causal link can be established between phenotypic plasticity and mutations that co-occur in times of environmental change, I don’t see what role plasticity could be said to play in evolution, except that of an artifact.

  56. Alf Hickey says

    The Dobbs article seems very confused to me. Sure, it is right to point out that a simplistic selfish gene theory in which one gene, expressed in one trait and coded for in one strand of DNA, can explain all of evolution is wrong, but he doesn’t offer a coherent explanation of how evolution actually works.

    Take this paragraph:

    “Those genetic distinctions aren’t enough to create all our differences from those animals — what biologists call our particular phenotype, which is essentially the recognisable thing a genotype builds. This means that we are human, rather than wormlike, flylike, chickenlike, feline, bovine, or excessively simian, less because we carry different genes from those other species than because our cells read differently our remarkably similar genomes as we develop from zygote to adult. The writing varies — but hardly as much as the reading.”

    So over the time span that separates worms from humans, what pray tell is doing the “reading” if not the genes themselves?

    Then again in what Dobbs says is the most important paragraph he says:

    “Wray and West-Eberhard don’t say that Dawkins is dead wrong. They and other evolutionary theorists — such as Massimo Pigliucci, professor of philosophy at the City University of New York; Eva Jablonka, professor of mathematics education at King’s College, London; Stuart Kauffman, professor of biochemistry and mathematics at the University of Vermont; Stuart A Newman, professor of cell biology and anatomy at the New York Medical College; and the late Stephen Jay Gould, to name a few — have been calling for an ‘extended modern synthesis’ for more than two decades. They do so even though they agree with most of what Dawkins says a gene does. They agree, in essence, that the gene is a big cog, but would argue that the biggest cog doesn’t necessarily always drive the other cogs. In many cases, they drive it. The gene, in short, just happens to be the biggest, most obvious part of the trait-making inheritance and evolutionary machine. But not the driver.”

    So again we are talking about the time span that separates worms from humans here, if genes are not the “driver” of evolution what is? Of course we should have a nuanced view of gene expression, but long term evolutionary trends simply make no sense unless understood as the process of natural selection working on genes.

    There are two definitional problems that cause confusions here. The first one, as pointed out above, is how to define ” the unit of selection”. I agree that it is best to take a pluralistic view. A plasmid, a cell, a whole organism, a gamete or even genitalia can probably be all though of the “unit of selection” under different circumstances.

    However, selection is only one of the fundamental steps in Darwinian evolution, the other one is reproduction. And genomes are the things that replicate, which is why they must have a central role above phenotype in any theory of evolution. The problem is that it is not so easy to define what a gene is. Obviously a one to one correspondence of traits to DNA strands is not going to work, but building a more complicated model is going to be very hard. For example, if certain epigentic factors are found to heritible over the long term, I think it makes sense to drop the “epi” and just say that they are part of the genome of an organism.

  57. davidwhitlock says

    Antiochus Epiphanes, I think you are not understanding the implications of what I am saying.

    Erik333’s question was:

    “Does the plasticity of gene expression talked about in the article really have the same (or reasonably similar) degrees of freedom in phenotype space as mutations do?”

    The difference between a sheep cell and a goat cell is the genome. What is the difference between a cell of sheep liver and a cell of goat pancreas? Where is the “developmental plasticity” that allows undifferentiated sheep cells to instantiate a fully competent goat liver? A liver of goat cells that can fully couple to an organism comprised of sheep cells?

    Why are most mutations neutral? Because development has sufficient plasticity to cope with those mutations. The plasticity of development is due to differential epigenetic programming.

    In other words, most gene mutations are “neutral” because the epigenetic programming of development has sufficient degrees of freedom to compensate for those gene mutations, and the process of development has sufficient robustness to actively select the “proper” epigenetic programming of particular genes so as to instantiate the particular epigenetic programming that does in fact compensate for those gene mutations.

    In other words, if epigenetic programming didn’t have the degrees of freedom to “neutralize” the effects of most gene mutations, most gene mutations would not be “neutral” (as is observed).

    The developmental systems that select and implement the “proper” epigenetic programming so as to neutralize most gene mutations are so robust as to not even be appreciated as being there. That is the problem with a “gene centric” view. It blinds researchers to very important stuff that is going on.

  58. Vilém Saptar says

    davidwhitlock @ 66

    The developmental systems that select and implement the “proper” epigenetic programming so as to neutralize most gene mutations are so robust as to not even be appreciated as being there. That is the problem with a “gene centric” view. It blinds researchers to very important stuff that is going on.

