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The comparison to jabberwocky is inevitable

Lots of people have been sending me this paper by Erik Andrulis, and most of you have done so with eyebrows raised, pointing out that it’s bizarre and unbelievable; some of you wrote asking whether it was believable, at which point my eyebrows went up. Come on people: when you see one grand cosmic explanation that is summarized with cartoons, which the author claims explains everything from the behavior of subatomic particles to the formation of the moon, shouldn’t you immediately sense crankery?

It’s also getting cited all over the place, from World of Warcraft fan sites to the Discovery Institute (those two have roughly equal credibility in matters of science), so I had to skim through it. I read it with rising concern: Erik Andrulis is a young assistant professor at Case Western Reserve University, and he’s published entirely sensible papers on RNA processing. This paper is so weird and out there that it is either an attempt to Sokal the field of origins of life research, or the man is seriously mentally ill. Either way, this is not going to help his career in the slightest.

The paper is titled Theory of the Origin, Evolution, and Nature of Life, and just the sweeping grandiosity of that title should set off alarm bells. Here is the abstract:

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Having skimmed through all 105 pages of this thing, I can tell you with confidence that it answers none of those questions. Just the fact that it is entirely non-mathematical and non-empirical (there aren’t any observations or experiments described at all), and that the entirety of the theory is built around diagrams sketched out by the author, should also tell you that this is not a useful or predictive theory.

It does not have an auspicious beginning. In addition to being constructed around cartoons and being a non-mathematical Theory of Everything, it has to introduce an elaborate collection of neologisms that make the whole paper painful to read.

In the theory proposed herein, I use the heterodox yet simple gyre—a spiral, vortex, whorl, or similar circular pattern—as a core model for understanding life. Because many elements of the gyre model (gyromodel) are alien, I introduce neologisms and important terms in bold italics to identify them; a theoretical lexicon is presented in Table 1. The central idea of this theory is that all physical reality, stretching from the so-called inanimate into the animate realm and from micro- to meso- to macrocosmic scales, can be interpreted and modeled as manifestations of a single geometric entity, the gyre. This entity is attractive because it has life-like characteristics, undergoes morphogenesis, and is responsive to environmental conditions. The gyromodel depicts the spatiotemporal behavior and properties of elementary particles, celestial bodies, atoms, chemicals, molecules, and systems as quantized packets of information, energy, and/or matter that oscillate between excited and ground states around a singularity. The singularity, in turn, modulates these states by alternating attractive and repulsive forces. The singularity itself is modeled as a gyre, thus evincing a thermodynamic, fractal, and nested organization of the gyromodel. In fitting the scientific evidence from quantum gravity to cell division, this theory arrives at an understanding of life that questions traditional beliefs and definitions.

Here’s a partial copy of his lexicon. It goes on quite a bit longer than what I’ve copied here.

Table 1. Gyromodel Lexicon

Alternagyre A gyrosystem whose gyrapex is not triquantal
Dextragyre A right-handed gyre or gyromodel
Focagyre A gyre that is the focal point of analysis or discussion
Gyradaptor The gyre singularity—a quantum—that exerts all forces on the gyrosystem
Gyrapex The relativistically high potential, excited, unstable, learning state of a particle
Gyraxiom A fact, condition, principle, or rule that constrains and defines the theoretical framework

Gyre The spacetime shape or path of a particle or group of particles; a quantum
Gyrequation Shorthand notation for analysis, discussion, and understanding gyromodels
Gyrobase The relativistically low potential, ground, stable, memory state of a particle
Gyrognosis The thermodynamically demanding process of learning and integrating IEM
Gyrolink The mIEM particle that links two gyromodules in a gyronexus
Gyromnemesis The thermodynamically conserving process of remembering and recovering IEM
Gyromodel The core model undergirding the theoretical framework
Gyromodule A dIEM particle in a gyronexus
Gyronexus A polymer of dIEM particles linked by mIEM particles
Gyrostate The potential and/or kinetic state that a particle occupies in its gyratory path
Gyrosystem A gyromodel with specific IEM composition, organization, and purpose
IEM Information, energy, and/or matter

I can’t help myself. You knew this was coming.

Twas brillig, and the slithy toves
Did gyre and gimble in the wabe:
All mimsy were the borogoves,
And the mome raths outgrabe.

Now I know that you are in lexical shock right now, but I’m about to make it worse. Witness the use of these terms in figure 1 of the paper, which will also reveal the kinds of diagrams he’s using.

“The levorafocagyre, in turn, is antichiral to the dextrasupragyre” is a nice sentence that about sums up the experience of reading this thing. Don’t believe me? Here are more excerpts that illustrate the grand, cosmic, and entirely uninformative nature of gyroexplanatory gyrobabble. Andrulis purports to explain everything from learning and memory (learning and memory by gyres, not the poor people trying to understand his paper):

The ultimate state of gyromnemesis is the stably adapted particle or gyronexus in the gyrobase. A particle thus adapts through learning and memory by completing one full cycle—a revolution— around the singularity. Taken together, gyrognosis defines IEM integration and assessment whereas gyromnemesis defines IEM storage and recovery. Finally, although a diquantal IEM (X”) undergoes gyrognosis as the gyrobase of a primary majorgyre, it undergoes gyromnemesis as the gyrapex of an alternagyre. Thus, gyre learning and memory are relative to the gyradaptive singularity.

To the formation of Earth’s moon:

Lunar Formation. The favored hypothesis for the formation of Earth’s Moon is from planetesimal impact on a proto-Earth proceeded by matter ejection, accretion, and gravitational capture [189,190]. However, the question of lunar origin has not been settled since there are competing, albeit antiquated hypotheses [191,192]. I also discovered the stunning admission that, “…shamefacedly, [astronomers] have little idea as to where [the Moon] came from. This is particularly embarrassing… [193].” The oxygyre models the Moon as a macroxyon that has a macroelectron within itself; this simple gyrosystem accounts for the known chemical composition of the Moon surface, oxides [194]. Regarding lunar origin, the macroxyon that is the Moon emerges from the macroelectron that is the Earth, concomitant with the emergence of Earth’s macroxyon [195,196].

Several additional points can be derived from this gyrosystem. First, the oxygyre explains water on and in the Moon [197-199]. Second, the gyrating effects of the macroxygyre model the rotation of the Moon on its axis. Third, the path of a less exergic macroxyon (Moon) around more exergic one (Earth) follows an ohiogyre path, or lunar orbit. Fourth, this oxygyre provides insight into how tidal cycling is linked to lunar orbit and axial rotation [200] since the Earth’s oceans (macroxymatrix) and Moon itself (a macroxyon) exert complementary attractorepulsive forces. Fifth, this theoretical union also helps clarify short-term chronobiological ([201]; see 3.8) and long-term geophysical [202] relationships. Sixth, the craters that cover planetary, lunar, and satellite surfaces [203-205]—most if not all of which are near-perfect circles—bear the signature of the macroelectron singularity and its strong thermodynamic force on the oxygyre [206].

You know what? That doesn’t explain anything!

While the strange terminology and nonsensical claims could be clues that this is an elaborate Poe of some sort, the story I’ve heard from some other sources is that Andrulis is not getting tenure and will be leaving Case next year, and that he seems to have a history of tuning in and out — so what this most likely is is a developing personal tragedy. I hope he gets the care he clearly needs; his other work suggests that this is an intelligent mind that is currently going off the rails.

Setting Andrulis aside, though, there are other problems here. How did this paper get published? It’s terrible: unreadable, incoherent, bizarre, and completely lacking in evidence or mathematical support. This is from the very first issue of a new journal, Life, which also contains a perfectly reasonable general summary of origins of life research by Stuart Kauffman alongside Andrulis’s ghastly dreck. There seems to be a complete lack of editorial discrimination at the journal; this is not the way to build a reputation. Or rather, it is, but not a desirable one.

And then there is Science Daily, which seems to be the source where most of my correspondents found this paper. Science Daily is an incredibly annoying source: all they do is republish, without any kind of intelligent assessment, press releases. They suck. What good is mindless regurgitation?

And finally, there’s Case Western Reserve University, which must bear a share of the blame. Where did the press release come from? Why, from the Media Relations office at CWRU. Somebody wrote the press release that begins like this:

The earth is alive, asserts a revolutionary scientific theory of life emerging from Case Western Reserve University School of Medicine. The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects—for example, planets, water, proteins, and DNA—are animate, that is, alive. With its broad explanatory power, applicable to all areas of science and medicine, this novel paradigm aims to catalyze a veritable renaissance.

It’s madness stamped with the Case Western Reserve University School of Medicine seal of approval. If Andrulis did Sokal the journal, he also Sokal’ed the institution that employs him. Who wrote that bullshit? Do they have anyone competent review their press releases before they mail them out to the whole wide world? Was there anyone thinking in all the steps from crank professor to PR department to journal editor to reviewers? There were so many points where this crackpottery should have been detected and rejected, and it didn’t happen.

(Also on Sb)


Science Daily has informed me that they have removed the press release from their site, and that it should never have made it through in the first place.

Also, apparently Case Western has removed the press release from their listings.

Comments

  1. says

    Well PZ, this is either an elaborate joke or the onset of schizophrenia. If the latter, I think it’s kind of cruel and unseemly to spend so much time trashing it, not to mention pointless. Lots of crazy people write crazy stuff, not worth your time.

    I would just leave it that the university’s PR department got pwned, and the journal is not a real journal. (There are lots of those Spamnals out there. I keep getting e-mails asking me to publish and be on editorial boards of bogus journals. You have to be careful, and certainly, they’ll take legitimate stuff as well as garbage, which can end up being embarrassing to the legitimate investigators.)

  2. jamessweet says

    I am sorry to say, but it reminds me a lot of a developing case of mild schizophrenia. The “everything is connected” delusion can become extremely powerful, and it can become particularly strange for those who are intelligent enough to identify real (but meaningless) patterns.

    I had a friend who started claiming to see plus signs and minus signs everywhere, shortly before he had a breakdown and jumped out of his window because he thought the CIA was after him. (And then a later incident where his roommate had to call the cops because he was naked in the basement screaming about being Jesus or something) What was interesting is that he really did find hidden plus and minus signs in the oddest of places, things I wouldn’t even have noticed. It all meant nothing of course — how significant is it that two perpendicular lines shows up in a lot of things? — but the point is, if he and I were both asked to find all of the plus and minus signs in a particular image, during his episode he would have found way more than me.

    I suspect something similar may be happening with Andrulis. He has this pattern fixed in his head, and, being a smart guy, is now identifying all sorts of hidden (but meaningless) instances of the pattern. Sad…

  3. bcwebb says

    His mind seems to have tranlated everything into a form of pig latin using the syllable gyre – Your first sentence translates as:

    Gyrelots gyre peogyreple gyrebeen gyring gyreme pagyrer Erikgyreandrulis….

    Very deep waters indeed.

  4. says

    I think I was very clear in identifying this as either a poor joke or a sign of mental illness, and if the latter, that I hope the fellow gets help now.

    However, that most definitely does not mean we should ignore tripe that gets published. It must be publicly criticized, and it must be made clear that this is bad science, because there are people, like those sad gomers at the Discovery Institute, who are reading it as representative of modern biology. That means the work should be trashed, while in this case the author should also be recommended for psychiatric help.

  5. says

    Turning and turning in the widening gyre,
    Things fall apart; the centre cannot hold;
    Mere anarchy is loosed upon the world.

    Yeats had a pretty-good theory then?

  6. Mario says

    The oxygyre models the Moon as a macroxyon that has a macroelectron within itself

    Dude, wait wat?

  7. says

    whoops

    Turning and turning in the widening gyre,
    The falcon cannot hear the falconer;
    Things fall apart; the centre cannot hold;
    Mere anarchy is loosed upon the world

    Loose me own mind next

  8. KG says

    John Nash is reported to have said that his (brilliant) work on game theory “came from the same place” as his (ludicrous) delusions of persecution. Sometimes, though by no means commonly, “great wits and madness are most near ally’d” as Dryden had it.

  9. ChasCPeterson says

    This is sure to draw that commentor–what was his name?–who was explaining all kinds of developmental processes in terms of cell vortices.

  10. pentatomid says

    “The ultimate state of gyromnemesis is the stably adapted particle or gyronexus in the gyrobase.”

    What? And here’s me thinking that the octogyromnemetic floool is completely supercalifragilisticexpialidocious in the context of inverse timey wimey wibbly wobbly jazz penguin.

    Ok, jokes aside, if this guy really is having mental health issues, obviously I hope he gets the care he needs. Honestly I do.

  11. says

    Fleury. There is a distinct similarity, but Andrulis carries it to an even greater extreme.

    Fleury still sends me occasional demands in email.

  12. Tualha says

    Turning and turning in the widening gyre
    The author cannot tell his ass from his elbow;
    Sense falls apart; the theory cannot hold;
    Mere gibberish is loosed upon the world.

    Poor guy, I suppose it probably is schizophrenia. Can’t imagine how this thing got published.

  13. consciousness razor says

    It’s also getting cited all over the place, from World of Warcraft fan sites to the Discovery Institute (those two have roughly equal credibility in matters of science), so I had to skim through it.

    Heh, that’s quite an insult to WoW fans.

  14. Gregory Greenwood says

    The earth is alive, asserts a revolutionary scientific theory of life emerging from Case Western Reserve University School of Medicine. The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects—for example, planets, water, proteins, and DNA—are animate, that is, alive. With its broad explanatory power, applicable to all areas of science and medicine, this novel paradigm aims to catalyze a veritable renaissance.

    So all the complex, pseudo-technical jargon from the paper was simply another formulation of the frankly ridiculous and long discredited Gaia hypothesis?

    I didn’t realise there was anyone left who took that pseudoscientific babble seriously anymore.

    Twas brillig, and the slithy toves
    Did gyre and gimble in the wabe:
    All mimsy were the borogoves,
    And the mome raths outgrabe.

    If, as appears to be the case, Andrulis is suffering from some sort of mental illness then I hope he gets the help he needs, but all the same I fear that the vorpal blade of this unfortunate paper may already have decapitated his career with a snicker-snack…

  15. radpumpkin says

    The hell is a “macroelectron?!” I’m still trying to figure out what he could mean by that, and I’m a chemist! I’m also having considerable problems understanding what possessed this guy to publish The Theory of Everything (TM) without any mathematical backing. Urgh…time to drink.

    Also, new rule: people who do not know how to set up mathematical solutions to quantum mechanical problems are hereby barred from using the term “quantum” on the internet. Under pain of cannonization.

  16. says

    So all the complex, pseudo-technical jargon from the paper was simply another formulation of the frankly ridiculous and long discredited Gaia hypothesis?

    I read a journal just last year talking about why more and more biologists are signing on to it!

  17. says

    I saw this soon after it hit the web. I quit after I hit the “gyres,” which obviously didn’t refer to anything except a pathetic fiction.

    It shouldn’t have taken more than a few seconds for the “reviewers” to recognize what a woo salad it was. Instead, I think they must have been completely baffled by the nonsense, and passed it in order to get it out of their sights.

    Chopra couldn’t have done worse, I don’t think, although he could have made it sappier.

    Glen Davidson

  18. says

    I’ve never heard of a journal called “Life”. I couldn’t find it on google, or in pubmed’s Journal list, or in the University of Michigan Library journal database.

    Searching through the other papers in this “journal”, there are such gems as “Is life unique?” (referencing Einsteins “minimum metaphysic”) and “Nature’s capricious character”.

    None of the articles contain primary research, they are all just crazy off-the wall pseudo-hypotheses drawing from pseudo-scientific concepts and logical fallacies. This is not, by any stretch of the imagination, a scientific journal! It’s like it was conceived out of a twisted collaboration between Kent Hovind, Deepak Chopra, and (for added schizo fun) Ken DeMyer!

    This kind of thing is why the American public is so confused about science. A handful of charlatans gets the same amount of stage time as the millions of competent, hard-working, and honest scientists.

  19. tomocar says

    I find it extremely unlikely that this is anything other than a Sokalism, in which case it’s doubly hilarious (first in its cleverness, and secondly in how many people bought into it) and the guy is a genius comic! You clearly nailed it PZ; the word “gyre” in jabberwocky is the dead giveaway. I love science humor!

  20. Dr. Audley Z. Darkheart, liar and scoundrel says

    Ha! Mr Darkheart graduated from Case and he’s always talking about how awesome it is (in terms of research). I’ll have to pass this along.

  21. DrewN says

    Gyre; a quantum.

    I don’t see what’s so difficult to understand about that. Gyre’s are clearly for selling weightloss gimmics and books about how to increase your luck on daytime tv. There’s also the common emperors-new-suit aproach to, um, science-esque words. If you don’t understand wtf he’s talking about, you’re clearly not as brilliant as the author.

  22. says

    Throughout history, many have come forward to claim to have solved the riddles of the Universe – only to be proven wrong. I am humbly submitting my book proposal in hopes that you will permit me to substantiate and defend my incommensurable, unfalsifiable, complete and consistent theory of everything.

    This made me laugh, this means it was a joke right?

  23. luke says

    I think it’s pretty clear that this is no Poe, anyway. I should also make it clear that I found that message board just now using google, I’m not a reader/contributer there!

  24. Randomfactor says

    Boy, are you guys going to look silly when this leads to antigravity and flying cars.

  25. Hercules Grytpype-Thynne says

    Third, the path of a less exergic macroxyon (Moon) around more exergic one (Earth) follows an ohiogyre path, or lunar orbit.

    Any word yet on the characteristics of the minnesotagyre?

  26. says

    This is my favourite part of the study:

    “Death is a consequence of gravitational collapse of the cellulogyre into its singularity (genon) due to unobstructed attractive force exerted by, on, and within all subsumed gyrosystems.”

    :-))

  27. Dave, the Kwisatz Haderach says

    Hmm, I’ve heard this somewhere before. The idea of the gyre, or spiral, as a fundamental property of life… Now where was it?

    Oh that’s right. It was an anime series called Tengen Toppa Gurren Lagann. Clearly, he is plagiarizing his ideas from Japanese shows.

    Now don’t spoil the ending of the paper for me. Cause if its anything like the cartoon, then the climax is a fight between mecha that are big enough to use galaxies as throwing stars.

  28. says

    Dr. Audley Z. Darkheart:

    Ha! Mr Darkheart graduated from Case and he’s always talking about how awesome it is (in terms of research). I’ll have to pass this along.

    It is awesome.

    They have a Center for Origins, and they started giving talks at The Happy Dog, a nice pub that serves hot dogs with a choice of 50 toppings. (Kim chi being one option. Peanut butter is another. It’s great. Just don’t combine those two.)

    Talks about the origins of the universe, life, and everything. In a pub. With gourmet hot dogs. What could be fuckin’ better?

  29. neuroturtle says

    Schizophrenic and/or manic wanderings taken seriously by the religious? That’s nothing new. Maybe a new religion will be born of it all.

  30. infraredeyes says

    Speaking of jabberwocky, the Guardian has a review by Mary Midgley of a book by Rupert Sheldrake, he of the “morphic resonance”. Actually, it’s more of a puff piece; Midgley is obviously very impressed by the book, which is cutely entitled “The Science Delusion”.

    I wonder how many books have come out under “The [fill in the blank] Delusion” titles in the last few years? Richard Dawkins must be running out of space for all the goats he’s been getting.

  31. seleucid23 says

    The WoW forum actually does a good job of taking this apart. Most of the people there called it as bull.

    Meanwhile the Discovery Institute use it as a stick to beat peer review.

  32. Antiochus Epiphanes says

    Talks about the origins of the universe, life, and everything. In a pub. With gourmet hot dogs. What could be fuckin’ better?

    Cleveland rocks.

  33. mudpuddles says

    Wow, what piques me most about this is the Science Daily thing. I mean, the fact that I didn’t realise how crap Science Daily was – I’ve used it occasionally as a resource to see what people in various sciences are researching, but I didn’t relise that all they do is reprint other people’s press releases with no scientific consideration or assessment whatsoever. I’ve just flipped through about 30 articles on there from the past few days, and every single one is simply a press release regurgitated word for word. At least 10 of those should never have been published on a “science” website – misleading article titles, bold claims of major discoveries before any peer-review and without the “discoverers” providing any support materials to back them up (other than press releases)…

    I’m disgusted with myself! That’s one site I will not be trusting again. Science Daily, you fail!

  34. Taz says

    Sounds like he read “Mimsy Were the Borogoves” by Lewis Padgett and incorporated it into his delusions.

    (A really good science fiction story, by the way.)

  35. unbound says

    Read a decent portion of it. I’m reminded of the Dark Sucker Theory more than anything else. Hopefully someone can confirm that this is just a joke…

  36. cybercmdr says

    Saw this last night at physorg.com. Yes, I know it’s not the best source but they make it easy to keep up on a lot of subjects. I’m kind of interested in everything in science, so that helps.

    My first impression was that this would be glommed upon by the ID community, either because they can twist it to support their claims or cite it as to how science gets things wrong. A lot of people fell down on the job for this to get published. Just goes to show that the process is not infallible, and sometimes it is rigged (as in faux journals used by the IDiots).

  37. Dr. Audley Z. Darkheart, liar and scoundrel says

    Nigel,
    Oh, I wasn’t saying that Case isn’t awesome, ‘cos it most definitely is. And Mr Darkheart got an amazing education there.

    I spent a little bit of time in Cleveland when we were dating and fell in love with the natural history museum. Donald Johanson worked for Case at the time that he disovered Lucy and the museum has a cool replica of her skeleton. Lucy! How fucking cool is that?

    I just think Mr Darkheart will get a kick out of this, erm, paper.

  38. Kaylakaze says

    As i said on SB:

    Anyone who has read Junji Ito’s Uzumaki knows what’s wrong with this guy.