    Pardon me if I’m being ignorant, I’m no biologist, but where do you suppose these robust developmental systems with degrees of freedom to neutralize mutations come from? I’m guessing these developmental systems themselves have been encoded in the genome. If this is true, then ultimately, you’re taking a gene centered view, aren’t you? Or is there some way they could be in the phenotype without being in the genome? Like maybe by being paths of least resistance or whatever that require no encoding or inheritance.

  59. gillt says

    Why are most mutations neutral? Because development has sufficient plasticity to cope with those mutations.

    I’m pretty sure there were lots of better reasons why nucleotide mutations are neutral.
    1. occur in non-coding regions and pseudogenes
    2. synonymous base substitution
    3. small population size

    The developmental systems that select and implement the “proper” epigenetic programming so as to neutralize most gene mutations are so robust as to not even be appreciated as being there.

    So you’re saying this despite the fact that DNA methylation patterns, a type of epigenetic programming, leads to deamination at methylated C residues in mammals? If anything, I thought this would be an argument for epigenetics increasing genetic diversity in a population.

  60. Antiochus Epiphanes says

    In other words, most gene mutations are “neutral” because the epigenetic programming of development has sufficient degrees of freedom to compensate for those gene mutations, and the process of development has sufficient robustness to actively select the “proper” epigenetic programming of particular genes so as to instantiate the particular epigenetic programming that does in fact compensate for those gene mutations.

     
    I don’t know where you are getting this, David. The only mechanism by which “epigenetic programming” could be thought to neutralize mutations is in post-transcriptional modification of individual RNA nucleotides*. I know that there are mechanisms of transforming uracil to cytosine, but I don’t think anyone knows exactly how extensively these kinds of changes serve to reverse mutations. Anyway, please feel free to elaborate or cite something, because I really am not sure what you are talking about.
     
    However, IF what you are saying is true one would expect to see quite a lot of substitution even at coding sites specifying aa residues of important function, or in rDNA…or essentially patterns of substitution that fit the neutral model across gene types. We don’t see that. Rather what we see is a much stronger degree of conservation of genes encoding necessary cellular functions.
     
    *As opposed to 5’capping, polyadenaltion, and intron splicing.

  61. davidwhitlock says

    No, you are still caught up in a gene-centered view. There is no center.

    The robustness of epigenetic programming is an emergent property of genomes. It is not reducible to “genes”.

    It is like the behavior of cognition is an emergent property of a brain. It is not reducible to neurons. The brain can compensate for the loss of neurons. It does that through plastic remodeling of the remaining neurons to do different things.

    Epigenetic programming could compensate for a mutation in an enzyme that results in lower activity by making more of that enzyme. The compensation of epigenetic programming happens on the scale of the organism, not the scale of the gene.

    Compensation for mutations are not necessarily at the site of mutations. A mutation in a P450 enzyme that degrades a certain product could be compensated for by the upregulation of a different enzyme that has cross-reactivity.

    There is no “gene” that does this, the behavior is an emergent property of the whole genome. It is thousands of DNA bits working together “in sync” in a never-before-occurring genome.

    It is like a 5 legged stool. Which of the legs are important? You can remove any leg, you can remove any two legs. It is only when you remove 3 legs that the stool doesn’t work.

  62. ChasCPeterson says

    I’m pretty sure there are different definitions of ‘epigenetic’ being used here.

  63. says

    Coming from Amazon jungle I can’t understand the mindset running at Western Sciences, principally, this debate about evolution and biogenesis. Who drives the evolution of my body ( from blastula to adult) is the body of my parents because they are my creator, they are the phenotype driven my genes. Then, logically, who drives the evolution of biological systems at Earth surface must be the creator of this planet, all its elements, included all biological systems. It is the phenotype that created and rules the genes. Its name? The Milky Way. But, then, Western Sciences does not have a model of galaxies that fits as the creator and ancestor and phenotype of the first cell system. That’s the problem. It is merely a job of connecting the seven kinds of astronomical bodies in a working system that you will understanding every step of evolution here. I did it and the face of LUCA (the Last Universal Common Ancestor e creator of life here) is shown in a theoretical model at my website, called “The Universal Matrix/DNA of natural Systems and Life’s Cycles”. Ok, I understand that a half-monkey from Amazon jungle can not teach evolutionary biology here, but, maybe I can tell something about natural logics.

  64. ChasCPeterson says

    I can’t understand the mindset running at Western Sciences

    I have a strong suspicion that it’s mutual.

  65. says

    Coming from Amazon jungle I can’t understand the mindset running at Western Sciences, principally, this debate about evolution and biogenesis. Who drives the evolution of my body ( from blastula to adult) is the body of my parents because they are my creator, they are the phenotype driven my genes. Then, logically, who drives the evolution of biological systems at Earth surface must be the creator of this planet…

    Congradulations, you just graduated to the sort of thinking that people had 500 years ago in the “Western Mindset” as well. The problem is, some where in the process, people realized that it just didn’t make any damn sense as an explanation. You had to keep making excuses for all the stuff that didn’t work in any sort of way close to what any intelligent creator might have come up with. And, it doesn’t help, at all, to just wave vaguely and proclaim that we just don’t, somehow, understand his genius (which would be 100% completely Western too, as long as you are religious, and looking for excuses for why “god” made things that contradict each other, don’t work rationally, or make no sense as part of a “grand plan”.)

    This is a purely human conceit, the idea that there is some creator some place, that is like us, and therefor, because *we* make things, he “makes things”. I say human conceit because, evolution doesn’t have a plan, but humans can plan. We don’t change with the environment, we change the environment to fit us. Every other animal is subject to the whims of the nature, living or dying, without one bit of say, at all, in when, or how. If the world changes too much for them, they neither adapt, nor can they adapt the world to save themselves. We, mere humans, at least once we learn the “basics” of changing things to fit us, can. The more we know, the more we can change. But, even we have limitations. We get better and better at it. 2,000 years ago, we had no idea how to deal with earthquakes. It was pure luck if building still stood, and a whole island of people was lost, due to them not seeing the signs they needed to leave. Today, we know what it means, and how dangerous it is to stay, even if, in the end, we can’t prevent it from happening. 1,000 years ago, a simple disease could wipe out 90% of the population of a whole continent. Now.. maybe it could still happen, if it really was nasty enough, but it would to be *far* nastier than the ones from back then, for us to have **no** way to deal with it, or contain it, or figure out how it spreads, etc. Even 20 years ago, people would have died from things we can either treat, repair, or control, well enough to keep them alive today.

    We shape our world, and every bloody conceited, hubris filled, fool, since the first day someone made a mud hut, because there wasn’t a cave nearby to live in, has been claiming that there must be some “bigger, invisible, creator, who, like us, made a giant mud hunt, lit fires on it, and thus created the sky!”

    You “insight” isn’t one. Its making unfounded assumptions about what might have “made” the world, based on the totally absurd hubris that there must be something out there, at least a bit, like yourself, who “made” the world. An idea based on the equally silly concept that, without the knowledge, no matter how basic, passed from your parents, and others, to you, about how to do those things, you would have any higher survival rate than any other monkey, if the world suddenly changed too much for you to keep living in it.

  66. says

    Kagehi, I can bring real natural facts as evidence for debunking every assertion you made in yours post. First of all you have read only the first sentence of my post and fast went answering it, then, you made a big mistake with yours unfounded saying that I am a believer in supernatural creators and a mystical. You can not show to us a document at any library of the world that my world view is a “sort of thinking that people had 500 years ago in the “Western Mindset”. I am based in modern Astronomy, Physics, Biology, Chemistry, which were not known at yesterday. Yes my insight, called “The Universal matrix/DNA of natural Systems and Life’s Cycles” is one, never produced before. You said that because you have no idea what’s my world view. Peterson, i his post above said the right short thing: While I can’t understand the causes that produced yours world view, it is mutual”. We live at different habitats.
    Yours says about “there is some creator some place, that is like us”, or “any intelligent creator might have come up with” or ” why “god” made things”, makes no sense as answer to my post. You are saying that, not me. But when you say “some where in the process, people realized that it just didn’t make any damn sense as an explanation” I can tell you that earlier in my young times, I realized that the gene centric view ( a bunch of atoms organized as chemical molecules) just didn’t make any sense as an explanation. This is mystical, this is no different from the existent religions, wake up man!
    There is no creator since there is no life’s origins, merely a long chain of causes and effects since the Big Bang, which produces the transformation of a unique natural system increasing its complexity, from atoms to galaxies to cell’s systems, to brain systems. If there is some supernatural agent, it is existing before the Big Bang and beyond this Universe, it is not my issue. Let’s go back to real facts here and now.