  39. stonyground says

    That little nonsense poem reminded me of Stanley Unwin. I would imagine that he will be completely unknown outside the UK, he appeared as one of the evil baron’s courtiers in the film version of Chitty Chitty Bang Bang. His speciality was talking a kind of gibberish that still managed to communicate meaning. He once did a series of Ads for tyres, Uniroyal I think. The tyres provided Maximost milodes, were outstandifold in the wetty grippers and thriftymost on your banky balancer. It has just occured to me that there are probably hundreds of old black and white clips of him on you tube.

  40. lauradiederich says

    Thanks for writing this post, PZ. My soil science proff mentioned this paper on the first day of class, and I was rather skeptical, but he couldn’t remember the name of the paper, and he misremembered the author. I shot him an email including this, hopefully he’ll respond favorably.
    I don’t think this post was mean spirited or a waste of time. It’s the job of the scientific community to call bullshit. It’s how we stay healthy, it’s how we stay confident in our perceptions, it’s how we grow. Andrulis may have been going through some stuff, that doesn’t make him a bad person or even necessarily a bad scientist. But bad papers are bad papers. Andrulis is excused, his paper is not. Any time bad science goes unchecked, it’s like ignoring an infection. If you don’t take care of it quickly, you get sepsis and die.

  41. savaga says

    I am thoroughly ashamed that such crap has come from my Alma Mater.

    To Erik Andrulis,
    Stop making an otherwise good research university look bad.

  42. coralline says

    The very first sentence of the introduction is a strawman, and *wrong*. That doesn’t lend a whole lot of credence to the whole thing.

    “How life abides by the second law of thermodynamics yet evolutionarily complexifies [...] is a fundamental mystery.”

    What I find especially amusing is that evolutionnews.org seems to be clueful enough to catch on, too: http://www.evolutionnews.org/2012/01/oh_now_we_under055641.html

  43. Sili says

    Whatever happened to the dude who suffered some kind of schizophrenic breakdown halfway through composing a poster? He showed up in the comments, but never to Fleuryan degrees.

    Poor fellow.

  44. Irene Delse says

    @ stonyground:

    Oh, that Stanley Unwin? Amusingly, it’s also the name of the original editor of The Lord of the Rings. Still the domain of fantasy, though ;)

  45. Ragutis says

    Talks about the origins of the universe, life, and everything. In a pub. With gourmet hot dogs. What could be fuckin’ better?

    Cleveland rocks

    I lived near Cleveland as a lad, and I can’t say that I remember anything about the rocks that was better than gourmet hot dogs. Then again, I’m not a geologist. ;p

    Dr. Audley Z. Darkheart, liar and scoundrel says:
    27 January 2012 at 1:47 pm

    I spent a little bit of time in Cleveland when we were dating and fell in love with the natural history museum.

    That was my favorite place as a kid up there. I was constantly bugging my mom to go again and again. Somewhere around here I have a pic of me on the Stegosaurus statue outside.

    Oh, and gyre. Gyre gyre quantum gyre. Gyre.

  46. benco says

    It’s like he looked at Feynman diagrams and thought, “Hey! I can draw too!” without understanding that there is a solid wall of math behind each of Feynman’s cute little pictures.

  47. says

    To quote from the forthcoming General Theory:

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc id lectus sodales augue placerat auctor vel et augue. Nulla dignissim sodales sapien. In aliquam risus et lorem euismod sit amet egestas risus sollicitudin. In laoreet, elit venenatis tempor venenatis, tellus magna venenatis lorem, sit amet gravida metus massa in lorem. Praesent tincidunt pellentesque ullamcorper. Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Aliquam varius accumsan diam, eu ornare ante sollicitudin vel. Aliquam non ipsum leo, non pulvinar justo. Nunc placerat porttitor arcu, nec interdum lacus tempor et. Donec sollicitudin mollis facilisis. Vestibulum quis lobortis magna.

  48. Anisopteran says

    @infraredeyes #47
    I nearly choked on my “Fruit’n’Fibre” the other meaning when they had Rupert Sheldrake (who I hoped had long ago disappeared up his own morphic assonance) “proving” that people’s pets were telepathic. On the BBC. But mysteriously, this story appears not to be mentioned anywhere on the BBC’s website.

    Odd, that.

  49. khops says

    This is all very concerning; I’m leaning towards the developing mental illness theory. I just met Erik Andrulis this summer at an RNA processing meeting. He seemed really nice, gave what I thought was a good and interesting talk (about the exosome and RNA degradation, none of this horseshit), and I’ve thought his work in the past has been good science. I just cited a paper or two of his in a grant. Interestingly he doesn’t look anything like that picture on his Case Western site. He pretty much looks like the Dude now from Big Lebowski… I sort of assumed it was more of an aging hippy chill guy thing and not a mental breakdown. I hope he gets help.

  50. Azuma Hazuki says

    Don’t be so quick to dismiss this idea…while it may be only one small pearl in 100+ pages of decaying oyster mantle, this idea of our reality having an inherent handedness or chirality isn’t so far-fetched.

    If the string/M-theory stuff is true, what we may be seeing here is the order and handedness with which our extended dimensions unravelled from what’s left of the Calabi-Yau spaces. Obviously I can’t properly visualize something in six dimensions (what I get looks like one of those loofah sponges, and bright blue to boot), but it’s a possibility. If nothing else, there may have been a handedness or chirality to the big bang “seed.”

  51. Richard Smith says

    Not so much Lewis Carroll as Pierre Culliford…

    The ultimate state of smurfomnemesis is the stably adapted particle or smurfonexus in the smurfobase. A particle thus adapts through learning and memory by completing one full cycle—a revolution— around the singularity. Taken together, smurfognosis defines IEM integration and assessment whereas smurfomnemesis defines IEM storage and recovery. Finally, although a diquantal IEM (X”) undergoes smurfognosis as the smurfobase of a primary majorsmurf, it undergoes smurfomnemesis as the smurfapex of an alternasmurf. Thus, smurf learning and memory are relative to the smurfadaptive singularity.

  52. DaveL says

    You know its going to be bad when the second sentence of the abstract includes a cognate of “paradigm.”

  53. Antiochus Epiphanes says

    Ragutis, nigel, Audley: I lived in the Cleveland are for 6 years, and worked at Case for three of them. Great place. I loved the museum, the symphony, little Italy*, and the Grog Shoppe**. CWRU is a really good school. I’m surprised that any of this flew.

    *Mama Santa’s!
    **The weather is another fucking story entirely.

  54. says

    Noooooo! I thought we were supposed to be WICCAN? Here I’ve spent the last month practicing saying “Principle of Plentitude” without giggling and now I’ve got to start adding gyre to everything to really, really describe reality? “Princigyre of Plentitude”? “Principle of Plentigrye”?

  55. says

    Antiochus Epiphanes:

    the Grog Shoppe

    I saw Bob Mould there. It’s a great venue. I need to get down there more often.

    I’m not sure how any of this flew, either. It seems a bit … how shall I say it … stupid? The comparison to Timecube was not inapt.

    I think during the talk on dark matter next month, I’ll create a hot dog and call it “the gyre.” It’ll be the most ridiculous combination of things ever to top a hot dog.

    Oh, and I’ll have another peanut butter porter.

    Or three.

    And then I’ll gyre.

  56. briandavis says

    I wonder where the dividing line is between ending up homeless explaining your theories to passersby, and ending up on the lecture circuit as the next Chopra.

  57. Gregory Greenwood says

    We Are Ing @ 23;

    I read a journal just last year talking about why more and more biologists are signing on to it!

    Aha! It is in a journal, so it must be true, amiright?

    ;-P

  58. says

    briandavis:

    I wonder where the dividing line is between ending up homeless explaining your theories to passersby, and ending up on the lecture circuit as the next Chopra.

    Simple. The first expounds on their beliefs because they think them true. The second preaches their beliefs because it makes them rich.

  59. fafhrd says

    @We Are Ing, #31: Wow, yeah, that statement does sound like a clear signal of intentional irony. Every one of those adjectives literally means “anti-scientific.” He’s going pretty damn far for the sake of a joke, though. I don’t know that much about the world of science publishing, but it seems to me like writing a paper runs a lot more risks than trolling a pseudoscience forum. Maybe he got bored with the latter?

  60. cybercmdr says

    #62: I’m sure the Intelligent Design people are going to use this one bent nail to refute the structure of peer reviewed science for decades. What they will refuse to understand is that peer review is the first step. Then the scientific community gets to look at it, and they can cry foul if the science is invalid (which has happened in this case). The process works, but this kind of crazy horseshit (horsegyre?) should never have gotten this far.

    I propose that from now on, if someone proposes a batshit pseudo-scientific idea, we can say that he/she is gyreating.

  61. Chris Booth says

    This reminds me of a pet peeve of mine; well, perhaps not a peeve, but a lot of people don’t seem to be aware of this, and it does irk me at times: Lewis Carroll (Charles Dodgson) did not make up the words “gyre” and “gimble” (the spelling is actually gimbal, but they are homonyms; gimble is a deliberate mis-spelling that turns it into a portmanteau of “gimbal” and “gimbled“, which is an old variant of “gimlet”). Lewis Carroll made up lots of other cool words, but not those two.

    Here is a peeve: the “g” “gyre” is pronounced as “j” as in “By Jew Jesus’s gyrating gingivitis, Ginger, Joe’s in the jakes!” Not as “g” in “Gosh, Greg, go grab some grog and grok Griselda’s gams!”

    In other words, the “g” itself gyred and gimbal’d in its sound, shifting from one side to the other so to speak: it gyres from “j” to “g” and gimbals from “g” to “j”. It is not strictly onomatopoeia or assonance, but it is a delightful example of Lewis Carroll’s playful transformations of sounds and words as he moves through forms and meanings….

  62. Chris Booth says

    Wow. Clearly this chap is going to have an uphill battle fighting the reactionary oppression of Big Math.

    (One thing Big Math has more than even Big Pharma: millions.)

    :-)

  63. 'Tis Himself, OM says

    Andrulis should have spent more time resting by the tum-tum tree in uffish thought.

  64. Dr. Audley Z. Darkheart, liar and scoundrel says

    AE,
    Mama Santa’s! Best. Pizza. Ever!

    Jesus, now I wish that I lived closer to Cleveland.

  65. chrislawson says

    Chris @85:

    Millions? You’re thinking too small, son. I say you’re thinking too small. Big Math has googols! And if they’re too small for you, there’s googolplexes. Googolplexes, I say! Not even Big Physics has googolplexes!

  66. Ichthyic says

    The whole thing sounds like Stuart Pivar and John A. Davison got together and created an artificial love child, who then wrote this paper.

  67. skgt says

    This isn’t the first thing he’s published on the topic.

    “Good advice austintorn! This should help significantly!

    Unity: Theory of Everything, Life, and the Universe
    http://www.scribd.com/doc/44194861

    I uploaded the theory to scribd.com as a PDF.

    I must advise the reader that this version of the model is from May of 2009; I have built substantially on it but have not updated the presentation. In other words, I have had to amend parts of the theory to suit facts I had not originally incorporated. Not major overhauls, but important nonetheless. Any questions that you might have about the gaps in the presentation I would encourage you to cite. I have dealt with many questions (raised by My bright Mind) already in a book that elaborates on this—indeed, most of my recent energies have been directed towards putting it into a book format for general audience; but you know this from my posts here and those at my blog.

    As the story goes, I have worked for the last six years on putting together an irreducible theory of everything. I started building models to understand results I got working with RNA and ribonucleases and then applied these models to major unsolved problems in physics, cosmology, linguistics, economics, theology, philosophy, psychology, and biology. The theory is incommensurable with the current worldview. Hence, it is controversial and revolutionary.

    I must warn anyone who downloads the PDF: the theoretical framework is quite dense, and, as such, may be rough going. It is not a manuscript, but a model in presentation format. A fast forward to the end of the document will provide a theoretical summary and implications. If you are willing to look at the whole work, I would be grateful for any comments or advice.

    As I have been unable to falsify the model, nor have I identified anyone who has been able to falsify it, by all estimations it is the correct model of reality. In other words, the Truth. Just like the great mystics have said, “I am the Truth.” Another way of saying this would be “Everything is Me.” Theory validates these claims. I, the Theoretician, am as skeptical any reader of the theory. I know and understand this skepticism as there is Only One I.

    Oh, and you are welcome to share it with anyone.

    Peace,

    Ik (Erik)

    And, thusly, I am no longer anonymous. ”

    From http://www.toequest.com/forum/your-toe-theory/5417-unity-18.html#post133889 – note that the scribd file has been deleted.

    While it would seem that this could be any Erik, the post used to contain his full name, and has since been edited out. Another poster quoting that post has copied

    “One. There is only One I, God, and it is the I we each use to refer to our self. There is Unity found in the One I. I is/am the Creator and the Creation.I is/am the source of all love. I is/am the source of all goodness. Knowing who I is/am is peace.Erik D. Andrulis 55″

    It’s the same guy, and he’s been working on this for a long time, having his views reinforced by a bunch of internet idiots obsessed with the Theory of Everything.

  68. chrislawson says

    coralline @62:

    I love how that Evolution News post sticks a bomb under peer review…and then uses a scene from Expelled to argue the case!

    What the DI is trying to say is: “peer review is a sham that stops our work from being published in respected journals”. What they are really saying, without meaning it, is: “it’s unfair that this crap gets published when our crap doesn’t.”

  69. truthspeaker says

    Chris Booth, your the last sentence of your post was wonderful. It’s even more fun when said aloud.

    It wasn’t until saying it aloud that I realized English “j” and “g” are pretty close together in the mouth. “J” is a labiodental affricate so the tongue is at the top of the mouth, close to the front. With “g” the tongue is at the top of the mouth, towards the middle or back.

    And you’re right, playing with that is something Lewis Carrol was good at.

  70. skgt says

    Since I cant edit, I’ll add here – so, it’s definitely not a joke, nor a short term mental deviation. This is somethign the guy would consider his lifes work, with the rest of his research serving to add a veneer of respectability. He appears to have also had a long running blog at http://thetheoryblog.wordpress.com/ – which again has been deleted since the publication of the paper.

    Other postings include

    “And now I have theoretical proof, derived from all of the available scientific, philosophical, psychological, theosophic, economic, political, etc. data. ”
    “Hi, I have been blogging for about three months now about the theory I have compiled. Here’s the cover letter I sent to publishing houses about the book I intend on publishing. The cover letter gives an overview of the theory, called Unity.

    Dear Editor,

    Throughout history, many have come forward to claim to have solved the riddles of the Universe – only to be proven wrong. I am humbly submitting my book proposal in hopes that you will permit me to substantiate and defend my incommensurable, unfalsifiable, complete and consistent theory of everything. T__ is a book that proves the Unity of the Universe, explains the origins of spacetime, chemical elements, Life, Man, and civilization, unifies the four fundamental physical forces, elucidates the true relationship among consciousness, mind, and matter, and resolves all extant anomalies, enigmas, and paradoxes. As the theoretical framework subsumes yet overturns entrenched worldviews and dogmas, T__ is controversial.

    T__ emerged from my own research on ribonucleic acid metabolism. As the story goes, I obtained inexplicable results, so I built models. Upon creating a heuristic, reified model with robust explanatory power, I applied the model to solve the major problems in cosmology, physics, chemistry, genetics, ontogeny, medicine, ecology, anthropology, linguistics, economics, law, psychology, religion, and epistemology, among other fields. What qualifications do I have that may engender confidence in the validity of this bold assertion? I have a tenure-track appointment at a prestigious American medical school, have 20 years experience in basic biomedical research, and have published 16 peer-reviewed manuscripts, including two first-author publications in the high-impact international journal Nature. Moreover, as part of research for T__, I read and became well versed in the theories, ideas, and observations of the most respected scientists, philosophers, theologians, mystics, and thinkers in the history of Humankind.

    T__ is a unique book in its scope and genre. Although this nonfictional publishing niche harbors works like A THEORY OF EVERYTHING by Ken Wilber (Shambhala, 2001), THE ROAD TO REALITY by Roger Penrose (Vintage, 2007), and NEW THEORIES OF EVERYTHING by John Barrow (Oxford University Press, 2008 ), none of these or kindred oeuvres delivers a theoretical synthesis of rationalism and mysticism, subject and object, noumenon and phenomenon, masculine and feminine, biotic and abiotic, and microcosm and macrocosm. In contrast, T__ presents this information and answers to quintessential ontological questions.

    I thought it might be a good idea to get commentary from members of this forum, as it appears there is an interest in such matters here.

    Just yesterday, I posted on how the theory, Unity, explains the origin and nature of CHNOPS and biogeochemical cycles in My Body and My Planet. Here is the link:

    http://thetheoryblog.wordpress.com/2…aning-to-life/

    I have spent the first three months on the blog introducing the core model, the axioms and principles that undergird it, and the Laws of Nature that emerge from the theoretical synthesis.

    I have already explained the origin, emergence, and evolution of water, carbon compounds, phospholipids, RNA, protein, and DNA. In the next few months, I will be discussing the elements of the model that deal with cosmology, astrophysics, particle physics, and metaphysics.

    Comments and criticisms are welcome either here – in this forum – or there, in the context of the blog.

    See y’all around.

    Peace,

    Ik”

    Something is seriously wrong here, and it has only been revealed now thanks to Life’s lack of publishing standards.

  71. truthspeaker says

    You can’t really say peer review is broken in this case. As PZ pointed out, Life is a brand new journal. It may have been created by someone unscrupulous to make a quick buck or it may have been created by another crank to publish crank stuff, I mean theories that run so counter to the dominant paradigm that the establishment won’t publish them.

    As for Dr. Andrulis, I suspect personal tragedy. Or maybe he’s pissed at not getting tenure and is Sokaling the institution that he thinks screwed him over. This only works if he’s quitting the field altogether.

  72. jjgdenisrobert says

    Reminds me of this French astrologer, Dom Neroman, who created this whole world schema based on platonic solids (but you see, Kepler used them to, so it *must* be scientific, no?) in a book called “La Lecon de Platon” (the absence of a cedilla on my keyboard is really bothering me right now). It’s just as nuts as what this guy did, but it at least has the advantage of being related, distantly, to the work of a real scientist (although not related in any meaningful way to his actual scientific work).

  73. Ichthyic says

    Since I cant edit, I’ll add here – so, it’s definitely not a joke, nor a short term mental deviation.

    doesn’t require it to be a short term mental deviation for schizophrenia to be involved; it sure sounds very similar to other writings from people I know to have suffered from mild schizophrenia.

    When you literally spend YEARS building an entirely new vocabulary, in order to describe things that are really just imagined views of already known things, there is a problem there.

    When it gets to the point where it DISPLACES your normal behavior and your career path? It’s gone beyond “problem” into the realm of thinking there is an underlying psychopathy involved.

    It’s sad to think that he had a crew of basically strangers on the internet enabling him as he moved further and further from reality, but it also wouldn’t surprise me in the least.

    I, like PZ mentioned, hope he at least gets himself checked out, and if there IS a problem, he still has time to restart his career.

    let this go on too long, and he ends up in the ranks of cranks like John Davison and his “prescribed evolutionary hypothesis”, as they rant from their computers in a lonely house.

    Hate to see it.

  74. Tualha says

    Ah, Mary Midgley. Poor Mary Midgley. She criticized The Selfish Gene and praises Sheldrake’s gibberish. In two hundred years, some grad student will write their thesis on the poor misguided Mary Midgley, and everyone will say, “Who?”

    Daz wins the thread.

    Googolplexes? Pah. I sneer at your googolplexes. You want a big number? Here’s a big number.

  75. Matt Penfold says

    Ah, Mary Midgley. Poor Mary Midgley. She criticized The Selfish Gene and praises Sheldrake’s gibberish. In two hundred years, some grad student will write their thesis on the poor misguided Mary Midgley, and everyone will say, “Who?”

    I think someone might have been playing a cruel practical joke on Midgely her entire academic life by substituting every book she plans to read with one with an identical title and cover, but with a text that the total opposite of that of the real book. What else could explain her persistent inability to understand these books ? Simple answer: She has not been reading the same books!

  76. XXIst Century (updated) Vole says

    chrislawson#88:

    Aaahh — Senator Claghorn and Foghorn Leghorn.

    Thanks for the memories!

  77. says

    Science Daily is kinda handy, when you don’t want to read through all 500 PLOS articles that get published each day to find the one that might interest you. I always go and look up the original release for anything I see on SD.
    As to Andrulis, he uses word salad, neologisms and associative loosening. All 3 clinical features of schizophrenia. A creative brain going off the rails, I’d say from a distance.
    Unbelievable this could get published.

  78. crissakentavr says

    Thinking of physical reality based upon orbits and attractions to repeating patterns isn’t entirely bunk, but breaks down in several places, especially empirically if not observationally.

    There is probably some benefit to dreaming in lingua like this, if not directly applicational to the real world. Reading it is like a trip out of reality.

    It would be nice if there were some patterns we’d find like this, but as far as I know, there aren’t; it just appears to be to the human brain when it is trying to pattern match without enough base information.

  79. Russell says

    If gyrognosis makes the mostest of the gonads of the monads, how come Liebniz didn’t discover DNA instead of calculus ?

    Stay tuned for DI Fellow Tom Bethell’s magisterial summary of this flummery for the dummery.

  80. WhiteHatLurker says

    To paraphrase a previous poster, my first reaction was “the journal Life? What is that?”

    To correct PZ, this is in the second volume of this, um, journal. The first volume was 48 pages, including a paper on making DNA movies (via bacteria) to communicate with life in the future or far away.

    One thing is that this paper has done a great deal to increase the journal’s notoriety. This paper alone has received a great deal of attention. (Much more than it is worth. I’ve been tempted too write a paper so bad that it would be cited by thousands of other papers fighting to destroy it. The impact would be impressive. I can’t decide what to do it on though.)

    While the author’s blog is gone, it is still in Google cache.

    ArsTechnica has a nice article on this story. Well okay, not nice, but … From their perspective all would have gone swimmingly, if it wasn’t for those kids research communication people at Case Western. If it weren’t for that press release, nobody would know about this. Maybe that was a cry for help.