    You said “evolution doesn’t have a plan, but humans can plan”. I am seeing no human planning of yours social system. I am seeing only that humans are mimicking the rules among animals that I am seeing here in the jungle, the division between few predators and a larger number of preys. Tomorrow in the morning I will wake up and going out I will see infinities directions that I can choose one accordingly to my freedom for choice; you will wake up and be driven to yours local work, you have no choice. What kind of plan is that? A plan against yourself ?!

    Evolution doesn’t have a plan?! What’s the real fact you can bring over the table for proving that? Different from yours gene centric view, I agree that anything material inside this material Universe is the carrier of the evolution process, so, there is no evolution with a plan. Dawkins is the one saying that genes has a plan, previewing the future, when trying to reproduce and spreading themselves. What absurdity! But, as a salvage man living among the salvage Nature, I learned to ask nature for answering my questions about existences. I don’t believe that nature plays dice with her creatures, so, I ask only to her. And about evolution or no evolution, Nature shows to me the evolution process that occurs at my face observing the 9 months of embryogenesis. Anything inside the womb has a plan, anything is able to preview what is coming next, bit there is evolution occurring there. because evolution is not the whole history, it is merely the several micro-steps of a real bigger process: reproduction. So, my Universe is merely a process of genetic reproduction, I don’t know what is being reproduced, it could be yours small atom that triggered the Big Bang, or a natural system too much complex. Reproduction is a plan in itself. And I can bring over the table my real fact as evidence: any pregnant woman. When you see evolution happening here, but believes that evolution have no plan, you are creating a mystical supernatural god called “Absolute Magical Chance”.

    In the jungle I can’t preview earthquakes because I have no scientific tools for pointing them to the right directions. You have the tools but you I can’t do it because you don’t know the right directions. Our difference is about the interpretations of the real known facts about this planet and the system surrounding it. We have a very different theoretical models. Of course, the two are no complete, but, since yours facts are the same of mine, it is an issue about interpretations.

    You said: “You would have any higher survival rate than any other monkey, if the world suddenly changed too much for you to keep living in it.” Do you believe that you and yours western stuff could have any higher survival rate than any other ancient native of Europe, if the world suddenly changed too much?! can you survive long time at the international space station? Have you built any bunker at Mars? Ok. My theoretical astronomical models are suggesting that this planet obeys a process of life cycle, the one that produced the life cycle that acts over yours own body. So, this planet is changing its shape, like yours body changed from blastula to baby. Bacterias existing inside babies can not exists inside blastula and vice-versa. I am waiting the day that you will prove that you are not a bacteria in relation to this planet and the evolving Cosmos. And I am surviving here more than any monkey did, due my knowledge. You can not coming here because you couldn’t survive more than a few weeks, because the the malaria gets you, not me.

    We should debating details about genes, but you went far away from the topic.

  67. says

    All I see is more assertions that a human-creator centric view somehow makes more sense than one supported by the facts. I didn’t go far away from anything, I was addressing your particular nonsense, which I am damn sure there isn’t one single person here, other than you, who isn’t either groaning, or laughing at. You are the one bringing in a lot of assertions about how it “must be planned”, purely based on your inability to accept that it might not be.

    Also, you are committing the single worse crime to scientific thought possible – you are inserting an unneeded entity, into the equation, for which you have no adequate description, of any kind, no way to test as a hypothesis, and no actual evidence, beyond your own desire for it to be a necessity.

    We get this all the time from every bloody bunch of religious people you can imagine. Its the same thing, every time. “We think something made it all. We can’t describe this thing. It changes shape depending on what we are talking about, and how badly we want to sound scientific. We have no evidence other than our own need for it to be true. We have no explanation for any, and all, contradictions to our view, other than to assert that its an ‘unknown’, and that, despite thousands of years of this stuff, somehow, if you damn scientists took it as seriously as we do, then maybe we actually would find evidence that wasn’t purely based on our need for it to be true. And, well… if you really push us on the subject, I guess we could say it was… er.. space aliens? That would make it plausible right, even if magic spirits, gods and other things are not?” Answer: Nope, still no evidence, and hell no, aliens don’t solve the problem, since you then just go and assert that somehow “they” had some magic sky fairy behind them instead. You still, at some point, either have to assert the ridiculous idea that something non-created “created” things, without there being any bloody logical reason to presume such a thing, never mind a single scrap of evidence to suggest its either true, nor even necessary, or… you have to allow that some process, exactly like the one we already are talking about, happened, without something guiding it. You can’t escape that problem by simple claiming there are infinite numbers of different “creators” all of which, in some wacky fashion, exist, recursively, to solve the problem, and without that.. asserting that there was one of them, to start with, just shoves the, “happened without someone to create the bloody, insanely, complicated thing, which was then able to create”, one step farther back in the queue.