  81. totalretard says

    Who would have suspected that live must evolve from quantum gravity, and the realization that diquantal effects are required is not short of pure genius. But don’t you think that some credit is due to Deepak Chopra and Maharishi Mahesh for inspiring such breathtaking wonders? Really, the only thing that Andrulis has added is his brilliant gyromodel, but again, that was probably cribbed from Elvis Presley.

    PZ, I think you’re just jealous that Andrulis beat you to the idea. You probably ignored it because this is what homeopathists have be trying to explain for centuries. Now I see how it all fits together.

    This will certainly be the quickest Nobel prize ever awarded.

  82. DLC says

    Wow.. . That’s some serious Jabberwocky. I wonder if his CHNOPS is sharper than my Vorpal Sword ?

    Snicker-snack!

  83. isochron says

    Can’t imagine how this thing got published.

    It’s an open access journal. The author pays the journal to publish the paper. The journal reviews the paper but it’s business model is diametrically opposed to the rejection of offered papers.

    I, for one, shall never publish in any journal that I have to pay to accept my papers.

  84. Midnight Rambler says

    I, for one, shall never publish in any journal that I have to pay to accept my papers.

    You’ll have a somewhat limited selection then. Even many good subscription-based journals have page charges, and there is general movement towards open-access publishing. Bear in mind that many of the major journals from Wiley and Elsevier charge several thousand dollars per year for library subscriptions.

    That said, there are a lot of online-only “journals” like this one that have sprung up in the last few years, that are essentially worthless. I get spam from them soliciting papers all the time, invariably totally unrelated to my own field. Hindawi Publishing and International Scholars Journals are the worst offenders. Anything called “International Journal of …” is almost guaranteed to be one of these. They publish anything, claiming to do peer review but usually doing about as much as Cosmology, and making money off of open-access fees. The sad thing is that they do publish some real research, but it not treated seriously because it’s in one of these flimsy journals.

  85. mudpuddles says

    infraredeyes #47, Anisopteran #69 & Tualha #99

    I picked up Sheldrake’s “The Science Delusion” in a book shop and opened it. Holy crap…. I actually felt significantly more stupid after just half a page.

    I then made the monumental error of looking him up and visiting his website (in a fit of morbid curiosity). Now the interwebs has done its magic and on every website I go to that has banner ads I’m plagued with Sheldrake adverts, including here on FTB. I have Sheldrake’s creepy head floating beside a line saying “What if Sheldrake was available to answer your questions now?”

    Mum got a shcok this morning when she heard me shout “I’d throw him through the fucking window!”

  86. mmLilje says

    So, according to him, the universe was created by Ulamog, the Infinite Gyre?

    These new-age religious beliefs keep getting sillier and sillier.

  87. richarddawkins says

    Although Jabberwocky is the obvious literary allusion, the following line of W B Yeats has always puzzled me:

    “Come from the holy fire, perne in a gyre”

    Yeats, great poet though he was, was also a mystic, who believed in fairies.

  88. isochron says

    I, for one, shall never publish in any journal that I have to pay to accept my papers.

    You’ll have a somewhat limited selection then. Even many good subscription-based journals have page charges, and there is general movement towards open-access publishing…

    Not in my field, fortunately. I did pay for extra pages (over the page limit) once or twice but out of 70 papers none was ‘pay to publish’. I have no objection to electronic journals (and have published in them on occasion) or to open access as a concept but ‘pay to publish’ is just very dangerous to peer reviewed science.

    I agree about the Hindawi and ISJ journals. They are crap. They keep sending e-mails asking me to join the editorial boards for some of their newer e-pamphlets. They just won’t take *Never!* for an answer.

  89. calis says

    This sheds some additional light on it:

    http://tinfoilpalace.eamped.com/2011/12/23/theory-of-the-origin-evolution-and-nature-of-life/

    I have spent the last 7 years or so working on a complete and consistent theory of the universe. I initially started out with a book, but that was a tough sell. So, I compiled a book proposal. That proposal was rejected by ~30 different publishing houses. I then tried literary agents. ~200 rejections ensued. I pared my theory down to a scientific manuscript that addresses topics ranging from quantum gravity to the origin and nature of cellular life. That manuscript was sent to and through 12 different peer-reviewed journals and article servers (arXiv) — where I had 4 decision appeals, 15 total rejections, and 1 retraction.

  90. Ichthyic says

    Now the interwebs has done its magic and on every website I go to that has banner ads I’m plagued with Sheldrake adverts, including here on FTB. I have Sheldrake’s creepy head floating beside a line saying “What if Sheldrake was available to answer your questions now?”

    *sigh*

    it’s cookie based.

    -clear your cookies
    -clear your browser cache

    other choices:

    -disable scripting for any site you don’t like the adbanners on.
    -install something like AdBlock Plus, and never be bothered by ads ever again, period.

  91. Russell says

    Which will come first?

    The Washington Times Op-Ed, the DI conference or the Conservapedia entry?

  92. an3rea says

    A few more informations from around the web… Erik D. Andrulis seems to have a twitter account
    https://twitter.com/#!/TheTheoretician

    He published his theoretical “insights” on a blog:
    http://thetheoryblog.wordpress.com/

    but he seems to have stripped all the content, some of which can still accessed through archive.org:
    http://wayback.archive.org/web/*/http://thetheoryblog.wordpress.com/

    There we can find a short history of his theory of everything:

    A bit of history here to give you insight into how I got into theory.

    I am a molecular biologist/cell biologist/geneticist/biochemist. I have trained in the model systems Saccharomyces cerevisiae and Drosophila melanogaster for ~20 years, and those are the two systems I use to study basic biological problems.

    When I arrived at my faculty position, I began work to understand a set of enzymes called ribonucleases (RNases), proteins that degrade or process RNA exonucleolytically (from one end of the RNA) or endonucleolytically (within the body of the RNA). One major intellectual gap in the field when I entered it was how these RNases functioned in vivo, that is, where they localized in the cell, how their activity was regulated as a consequence of cell cycle progression, their post-translational modifications and how they assembled into function protein complexes.

    I’m aware that’s a mouthful, but more to come.

    Anyhoo, it turned out that one of these proteins had a whole bunch of domains that were interesting from a bioinformatic standpoint. So, I started making point-directed mutants and truncations of the protein and putting them into cells to see where these localized, how they interacted with cellular proteins, etc. That’s when the surprises started happening.

    You see, I could make the cell do the craziest things, as many of the mutant proteins had dominant-negative effects. Some caused cells to arrest in cytokinesis, others caused premature chromosome condensation (an uncoupling of cell cycle found in cancers). Others fiddled with microtubules, cell size, nucleocytoplasmic transport, mitochondrial DNA maintenance, and de novo membrane synthesis.

    Basically, the gist is that my enzyme could control the cell. How is that possible, I asked myself? No one is going to believe that one protein can do all of this!

    And that’s when I realized that it wasn’t the protein, I surmised it was the substrate: RNA. By perturbing the RNA—>NMP (Where NMP = AMP, GMP, CMP, UMP) reaction, you could wreak havoc on all aspects of the cell. Indeed, when I looked at the literature, I found one peculiar, unsolved finding that defied explanation: ATP was involved in all major signalling pathways, GTP in translation and transport, CTP in lipid metabolism, and UTP in carbohydrate metabolism. In other words, those 4 nucleotides represent the 4 major control pathways of the cell. So, RNA was the key that unlocked the veritable theoretical door for me.

    So, after examining the central dogma and found all of the flaws (more about this for those interested), I began making models. So, instead of DNA goes to RNA goes to protein, I was able to uncover the appropriate order and positioning of these important components within all living cells. That is, ribogyre aminogyre deoxygyre.

    I think this really is some kind of psychosis in progress.

  93. an3rea says

    Here is more of his own account:

    http://web.archive.org/web/20100726165015/http://thetheoryblog.wordpress.com/

    I got a little ahead of my story line, so I need to go back a little bit.

    So, at the point when I started getting all of these weird results (see last post), I tried to put them into context. How could this RNase affect nucleocytoplasmic transport, membrane formation, mitochondria, cell cycle, microtubules and RNA? I realized one thing right away—this was a formula for regulating the eukaryotic cell.

    Now, I knew that one of the major unsolved problems in science is the emergence or origin of the eukaryotic cell. That is, the current cell types have such a large morphological gap between them (for example, prokaryotes have no nucleus, have a nucleoid, have a circular genome, and have no intracellular organelles) but eukaryotes have all that stuff.

    The argument has always been that the reason that the gap exists between the prokaryotic and eukaryotic world is that the intermediary cell types have been culled. But, and I repeat but, this is a big assumption. As a theoretician, I cannot accept any assumption—Especially in light of the way the fact that major saltations occur at many levels in the observable world, and even this saltationary model has made its way into mainstream evolutionary thinking with punctuated equilibrium. One saltation that you may not consider related to this point, but I now know is, is the way that energy moves as quantized packets. Please refer to Planck’s original studies and you can verify for yourself that photons moves saltationally.

    Anyhow, so, I began to read the primary literature. I found conflicting models, inconsistencies, and dogmas. Then, I turned to books. Authors like Christian deDuve, Lynn Margulis, Nick Lane, Alexander Oparin, Franklin Harold, Ernst Mayr, Marlene Zuk, George Williams, John Maynard Smith, Wallace Arthur, Paul Davies, Fred Adams, Brian Goodwin, Robert Hazen, Francois Jacob, Iris Fry, John Gribbin, Jan Sapp. And many more. I found the same thing: no one knew how the eukaryotic cell emerged. It was all speculation.

    The most widely accepted model for the emergence of the eukaryotic cell is serial endosymbiotic theory (SET), articulated by Lynn Margulis. However, there are many problems with this theory, and I’ll mention a couple here: (1) SET presumes that one cell ‘engulfed’ another, creating a symbiotic relationship. However, in order for this to happen, the cell that does the engulfing must have the appropriate molecules to achieve this feat called phaocytosis. But no extant cell type, archaea or eubacteria, have these molecules. So, intellectual bending-over-backwards must be performed to say that the cell that ‘evolved’ this phagocytosis no longer exists on its own in nature. Convenient, as one can never empirically challenge the theory. (2) SET does not address any of the other emergent features of the formation of the eukaryotic cell, including, but not limited to: (a) the saltation from circular, non-chomatinized DNA to telomere-capped, chromatin-packaged chromosomal DNA; (b) the saltation from no organelles to the presence of a vast intermembrane system including the Golgi appartus, endoplasmic reticulum, lysosome, peroxisome. (c) the saltation from a non-compartmentalized nucleoid to a wholly compartmentalized nucleus, with exquisite and rococo protein complexes called nuclear pore complexes that allow for passage in and out of the nucleus; (d) the saltation from the absence of introns to the emergence of introns within gene-coding regions; (e) the saltation from a small number of eubacterial genes, or open reading frames, to a large number of genes with roles specialized to the purpose of the eukaryotic cell. There are many more reasons why SET is incapable of explaining the emergence of the eukaryotic cell, but I hope this provides a good picture.

    Anyways, so I got to thinking more about RNA. It was well known that ATP –> ADP + P is the major energy process in the cell, where ATP is adenosine triphosphate and ADP is adenosine diphosphate. The free P, called orthophosphate, liberates or transfers a lot of stored energy in something called a high-energy phosphate bond. This occurs with the other nucleotides as well (GTP –> GDP, UTP–>UDP, and CTP–>CDP). It is also known that (ATP + CTP + UTP + GTP)n —> (RNA + 2P)n, where RNA is the nucleotide polymer (AMP-CTP-UMP-GMP)n and n is any number and 2P is called pyrophosphate. For theoretical clarity, we would call RNA as (NMP)n. Likewise, we would group the nucleotides as NTPs and NDPs, where s represent the pool of nucleotide tri- or diphosphates. So, the reactions would be:

    NTPs –> NDPs + P
    NTPs –> (NMP)n + 2P

    For those chemists out there, you know that these reactions go both ways, and removing the ‘s’ for simplicity’s sake:

    NTP NDP + P
    NTP (NMP)n + 2P

    Because the NTP is shared between both reactions, it can be theoretically compressed further:

    NTP NDP + P + (NMP)n + 2P

    Note that reactions that go in two directions can be viewed also as a circle, or a cycle. Alas, I cannot do this justice here, by try to envision NTP at the top of the circle as the high energy state, the triphosphate. As it releases a P, it falls to the low energy state, NDP. The P would be the singularity in the center of the cycle. Now, envision that cycle in 4-dimensions (spacetime) rather than 2D space and you have a gyre – this is called a ribogyre. As it releases 2P, it falls to the low energy state that is more stable than NDP, that is, (NMP)n, or RNA. This also can be viewed as a similar cycle, with 2P as the singularity in the center of circle.

    Since it was theoretically compressed above, please now try to overlay, in your mind’s eye, these two cycles, or gyres, and what you get is a double helix.

    More later.

  94. Ichthyic says

    The term “word salad” comes to mind.

    that’s just it, though. All the energy-oriented reactions he’s talking about involving phosphate cycles are accurate enough, from my recollection.

    It’s just that he then starts overlaying a perfectly reasonable explanation of these reactions as “cycles” (which we actually DO use when we teach these things – http://www.doctortee.com/dsu/tiftickjian/cse-img/biology/enzymes/atp-cycle.jpg for example), with this completely inane and irrelevant gyre-jargon he’s invented.

    There is a clear conflation in this person’s mind between pattern and process, where to him, the pattern itself explains the process.

    It’s like if I gave you a complex matrix equation, and tried to explain how it worked by saying:

    “See? SQUARE!”

    Indeed, there is a square pattern to a matrix… but it hardly explains what’s going on in it.

    I expect with people like this, there is some breakdown in how the mind processes pattern recognition and logic.

    makes me wonder if there is not just a chemical imbalance, but a physical one; maybe something interfering with distinct lateral processing?

    something like the exact opposite of what is sometimes seen when there is damage to the corpus callosum?

    instead of “split brain”, this guy is exhibiting “merge brain”.

  95. Chris Booth says

    richarddawkins @ # 121:

    Although Jabberwocky is the obvious literary allusion, the following line of W B Yeats has always puzzled me:

    “Come from the holy fire, perne in a gyre”

    Yeats, great poet though he was, was also a mystic, who believed in fairies.

    That line from “Sailing to Byzantium” is quite rich.

    To “perne” is to rise in the air like smoke. “Gyre” is a word that has been around since its Greek root “gyro-“, and exists in the word-hoard of English. Neither Lewis Carroll nor Yeats invented it.

    Yeats, a follower of Madam Blavatsky believed in cycles of history. The holy fire (remember the text of Handel’s Messiah–“God’s love is like a refining fire”?) refines the soul, allows the dross to be poured away, leaving the pure “gold”. The dross is imperfect flesh (the dying animal). Subject to age, imperfection, degradation, diminution, decline, humiliation, he longs for the perfect, untarnishable purity of a form of gold (“such a form as Grecian goldsmiths make”), a form that is, unlike a poet’s, both artist and artwork (youth and beauty; think Keats here, too). Anyway, the smoke of a purifying fire–or the earthly smoke of goldsmiths’ smithies–will rise from those smithies, gyring–spiraling–outward; the thousand-year cycle that he saw as the pattern of rise and fall of civilizations would be where the spiral returns to the same place on the circle, but in another time: Greece/Rome…Byzantium…20th-Century Europe. He saw the purified artist-creator as being the highest aspiration of humanity, and the sages, having their impure physical limitations burnt off as smoke become the artist and the art. They are the gold mosaic and the goldsmith.
    Yeats’ next line is “And be the singing-masters of my soul”. He asks the ideal artists, the Byzantine artists, to teach him to be their equal as a craftsman and pure artist–this is why he asks them to be his singing-masters. Not to teach him singing per se, as they were visual artists. But he admired Byzantine art as art of the highest order, and wished to attain that level of artistry in his Irish-voiced English verse.

    [As to Yeats' mysticism: Ezra Pound used to fondly refer to Yeats' talk of these things as "Uncle Willie's spooks".]

    The line you quoted is in the imperative. That is fascinating (or is to me, at least). :-) Picture a mosaic of saints, in lovely bright tiles and gold, singing hymns while martyred in fire. Or standing in purgatorial flames singing Hosannas as the refining fire of God’s love painfully purifies them. Yeats sees this as a metaphor for himself. “Singing” as a metaphor for poetry, the purgatorial flames as a metaphor for that which purifies his soul and artistry, the suffering that is the soul of art. (For almost 200 years now, people have trivialized the music of Felix Mendelssohn, whose birthday is Friday, for being too facile, because, talented little rich boy, he never suffered–ha.) The line is in the imperative because Yeats is imploring them to reach out over the millennium that separates them to teach and/or inspire him to be such an artist.

    Well, one could go on. “Sailing to Byzantium” is one of the great poems of English, and it is so rich.

    But Yeats has two “Byzantium” poems “Sailing to Byzantium” and “Byzantium”, which is an interesting contrast to it. And he uses the word “gyre” in “The Second Coming”–the first stanza, which is also the epigraph to Achebe’s Nobel-Prize-winning novel Things Fall Apart….As an African, you must be familiar with Achebe’s novel. ;-)

  96. TheDancingGeek says

    Spirals (gyres) as the basis of everything in the universe? Why, this man isn’t crazy. He’s just a big fan of Gurren Lagann!

  97. lpetrich says

    Reminds me of George Francis Gillette’s “spiral universe”:

    Each ultimote is simultaneously an integral part of zillions of otherplane units and only thus is its infinite allplane velocity and energy subdivided into zillions of finite planar quotas of velocity and energy.

    In all the cosmos there is naught but straight-flying bumping, caroming, and again straight flying. Phenomena are but lumps, jumps, and bumps. A mass unit’s career is but lumping, jumping, bumping, rejumping, rebumping, and finally unlumping.

    He explains his “backscrewing theory of gravity”:

    Gravitation is the kicked back nut of the screwing bolt of radiation.

    Gravitation and backscrewing are synonymous. All mass units are solar systems…of interscrewed subunits.

    Gravitation is naught but that reaction in the form of subplanar solar systems screwing through higher plane masses.

    From Martin Gardner’s Fads and Fallacies in the Name of Science.

  98. lpetrich says

    Diagrams? GFG has some also, like of a “laminated, solid, solid, solid, solid” and “the all cosmos doughnut”.

  99. dovhenis says

    Universe-Energy-Mass-Life Compilation
    http://universe-life.com/2012/02/03/universe-energy-mass-life-compilation/

    A. The Universe

    From the Big-Bang it is a rationally commonsensical conjecture that the gravitons, the smallest base primal particles of the universe, must be both mass and energy, i.e. inert mass yet in motion even at the briefest fraction of a second of the pre Big Bang singularity. This is rationally commonsensical since otherwise the Big would not have Banged, the superposition of mass and energy would not have been resolved.
    The universe originates, derives and evolves from this energy-mass dualism which is possible and probable due to the small size of the gravitons.
    Since gravitation Is the propensity of energy reconversion to mass and energy is mass in motion, gravity is the force exerted between mass formats.
    All the matter of the universe is a progeny of the gravitons evolutions, of the natural selection of mass, of some of the mass formats attaining temporary augmented energy constraint in their successive generations, with energy drained from other mass formats, to temporarily postpone, survive, the reversion of their own constitutional mass to the pool of cosmic energy fueling the galactic clusters expansion set in motion by the Big Bang.

    B. Earth Life

    Earth Life is just another mass format. A self-replicating mass format. Self-replication is its mode of evolution, natural selection. Its smallest base primal units are the RNAs genes.
    The genesis of RNAs genes, life’s primal organisms, is rationally commonsensical thus highly probable, the “naturally-selected” RNA nucleotides. Life began/evolved on Earth with the natural selection of inanimate RNA, then of some RNA nucleotides, then arriving at the ultimate mode of natural selection, self-replication.

    C. Know Thyself. Life Is Simpler Than We Are Told

    The origin-reason and the purpose-fate of life are mechanistic, ethically and practically valueless. Life is the cheapest commodity on Earth.
    As Life is just another mass format, due to the oneness of the universe it is commonsensical that natural selection is ubiquitous for ALL mass formats and that life, self-replication, is its extension. And it is commonsensical, too, that evolutions, broken symmetry scenarios, are ubiquitous in all processes in all disciplines and that these evolutions are the “quantum mechanics” of the processes.

    Human life is just one of many nature’s routes for the natural survival of RNAs, the base primal Earth organisms.

    Life’s evolution, self-replication:

    Genes (organisms) to genomes (organisms) to monocellular to multicellular organisms:

    Individual monocells to cooperative monocells communities,“cultures”.
    Monocells cultures to neural systems, then to nerved multicellular organisms.

    Human life is just one of many nature’s routes for the natural survival of RNAs, the base Earth organism.
    It is up to humans themselves to elect the purpose and format of their life as individuals and as group-members.

    Dov Henis (comments from 22nd century)
    An Embarrassingly Obvious Theory Of Everything
    http://universe-life.com/2011/12/10/eotoe-embarrassingly-obvious-theory-of-everything/

  100. says

    The title is biased — as is the article.

    “You know what? That doesn’t explain anything!” This quotation shows that the author either lacks the skills or the mental discipline to even try to understand the preceding excerpt.

    “It’s terrible: unreadable, incoherent, bizarre, and completely lacking in evidence or mathematical support.” Ditto. No mathematical support is needed or even wanted. The author clearly is not willing to do the hard work of figuring the paper out.

    “It’s madness stamped with the Case Western Reserve University School of Medicine seal of approval.” Wrong. It is a radically new interpretation of a variety of systems. The paper is coherent and interlinking — unlike all other theories. For example, we have no overarching theory of chemistry!

    Case Western has removed the press release from their listings — because it is cowardly.

    Its press office was bullied by two physicists who were “embarrassed” (threatened really) that a non-physicist would dare to trespass in their sacred territory. Science is about defending one’s turf — and getting grants that support pet theories.

    The paper is genuine. That’s right. It is an entirely serious work — meant for serious consideration. It requires HARD mental labor to begin to understand it, so most people will take the easy route and dismiss it.