    I am not even going to try to address the actual absurdities themselves in your post, there are entire websites dedicated to trying to do that, and much more qualified people to answer them. The only thing, therefor, I am addressing, is the absurd notion that because you can make a hat, or what ever, someone/thing had to make you, instead of the simpler, more likely, and, based on actual evidence, far more plausible, conclusion that your ability to make that hat is an artifact of a non-creation, with no creator, and its purely your own inability to abandon the idea that everything “must be” created, based on a plan, that keeps you from seeing it.

    In fact, its commonly listed as the single biggest problem in getting people to understand genetics, as it really works, never mind evolution – the presumption that because people create, and can plan, the universe had to be made by something that does too. That you can’t grasp, or accept this, is a sign not of bringing a new (instead of ancient and tested to the point of it being completely rejected) view to the subject, but a complete and utter failure to understand them, or any of the vast array of other sciences that indirectly support them.

  68. says

    Oh.. And just to be clear, you also make the completely mad assertion that your parents “made you”, as though they somehow, mystically, or something, sat down and picked each and every allele you had, instead of just tossing a lot of randomized bits of his genes in with a random bit of hers, and hoped it functioned, instead of, as happens 60% of the time, completely went wrong, and failed to produce a baby. If this qualifies, somehow, in your mind as “guiding”, never mind “creating”, then… your position on the subject is even more incomprehensible and meaningless than it already appeared to be to start with. It also “proves” you have no clue what you are talking about, at all, and are just pulling out random ideas, in hopes that someone who actually does understand this stuff will think you have an amazing insight (rather than the need to go back to school for a few years, preferably for a non-religious education).

  69. Nerd of Redhead, Dances OM Trolls says

    Yes my insight, called “The Universal matrix/DNA of natural Systems and Life’s Cycles” is one, never produced before.

    Until you publish it in a peer reviewed scientific journal, it doesn’t exist, except in your mind. You have nothing until it is published.

    I see NO citations to the peer reviewed scientific literature. All you have is bad sophistry.

  70. says

    78 -Kagehi said: “Oh.. And just to be clear, you also make the completely mad assertion that your parents “made you”, as though they somehow, mystically,..

    You are such addicted to think inside the box that you never will understand one word of a giant world view outside the box. Everything you said about my post is wrong again!

    The assertion that my parents made body without their planning has no foundation on mystical or magical thinking! My parents made me as merely tool used by Nature and its natural methods. Yours world view based on “the blind evolution made my body” is a exceptional claim requiring exceptional evidences, which you don’t have, I will not extend this debate because you never stands on topic, on facts, real proved facts.

    Yours presumption that the Universe was not tunneled for producing biological systems and consciousness – although knowing that inside this Universe there are wombs tunnelled for producing biological systems and consciousness – is a behavior of someone going far away from the rational logics for to arrange a mystical belief ( never seen at any place and time: where did you see biological systems and consciousness being created by blind evolution?! How do you know that evolution is blind?!), to fit inside the box of a current doctrine. The Matrix/DNA Theory is a totally different exercise of logics and reason.

  71. says

    79 – Nerd of Redhead, Dances OM Trolls
    You said: “Until you publish it in a peer reviewed scientific journal, it doesn’t exist, except in your mind. You have nothing until it is published.”

    But… who said to you that yours Science and yours scientific method are the owners of Nature?! Don’t you know about relativism? Each observer at different point in space/time see Nature from his/her limited perspective. We – me and you – standing on very different locations, we are surrounded by different views of Nature, so, yours “peer review” has nothing to do about my world view.

    Yes, it is published on my way to do things. If you want know see my website “The Universal Matrix of Natural Systems and Life’s Cycles Theory” (Google it). Now, if you want saying that it has no connection with the real world, try to debunk it, bringing on the table any real proved fact, not yours theories.

  72. Nerd of Redhead, Dances OM Trolls says

    The assertion that my parents made body without their planning has no foundation on mystical or magical thinking!

    Unevidenced assertion, dismissed without evidence. Back to where you were months ago. Back up your inane and fuckwitted idea with third party scientific evidence, or shut the fuck up about it. The middle ground, where you can’t put up, but won’t shut the fuck up, is for liars and bullshitters. Thanks for supplying us with prima facie evidence for the legitimacy of your ideas. Namely, the outhouse hole.