    “Well PZ, this is either an elaborate joke or the onset of schizophrenia.” The paper is no joke. I have known Erik for years, and he is in full control of his mental facilities.

    To those of you put off by the new words, do you ignore studies that include words such as prednisone and pyridine too? Those words are neologisms — as are most for pharmaceuticals and chemistry.
    All of science is loaded with jargon.

    Because the paper is heterodox and VERY dense, few people will have an inkling as to what it means. Much more fun to mock something complex and new than to struggle to understand it.

    I have advanced degrees in science and have read the paper. I have had extensive exchanges with Erik over several years regarding its contents.
    In addition, I have access to additional supporting material which is MUCH more expansive.I have quizzed Erik repeatedly over its contents. He has corrected errors and overstatements and given consistent answers.
    Science is about protecting the status quo — and defends it jealously.

    Also, for your consideration: http://milesmathis.com/erik.pdf

  101. KG says

    I have advanced degrees in science – nettleingenting

    Oh well, you must be right, then, even though you haven’t actually told us what the paper is about. End of argument.

  102. Nerd of Redhead, Dances OM Trolls says

    Science is about defending one’s turf

    That alone tells me you aren’t a scientist.

  103. says

    nigelTheBold, Abbot of the Hoppist Monks

    The paper is theory, not hypothesis, as it has an enormous amount of supporting facts both in it and in unpublished material. Check some of the references if you are skeptical.

    The paper predicts that RNA is the genetic template on which DNA forms. Therefore, the paper predicts that there would be a pool of RNA that has no genomic complement (unannoted RNA). If you find RNAs that have no DNA template, how does the RNA come to be made?

    The unannoted RNA is made through polymerization of nucleotides driven by the chemical energy stored in the high energy phosphate bond (and that energy is deposited there by all the metabolic pathways of the cell).

    One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement. There should some level of sequence contraints, structural constraints, specification, and functionality to this unannoted RNA.

    So, how does a new gene come to exist?

    Another positive prediction is that one should expect to find changes in annoted RNA (made from DNA) that ultimately drives changes in DNA. RNA based mutagenesis of DNA!

    That is to say, RNA is the driver of evolution, and evolution is not “random.” Random is a philosophical term adopted by science because “by a method that we don’t know,” while being more honest, reveals the ignorance in much of science.

    On a fuller note, the paper is about both how reality is, and WHY it is. Since science explains how but not why, the paper is science because it explains how, but it goes beyond science by explaining why. An enormous accomplishment equivalent to going from medieval thinking, to the Renaissance and, more aptly, to the Enlightenment.

    By the way, the Enlightenment met a LOT of resistance (think of poor Galileo), but the Western world now takes it for granted.

    Keep in mind, Galileo had only the church to enrage. Now, we have the scientists.

  104. KG says

    Keep in mind, Galileo had only the church to enrage. Now, we have the scientists. – neetleingenting

    Well quite, no new idea has been accepted in science in the last century, has it?

    Keep going, please. I’ve still got a few spaces left empty on my crank bingo card at this point.

  105. PFC Ogvorbis (Yes, they are) says

    The paper is theory, not hypothesis

    Er, I do not think those words mean what you think they mean. Theory has a very definite definition for those with degrees in science. And for actual scientists. C’mon, you can do better than that. I mean, I’m just a lowly historian and even I can spot the shit in that statement.

  106. Matt Penfold says

    The paper is theory, not hypothesis, as it has an enormous amount of supporting facts both in it and in unpublished material. Check some of the references if you are skeptical.

    The unpublished material must be discounted, since it is unpublished. Really, why say something so silly ?

  107. Ariaflame, BSc, BF, PhD says

    The paper is theory, not hypothesis, as it has an enormous amount of supporting facts both in it and in unpublished material.

    Evidence. Data. Predictions. Is this hypothesis falsifiable? If not, then fail. And for the unpublished material? That’s like claiming the lurkers support you in email.

    Claiming that science supports the status quo really does suggest that you are not a scientist. Sure, science can be slow to accept new theories. Because one of the things that scientists do is to examine hypotheses and proposed theories and see how they stack up against evidence. And for actual experimental things if the effect is reproducible. It may be a slow process sometimes, but it filters out a lot of woo.

    Part of the problem is that human beings, and scientists are no exception, are really good at seeing patterns. So good in fact that they see patterns that aren’t actually there. To the point where they can convince themselves that those perceived patterns represent something meaningful. Like the face on mars, or people who see jebus on a piece of toast.

    It is important then for a scientist to try to examine their work for any biases or preconceptions they may have brought with them. And to think of every way in which their hypothesis might be wrong and ways to test for that. And then to do those tests. Because the easiest person to fool is yourself.

  108. says

    Why say something so silly? Take your pick:
    a) They don’t want to but it’s the best they’ve got.
    b) They don’t realize it’s silly because they themselves are very, very silly.

  109. Mr. Fire says

    For example, we have no overarching theory of chemistry!

    BWAHAHA

    And what, pray tell, does that even mean?

  110. KG says

    Ah a degree in Science! Of course…did you do your grad research on the Ultimate Nullifier Device or the Doomian Chronoengine? – We Are Ing

    I was betting on the extraction of zero-point energy from unobtanium.

  111. Nerd of Redhead, Dances OM Trolls says

    The paper is theory,

    Nope, not close. Defineitely not a scientific theory. Has a long way to go to meet that criteria.

    The paper predicts that RNA is the genetic template on which DNA forms.

    Citation to the peer reviewed scientific literature needed, as the science says otherwise.

    The unannoted RNA is made through polymerization of nucleotides driven by the chemical energy stored in the high energy phosphate bond.

    And where and how does this happen? To form polymers one need to keep feeding growing chains. Nature does this with enzymes. How is this different from what happens now? Actually, as a chemist, this just sound like gobbledy-gook.

    So, how does a new gene come to exist?

    Mutation, duplication, and natural selection. Next stoopid question.

    RNA based mutagenesis of DNA!

    Sorry, it is know that mutagenesis of DNA occurs due to errors in replication. You have about 100-150 mutations from your parents due to those errors.

    That is to say, RNA is the driver of evolution, and evolution is not “random.”

    Why isn’t it random? Where does this “order” come from? That bullshit sounds really random.

    By the way, the Enlightenment met a LOT of resistance

    Which has nothing to do with this pile of bovine excrement. The delusional ramblings of anybody is not real science. Real science isn’t in that paper. Delusional thinking is.

  112. says

    nettleingenting:

    Thanks for the reply.

    Keep in mind, Galileo had only the church to enrage. Now, we have the scientists.

    I’m not sure what you’re seeing is rage, and there’s a qualitative difference between the church and scientists. While scientists may at first resist new ideas, they are, as a whole, forced by their very ideology to be open to evidence. At the moment, it seems that’s what this idea lacks — supporting experimental evidence.

    I’d say resistance is a good thing. In fact, the more revolutionary the hypothesis, the more resistance there should be. This is not only natural, but a necessary part of the scientific method. If an idea can’t stand up to scrutiny (and that includes ridicule), it isn’t much of an idea. If it weren’t for resistance, for a certain intellectual barrier to entry, every crackpot idea out there would have equal weight.

    Science is essentially conservative because true discoveries are almost always incremental, building on the knowledge gained before, one small piece at a time. Quantum theory didn’t just spring full-blown from nothing — it built on inconsistencies in research data, and from the descriptive theories already in existence.

    On a fuller note, the paper is about both how reality is, and WHY it is. Since science explains how but not why, the paper is science because it explains how, but it goes beyond science by explaining why. An enormous accomplishment equivalent to going from medieval thinking, to the Renaissance and, more aptly, to the Enlightenment.

    And this is the reason there should be a lot of resistance to the idea. There have been a lot of people who make similar claims, and in pretty much all cases, the ideas are crackpottery. The skepticism you see is strictly in proportion to the claims made. As the claims are outrageous (however true they might be), so is reaction. Erik’s presentation (including the press release) reeked of hyperbole and excessiveness, which is one of the hallmarks of a crackpot.

    If Erik’s ideas are sound, if they are predictive and useful, he will be vindicated. If his ideas are not sound, if they aren’t congruent with reality, that too will be shown.

  113. Mr. Fire says

    This quotation shows that the author either lacks the skills or the mental discipline to even try to understand the preceding excerpt.

    Courtier’s Reply.

    It requires HARD mental labor data to begin to understand it,

    FIFY. Without results, the coolest idea in the world is a just-so story.

    To those of you put off by the new words, do you ignore studies that include words such as prednisone and pyridine too?

    Analogy fail. These are names given to things that had already been confirmed to exist, or at least had strong data upon which the names were based.

    Well, that, and there is an order of magnitude between mundane chemistry terminology and the hubris of an unjustifiable grand theory of everything.

    I have quizzed Erik repeatedly over its contents.

    Which of you is Pinky and which of you is The Brain?

    That is to say, RNA is the driver of evolution, and evolution is not “random.”

    um

    wut

    Even if the well-established RNA Hypothesis turns out to be accurate, how is mutation of RNA any less random?

    Jesus, you’re a sausage machine of crank, aren’t you?

  114. PFC Ogvorbis (Yes, they are) says

    Keep in mind, Galileo had only the church to enrage.

    Keep in mind that Galileo was friends with the Pope. Or at least they had been. But then, Galileo had lots and lots of former friends. What really pissed off the Pope was not that Galileo claimed that the earth orbited the sun, or even that Galileo’s math didn’t accurately predict the orbits (he thought that Keppler’s ideas on elipses were ridiculous (and ridiculed them)). No, the Pope got really pissed when Galileo released his book as a conversation between Simplicis and somebody else, and put the Pope’s writings (the Pope at the time (one of the Barberini Popes, if I recall correctly) had a very good reputation as a natural philosopher) as Simpleton’s argument. And published it in Italian so that everyone would be able to see that the Pope was a simpleton. So enraging the church had as much to do with Galileo’s style (or lack thereof), with Galileo’s ability to piss off other natural philosphers, with Galileo’s take-no-prisoners egotistical way of engaging his fellow philosophers, as it did his writings about a sun-centered system.

  115. says

    I am impressed with the hostility and willful ignorance of this forum — but not particularly surprised. Arguing is so much more fun than reasoned debate. Let’s ramp up the hate! Rock on guys!

    Clearly, many of you don’t understand the questions at hand.

    I wonder if anyone here really made the tough slog of sitting down for hours to understand the paper, so as to be able to make specific critical comments or even come up with substantive questions. For some strange reason, I have my doubts.

    Supporting experimental evidence is throughout the paper, so clearly anyone who claims otherwise hasn’t bothered to spend, oh, an afternoon STUDYING the paper. Better just to kick back with a six pack and watch the game!

    Matt Penfold
    Unpublished material should rarely be discounted. When speaking on the paper, scientists don’t just read their paper. Good grief, this is what the Gordon Research Conference is all about! Talking about unpublished data!

    nigelTheBold, Abbot of the Hoppist Monks
    Happy to respond to a thoughtful question.
    Science is indeed conservative — as much as any religion. Of course science has produced new results and new theories, albeit with a grant funding rate of 8% (!), that rate is decreasing and discoveries are increasingly of peripheral utility. As two scientists told me when I asked them what that funding rate meant, they both said, “the death of science.”

    My point about defending the status quo is that scientists are very quick to reject heterodox theory and are also very quick to defend their theory against a colleague’s.

    Erik has definitely told me he has been treated with outright hostility, so rage is the right word. By the way, he does have some scientists who support him. One of them told him “Keep in mind, Galileo had only the church to enrage. Now, we have the scientists.” So, I was not expressing my opinion alone.

    “If Erik’s ideas are sound, if they are predictive and useful, he will be vindicated. If his ideas are not sound, if they aren’t congruent with reality, that too will be shown.” Neither is necessarily the case. If people want to be willfully ignorant and just stick with “what works good enough,” Erik’s theory will be treated with indifference regardless of whether it is wholly right, partly right, or wrong.

    By the way, I really like ale made by trappist monks. It seems you have some in you, if just enough to give you that mild sense of serenity that comes after the first few sips.

    For those of you who would deconstruct my posts with slurs, that’s fine. You clearly don’t take the time to consider alternative views — save for ridicule.

    Here’s one last nettle for you!
    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally in your interest in this paper.

  116. says

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally in your interest in this paper.

    It’s unfalsifiable according to the author.

    That was easy.

  117. says

    We Are Ing

    “It’s unfalsifiable according to the author.”

    Falsify it then. Prove him wrong. A simple task, right? Easy?

    I notice you ignored the simple task I gave. Was it too hard?

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally insincere in your interest in this paper.

  118. says

    I didn’t

    Being unfalsifiable is a fundamental flaw in the paper.

    We’re done. there’s no need to start the race when the car lacks an engine.

  119. Ariaflame, BSc, BF, PhD says

    You claim to be a scientist and do not know what unfalsifiable means? Major major fail.

    Chiropractor maybe? They seem to get a lot of woo, or maybe homeopath.

  120. says

    Unfalsifiable means unable to falsify. Not that it cannot be proven but that it is structured in a way that it cannot be tested. Something like that is thus in a universe where it’s truth and untruth are indistinguishable. To test the hypothesis you will have to refine it to have an impact.

    If X happened how can we demonstrate it.

    Well if X happened we should see Y, do we see Y?

    If so go to “do we see Z” if not then X is wrong.

  121. says

    You guys are being silly.

    I guess I am simply stirring up the hornet’s nest more.

    Of course I know what unfalsifiable means. Geez. English is my first language.

    Unfalsifiable means that it can’t be proven false.

    Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    So, prove it false! Come on guys, you can do it. Right?
    Actually, judging from the level of discussion here, I think few if any of you can.

    I repeat my simple challenge.

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally insincere in your interest in this paper.

  122. says

    As two scientists told me when I asked them what that funding rate meant, they both said, “the death of science.”

    Yeah. Ain’t that the truth. At least, the death of science in America. Fortunately, some other countries work hard to keep science alive (such as China).

    My point about defending the status quo is that scientists are very quick to reject heterodox theory and are also very quick to defend their theory against a colleague’s.

    But they still have to defend. It’s not like religious dogma, which is impervious to logic and data. I merely contend your comparison of scientists to the church is hardly warranted. And it’s not like scientists haven’t defended their own pet hypotheses against others in the the long history of science.

    More importantly, though, young scientists haven’t staked their territory yet. Ideas that are resisted by one generation are often embraced by the next. I recall the resistance met by string theory (which really isn’t much of a theory even yet) back in the early 80s. Now it is the dominant hypothesis in QM, rightly or wrongly.

    Me, I’m not qualified to judge this paper. It’s not as obviously quackery as Timecube, for instance. I do have experience spotting quackery in general, though. And this paper, and the way it was presented, has many of the hallmarks of quackery — grandiose claims, a lack of mathematical rigor, no references to vetted papers, no supporting research, and no proposed tests.

    That may change in time, of course. Hopefully Erik will be able to formulate some tests, and demonstrate how QM and relativity are derived from his hypothesis (including the mathematical relationships we’ve observed in nature).

    Until then, I’ll throw this into the pile of potentially interesting ideas about the fundamental nature of the universe, somewhere between the holistic universe and causal dynamical triangulations.

  123. says

    Unfalsifiable means that it can’t be proven false.Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    Unfalsifiable=/= true
    falsifiable=/= false

    In this case falsifiable== more or less verifiable

    It isn’t that it’s an incorrect claim. It’s that it’s evident of inherently flawed methodology. Basically you cannot propose a claim that is philosophically a closed loop and proclaim it true because it cannot be falsified.

    It’s the problem of the invisible dragon.

    As I said before, in science the hypothesis must be falsifiable.

    There is no real standard of evidence to prove 100% something, so you try to DISPROVE it and use the process of elimination and strength of it’s stance to show how it conforms to all onslaught of evidence.

    In science falsifiable == verifiable.

  124. Nerd of Redhead, Dances OM Trolls says

    I”t’s unfalsifiable according to the author.”

    That statement puts it in the classificaiton of so wrong, it’s not even wrong, just bullshit. Obviously no attempt at falsification was made by referring each claim to the peer reviewed scientific literature for confirmation had occurred. The paper would require hundreds, if not thousands, of literature references. This sounds like a crank who thinks their idea is so good they doen’t have to do the necessary “showing the evidence” to back it up.

    I am impressed with the hostility and willful ignorance of this forum

    I’m impressed by your willful ignorance, and the inability to consider the paper comes from a crank. You also appear to think that outsiders make big revolutions in science. No, they don’t. The scientists who make the paradigm shifts have a thorough understanding of the subject. That is not the case here.

    Prove him wrong. A simple task, right? Easy?

    Already done above. But, in science, we don’t have to prove such idiocy wrong. The burden of proof is on the author, not those refuting him. The author must show they are right by copious citations to the scientific literature that contains the evidence that backs up their claims. You again show a failure to understand how science operates, and how the scientific method really works.

  125. PFC Ogvorbis (Yes, they are) says

    I am impressed with the hostility and willful ignorance of this forum — but not particularly surprised. Arguing is so much more fun than reasoned debate.

    Yup. Hostility to your willful ignorance.

    And arguing is debate. And you have, so far, given absolutely nothing on your side.

    Unpublished material should rarely be discounted.

    If a paper is unpublished, it doesn’t actually exist to the scientific community. If it has been published, that means that it has been subjected to rigorous peer review. Which means others can read it. And respond to it.

    By the way, I really like ale made by trappist monks. It seems you have some in you, if just enough to give you that mild sense of serenity that comes after the first few sips

    Wait. If we are not immediately swayed by the paper, or your defence of the paper, we are drunk? That’s your argument?

  126. Mr. Fire says

    Um, no-one is saying that unfalsifiable is an incorrect description of the paper, dullard.

    They’re saying that the fact that it is unfalsifiable makes it effectively useless.

    But I’m still betting that despite being able to regurgitate a superficial definition of the word ‘unfalsifiable’, you still don’t grok it. Perhaps if you put in the HARD mental labor required, though.

  127. says

    nettleingenting:

    Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    Ah, man. I thought you were arguing in good faith.

    You claimed to be trained as a scientist, and yet you don’t seem to understand the basic principles of the scientific method. Your defense of the proposal as a theory should’ve given me my first clue. Your inability to grasp the importance of falsifiability, though, is inexcusable.

    That’s one of the most fundamental attributes of science.

  128. says

    nigelTheBold, Abbot of the Hoppist Monks

    I think you don’t know the history of Judiasm and Christianity.

    Rabbis would repeatedly debate — and defend — various position. Thus, we have not just the Jewish Bible, but also the Midrash, and most important for this subject the Mishna (not sure about the spellings). The Mishna is specifically about Rabbis defending various positions and interpretations.

    As for Christianity, we have the Jesuits, an order with a specific duty to debate positions within Catholicism. Moreover, the Catholic Church itself debates a variety of positions. To wit, less than 100 years ago they changed dogma from “Jesus was killed by the Jews.” They finally acknowledged that previous position was not helping the Jews, you see.

    Coincidentally, in science we had the ultraviolet catastrophe, where black bodies would emit more energy than they absorbed once exposed to UV (all is mathematical theory). Science clung to this broken theory (it had nothing else to use) until Planck came up with the idea of quanta of photons.

    Science will stick with broken theory until something better comes along AND is understood. As I recall, Einstein’s general theory of relativity (incredibly radical at the time) took about 10 years to be accepted!

    “Until then, I’ll throw this into the pile of potentially interesting ideas about the fundamental nature of the universe…”

    Yours is a good mind. Why are you even on this forum?

    We Are Ing
    Yours may be a good mind, but you don’t appear to want to use it much.
    The problem of the invisible dragon sounds less clever than string theory. The difference is that invisible dragons would have bulk, cause disturbances in the air, potentially make noise, give off heat,etc. So, we can test for those. We can’t test for string theory. Neither have we isolated a quark. Sure, we can measure for quarks, but measurements necessarily change the system. So, again, we have not isolated a quark, we just see something moving through a barrier and call it evidence — whatever it is.

    Science is not about proving — only about disproving and removing what is demonstrably not true. Notice that science is not about removing what is NOT demonstrably not true.
    You clearly are not capable of the challenge I put forth, so don’t worry about it. Chill out, and have a fine day.

    To others, I repeat the simple task.

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally insincere in your interest in this paper.

  129. says

    @Nettle

    I have been patient with you and explained without insults or vitriol or hostility. And you respond to me very rudely. Please explain or defend yourself before I bother to repeat it for you again.

  130. says

    The problem of the invisible dragon sounds less clever than string theory. The difference is that invisible dragons would have bulk, cause disturbances in the air, potentially make noise, give off heat,etc. So, we can test for those. We can’t test for string theory.

    The dragon can phase at will. It’s hiding because you scare it.

    The invisible dragon is a thought experiment to demonstrate why hypothesis have to be testable/falsifiable in order to be taken seriously. The invisible pet dragon is unfalsifiable, it’s existence is indistinguishable from it’s falseness.

    String theory is mislabeled and I have heard people argue that it is of questionable falsifiability but it has inherent claims to it, and inherent potential experiments that can be done to disprove it.

    You’re just wrong on quarks as the wiki documents the history of their evidential proof

  131. says

    nigelTheBold, Abbot of the Hoppist Monks

    Good grief, man. Claiming that something is unfalsifiable does not make it unfalsifiable! It’s just a claim and claims can be wrong.

    PFC Ogvorbis (Yes, they are)
    Arguing is not debating. The two words are different.
    “The scientists who make the paradigm shifts have a thorough understanding of the subject.” Sure. And that is the case here. Erik has a clear understanding of his subject.
    “If a paper is unpublished, it doesn’t actually exist to the scientific community” Wrong! The Gordon Research Conference is SPECIFICALLY for the discussion of unpublished work.
    “I’m impressed by your willful ignorance, and the inability to consider the paper comes from a crank.” You clearly have not STUDIED the paper, so your criticism has no value.

    Mr. Fire
    How do you test a mathematical description of something unmeasurable? Neater trick: how do you isolate a quark?