  73. says

    Don’t you know about relativism? Each observer at different point in space/time see Nature from his/her limited perspective.

    I love this sort of abject gibberish. So what if two people see different parts of the same bloody wall and one thinks a stain on the thing looks like a duck, but the other one says its a camel, which is the sort of nonsense you are getting at. Science represents the “intersection” of those perceptions. Its the things that everyone can agree is there, or which, by moving someone in to the same position in space, or what ever such silly obfuscation you prefer, they will *also* see, from that point. Its also about comparing those measures against other measures, taken with instruments, which have the “same” observed result, regardless of who is doing the observing, and then comparing those 100% predictable results to the errors from purely human perception. And, above and beyond all of that, its understanding how and why those human perceptions work. Which is to say, what the same bloody data is that goes in, in all cases, with all people, and how the brain as a system that builds patterns out of a fraction of that data, sometimes screws up, badly, and gets entirely wrong results, from data that is otherwise 100% predictable, and nothing like what is perceived by the eyes, or ears, or nose, etc., when compared.

    Without this understanding we couldn’t design synthetic scents, which smell like predictable things. We wouldn’t use mathematical models to make 3D images, that look like the real world, in a computer. We couldn’t have come up with the newest touch screen tech, which uses small current changes to trigger the skin to tighten, or loosen, and, in doing so, exactly as predicted, **making it feel like** you where touch a non-smooth surface, like a pineapple. Its our understanding of the limitations, and function, and malfunction, or human senses, compared to real data, collected by 100% predictable means, that lets us do these things. No one has **ever** come up with anything, based on the absurd idea that everyone sees things differently, so somehow reality itself is somehow disconnected from tangible, predictable phenomena, and is instead, somehow manufactured by observation, in the dead opposite of how the universe works.

    Anything suggesting otherwise provides no bloody useful predictive value, and is indistinguishable from the silly nonsense that “magical theory” was predicated on, where nothing is predictable, everything is explained from personal perspective, and, despite the fact that this never happened, casting a spell can change the universe (except when the subject is immune, or protected, or strong willed, or something interfered, or it was the wrong moon phase, or evil spirits intercepted the spell, or…. blah, blah, blah, gibberish.)

    When you make wild, absurd, unbelievable, claims, which contradict how everyone else bloody thinks the universe works, its your bloody job to prove it is right, not someone else’s to “debunk” it. There have been many times that science has been shaken, and come out stronger, precisely because someone had such an idea, and had bloody solid evidence, which better explained what was already observed, instead of completely contracting it, or failing to explain existing facts already known about the subject. None of these people who managed these drastic shifts in assumptions did it by insisting they had it right, whining about how everyone else was being unfair, or didn’t understand, or restating the same assertions 50 different ways, without one scrap of fact to back any of it up, while saying that it was up to everyone else who needed to “debunk” them. They did it by providing the bloody evidence that they where right.

  74. says

    Nerd of Redhead, Dances OM Trolls

    You said: Unevidenced assertion, dismissed without evidence.

    The unique explanation I have for your post is that I am doing errors about English language , which is not my native language. It is not possible that you believe that my parents has planned ( has elaborated the design) when they made my body. It is not possible that you can’t understand what I am saying:

    My parents made my body, so, this planet and the galaxy to who this planet belongs made biological systems here. That’s my affirmation, my final conclusion and any other alternative about who created life here is not rational.If religious, mystical people believe that something supernatural came here creating life it is pure imagination, since never nobody saw anything supernatural. If other opposite kind of religious people believe that life emerged here by chance, by statistical probability, as I think you believe, it is mystical, not rational belief. Because my body was not emerged by chance or statistical probability inside my mother’s body. neither life emerged by chance inside the Milk Way body. What’s wrong about that?!

    But… this wrong world view that you advocates is the cause our knowledge is going so slow, the dominant scientific thought is doing that human sciences is leading Humanity to lose the game. Before this “scientific enterprise” (1800’s?) there were 500 million people suffering due bad life’s conditions, today there are 7 billions in this situation. Slaves of work being vampirized by humans predators and science have doing nothing for them. You are fired, your opportunity was passed off, we need another kind of scientific thought and method.