    You guys are intellectually lazy to an incredible degree.

  132. Antiochus Epiphanes says

    nettleingenting: I read the paper and couldn’t detect much of an explanation or the identification of something needing explaining. Maybe I missed the point, but Andrulis is certainly at least partly to blame. Many of the most important scientific papers in history were over abstruse concepts, and yet even a novice could detect in general what was being communicated.
    I’m glad that you have provided some more succinct context. However, I don’t find that what you have written sheds as much light on the paper as you may have hoped.

    The paper predicts that RNA is the genetic template on which DNA forms.

    Certainly, we know that this occurs in isolation (retrovirus lysogeny), but we also know that the vast bulk of DNA is replicated from DNA template. I’m not sure whether you are referring here to the RNA-world hypothesis, simply because the prediction appears to be in relationship to things that are happening now.

    Therefore, the paper predicts that there would be a pool of RNA that has no genomic complement (unannoted RNA). If you find RNAs that have no DNA template, how does the RNA come to be made?

    Thousands of EST libraries have failed to detect any such thing to my knowledge. It would certainly be big news if they did, but this hardly speaks to the central role of annotated RNA in directing *gag* evolution.

    The unannoted RNA is made through polymerization of nucleotides driven by the chemical energy stored in the high energy phosphate bond (and that energy is deposited there by all the metabolic pathways of the cell).

    All cellular processes requiring catalytic energy rely on energy in phosphate bonds. However, in the case of the polymerization of RNA nucleotides, RNA polymerase is required for this transformation to take place. Does Andrulis propose a mechanism?

    One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement. There should some level of sequence contraints, structural constraints, specification, and functionality to this unannoted RNA.

    But we have no evidence of that and new transcriptomes are sequenced daily. The preponderance of evidence is against this “theory”.

    So, how does a new gene come to exist?

    Duplication and divergence.

    Another positive prediction is that one should expect to find changes in annoted RNA (made from DNA) that ultimately drives changes in DNA. RNA based mutagenesis of DNA!

    OK. But we don’t find annotated RNA. Even if we did, with no sequence-sequence correspondence with existing DNA, it is difficult to imagine a mechanism by which this might happen.

    That is to say, RNA is the driver of evolution, and evolution is not “random.” Random is a philosophical term adopted by science because “by a method that we don’t know,” while being more honest, reveals the ignorance in much of science.

    You haven’t provided a mechanism for the directing action of your non-existent annotated RNA to “drive” the evolution of anything. But whatevs. Two points. 1) That isn’t really what random means. Mutation is said to be a random process in evolution, not because we don’t understand the mechanism by which it occurs, but because mutations occur without respect to the function of the loci in which they occur. The are random in regard to phenotype and by extension selection pressure. 2) Evolution is not a completely random process anyway. At least according to orthodox evolutionary theory.

    On a fuller note, the paper is about both how reality is, and WHY it is. Since science explains how but not why, the paper is science because it explains how, but it goes beyond science by explaining why.

    Why what? What does this paper purport to explain?

    An enormous accomplishment equivalent to going from medieval thinking, to the Renaissance and, more aptly, to the Enlightenment.
    By the way, the Enlightenment met a LOT of resistance (think of poor Galileo), but the Western world now takes it for granted.
    Keep in mind, Galileo had only the church to enrage. Now, we have the scientists.

    Has Andrulis been put on house arrest or something? His ideas are being attacked, not because they are heterodox, but because they are incoherent.

  133. says

    nettleingenting:

    Good grief, man. Claiming that something is unfalsifiable does not make it unfalsifiable! It’s just a claim and claims can be wrong.

    Very true.

    It’s just very troubling that the person who formulated the hypothesis claims it is not falsifiable. If the person who understands the proposition best cannot think of a way to falsify the proposition, it’s a claim with some weight behind it.

  134. PFC Ogvorbis (Yes, they are) says

    “The scientists who make the paradigm shifts have a thorough understanding of the subject.” Sure. And that is the case here. Erik has a clear understanding of his subject.

    Why don’t you argue with what people actually write? If you are going to randomly assign statements under my ‘nym, you are populating both sides of the debate. And you are correct. This is not a debate. This is not even an argument (no matter what definition you use). This is you makeing shit up and then arguing against it.

  135. Mr. Fire says

    Yours is a good mind. Why are you even on this forum?

    What you don’t understand is that I and probably most other people are of a similar sentiment to nigel’s. I shall accept Andrulis’ hypothesis when he a) makes it coherent; b) provides a mechanism for testing it; c) validates it thoroughly with meaningful results. Until then, it’s garbage.

    To others, I repeat the simple task.

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally insincere in your interest in this paper.

    Repetition of a bullshit demand doesn’t make it any less bullshit.

    He doesn’t have theory. He has manic, unfounded, ridiculous assertions pulled from nowhere and justified with nothing.

    Oh, and:

    Also, for your consideration: http://milesmathis.com/erik.pdf

    Let’s get some meat on that:

    The slur “crackpot” is aimed at Erik Andrulis, whom I had not heard of before today and whose article I have not read. I don’t need to read it because this defense is not a defense of Andrulis’ theory, it is a defense of Andrulis’ right to publish his theory without being called a crackpot by mainstream gatekeepers and propagandists.

    So, um, yeah.

  136. Nerd of Redhead, Dances OM Trolls says

    Erik has a clear understanding of his subject.

    Not that I see, and I’m a chemist. Incoherant crank all the way. You need to back up your assertions with evidence too. I see nothing.

  137. Antiochus Epiphanes says

    nettleingenting: I will also say that it would appear that Andrulis purposefully made is manuscript, Sokalish, by redefining words in strange ways. For example

    Amino: Of or relating to sulfur compounds (particles), amino acids, polypeptides

    The word “amino” has never generally referred to sulfur compounds. When amino acids have sulfur in them, the sulfur is restricted to side-chains. There are only two canonical* amino acids that incorporate sulfur.

    Or

    Electro: Of or relating to visible matter particles, chemical elements, planetary cores

    Rather than indicating negative charge.
    Or,

    Ribo: Of or relating to nitrogen particles, nitrogenous bases, RNA

    Rather than indicating a ribose component, which is strangely enough a sugar devoid of nitrogen.

    Also, there is a lot in that paper that has nothing to do with whatever it is you were trying to explain.

    *See. I can do it too.

    PFC Ogvorbis

    This is you makeing shit up and then arguing against it.

    I have an idea for a new blog.

  138. Nerd of Redhead, Dances OM Trolls says

    Anyone else think nettleingenting might be the author or a good friend of the author? Hence its resistance to the “crank” epithet, no matter how well deserved?

  139. PFC Ogvorbis (Yes, they are) says

    You know…I make shit up and then argue against it. It’s so easy, really.

    You could call it Strawman.com.

    It isn’t taken.

    Yet.

  140. says

    Antiochus Epiphanes,
    you seem to be particularly reasonable, so I will share with you a thoughtful explanation of part of the paper that I made else where.
    By the way, the neologisms and atypical use of words (such as amino to mean containing sulfur) were necessary because Erik is defining a new paradigm. In the case of amino, the amino acids cysteine and methionine are the biochemicals where sulfur first emerges in his heirarchy of gyres. Very logical.

    To those of you unfamiliar with biochemistry, don’t even try to understand what follows. Really. You won’t stand a chance of understanding, and I’m mostly talking about contemporary biochemistry, nothing special, but inscrutable to the non-biochemist.

    The query made to me was as follows.

    Otherwise you seem to be playing the “I can understand Andrulis’s paper because I have advanced degrees in science” ploy. But I (and lots of others too) have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). Of course that doesn’t rule out the possibility that I can’t recognize paradigm-shifting brilliance when I see it, but it’s usually the case that remarkable insights in molecular life sciences are amenable to rather simple explanations (by far the hardest part of obtaining astonishing insight in molecular biology in its broadest sense is in overcoming experimental/technical issues).
    So Andrulis’ states (using straw-man, and non-sequitur type illogic) in his introduction : “Finally, the RNA (ribonucleic acid) world hypothesis posits that ribonucleotide-based genetic systems evolved prior to protein and deoxyribonucleic acid (DNA). This hypothesis does not fit well with the central dogma and is unable to resolve precisely how the translation apparatus, genetic code, and biometabolic pathways evolved [7-9].”
    Yor task, nettle, (since you understand Andrulis’ paper very well), is to explain to us in simple terms how Andrulis’s hypothesis “resolves precisely how the translation apparatus, genetic code, and biometabolic pathways evolved”.

    To which I replied as follows.

    Nice, you and I both have similar experience, as I have worked in chemistry, biochemistry in molecular biology laboratories in Cambridge and Southern California. I didn’t mean it as a “ploy.” I meant it to be genuine. But I digress.

    Frankly, I don’t see the illogic nor do I see the non-sequitur nature of that quote you gave. Perhaps that’s because I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma) and the central dogma says nothing about the origin and evolution of RNA. The point Erik was trying to make is that current models/theories/hypotheses/ideas are ad hoc and thus should be considered provisional at best and wrong at worst. Could you point out the illogic there?

    As for how theory treats those three problems (translation apparatus, genetic code, and biometabolic pathways), I would call your attention to where these problems are treated:

    – p. 43 Origin of the genetic code

    Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system. The tri-quantal system (as he calls it) is the tri-nucleotide, with each component of the system having a relative amount of energy (see section 2.4.5, pp. 13-14), “(i) a high energy (exergic), unstable, excited form; (ii) an intermediate energy, quasi-stable, transition form; and (iii) a low energy, stable, ground form.” My read of this is that the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code. Is there a problem with the interpretation that I am missing?

    Erik has proposed that the code evolved autocatalytically, from the metabolism of the orthophosphate bonds between the 2nd and/or 3rd nucleotides. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems. I assume you are familiar with their work.

    – pp. 45-48 Specificity of genetic code; origin of translation apparatus.

    Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s). Again, points for Erik, as this is, in fact, what one observes in existing cells (in fact, to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins; more points). The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA. And, just as the rRNA can cycle in and out of the quarternary complex, Erik models the mRNA cycling in and out that previously mentioned ternary complex. Both cycling phenomena are depicted accurately by the gyre and the latter of the two reveals a co-adaptational relationship between the aa-tRNA and the mRNA.

    My only problem in understanding is how the genetic information of RNA is transferred to the link between the amino acids that make up the polypeptide chain. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.) Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.) He relies on an axiom (the tenth one) to take this position. Seeing as this axiom applies to all systems in his theory, and finding no experimental evidence to refute it, I cannot dismiss it outright as wrong.

    – pp. 30-60 Biometabolic pathways

    Other than page 35, Erik does not use the term “biometabolic pathways” (because he did raise it up front, points against Erik). Perhaps the reason for this oversight is that every single pathway in the cell is a biometabolic pathway? In this regard, these 30 cited pages contain a large amount of discussion of many distinct aspects of cellular metabolism. If there’s one particular example you wanna go over, lemme know.

  141. Mr. Fire says

    How do you test a mathematical description of something unmeasurable?

    Look at the link I provided and you’ll see what has been said about that.

    Neater trick: how do you isolate a quark?

    More bullshit demands. Ing referred to this above.

    There is evidence for their existence, in fulfilment of the predictions. Deep Inelastic Scattering, for example. You don’t need to catch a quark in a bottle to have good reason to think it exists.

    Can you isolate an electron?

    You guys are intellectually lazy to an incredible degree.

    While you’ve been Gish Galloping across the fields of chemical nomenclature, the RNA World Hypothesis, particle physics and more, all while not having a clue what you’re talking about nor answering any of the objections to the intellectual skidmarks that you’ve left behind in each case.

  142. says

    Mr. Fire

    You don’t have an inkling of biochemistry, and I suspect a you have avery poor grasp of science in general.

    I don’t know why you make yourself look so ignorant with such statements of “While you’ve been Gish Galloping across the fields of chemical nomenclature, the RNA World Hypothesis, particle physics and more, all while not having a clue what you’re talking about” when I have repeatedly demonstrated that I do know what I’m talking about. Your comment would be funny were it not a reflection of someone willfully ignorant.

    By the way, you can isolate an electron. Thus, we can study an electron.

    Up and down quarks can’t be isolated singularly, therefore we can’t study them.

    If deep inelastic scattering is correct, then why is the idea of color confinement used to say that we can’t isolate up and down quarks, and therefore therefore they can not be directly observed?

    You can’t have it both ways!

    The more you spread your ignorance, you more foolish you look. Please stop, if only for your own sake.

  143. Mr. Fire says

    From Erik Andrulis’ own webpage:

    Extending upon this RNA research, I recently compiled an incommensurable, trans-disciplinary, neologistical, axiomatic theory of life from quantum gravity to the living cell.

    incommensurable = incapable of being judged, measured, or considered comparatively.

    ++++++++++++++++

    nettleingenting:

    How does one go about showing that gyres exist and are meaningful for science?

  144. says

    Mr. Fire,

    It is incommensurable, as it compares with no extant theory, yet subsumes all of them. Geez, you clearly don’t want to study the paper. Too hard, I guess

    “How does one go about showing that gyres exist and are meaningful for science?

    You look.

    Fingerprints
    waves
    tornados
    cell cycle
    metabolism
    circadian rhythms

    Utility: gyres unify all of science, thus we see how the turnover of high energy phosphates, for example, is tied in to the cell cycle.

    You would know all this if you just read the paper, but you didn’t. So, you remain ignorant. Your choice.
    Why bother trying to learn something difficult, I guess.

  145. says

    Along with deep inelastic scattering, there’s also the evidence provided by electron/positron annihilation. So far, the quark model has proven effective at predicting new an unique features of the universe, not least of which is the standard model family of particles.

    While it might eventually prove to be an inadequate model, it has proven itself useful. That’s an important hallmark of a good theory.

  146. Nerd of Redhead, Dances OM Trolls says

    Up and down quarks can’t be isolated singularly, therefore we can’t study them.

    You lie. We know quie a bit about them. And Mr. Fire is a chemist. He smells bullshit when it is presented, even by you.

    then why is the idea of color confinement used to say that we can’t isolate up and down quarks, and therefore therefore they can not be directly observed?

    Easy, mathematical models describing their behavior. QuantumChromoDynamics.

    You can’t have it both ways!

    You can’t keep making unscientific assertions like the above without being called a liar and bullshitter. You aren’t showing any scientific understanding.

    The more you spread your ignorance, you more foolish you look. Please stop, if only for your own sake.

    So speaks the ignorant fool who fails to understand the need for a theory to be supported by citations to the evidence, hence falsifiable.

    But you have already put the hole well ever your head. You need to remember the first rule of holes.

  147. says

    nigelTheBold, Abbot of the Hoppist Monks

    Your points are well taken. I am not arguing that present theory predicts nothing. I am simply pointing out that while we can theorize about these particles, we can make measurements relating to them, but we can’t isolate them.

    “While it might eventually prove to be an inadequate model, it has proven itself useful. That’s an important hallmark of a good theory.”

    A theory is good until it is broken. Again, think black body radiation and the ultraviolet catastrophe. The theory of light had pretty darned good predictive power — with the nasty exception that uv light shined at a black body would give off more energy than was put in!
    Below uv, theory predicted that the energy that went in would be the same that the black body radiated out. Seems fine to me. All we have to do is ignore uv and higher energy radiation, and the theory held together.

    Of course, it was hopelessly broken, but science had no alternative, until a guy named Planck suggested that photons had quantum, steps, of energy. Problem solved.

  148. says

    Nerd of Redhead, Dances OM Trolls

    Studying the effect of particle is not the same as studying the isolated particle.

    So, my comments regarding quarks are correct.

    I am not sure why you confused the two ideas.

    Too, mathematical models are as good as the data on which they are based. They’re only models that are intended to predict and describe. They are not observations.

  149. says

    nettleingenting:

    I am not arguing that present theory predicts nothing. I am simply pointing out that while we can theorize about these particles, we can make measurements relating to them, but we can’t isolate them.

    Absolutely true. I’m just not clear on the point you are attempting to make, I guess. I’d gathered it was something along the lines of, “You can’t isolate quarks, so what proof do you have that quarks exist?”

    But I guess that’s not what you’re saying.

    A theory is good until it is broken.

    Or until something with more predictive power comes along. But yeah — we’re definitely in agreement on that.

    Of course, it was hopelessly broken, but science had no alternative, until a guy named Planck suggested that photons had quantum, steps, of energy. Problem solved.

    Yep. And that’s how it typically works: a theory or hypothesis is found to be in opposition to observed reality, people scratch their heads a bit, and someone thinks up something clever based on the observations that caused the conundrum.

    While I’m having trouble grokking all the jargon in Erik’s paper, I thought maybe I’d be able to figure out exactly which inadequate models were being addressed by the paper. So far it seems he’s saying, “Things in the universe exhibit cyclic patterns, so it’s cycles all the way down.”

    I’m hoping to have that “Ah-HA” moment where the jargon starts fitting together in my head. But I think it’s going to take a bit more time.

  150. Nerd of Redhead, Dances OM Trolls says

    So, my comments regarding quarks are correctNope.They’re only models that are intended to predict and describe. They are not observations.They are based on observations ,and can have predictive power, and have been used to look for new particles. Unlike the alleged scientiic theory you are defending. It isn’t a scientific theory until fully back up by solid and conclusive evidence, which appears to be lacking.

  151. KG says

    By the way, the neologisms and atypical use of words (such as amino to mean containing sulfur) were necessary because Erik is defining a new paradigm. – nettleingenting

    Crap. Whether you are “defining a new paradigm” (there’s another square of my crank bingo card filled!) or not, you do not seek to redefine well-established existing terms in ways that are inconsistent with current use unless you are either seeking to confuse your audience, or are yourself confused.

  152. Nerd of Redhead, Dances OM Trolls says

    Dang, blockquoe fail #203.

    So, my comments regarding quarks are correct

    Nope.

    They’re only models that are intended to predict and describe. They are not observations.

    They are based on observations and well accepted scentific theory, and can have predictive power, and have suggested the existence of new particles. Unlike the alleged scientific theory you are defending. It isn’t a scientific theory until fully back up by solid and conclusive evidence, which appears to be lacking.

    It isn’t a theory just because you call it one. I don’t and won’t call it a scientific theory until it meets my professional criteria, as it lacks (and I suspect will always lack) the proper evidence to back it up.

    I’ll simplify it for you. Ideas =/= scientific theory. The paper had an idea. Ideas + evidence = scientific theory. The paper lacked the evidence.

  153. Mr. Fire says

    More desperate grasping from the crank.

    when I have repeatedly demonstrated that I do know what I’m talking about.

    Would that be in bullshit factual, epistemological, and reading comprehension fails like:

    “overarching theory of chemistry

    “Science is about protecting the status quo — and defends it jealously.

    “Also, for your consideration: http://milesmathis.com/erik.pdf

    “That is to say, RNA is the driver of evolution, and evolution is not “random.”

    “it goes beyond science by explaining why.

    “Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    “The difference is that invisible dragons would have bulk, cause disturbances in the air, potentially make noise, give off heat,etc. So, we can test for those. We can’t test for string theory.

    And then the hemorroid cherry on the shit sundae:

    “How does one go about showing that gyres exist and are meaningful for science?

    You look.

    Fingerprints
    waves
    tornados
    cell cycle
    metabolism
    circadian rhythms

    Wow. Just-so, self-fulfilling circular bullshit and confirmation bias. Keep crankin’!

  154. says

    Ok Nettle. This is gone on far enough. You have been treated with undeserved understanding and patience and responded with insults. You’re playing a game and I’m done playing now. Why don’t you go nettle somewhere else now?

  155. says

    “That is to say, RNA is the driver of evolution, and evolution is not “random.”

    I am done with him, but this one I missed and especially irked me.

    There are RNA viruses RIGHT NOW…they evolve. This is not even wrong.

  156. says

    In the case of amino, the amino acids cysteine and methionine are the biochemicals where sulfur first emerges in his heirarchy of gyres. Very logical.

    What the hell is so very logical here. The word amino has always, as far as I can tell anyway, referred to the presence of nitrogen (mor specifically an amine group). ‘thio-‘ is generally used to refer to stuff containing sulfur. Why does Andrulis feel that his ‘introduction of new concepts’ requires completely redefining existing concepts. Why doesn’t he just use existing terms. Listen nettleface, if this is your idea of very logical, then you’ve got issues.

    Also:

    You guys are being silly.

    I guess I am simply stirring up the hornet’s nest more.

    Of course I know what unfalsifiable means. Geez. English is my first language.

    Unfalsifiable means that it can’t be proven false.

    Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    So, prove it false! Come on guys, you can do it. Right?
    Actually, judging from the level of discussion here, I think few if any of you can.

    I repeat my simple challenge.

    Ok, now I know it. You’re a liar. Why do I say this? Well you claim to be a scientist, yet you have no idea what the term unfalsifiable means. Unfalsifiable=untestable=scientifically worthless. A good scientific theory is falsifiable, but not false. For example Darwin’s theory of evolution can be falsified, for example by finding a fossil rabbit in Cambrian strata. However, it has never been falsified and has the evidence on it’s side, making accurate predictions about the natuural world.
    But in any case, please tell me how you became a scientist without understanding the basic concept of falsifiability? That is if you really are a scientist.

  157. Mr. Fire says

    Nettleingenting, what do you think of the work of Vincent Fleury and Stuart Pivar, who have similar groundbreaking theories of lots-of-stuff?

    If so, do you consider them more substantiated or less substantitiated than your Erik’s seminal paper?

  158. says

    nigelTheBold, Abbot of the Hoppist Monks

    Good for you that you have the intellectual curiosity to read the paper. Hopefully, you have the mental fortitude to make it through. I find it a tough slog.

    I find it easier first to ignore most of the neologisms and focus on the quasi-scientific diagrams (or equations if you prefer).

    KG,
    you are being foolish. All of science is neologisms and newly defined language. The words Sodium Azide and Wittig Reaction would mean nothing 300 years ago. Hell, science has gone through several paradigm shifts where new words have had to be defined, but I suspect you don’t know or care. For example, the phlogiston theory was replaced (a paradigm shift) by the idea of oxygen. What the heck is oxygen? A word that was invented by early chemists to explain what allows fires to burn and animals to breath. Not good enough for you? How about the idea that an oxidizer DOES NOT HAVE TO BE OXYGEN! I presume you think such an idea to be baloney, but you clearly have your mind set on the bizarre idea that language is immutable. The linguistic term for such an insipid idea is “the etymological fallacy,” where one presumes that a word means what its root means.

    Nerd of Redhead, Dances OM Trolls
    The paper is loaded with evidence. You clearly lack both the interest and probably the intellectual ability to even read the paper, let alone understand it. In a previous post (scroll up) I gave a long list of evidence. Again, you probably either ignored it or didn’t understand it because it was biochemistry.

  159. says

    Oxidizers are compounds which are capable of reacting with and oxidizing (i.e., giving off oxygen) other materials.

    How about the idea that an oxidizer DOES NOT HAVE TO BE OXYGEN

    Just pointing out.

  160. says

    Oi, nettleface, amino is an existing term. It refers to compounds containing an amine group. Why is it ‘very logical’ for Andrulis to start using it for things containing sulfur, something for which there is already another term: thio?

  161. says

    We Are Ing

    “Amino is not a neologism”

    I will graciously assume that you are intelligent and have simply misunderstood me.

    About the word Amino, I did not state it was a neologism. Rather, I said Erik uses the word to focus on sulfur as opposed to the amine. He does so because cysteine and methionine are the first molecules to incorporate sulfur. So, Erik is just trying to emphasize that while nitrogen emerges biologically with RNA, sulfur emerges biologically with amino acids.

    You would know all this if you read the paper, but for reasons known only to yourself, you clearly would prefer to argue from a position of ignorance.

  162. says

    nettleingenting:

    Good for you that you have the intellectual curiosity to read the paper. Hopefully, you have the mental fortitude to make it through. I find it a tough slog.

    Well, frankly it’s not entirely intellectual curiosity. I’m really quite a dullard with more interest in shiny things and things that move quickly and erratically. There’s a lot of, “What the hell is nettleingenting talking about?” going on. Also, I’m a bit masochistic.

    So far, though, from what little I can glean, the evidence presented isn’t terribly persuasive. It still seems an exercise in pattern recognition rather than a cohesive hypothesis. But that could just be me. It’s reeeeeeaaalllly hard to tell.

  163. says

    We Are Ing

    “Oxidizers are compounds which are capable of reacting with and oxidizing (i.e., giving off oxygen) other materials”

    Have you not taken basic chemistry? Your definition is nonsensical.

    When you oxidize something, like coal, you do NOT give off oxygen. You give off carbon dioxide, which is not oxygen. Don’t believe me? Try breathing pure carbon dioxide.

    Another example is rust. Try breathing rust.

    Yet another example is the oxygen used in the space shuttle main tank. It oxidizes the liquid hydrogen to form water. Try breathing water.

    Afterwards, try breathing oxygen. Big difference, hunh?
    That’s because your body needs oxygen to perform oxidative reactions.

    Other oxidizers include fluorine and chlorine.

  164. Nerd of Redhead, Dances OM Trolls says

    The paper is loaded with evidence.

    No, it is loaded with allegations and sophistry. For example, what is the evidence (citation) that RNA causes DNA mutations? Put up or shut up.

    In a previous post (scroll up) I gave a long list of evidence.

    You don’t get it. This is evidence: Lenski. A citation to the peer reviewed scientific literature. A citation for each questionable claim that is made is required. The fact you don’t get it, tells me you aren’t a scientist, which I am.

    He does so because cysteine and methionine are the first molecules to incorporate sulfur.

    Citation needed! (see how that works)?

  165. Mr. Fire says

    KG,
    you are being foolish. All of science is neologisms and newly defined language. The words Sodium Azide and Wittig Reaction would mean nothing 300 years ago.

    sodium azide and the Wittig olefination were not terms expropriated from a pre-existing usage and then confusingly redefined, the way ‘amino’ was here, moron.

    Not good enough for you? How about the idea that an oxidizer DOES NOT HAVE TO BE OXYGEN!

    An embarrassing fail for someone who claims to be a chemist.

    You can see why the generalization of the phrase oxidation came about historically: it was a specific phenomenon thought to be traceable to one source, that ended up having a number of sources.

    There is no such excuse for ‘amino’ – where the term is specifically associated with the nitrogen atom.

    Hence KG’s inference that Andrulis was either ignorant or disingenuous.

    You were a crank from your first post, but now you’re really starting to show fatigue.

  166. KG says

    KG,
    you are being foolish. All of science is neologisms and newly defined language. The words Sodium Azide and Wittig Reaction would mean nothing 300 years ago. – nettleingenting

    You are being dishonest. Inventing new terms may be necessary; redefining old ones in ways which are both idiosyncratic and completely inconsistent with their existing meaning is not: as I said, it indicates either confusion, or the desire to confuse.

  167. Nerd of Redhead, Dances OM Trolls says

    sulfur emerges biologically with amino acids.

    I suspect it would first emerge as an anaerobic energy source. At least I’ve seen articles to that effect. Again, citation needed.

  168. says

    sodium azide and the Wittig olefination were not terms expropriated from a pre-existing usage and then confusingly redefined, the way ‘amino’ was here, moron.

    Yeah, I’ve been trying to get that point accross, but apparently nettleface doesn’t read my posts. Maybe it’s because I called him nettleface. Meh.

  169. Mr. Fire says

    When you oxidize something, like coal, you do NOT give off oxygen.

    Yeah so Ing’s point there had a mistake.

    You then see fit to rub it in with several repetitive paragraphs, rather than adressing more substantial things.

    Someone’s trying to puff up their credentials.

    Bored now.

  170. Nerd of Redhead, Dances OM Trolls says

    Oh, and nettles, the reason Einstein’s theory took 10 years to be accepted was that he made predictions in his publication that would falsify his general theory of relativity. It took that long to prepare and make the actual empirical measurements (gravitational lensing by the sun). They were made and found to correspond to his theory. Now, what falsifiable predictions are in the cranks paper?

  171. says

    Again, nettleface, why does Andrulis use an existing term (amino) for something different from its common usage (compounds containing sulfur, apparently) for which there is also an existing term (thio)? Why, according to you, is this so ‘very logical’? Is he deliberately trying to be confusing?

  172. says

    just for clarity, the ‘compounds containing sulfur’ in my previous comment refered to the ‘something differet from its common usage’, not to the ‘common usage’-part. sorry if that wasn’t clear.

  173. Mr. Fire says

    Seriously, nettleingenting, you have demonstrated no more of an understanding of Andrulis’ paper than we have.

    Your references to experimental support through RNA and other things give no reference to gyres, but at best simply reassert existing findings and try to link them together through these mysterious and unfalsifiable shibboleths.

    When pressed for how they connect to gyres, the best you can vomit up is this laughable, circular horseshit:

    “How does one go about showing that gyres exist and are meaningful for science?

    You look.

    Fingerprints
    waves
    tornados
    cell cycle
    metabolism
    circadian rhythms

    I mean, are you not embarrassed with yourself for writing this?

  174. says

    Nerd of Redhead, Dances OM Trolls

    “No, it is loaded with allegations and sophistry. For example, what is the evidence (citation) that RNA causes DNA mutations? Put up or shut up.”
    I already explained the evidence in a previous post, but you were not capable of understanding, I suspect. Either that, or you didn’t care. I suspect the former.
    Study the paper, then I will dignify your question with an answer.

    Mr. Fire
    “sodium azide and the Wittig olefination were not terms expropriated from a pre-existing usage and then confusingly redefined, the way ‘amino’ was here, moron.”
    You are willfully confusing my explanations, and using an ad hominem remark for some strange reason. The first two words I explained as neologisms. The word amino I explain as have a a shifted meaning.
    Words are redefined all. the. time. You graciously provided me with a perfect example. Moron used to be a scientific term referring to the most mentally retarded individuals. Thus, it was a classification, not an insult. Psychiatry and psychology have long since stopped using the term. So, does that mean moron still has its original meaning>? Clearly not. It is now meant as an insult, not a neutral description. But then, you knew all that right?

    In a related vein, Erik is shifting the readers’s attention from the amine part of the amino acid to the emergence of sulfur in biological systems. He does this because nitrogen emerges earlier, in RNA.

    I told you this, but you willfully twisted my statements in a way that serves your petty (and bizarre) point of view. I would presume you would just be teasing me if you weren’t so spiteful. What’s wrong, dude?

    KG
    You are being presumptive. The idea that the Earth was the center of the solar system was redefine to be that the Sun was the center of the solar system. A “solar-centric” viewpoint was a new term necessary to describe a new paradigm.
    More important, redefining old terms is both necessary and happens all the time. See my explantation of moron above. Its redefinition was bizarre and inconsistent with its preceding meaning. Previously, a moron was a psychological term referring to an individual incapable of anything but assisted living. Now, a moron can, as I proudly demonstrate, debate with even people on the internet like you.

    So, which is it? Is a moron a neutral, scientific term referring to a person incapable of basic human interactions?
    Or is moron a negative term referring to someone with whom you disagree because you think their point of view invalid?

  175. Nerd of Redhead, Dances OM Trolls says

    Nettles, get back to us when one of the unevidenced predictions in the paper is properly falsified with empircal evidence. Until then, all it is, is an idea, not a proper scientific theory.

  176. says

    In a related vein, Erik is shifting the readers’s attention from the amine part of the amino acid to the emergence of sulfur in biological systems. He does this because nitrogen emerges earlier, in RNA.

    And this is a good reason to use words in a confusing way… Why exactly? Why should the ‘fact’ that sulfur emerged in aminoacids first matter to the use of the word ‘amino’? After all, amino acids are so called because they have an amine group, not the other way round. I don’t care what Andrulis is trying to amphesize. Amino has a meaning in science, and it’s not ‘containing sulfur’ (for which there is already a word ‘thio’).

  177. Mr. Fire says

    Ha.

    You do not understand what an ad hominem is, nettleingenting. I can therefore assume that you do not understand anything else.

  178. says

    Nerd of Redhead, Dances OM Troll

    Get back to me when string theory is falsified with empirical data.

    pentatomid
    Yes this usage is important. Yes thio exists, so does mercapto. The point of the usage, as I have explained, is to emphasize that with amino acids comes sulfur. It’s the sulfur that is special, so Erik focusses on that. It just happens to emerge with amino acids, so that is what should define them — not the amino or the acid. Focus on the emergence of sulfur which, critically, happens with amino acids. He’s saying that the attention to the amino acid is misplaced and that the incorporation of sulfur in cellular systems is key. Confusing, yes. Logical, yes.

    Mr. Fire
    You are confused — and making yourself look foolish again.

  179. says

    See, to me, what Andrulis is doing by redefining the meaning of ‘amino’ to ‘emphasize the fact that sulfur arose first in aminoacids'(citation needed, nettleface) is something like the following (and I know the analogy I’m about to give isn’t perfect).
    Suppose I’m writing a paper on some Mirid bugs. The species I’m writing about is a bright green species with white stripes all over its body. However, the particular bright green color arose first in a different species, which doesn’t have white stripes, but has black dots all over its body. Hence the color green shall now be refered to as ‘having black spots’, to emphasize this fact.

  180. says

    pentatomid

    An elaboration/clarification
    Mercapto is inherently confusing. I have worked with, say, mercaptoethanol. Fun for pranks sure. But, I have never, ever used it with mercury. Maybe its just me, but I think mercaptoethanol would make no sense to a layman, were you to say, you see, the mercapto means it has sulfur.

  181. says

    You do not understand what an ad hominem is, nettleingenting. I can therefore assume that you do not understand anything else.

    Ah, there you go again, thinking language is immutable.
    Keep in mind that nettleingenting reserves the right to re-define words willy-nilly as required by his new paradigm. And English is his first language, not his last.

    “To control the infinitive is to rule the entire compost!”
    –Xeres Furd

  182. says

    pentatomid
    1, you want a citation? Read the paper and then will talk.
    2. nettleface? Flattery will get you nowhere.
    3. Heck, even the present “central dogma” shows that sulfur is nowhere to be found in the cell until the production of cysteine and methionine. This is basic biochemistry.
    4. You do not have to like Erik’s reasoning and focus on sulfur. I’m just the messenger.
    5. Shoot the messenger if you don’t like the message.

  183. says

    I’m sorry, but I still don’t see how any of this makes changing the meaning of ‘amino’ a usefull exercise. Using a word in a different way from the rest of the world, even if it would ‘make more sense’, is, as a behavior, not a logical thing to do, as it is detrimental to getting your message accross. Especially in this case, since there is no obvious need to do so.

  184. Therrin says

    Keep in mind that nettleingenting reserves the right to re-define words willy-nilly as required by his new paradigm. And English is his first language, not his last.

    No no, Erik’s the only one allowed to redefine words. Nettle is merely the self-referential glossary that leaves one flipping between Dunning and Kruger for hours.

  185. KG says

    nettleingenting,

    You are being presumptive. The idea that the Earth was the center of the solar system was redefine to be that the Sun was the center of the solar system. A “solar-centric” viewpoint was a new term necessary to describe a new paradigm.

    That is not a redefinition of an existing term. It is utterly absurd and dishonest to refer to a new theory as a redefinition.

    More important, redefining old terms is both necessary and happens all the time. See my explantation of moron above. Its redefinition was bizarre and inconsistent with its preceding meaning.

    More dishonesty. That was not a redefinition within science, let alone an attempt by one person in a single paper to redefine existing scientific terms that have clear, commonly understood and current scientific meanings. It was the adoption of a scientific term into everyday language, parallel to those of “ecology” and “quantum” more recently. None of these adoptions changed the scientific meaning of the terms.

  186. says

    pentatomid
    words change meaning all the time — and in important way.

    For example, the world used to use the word homosexual as the description of a disease. Only slowly did the concept emerge that the word homosexual did not refer to a disease. The word was slowly being used in a different way than the rest of the world (some parts still hold homosexuality to be some sort of illness).

    So, how was this not a logical thing to do? Is the new usage of the word homosexual detrimental to getting your message across? Should we return to its old usage just because “it seems to work fine and everybody understood it”? Seems illogical.

    More logical is to accept its new meaning and realize that there will necessarily be confusion, as indeed we find with the word homosexual. Michele Bachmann’s husband claims to be able to “cure” homosexuality. So, is it back to being a disease? Confusing!

    Keep in mind, Erik is defining a new paradigm. Much as the word ether changed its meaning in the shift to modern science, so are words changing to fit Erik’s paradigm.

  187. KG says

    I’d currently be willing to make a small but significant bet that “nettleingenting” is none other than Erik Andrulis.

  188. says

    3. Heck, even the present “central dogma” shows that sulfur is nowhere to be found in the cell until the production of cysteine and methionine. This is basic biochemistry.

    It may well be basic biochemistry (even though I don’t remember ever having encountered this claim when I took basic biochemistry at university, but that could be me. It never was my strongest subject), nevertheless: Provide citation please. Shouldn’t be too hard to find, if it’s so basic. Right?

  189. says

    KG

    You remind me of Galileo’s comment on his critics.

    Looking at the moon through a telescope, he found it was not a perfect sphere but covered with craters. His critics did not believe him — and refused to look through his telescope because they KNEW the moon had to be a perfect sphere. They said, well, if you see craters, then we know the moon must be surrounded by a perfect INVISIBLE sphere. Galileo, who was wonderful with this kind of stuff replied, well then, how do you not know that the perfect invisible sphere is surrounded by an invisible sphere of craters.
    Their reply, with ire, was that we KNOW things are immutable.

    To which Galileo said, I wish they were all like their beliefs. Immutable, unchangable, and incapable of spreading their ignorance.

    KG, you are very much like Galileo’s critics. Perhaps, you are a fan of retro-futures.

  190. Mr. Fire says

    Nope, nettleingenting. You just really don’t understand what an ad hominem is.

    I was hoping you’d be the first to get it, but I guess the quest continues.

    +++++++++++++

    In more relevant vein: nettleingenting, why do you insist on using circular arguments and just-so stories, such as tornadoes and fingerprints, justify the existence of gyres?

  191. says

    I’m no scientist, but as a linguist I can tell that nettle has trouble understanding the difference between concept and word.

  192. says

    pentatomid

    check any biochem textbook. sulfur is nowhere to be found until you get to cysteine and methionine.

    I have taught biochemistry, so it is one of my strong subjects.

    Asking for a citation or reference on this subject is like asking for a reference on DNA having genes. Silly.

  193. Mr. Fire says

    The homosexual gambit has to be the most bizarre strawman I’ve seen in a long time.

    Therrin’s right. You’re really starting to melt down into grandiose, deranged rambling, nettleingetting.

  194. Nerd of Redhead, Dances OM Trolls says

    Still waiting for your evidence nettles. Silent as far as peer reviewed scientific literature citations for gyres in biology, cosmology, etc. I wonder why that is???

    KG, you are very much like Galileo’s critics.

    Nope, KG is a realist, unlike you. There is no evidence for gyres, as you haven’t presented any. Putting an idea out is not the same as putting out a true scientific theory, which requires solid and conclusive evidence. Oh, and give up the sockpuppeting Andrulis.

  195. says

    words change meaning all the time — and in important way.

    As has been pointed out to you, yes we know words change their meaning, but hardly in this manner. This has all been pointed out to you, in particular by KG. Also, the analogy with homosexuality fails completely: homosexuality still means being sexually attracted to the same gender. This used to be regarded as a disease and now it isn’t anymore, but the basic meaning (sexual attraction or behaviour between individuals of the same gender) hasn’t changed. Now if homosexuality had suddenly come to mean ‘the color blue’, then that would be closer to what Andrulis is doing here. Surely you can see that someone referring to smurfs as homosexual is not exactly productive if all he wants to do is make a statement on the color of smurfs.
    Seriously, changing the meaning of amino from ‘containing an amine group’ to ‘biochemical compound containing sulfur’ is in no way logical. I, and others here, have given you reasons why. You’ve failed to adress them and only repeated why Erik Andrulis apparantly chose to execute this change. Having a reason to do something, however, does not equate to having a logically sound and good reason to do something.

  196. says

    Mr. Fire
    “grandiose, deranged rambling”
    You are not making sense again. I presented a coherent change in the meaning of a word. What is grandiose about that? Absolutely nothing, but you see so full of outright hatred, that logical won’t stop you from making untenable comments. Weird.

    Nerd of Redhead, Dances OM Trolls
    “There is no evidence for gyres”
    I prvoided some simple ones here, and the paper is loaded with evidence. But you don’t care, I know.

    There are those that see; there are those that see when they are shown; and there are those that refuse to see.
    Nerd of Redhead, Dances OM Trolls, you are the last.

    You have been shown the paper, but gosh it’s hard to understand!

    Far easier to just argue for its own sake about something about which you remain willfully ignorant.

    Why bother learning anything difficult and new, right?
    Just watch Dancing with the Stars with a bowl of popcorn. Now that’s more like it.

  197. Nerd of Redhead, Dances OM Trolls says

    You have been shown the paper, but gosh it’s hard to understand!

    Nope fuckwitted idjit, it is easy to understand, as a 30+ year practitioner of science, and a 25+ year skeptic. It is crankdom at its best. Full of sound and fury, but not proper scientific evidence, lacking the scientific rigor to make it into even a bad paper, which is the best it can hope for. Nothing but inane ideas badly expressed. Boring and irrelevant, just like all your posts to date. Care to play some more?

  198. KG says

    nettleingenting@245,

    You can’t answer my point, so you babble nonsensically about Galileo. A sure sign of the crank.

  199. says

    Actually I’m wrong but not wrong

    The dangerous materials definition of an oxidizing agent is a substance that is not necessarily combustible, but may, generally by yielding oxygen, cause or contribute to the combustion of other material (Australian Dangerous Goods Code, 6th Edition). By this definition some materials that are classified as oxidizing agents by analytical chemists are not classified as oxidizing agents in a dangerous materials sense. An example is potassium dichromate, which does not pass the dangerous goods test of an oxidizing agent.

    I made the mistake because I tend to think of Oxidizers as the safety classification while thinking of oxidizing agents as those involved in redox.

  200. says

    Nah, since you seem to know everything about everything, I’ll be glad if you get back to me after you’ve read an introductory book on semantics.

    (My comment was merely a popcorn eating from the sidelines kind of statement anyways.)

  201. says

    It still is my point that you don’t know what you’re talking about.

    Have you not taken basic chemistry? Your definition is nonsensical.

    Because I find it hard to believe someone could actually be around chemicals and not have noticed this usage.

  202. KG says

    I presented a coherent change in the meaning of a word. What is grandiose about that? – nettleingenting

    Even if it were coherent, it would still be the height of grandiosity for a single scientist to presume that they could, unilaterally, completely alter the meaning of a well-understood scientific term.

  203. says

    pentatomid
    Your criticisms are mostly fair. The reference to the color blue is strange. The change of *focus* is the key to what Erik is doing. You don’t have to like it, but he is simply saying we should notice the emergence of sulfur.

    The fundamental meaning of homosexual HAS changed, but I guess you don’t consider the idea of a sick person becoming totally healthy after a bunch of psychologists voted on the idea to be a dramatic change. I can’t think of any physical disease cured by a bunch of psychologists voting.

    Sure, part of the original meaning of homosexual persists, and you may consider it to be the core part. But then, I suspect if you were a homosexual subjected to “treatments” you would probably be thinking that you were sick first — and that your sickness was the homosexuality. Just my speculation, I admit.

    Again, I just explained Erik’s reasoning for the focus on sulfur. I can understand why you disagree. Not really a big deal.

  204. says

    You do not have to like Erik’s reasoning and focus on sulfur. I’m just the messenger.

    I strongly suspect this is a lie.