  75. says

    to Kagehi:

    You said: “I love this sort of abject gibberish. So what if two people see different parts of the same bloody wall and one thinks a stain on the thing looks like a duck, but the other one says its a camel, which is the sort of nonsense you are getting at.”

    Com’on, nobody is stupid here for saying such thing as duck or camel, you don’t understand why I said relativism. You got yours world view at a urban city from 20 century, I got mine at a jungle that is virgin habitat testimonial of life’s origins, millions years ago. This is different time. You got yours seeing the Empire State and taxi drivers, I got mine seeing trees and serpents. This is different space. Different observers located at different points in time/space. Is it wrong?!

    You said: “Science represents the “intersection” of those perceptions.”

    Not the human science, as it has been applied. I have hundreds of topics as evidence that yours science is out off the right track. We can debate it, if you want. Do you know something? That Physics married with Math wishes to get a Theory of Everything is the most irrational and mystical behavior. This Universe has produced a human body. If you apply Physics and Math over a human body trying to get a Theory of Everything of The Human Body, you will not advance from the mechanistic bone skeleton. But the most complex part of the human body begins beyond the skeleton, with the soft meat, the brain producing thoughts. Yours team, driving sciences today, never will have the idea that the Universe, a Theory of Everything, can not be explained without Biology, Neurology, Psychology… you forgot that the Universe is the father/ mother of humans bodies. You believe that the Universe is magical, creating things that it has no information for. Go to my website and see how works a living, biological and conscious Universe as must be our genetic producer. See how this galaxy described by Newtonian mechanics has an invisible coberture of biological organization of matter. Or go living in the jungle for to learn another relativistic point of view.

  76. a_ray_in_dilbert_space says

    Louis Morelli,
    The mindset running in western science is pretty simple–ideas have to prove their merit by increasing understanding, specifically by making a nontrivial prediction that is subsequently verified. You are welcome to play.

  77. says

    Do you want know how relativism worked in my method?

    1) I am big, a cell system is microscopic. I am microscopic, this galaxy is macroscopic. I see a cell system from outside, I can know its periphery very well, but I can’t see the interior well, there are a lot of things that humans does not know about cells.

    2) I see a galaxy from inside, I can know its interior very well, but I can’t see its periphery, there are lots of things humans does not know about galaxies.

    3) But… I am sure that this galaxy is an ancestral of cells systems. Of course, it is! So , I will apply what I know about the periphery of cells systems over the unknown periphery of galactic systems, calculating the reverse mechanisms of evolution, and I will apply what I know about the galactic interior over the unknown things of the cell’s interior, calculating not the reverse but the normal steps of evolution. This is merely 10% of my method, it has lots of other techniques, the final result is a very different picture of all existences. You don’t need to travel to another point in time’space for seeing things from that perspective if you can do it with yours intelligence. But… be rational, do not bring on here mystical, magical thinking, like life’s emerging inside galaxies by statistic probabilities… neither bring on those supernatural beings from the other team …

  78. says

    to: a_ray_in_dilbert_space

    You said: “…ideas have to prove their merit by increasing understanding, specifically by making a nontrivial prediction that is subsequently verified.”

    That’s why the jungle told me, 30 years ago, an absurd idea about what is this world, an idea that I can’t believe in it, but in these 30 years I am seeing news, scientific papers, images from Hubble, etc., which were the right nontrivial predictions made by that idea – that I realized there is something wrong with my skepticism. At my website I had posted some of those predictions that were confirmed, I have counted hundreds of them ( portuguese section, Artigos).

    At another hand, I am seeing everyday a scientific discovery, or an image from Hubble, etc., suggesting that the academic theoretical models need be changed.

    Of course my models are not complete, there are lots of errors, maybe is everything wrong. But they are under test because the whole theory is falsifiable. There are no black holes in my working galaxies because I never saw black holes and I never saw nature reaching the point of singularity. This is an absurd idea.

  79. Nerd of Redhead, Dances OM Trolls says

    Word salad from a liar and bullshitter without evidence. You have nothing to say that makes cogent sense. Try peddling your bullshit elsewhere, or link to real evidence to show your ideas have merit. They don’t without evidence.

  80. a_ray_in_dilbert_space says

    Louis,
    Eu falo Portugues. I am sorry, but you have to specify where to look for your validation in advance. It is not enough to subsequently come across an article or result that seems to be in accord with your theory. That is not prediction, but prophecy. You need to specify a concrete falsifiable prediction and how to falsify it, or you aren’t doing science.