    I can’t imagine anyone other than a troll looking for lulz or the author themselves going around in circles this long in impotent defense

  205. says

    The fundamental meaning of homosexual HAS changed, but I guess you don’t consider the idea of a sick person becoming totally healthy after a bunch of psychologists voted on the idea to be a dramatic change. I can’t think of any physical disease cured by a bunch of psychologists voting.

    FFS. The definition didn’t change at all, the prognosis that it was a disease did.

    Red Pandas and Great Pandas both have the definition Panda, since we started investigating we’ve corrected an error and seen that red pandas are not bears and are closer to weasels and skunks while Great Pandas are bears. Their definition is the same they just go on a different shelf.

  206. says

    A gyrosystem whose gyrapex is not triquantal

    This is where I start to have problems with the theory. If a gyrapex is not triquantal, would not any vit in nearby paravot be less than instantly regfo? And any new vit be inverted due to the excessive plig?
    It would also seem to imply a central grand knusp zilping a massive and glorious whonbley. And this is indefensible, given the mighty philharmonic gesticulative nature of the emissions and the 641-faceted implosion that results when a fejrath strikes a non-anti fejrath.
    Or is everyone too lazy to understand?

  207. Therrin says

    Sure, part of the original meaning of homosexual persists, and you may consider it to be the core part.

    The etymological part? Yeah, I consider that pretty “core”.

  208. Nerd of Redhead, Dances OM Trolls says

    Again, I just explained Erik’s my reasoning for the focus on sulfur. I can understand why you disagree. Not really a big deal.

    FTFY. What is a big deal Erik is your lying about who you are. Little lie, big lie.

  209. says

    pelamun
    A strange, sarcastic comment that contradicts your earlier one. But ok.

    Nerd of Redhead, Dances OM Trolls
    “Nope fuckwitted idjit,” such flattery makes me blush.
    “it is easy to understand, as a 30+ year practitioner of science, and a 25+ year skeptic”
    No. With your experience you have too much invested in the present theories of science to spend precious time on a radically new theory. You have absolutely every reason to stick to “what works” and avoid the radically new.
    This paper is not for you.

    KG
    “Even if it were coherent, it would still be the height of grandiosity for a single scientist to presume that they could, unilaterally, completely alter the meaning of a well-understood scientific term.”

    Ah, so you are redirecting your criticism toward Erik and now. Well, here I can agree with you. I’ll go further. The entire paper is grandiose.

    We Are Ing
    Your comment doesn’t really make sense. Just to be clear, an oxidizer causes oxygen to bind to something. Sure, oxygen may be released first, but then it has to bind to something to be an oxidizer. A tank of oxygen that just is releasing oxygen into a room is not an oxidizer.

    In contrast, a tank of oxygen feeding an acetylene torch, IS an oxidizer because it is oxidizing the acetylene to form a flame.

  210. says

    Your comment doesn’t really make sense. Just to be clear, an oxidizer causes oxygen to bind to something. Sure, oxygen may be released first, but then it has to bind to something to be an oxidizer. A tank of oxygen that just is releasing oxygen into a room is not an oxidizer.

    In contrast, a tank of oxygen feeding an acetylene torch, IS an oxidizer because it is oxidizing the acetylene to form a flame.

    Wait wait wait wait wait…this is the definition that right before you said was wrong and that I was an idiot for making? You realize that right?

  211. Nerd of Redhead, Dances OM Trolls says

    Erik, you do realize that defending your inane paper like you have all afternoon is utterly and totally unprofessional. Do you really want your department head to hear about it?

  212. truthspeaker says

    Science will stick with broken theory until something better comes along AND is understood.

    Yes, that’s the idea. That’s the strength of science.

  213. says

    We Are Ing

    We are misunderstanding each other on this subject. The whole point of oxidation is NOT the release of the oxygen, as oxygen can be released without any effect. The point is the binding of the oxygen to something. It is the binding that is the oxidation.

    I hope that explanation clears the matter of oxidizer up.

  214. truthspeaker says

    • Galileo

    • You haven’t taken the effort to understand my radical new theory.

    • Anybody who ignores my idea has a vested interest in stifling innovation.

    • I’m being persecuted or silenced because my idea is so radical.

    Did I miss any? I only need one more for Bingo.

  215. says

    Nerd of Redhead, Dances OM Trolls

    “Erik, you do realize that defending your inane paper like you have all afternoon is utterly and totally unprofessional. Do you really want your department head to hear about it?”

    Your comment made me laugh a bit.

    I don’t think the department head will care, since I am not Erik, though I’m flattered you would think so.

    I do know Erik well, as I have indicated before.

  216. says

    Ing, I’m not familiar with Adventure Time or Ricardo, but if you spent, say, a paragraph talking about them it would contain more real, useful information than Eric/Nettles entire output here.

  217. truthspeaker says

    pentatomid says:
    13 February 2012 at 4:30 pm

    See, to me, what Andrulis is doing by redefining the meaning of ‘amino’ to ‘emphasize the fact that sulfur arose first in aminoacids’(citation needed, nettleface) is something like the following (and I know the analogy I’m about to give isn’t perfect).
    Suppose I’m writing a paper on some Mirid bugs. The species I’m writing about is a bright green species with white stripes all over its body. However, the particular bright green color arose first in a different species, which doesn’t have white stripes, but has black dots all over its body. Hence the color green shall now be refered to as ‘having black spots’, to emphasize this fact.

    It’s the science equivalent of Cockney rhyming slang. As a student of linguistics, I approve.

  218. KG says

    Ah, so you are redirecting your criticism toward Erik and now. Well, here I can agree with you. I’ll go further. The entire paper is grandiose. – nettleingenting

    I’m assuming that you are Erik.

    You do realise that “grandiose” is not generally a term of approbation?

  219. says

    @Nettle

    Noooooooooooooo…in the safety classification an oxidizer is something that contributes to combustion typically by yielding oxygen.

    In chemistry oxidizers remove electrons.

    Your original point seemed to be that one would think oxidizing equations needed oxygen.

    The word oxidation originally implied reaction with oxygen to form an oxide, since (di)oxygen was historically the first recognized oxidizing agent. Later the meaning was generalized to include all processes involving loss of electrons.

    Substances that have the ability to oxidize other substances are said to be oxidative or oxidizing and are known as oxidizing agents, oxidants, or oxidizers. Put another way, the oxidant (oxidizing agent) removes electrons from another substance; i.e., it oxidizes other substances, and is thus itself reduced. And, because it “accepts” electrons, it is also called an electron acceptor.

    Oxidants are usually chemical substances with elements in high oxidation states (e.g., H2O2, MnO−
    4, CrO3, Cr2O2−
    7, OsO4), or else highly electronegative elements that can gain extra electrons by oxidizing another substance (O2, F2, Cl2, Br2)

    I’m baffled with how you’re now getting the definition wrong. Because now you seem to be imply that oxidation requires some oxygen in the equation.

    http://www.newton.dep.anl.gov/askasci/chem03/chem03893.htm

  220. says

    truthspeaker
    • Galileo
    I don’t know what you mean here. I will presume you are saying that it is the height of arrogance to compare a radical new theory to a historical figure who created radically new theories. Not sure why this comparison is an issue at all, though.

    • You haven’t taken the effort to understand my radical new theory.
    It’s HARD to learn the radically new. Why bother trying? Hell, why continue to learn anything after graduation?

    • Anybody who ignores my idea has a vested interest in stifling innovation.
    This claim is absurd. Most people either won’t care or try. Those who wish to stifle innovation are the minority.

    • I’m being persecuted or silenced because my idea is so radical.
    I would say Erik is being ostracized and you do know that CWRU retracted their publicity because two physicists were “embarrassed” (threatened) by having a mo bio professor have the audacity to tread on their sacred ground.

    Did I miss any? I only need one more for Bingo.
    I would say you missed the entire point of the paper, and that you probably will choose to ignore its content rather than do the tough mental labor of trying to understand it.

    So, Bingo!

  221. says

    The definition of homosexuality changed due to changing social attitudes. The label, though somewhat offensive due to the original definition, would still apply to the exact same people. The target objects (in this case, people) remains the same. Our social attitudes about those objects (in this case, people) has changed.

    It seems the re-definition of amino changes the group of objects to which it applies. This is a radical and senseless re-definition, one that is far more confusing than helpful, most especially to those who use the term precisely — that is, practicing scientists, the very audience Erik hopes to target.

    It doesn’t make the concepts clearer. Instead, it obfuscates and misdirects. This will tend to have the exact opposite effect intended.

    Unless, that is, obfuscation and confusion is the intent.

  222. says

    We Are Ing

    It’s simply a matter of focus. “Put another way, the oxidant (oxidizing agent) removes electrons from another substance; i.e., it oxidizes other substances, and is thus itself reduced. And, because it “accepts” electrons, it is also called an electron acceptor.” That is the oxidative process.

    I already said that fluorine and chlorine can also act as oxidizers.

    KG
    I’m assuming that you are Erik.
    Assume away.
    I will assume you are the Queen of Norway.
    I know with certainty that you are wrong in your assumption, as I am not he. I’ve already said that I know him, though.
    I have no idea if you are indeed the Queen of Norway, though.

    You do realise that “grandiose” is not generally a term of approbation?
    yep.

  223. Ariaflame, BSc, BF, PhD says

    In any case, unless Erik provides some indication of what it would take to prove his hypothesis or idea wrong it can be safely put on the shelf with the other interesting, or in this case baffling ideas about the universe. If the is no way to test it, then we have no obligation to take it seriously.

    Arguing about minutiae and his misappropriation of scientific terms doesn’t address this.

    The reference to the uv catastrophe is misleading because in that situation new science was needed to explain something that the established theories failed at. Here there does not appear to be any such failure of current theories.

  224. says

    It’s simply a matter of focus. “Put another way, the oxidant (oxidizing agent) removes electrons from another substance; i.e., it oxidizes other substances, and is thus itself reduced. And, because it “accepts” electrons, it is also called an electron acceptor.” That is the oxidative process.

    I already said that fluorine and chlorine can also act as oxidizers.

    I KNOW THAT YOU FUCKING IDIOT! That’s what I said.

    You said

    We are misunderstanding each other on this subject. The whole point of oxidation is NOT the release of the oxygen, as oxygen can be released without any effect. The point is the binding of the oxygen to something. It is the binding that is the oxidation.

    Which is wrong in BOTH senses of the term. The strict chemical sense it is wrong because oxygen isn’t required, in the materials safety sense it is wrong because they’re concerned with the YIELDING of oxygen, not it’s binding.

  225. Nerd of Redhead, Dances OM Trolls says

    You haven’t taken the effort to understand my radical new theory IDEA.

    It’s only an idea, not a theory. It does’t have the evidence required to be a theory.

    I’m being persecuted or silenced because my idea is so radical.

    Har. You aren’t being persecuted, as nobody is coming knocking on your door. You aren’t being silenced. Your inane and stoopid paper is still out there. Nobody expects you take it back. We just expect you to take your lumps for being a doofus like any responsible adult should. The best thing you can do is to just lay low and let it blow over. People have short memories.

    I don’t know what you mean here. I will presume you are saying that it is the height of arrogance to compare a radical new theory to a historical figure who created radically new theories. Not sure why this comparison is an issue at all, though.

    Galileo had real enemies, who threatened him with torture. You aren’t being threatened at all. Galileo also had the conclusive evidence that you lack. There is no comparison except in your paranoid and delusionally romantic mind.

    I would say Erik is being ostracized and you do know that CWRU retracted their publicity because two physicists were “embarrassed” (threatened) by having a mo bio professor have the audacity to tread on their sacred ground.

    No, it came about because of arrogance and stupidity on Erik’s part. If he really had the evidence, no problem. But there is no evidence for the gyres…

  226. says

    nigelTheBold, Abbot of the Hoppist Monks

    “It seems the re-definition of amino changes the group of objects to which it applies.”

    Only at first blush and for those who don’t know enough biochem to know that the amino acids cysteine and methionine are the primary carriers of sulfur

    From the paper: of or relating to sulfur compounds, amino acids, polypeptides

    While the introduction of the word sulfur is novel, it is logical as I previously indicated and notice that “amino acids, polypeptides” are there too. So, I think this idea is not really that confusing. The redefinition is merely an expansion on of the definition.

    I hope that clears up the amino argument.

  227. KG says

    CWRU retracted their publicity because two physicists were “embarrassed” (threatened) by having a mo bio professor have the audacity to tread on their sacred ground. nettleingenting

    The press release is still there, at the other end of PZ’s link. One only has to read it to know that the paper it refers to is almost certainly a complete load of tosh. Just so everyone can judge this for themselves, here it is:

    Newswise — The earth is alive, asserts a revolutionary scientific theory of life emerging from Case Western Reserve University School of Medicine. The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects—for example, planets, water, proteins, and DNA—are animate, that is, alive. With its broad explanatory power, applicable to all areas of science and medicine, this novel paradigm aims to catalyze a veritable renaissance.

    Erik Andrulis, PhD, assistant professor of molecular biology and microbiology, advanced his controversial framework in his manuscript “Theory of the Origin, Evolution, and Nature of Life,” published in the peer-reviewed journal, Life. His theory explains not only the evolutionary emergence of life on earth and in the universe but also the structure and function of existing cells and biospheres.

    In addition to resolving long-standing paradoxes and puzzles in chemistry and biology, Dr. Andrulis’ theory unifies quantum and celestial mechanics. His unorthodox solution to this quintessential problem in physics differs from mainstream approaches, like string theory, as it is simple, non-mathematical, and experimentally and experientially verifiable. As such, the new portrait of quantum gravity is radical.

    The basic idea of Dr. Andrulis’ framework is that all physical reality can be modeled by a single geometric entity with life-like characteristics: the gyre. The so-called “gyromodel” depicts objects—particles, atoms, chemicals, molecules, and cells—as quantized packets of energy and matter that cycle between excited and ground states around a singularity, the gyromodel’s center. A singularity is itself modeled as a gyre, wholly compatible with the thermodynamic and fractal nature of life. An example of this nested, self-similar organization is the Russian Matryoshka doll.

    By fitting the gyromodel to facts accumulated over scientific history, Dr. Andrulis confirms the proposed existence of eight laws of nature. One of these, the natural law of unity, decrees that the living cell and any part of the visible universe are irreducible. This law formally establishes that there is one physical reality.

    Another natural law dictates that the atomic and cosmic realms abide by identical organizational constraints. Simply put, atoms in the human body and solar systems in the universe move and behave in the exact same manner.

    “Modern science lacks a unifying, interdisciplinary theory of life. In other words, current theories are unable to explain why life is the way it is and not any other way,” Dr. Andrulis says. “This general paradigm furnishes a fresh perspective on the character and meaning of life, offers solutions to protracted problems, and strives to end divisive debates.”

    One debate swirls around the scientific merit of James Lovelock’s popular Gaia hypothesis. By showing that the earth is theoretically synonymous with life, Dr. Andrulis’ paradigm substantiates the Gaian premise that all organisms and their surroundings on earth are closely integrated to form a single self-regulating complex system.

    Another legendary quarrel is that between biblical creationists and neo-Darwinian evolutionists. In demonstrating that the origin and evolution of life is a consequence of natural laws and physical forces, this theory synthesizes arguments and dispels assumptions from both sides of the creation-evolution debate.

    To test his paradigm, Dr. Andrulis designed bidirectional flow diagrams that both depict and predict the dynamics of energy and matter. While such diagrams may be foreign to some scientists, they are standard reaction notation to chemists, biochemists, and biologists.

    Dr. Andrulis has used his theory to successfully predict and identify a hidden signature of RNA biogenesis in his laboratory at Case Western Reserve University School of Medicine. He is now applying the gyromodel to unify and explain the evolution and development of human beings.

    Note the absurd reference to “the creation-evolution debate”. There is of course no such debate within the scientific community; a paper that “synthesizes arguments” from scientists on the one hand, and a parcel of ignorant ideologues on the other, is bound to be drivel. Of course, this could be the ignorance of those responsible for the press release, but if so, Andrulis himself should have, and preseumably would have, protested.

  228. Nerd of Redhead, Dances OM Trolls says

    Nettles/Erik, long past time to fade into the bandwidth, which was really prior to your first post. Why are you afraid to do so???

  229. says

    We Are Ing
    Ok. I accept your criticism. I have been too narrow in my definition.

    Ariaflame, BSc, BF, PhD
    In any case, unless Erik provides some indication of what it would take to prove his hypothesis or idea wrong it can be safely put on the shelf with the other interesting, or in this case baffling ideas about the universe. If the is no way to test it, then we have no obligation to take it seriously.

    A fair criticism.

    Arguing about minutiae and his misappropriation of scientific terms doesn’t address this.

    Ditto

    The reference to the uv catastrophe is misleading because in that situation new science was needed to explain something that the established theories failed at. Here there does not appear to be any such failure of current theories.

    Not true. Present science has plenty of theories that don’t quite work or don’t really work. I am not very knowledgeable about failures and omissions of present science, but if you are curious, check out this post.
    http://milesmathis.com/erik.pdf
    The author mentions several problems in contemporary science.

    Nerd of Redhead, Dances OM Trolls
    Again, the paper presents loads of evidence of gyres, but you don’t care enough to study the paper, and you ignore natural phenonomena like ocean currents, tornadoes, the orbit of the moon, etc. The evidence is overwhelming, but you are willfully ignoring it.

  230. KG says

    While the introduction of the word sulfur is novel, it is logical as I previously indicated and notice that “amino acids, polypeptides” are there too. So, I think this idea is not really that confusing. The redefinition is merely an expansion on of the definition.

    I hope that clears up the amino argument. – nettleingenting

    The term “amino” has a precise, agreed meaning in chemistry. It does not include the vast majority of sulphur compounds. Redefining “amino” to include all sulfur compounds because some amino acids include sulfur is like redefining “crustacean” to include all animals with eight limbs, because some crustaceans have eight limbs. It’s nonsense. It’s daft. It’s ludicrous dribble.

    I hope that clears up the amino argument.

  231. KG says

    Again, the paper presents loads of evidence of gyres – nettleingenting

    Can you really be as stupid as you appear? Nobody is denying that there are gyres. That does not imply that gyres explain life, the universe and everything. Really, the claim that they do makes no more sense than the humorous claim in The Hitchhiker’s Guide to the Galaxy that the answer to the ultimate question is 42.

  232. says

    KG,
    “The press release is still there, at the other end of PZ’s link.” Right. I did not say it was totally unavailable.

    “Note the absurd reference to “the creation-evolution debate”. There is of course no such debate within the scientific community;” Correct. But there still are people (like those who write scientific textbooks for Texas) who believe and promote creationism. So, there is an ongoing debate.

    Nerd of Redhead, Dances OM Trolls

    Again, I am not he. Erik would never waste his time here. In fact, he told me specifically to avoid this hole of hate, but I figured posting here would be fun.

  233. says

    KG,
    The majority of biological sulfur is in amino acids. Can you name any other biological molecule that contains as much sulfur as all the cysteine or all the methionine in organisms? No, Most of the sulfur is in those two amino acids. Nothing else comes close.

    “Nobody is denying that there are gyres.”
    You aren’t paying attention. One of your fellow haters was indeed denying the evidence of gyres.

    Now, if you can’t pay attention to others comments in this forum (and my responses), then you don’t stand a chance of understanding the paper.

    Don’t try.

    Just relax.

  234. 'Tis Himself, OM says

    Erik would never waste his time here. In fact, he told me specifically to avoid this hole of hate

    We’re not worth Erik’s time so instead we get the second string to try to peddle his bullshit to the intelligentsia.

  235. 'Tis Himself, OM says

    The majority of biological sulfur is in amino acids. Can you name any other biological molecule that contains as much sulfur as all the cysteine or all the methionine in organisms? No, Most of the sulfur is in those two amino acids. Nothing else comes close.

    So what? That still doesn’t mean Erik can usurp a legitimate scientific word with a universally (except for Erik) agreed upon meaning just because he’s run out of suffixes and prefixes to stick on the word gyre.

  236. says

    ‘Tis Himself, OM
    “We’re not worth Erik’s time so instead we get the second string ”
    Yes. Many of you have clearly indicated you aren’t worth any of his time.
    Second string? I am truly flattered! All through HS sports I was usually third string!

    “So what? That still doesn’t mean Erik can usurp a legitimate scientific word”

    More willfull ignorance. You clearly have not read the paper.

    From the paper: of or relating to sulfur compounds, amino acids, polypeptides

    The majority of biological sulfur is in amino acids! Why does it make you so uncomfortable to address this simple fact explicitly?

  237. KG says

    nettleingenting,

    So, there is an ongoing debate.

    There is, as I said, no scientific debate; and the press release specifically says that the paper “synthsizes arguments” from “both sides” of the debate. So it is saying the paper takes the arguments of the ignorant ideologues seriously, and incorporates them. Either the author approves this implication, or he does not. Which is it?

    The majority of biological sulfur is in amino acids.

    That’s completely irrelevant. It wouldn’t matter if all biological sulfur was in amino acids, the attempt at redefinition is still daft.

    You aren’t paying attention. One of your fellow haters was indeed denying the evidence of gyres.

    No, he wasn’t. He was denying the existence of the gyres, i.e. those in the paper – the ones that explain life, the universe and everything.

  238. KG says

    Well, I’m off to bed. Idiot Erik will no doubt continue his dribblings for a few hours yet. Have fun!

  239. Nerd of Redhead, Dances OM Trolls says

    More willfull ignorance. You clearly have not read the paper.

    Nobody has to read your idiocy. The paper crankdom, as everybody with half a mind could see from the description.

    The majority of biological sulfur is in amino acids! Why does it make you so uncomfortable to address this simple fact explicitly?

    And this has to do with gyres how???? Irrelevancy and arrogance.

    Again, I am not he. Erik would never waste his time here. In fact, he told me specifically to avoid this hole of hate, but I figured posting here would be fun.

    And why should I believe a liar and bullshitter, and confessed troll, who doesn’t understand how science operates? Again, Erik, this is utterly and totally unprofessional, even if he sent a loser like you to defend his sorry ass, which shows his desperation if true.

  240. says

    Ok.