  81. a_ray_in_dilbert_space says

    Louis, I also take offense at your suggestion that science has failed humans on a moral scale. Do you have any idea where we would be if not for antibiotics, if not for antimalarials–hell if not for cell phones. Science has done far more for the poor of the world in its 400 short years than all of the religion or philosophy of the previous 5000 years, and it continues to do more than all the mystics, shamans, politicians, priests and philanthropists combined.

  82. says

    a_ray_in_dilbert_space:

    You said: “You need to specify a concrete falsifiable prediction and how to falsify it, or you aren’t doing science.”

    I never said I am doing science as you understand it.I have no such pretension, I am a curious philosopher, a naturalist philosopher, agnostic, trying to understanding the origins end functionality of the whole biosphere of Amazon jungle, so, I need separate everything into systems and after that, putting all systems altogether for getting a big picture, and I did it. My method is the ancient first steps of Greek philosophy, comparative anatomy between living and non-living systems for calculating the links between them, which give a new understanding about universal evolution. But… all my life I have following yours science, because the reductionist method has been half of the sources where I get my data, the another half is the jungle.

    As said Einstein, one can not in life to prove that his universal theory is the right one, and he don’t have to prove it, he need to show that the theory makes sense, rational sense. That’s what I am doing after getting my whole picture, testing it against every new known fact in the last 30 years, and after doing my website, already posting there hundreds or thousands of right predictions from my models.

    Only for your sake, if you want to know how it works, see only one of these thousands of evidences that the theory makes sense: http://theuniversalmatrix.com/pt-br/artigos/?p=333 ( ATP Sintase: Como a Terra Copiou do Céu esta Extraordinária Engenharia! ) – or ATP Synthase: How Nature at Earth Has Copied from the Sky this Extraordinary Engineering . There are a synthese in English too, the article is not finished. Go there, see it, come back making yours criticism, because I know, you will not understand the whole thing.

  83. says

    a_ray_in_dilbert_space

    You said: Louis, I also take offense at your suggestion that science has failed humans on a moral scale.

    500 millions humans slaves at 400 years ago; 7 billions (90% of the world population?) humans slaves today. Against numbers, there are no minded produced arguments.

    I will not remember the evidences that our planet is sick, changing climate, due we are not sure of it is man made illness.

    But… accordingly to the results of my investigation, the worst thing that human science is doing is leading Humanity towards the Admirable New World, under the rules of a Big Brother. It will be the premature abortion of this new natural system being generated here, called “consciousness”, for to be eternal zombie.

    There are three fundamentals problems with human science in the last 400 years:

    1) The supreme, honest, altruistic, goal of the founding fathers at the Illuminism, was denied by the disciples and science sold its soul to the dominant class of human predators, feeding the selfish gene. All science’s production has been delivered gratefully to these predators, giving them power, feeding a monster, becoming anti-human;

    2) While the founding fathers were fighting the mysticism and its prejudices to human kind, the disciples built another mystical world view, changing the magical God by the magical blind Universe and science lost the right way. But, like the ancient deist mysticism was based on memory registered at our genetics, this new mysticism is also based on it. It is a genetic process coming from our creator, which is described by Newtonian mechanics, then, science is driven to grasp the mechanical aspect of every natural phenomena, while every phenomena has lots of another kind of matter organization, others invisible natural systems acting here due the hierarchy of systems, etc. That’s why science is driving us, our youngers today, towards a mechanical state of human society;

    3) Science must be a feed-back process between the reductionist method and the systemic method. Reductionism gets data about details and systemic approach try to connect these data into big pictures, building good theories that feeds the search for reductionism. But, systemic method does not provides profit in money, nobody is funding it. Systemic thinking was born with Margullis ( the symbiotic theory), Fritjof Capra (The Tao of Physics) and others, till Bertalanffy making what francis bacon did with reductionism, collecting every dispersive data into a General Systems Theory. Bertalanffy could not advance because no human being was discovered yet what is a real natural system, the unique tentative today is my suggestion called “The Universal Matrix/DNA for Natural Systems”. So, The general theory about natural systems was killed and Wiener, Rosenberg, who were mathematicians/physicians took the control and deviate it from natural to artificial systems, creating cybernetics and this whole scientific enterprise today dominated by the electro-mechanical brain of computers.

    Nope, my friend. There are 7 billions human beings being tortured today at this absurd human condition of existence, the planet is dying… to the hell with this kind of science! Go back to the intentions of the founding fathers, do what I am doing, alone, paying it with my hard work, not being a traitor.