    You guys have now bored me.

    Your closed minds and bizarre misinterpretations of what I say have grown tiresome.

    Also, your need to hurl insults at me just reveals that many of you are terribly insecure. Such a shame.

    I’m sure you’ll have fun tormenting the next person trying to contribute constructively!

    Nonetheless, I wish you all well.

  241. Mr. Fire says

    check out this post.
    http://milesmathis.com/erik.pdf
    The author mentions several problems in contemporary science.

    Oh good Christ. Are you still plugging this crackpot bullshit? The post that says utterly demented, paranoid craziness like:

    Who is Jesse Emspak? A top physicist or chemist? No. He is a freelance journalist who is a mutual funds reporter for Investor’s Business Daily and other such places when he isn’t providing agitprop for Discovery News or Space.com. Sounds fishy to me already. I am just going to assume he is with some government agency until he proves he isn’t. This is a good bet, since most of what you read under major mastheads—on the internet and off—is written now by government agencies or at their behest.

    +++++++++++++++++++

    In a totally unrelated point, I’d like to ask you what you think an ad hominem is.

  242. Nerd of Redhead, Dances OM Trolls says

    You guys have now bored me.

    We were bored from your first insipid post.

    Your closed minds and bizarre misinterpretations of what I say have grown tiresome.

    Scientific minds that require actual evidence, not just claims. We are tiresome to the liars and bullshitters.

    Also, your need to hurl insults at me just reveals that many of you are terribly insecure. Such a shame.

    Well, if you ever provided real evidence, and didn’t keep avoiding that issue, your treatment would have been different. But you behaved and responded like a troll, not an honest person in a discussion.

    I’m sure you’ll have fun tormenting the next person trying to contribute constructively!

    Hopefully they will back up their inane claims with real evidence. It does make a difference. Hint, the links you presented to peer reviewed scientific literature? OH, that’s right, you didn’t link…

  243. says

    nettleingenting:

    Only at first blush and for those who don’t know enough biochem to know that the amino acids cysteine and methionine are the primary carriers of sulfur

    And that has to do with the word “amino,” how exactly?

    If Erik is that unconcerned with precise language in a field in which precise language is paramount, that’s his business. But he shouldn’t be so surprised when this results in ridicule. And the stupid thing is, he could have avoided that criticism simply by using the “thio” prefix.

    Plus, thiogyre has a really great sound to it, don’t you think? I’m sure it’s important. Revolutionary, even.

    In any case, I’m a bit confused. Would “amino” still include all amino acids, or only the two with sulfur?

  244. 'Tis Himself, OM says

    Listen, you stupid, smug twit, amino is a term with a specific chemical meaning. So what if a couple of amino acids have sulfur, most amino acids do not. As has been pointed out, there’s another term, thio, used to describe compounds containing sulfur. There’s no reason for Erik to try to redefine a term with an agreed upon meaning when there’s already another term with the definition Erik is trying to use.

    Also, your need to hurl insults at me just reveals that many of you are terribly insecure.

    No, asshole, the reason you’re insulted is you’re an arrogant, pompous prig defending the indefensible.

  245. says

    After an initial read-through, I have to admit I have no fucking clue what the paper is about.

    The proposal is put forth not to explain anything unusual. It was not prompted by a specific lack, but a general one: the fact that we don’t have a grand unified theory of everything. It’s like the author realized this lack, and thought to himself, “There’s gotta be an explanation for everything.”

    And, seeing that swirls and cycles exist in all kinds of things, from galaxy clusters down to DNA strands and smaller, through magnetic fields to ocean waves, the author decided, “Yeah. Swirls and cycles. It’s all swirls and cycles, all the way down. There’s gotta be a great word for that.”

    Unlike Galileo, there are no bits of strange data to explain, that run counter to existing theories. There’s no measurements of the movement of the planets running contrary to accepted models. Unlike Galileo, there is less concern with congruence with reality, and more with the internal consistency of the model itself.

    As for the claim of “life,” I’m still not clear on how that’s achieved.

    The lack of mathematics is notable. There is no clear way that I can see to draw any of the known relationships from this proposal, let alone a clear path to reconciling QM with general relativity — the ultimate test of any theory of everything.

    For some reason, the paper reminded of of the Exceptionally Simple Theory of Everything, only without any kind of mathematical rigor. Lisi, at least, has proposed a full model open to analysis and critique (the primary critique focusing on the problem of non-chirality). Also, there is a logical basis for proposing an E8 lie group as the fundamental framework of everything, whereas the gyre concept seems to have no such logical basis.

    All-in-all, the crank-index is pretty damned high, mostly due to its non-standard use of standard language (which is fairly pervasive, and not limited to “amino”), special cases, and general lack of predictive power. As for its purported “explanatory” power, I’ll wait to see if anyone can derive general relativity and/or quantum mechanics from it. Without that, it hasn’t explained shit.

  246. Mr. Fire says

    Post-game analysis:

    nettleingenting has not provided any actual evidence that they themselves understand what a gyre is, let alone that it is real.

    The initial post @140 contained dismissive and content-free Courtier’s Replies along the lines of:

    It requires HARD mental labor to begin to understand it, so most people will take the easy route and dismiss it.

    It was footnoted with a link to a screed from a unhinged crank.

    +++

    When then pressed for information about positive predictions the paper made, they saw fit @146 to paraphrase a half-baked, bastardized mishmash of facts and hypotheses that already exist (and of course with zero attempt to explain how the fuck gyres come into it).

    This was footnoted with the classic crank gambit of comparing the subject to Galileo. It’s like the crank Godwin or something.

    +++

    The post @160 consisted of whining and more Courtier’s Replies coupled with sneering demands to read the entire paper. All while not making any attempt to divulge what they understand about it.

    This was footnoted with the absurd (and gramatically-challenged) attempt to shift the burden of proof on everyone else:

    If you can’t explain the theoretical flaws in the paper’s explanation of the cell cycle, then you are intellectually lazy and are totally in your interest in this paper.

    Still no attempt to divulge their understanding of gyres.

    +++

    Posts 162 and 167 revealed an either embarrassing inability to grasp the idea of falsifiability or an embarrassing fail at reading comprehension.

    Footnoted by the same inane demand as in 160.

    +++

    Posts 176 and 179: some chest-beating and burden of proof-shifting. No light shed on gyres.

    +++

    Post 190 is where the ridiculous attempt to justify redefining ‘amino’ as ‘a sulfur containing compound’ begins.

    There are references to some interesting, pre-existing concepts in biochemistry, such as the Wobble Pairs and autocatalysis. And then with a swish of the hand the insinuation is made that Andrulis’ theory somehow explains these as well as or better what is currently out there. I don’t know whether this is clumsiness, or an underhanded attempt at blinding with science.

    Oh, and no mention of gyres.

    +++

    In 196 they are finally pressed into talking about gyres, which is where they come up with this chestnut:

    “How does one go about showing that gyres exist and are meaningful for science?

    You look.

    Fingerprints
    waves
    tornados
    cell cycle
    metabolism
    circadian rhythms

    Utility: gyres unify all of science, thus we see how the turnover of high energy phosphates, for example, is tied in to the cell cycle.

    If only I would just read the whole paper I would understand what this non-explanation means! nettleingenting sure isn’t going to provide any clues! That would involve actually having to say something meaningful!

    +++

    Things circle around for a bit with the same bullshit getting re-asserted. At 228, nettleingenting makes the signature dumbass move of not knowing what an ad hominem is.

    +++

    After that, more dancing about the amino bullshit, more pomposity, more something-something-I-don’t-care-because-my-eyes-are-glazing-over.

    Oh, and no explanation of what gyres are.

    +++

    Finally @302: a textbook flounce. Multiple standard sneering parting shots.

    Will they stick to it though? Or will the gyres – whatever the fuck they are – bring nettleingenting back?

  247. says

    Holy Handgrenade, how dense can you get. Seriously.

    “So what? That still doesn’t mean Erik can usurp a legitimate scientific word”

    More willfull ignorance. You clearly have not read the paper.

    From the paper: of or relating to sulfur compounds, amino acids, polypeptides

    The majority of biological sulfur is in amino acids! Why does it make you so uncomfortable to address this simple fact explicitly?

    First of all, you don’t have to have read the paper to understand that the redefenition of an existing word with a very precise meaning in science is just a very stupid idea. End of. You’re done.
    Secondly, noone here is uncomfortable with adressing ‘this simpe fact’, since we have adressed it. Adressed it by saying: so fucking what. Seriously, I don’t care if all the sulfur in the galaxy was in a couple of amino acids. That still would not be a good reson to use a word meaning ‘containing an amine group’ to suddenly denote ‘sulfur compounds, amino acids, polypeptides’. Not in the least because there are still amino-compounds (the real defenition, not Erik’s weird ass nonsense) not covered in the new definition. Aminoacids aren’t the only things ‘amino’, mister I’m so good at biochemistry nettleface.

    Also, he has no idea how a language actually evolves.

    check any biochem textbook. sulfur is nowhere to be found until you get to cysteine and methionine.

    I have taught biochemistry, so it is one of my strong subjects.

    Asking for a citation or reference on this subject is like asking for a reference on DNA having genes. Silly.

    Asking for sources is NEVER silly, even if that source was a general biochemistry book or website. Given the nonsense nettleface is spouting, I can’t go and assume that he’s corect on this. That’s like assuming Kent Hovind knows something about carbon dating.

    When asked about falsifiability, he responds:

    Of course I know what unfalsifiable means. Geez. English is my first language.

    Unfalsifiable means that it can’t be proven false.

    Naturally, if “unfalsifiable” is an incorrect claim, the paper can indeed be proven false!

    So, prove it false! Come on guys, you can do it. Right?
    Actually, judging from the level of discussion here, I think few if any of you can.

    Demonstrating that he has absolutely no idea what unfalsifiable means. As I have stated before, a good scientific theory is falsifiable, but not false.

    When asked for evidence, he just names random cyclical events and, well basically, things that look sort of roundish. Why exactly are these things evidence for Andrulis’ wonedrfull magical ‘theory’? Oh right, I probably haven’t done enough hard work to understand. Tell me, do I need to have faith as well? Every time someonedisagrees with him, nettleface goes on to claim that they haven’t studied the paper, are ignorant or can’t comprehend him.

    Arrogant and dishonest, that’s what this guy is.

  248. KG says

    Asking for a citation or reference on this subject is like asking for a reference on DNA having genes. – nettleingenting

    This prime piece of idiocy has not been commented on. “DNA having genes”? WTF is that supposed to mean?

  249. says

    nigelTheBold

    And the stupid thing is, he could have avoided that criticism simply by using the “thio” prefix.

    Yep. I’ve mentioned that to old nettleface a couple of times now. His reply was yet another rehashof Andrulis’ reasons for doing this:

    Yes this usage is important. Yes thio exists, so does mercapto. The point of the usage, as I have explained, is to emphasize that with amino acids comes sulfur. It’s the sulfur that is special, so Erik focusses on that. It just happens to emerge with amino acids, so that is what should define them — not the amino or the acid. Focus on the emergence of sulfur which, critically, happens with amino acids. He’s saying that the attention to the amino acid is misplaced and that the incorporation of sulfur in cellular systems is key. Confusing, yes. Logical, yes.

    Followed by this, which I don’t really get.

    An elaboration/clarification
    Mercapto is inherently confusing. I have worked with, say, mercaptoethanol. Fun for pranks sure. But, I have never, ever used it with mercury. Maybe its just me, but I think mercaptoethanol would make no sense to a layman, were you to say, you see, the mercapto means it has sulfur.

  250. says

    pentatomid:

    Yep. I’ve mentioned that to old nettleface a couple of times now.

    Yeah. I basically stole it from you, as it’s been far too long since I’ve taken any chemistry to recall that off the top of my head. As a physics major, I never bothered committing those to memory past the semester.

    What I don’t get (and I didn’t quite get from the paper) was why Erik was making such a big deal about it. Sure, biologically it shows up almost exclusively in a couple of amino acids. But so what? What’s the big deal? What was he trying to demonstrate?

    There certainly wasn’t an over-arching premise here, other than “gyres are everywhere.” There’s a half-assed attempt at replacing quarks, but without any kind of actual physics. There was no attempt to demonstrate how to adapt a Feynman diagram, for instance, something which should be basic (especially considering there’s little math involved), and that (or something like it) is necessary to demonstrate that the model fits with observed reality.

    Anyway. I just don’t get what the paper was supposed to address, and I’m not sure all the things that were big deals in the paper are really big deals in reality.

  251. Antiochus Epiphanes says

    Look, Erik…errrr, nettleingenting, if you are still around: It would seem that the only two people who understand this revolutionary manuscript are you two. I’m not talking about just here. I mean among your colleagues. It is clear that you, ummm, I mean Erik, have failed to communicate something important. It’s not at all like Galileo peering through a telescope and declaring “craters!”‘ but more like if he declared “spaghetti sauce!”. Even, with understanding of the repurposed use of commonplace terms, I quickly get lost in the prose of this MS rather than in the concepts.

  252. KG says

    It’s not at all like Galileo peering through a telescope and declaring “craters!”‘ but more like if he declared “spaghetti sauce!” – Antiochus Epiphanes

    Now that’s just silly – IIRC, the spaghetti tree hadn’t even been discovered in the 16th century!

  253. says

    Ok. I accept your criticism. I have been too narrow in my definition..

    No your definition was just wrong. There were two possible contexts and it was wrong for both of them. Let me point out that your haranged and insulted me for using the definition of one context, while seemingly being ignorant of them.

    Now, IIRC the Redox reaction is one of those big important ones in chemistry that anyone seeking to overturn the paradigm of chemistry and physics should be very familiar with.

    Asking for a citation or reference on this subject is like asking for a reference on DNA having genes

    Jesus fucking christ.

    DNA is a chemical structure. Gene is the conceptual unit given to lengths of DNA or RNA

    A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a polypeptide or for an RNA chain that has a function in the organism.

    Again note with your odd focus on the RNA world that everyone knows RNA works perfectly fine as a genome medium. In fact IIRC the reason why life on earth probably has selected for DNA medium over RNA is that despite the fact that both have equal coding capacity, DNA as a double strand can be broken while preserving the information and it allows for autocorrecting mechanisms.

  254. says

    Asking for a citation or reference on this subject is like asking for a reference on DNA having genes. Silly.

    I hadn’t gone into the ‘DNA having genes’ thing before, since I thought I vaguely knew what nettleface was on about and his main point was that me asking for references was somehow ridiculous,so I chose to adress that. Having thought about it, though, makes me wonder if I did know what he was meant. After all, If netleface really is a biochemist, defending a theory with a lot of focus on RNA and DNA, this seems at best a very weird way of saying things, and at worst (and more likely) yet another display of his complete lack of understanding of, well, anything.
    Seriously, DNA has genes is a completely meaningless thing to say.

  255. Antiochus Epiphanes says

    An elaboration/clarification
    Mercapto is inherently confusing. I have worked with, say, mercaptoethanol. Fun for pranks sure. But, I have never, ever used it with mercury. Maybe its just me, but I think mercaptoethanol would make no sense to a layman, were you to say, you see, the mercapto means it has sulfur.

    As usual, I’m not sure what the point was other than to demonstrate that the root “mercapto” was derived from mercury capitans, I guess because sulfhydryl groups bind mercury, but that’s not what that root means anymore.

    IDK.

  256. Owlmirror says

    For example Darwin’s theory of evolution can be falsified, for example by finding a fossil rabbit in Cambrian strata.

    I have argued against this elsewhere.

    The components of the theory of evolution are falsifiable observations about reproduction and survival. But “falsifiable” does not mean that an anomaly would prove the explanation false; the diversity of life on Earth would still be best explained by evolution, and a putative new anomaly would require a parallel explanation.

  257. says

    The components of the theory of evolution are falsifiable observations about reproduction and survival. But “falsifiable” does not mean that an anomaly would prove the explanation false; the diversity of life on Earth would still be best explained by evolution, and a putative new anomaly would require a parallel explanation.

    Okay, fine, my example wasn’t the best example out there. But my point about falsifiability still stands: nettleingenting doesn’t know what it means.

  258. says

    Ok. I’m back to offer you more material to misunderstand, ignore, or kick around. With the possible exception of nigelTheBold, Abbot of the Hoppist Monks, you guys seem incapable of deep critical thinking but are very skilled with making irrelevant comments and hurling insults.
    Bearing you no grudge and as a person who tries to be kind, I offer you an exchange from elsewhere to let you rejoice in your intellectual laziness!

    nigelTheBold, Abbot of the Hoppist Monks
    “And that has to do with the word “amino,” how exactly?

    If Erik is that unconcerned with precise language in a field in which precise language is paramount, that’s his business. But he shouldn’t be so surprised when this results in ridicule. And the stupid thing is, he could have avoided that criticism simply by using the “thio” prefix. ”

    As I indicated before, the full definition includes amino acids and peptides. Sulfur is found apart from cysteine and methionine only 30% of the time. So, Erik is emphasizing this critical biological fact by stating that amino includes (but is not only) sulfur. You don’t have to like that association, but a majority of the time, it is true. There is another important reason, but I already explained it. If you missed it, oh well.

    So, here is fun stuff for you to misunderstand. I’m sure you won’t let your ignorance stop you from making fools of yourselves. By the way, after these posts, I won’t play with you today.
    1. a critical comment
    2. my answer
    3. a non-response to my answer
    4. my final answer to the critic.

    1. a critical comment

    nettle, my comments identifying very specific examples of illogic were described here:

    http://retractionwatch.wordpress.com/2012/01/28/case-western-explains-why-it-withdrew-press-release-about-andrulis-origin-of-life-paper/#comment-9679

    perhaps you might want to address those specifically on that thread.

    Otherwise you seem to be playing the “I can understand Andrulis’s paper because I have advanced degrees in science” ploy. But I (and lots of others too) have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). Of course that doesn’t rule out the possibility that I can’t recognize paradigm-shifting brilliance when I see it, but it’s usually the case that remarkable insights in molecular life sciences are amenable to rather simple explanations (by far the hardest part of obtaining astonishing insight in molecular biology in its broadest sense is in overcoming experimental/technical issues).

    So Andrulis’ states (using straw-man, and non-sequitur type illogic) in his introduction : “Finally, the RNA (ribonucleic acid) world hypothesis posits that ribonucleotide-based genetic systems evolved prior to protein and deoxyribonucleic acid (DNA). This hypothesis does not fit well with the central dogma and is unable to resolve precisely how the translation apparatus, genetic code, and biometabolic pathways evolved [7-9].”

    Yor task, nettle, (since you understand Andrulis’ paper very well), is to explain to us in simple terms how Andrulis’s hypothesis “resolves precisely how the translation apparatus, genetic code, and biometabolic pathways evolved”.

  259. says

    2. my answer

    Nice, you and I both have similar experience, as I have worked in chemistry, biochemistry in molecular biology laboratories in Cambridge and Southern California. I didn’t mean it as a “ploy.” I meant it to be genuine. But I digress.

    Frankly, I don’t see the illogic nor do I see the non-sequitur nature of that quote you gave. Perhaps that’s because I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma) and the central dogma says nothing about the origin and evolution of RNA. The point Erik was trying to make is that current models/theories/hypotheses/ideas are ad hoc and thus should be considered provisional at best and wrong at worst. Could you point out the illogic there?

    As for how theory treats those three problems (translation apparatus, genetic code, and biometabolic pathways), I would call your attention to where these problems are treated:

    – p. 43 Origin of the genetic code

    Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system. The tri-quantal system (as he calls it) is the tri-nucleotide, with each component of the system having a relative amount of energy (see section 2.4.5, pp. 13-14), “(i) a high energy (exergic), unstable, excited form; (ii) an intermediate energy, quasi-stable, transition form; and (iii) a low energy, stable, ground form.” My read of this is that the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code. Is there a problem with the interpretation that I am missing?

    Erik has proposed that the code evolved autocatalytically, from the metabolism of the orthophosphate bonds between the 2nd and/or 3rd nucleotides. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems. I assume you are familiar with their work.

    – pp. 45-48 Specificity of genetic code; origin of translation apparatus.

    Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s). Again, points for Erik, as this is, in fact, what one observes in existing cells (in fact, to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins; more points). The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA. And, just as the rRNA can cycle in and out of the quarternary complex, Erik models the mRNA cycling in and out that previously mentioned ternary complex. Both cycling phenomena are depicted accurately by the gyre and the latter of the two reveals a co-adaptational relationship between the aa-tRNA and the mRNA.

    My only problem in understanding is how the genetic information of RNA is transferred to the link between the amino acids that make up the polypeptide chain. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.) Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.) He relies on an axiom (the tenth one) to take this position. Seeing as this axiom applies to all systems in his theory, and finding no experimental evidence to refute it, I cannot dismiss it outright as wrong.

    – pp. 30-60 Biometabolic pathways

    Other than page 35, Erik does not use the term “biometabolic pathways” (because he did raise it up front, points against Erik). Perhaps the reason for this oversight is that every single pathway in the cell is a biometabolic pathway? In this regard, these 30 cited pages contain a large amount of discussion of many distinct aspects of cellular metabolism. If there’s one particular example you wanna go over, lemme know.

  260. says

    3. the critic’s non-response to my answer

    Frankly, I don’t see the illogic nor do I see the non-sequitur nature of that quote you gave. Perhaps that’s because I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma)

    Nettle, I explained the illogic of that quote in the post to which I linked above. Simply put, the “RNA world” theory is a theory that addresses the early stages of life evolution (i.e. that early RNA molecules played the role of both biological catalysts and carriers of genetic information). The central dogma is a (partial) description of the flow of genetic information in extant organisms in a 4.6 billion year old Earth. It’s a strawman argument and a non-sequitur to insinuate that the “RNA world” theory should explain observations pertaining after 4 billion years of evolution. That illogic ignores the entire contingent nature of evolution over virtually the entire history of the earth. The “RNA world” doesn’t explain the origin of the eukaryote (engulfing of primitive cells to produce mitochondria in extant animal cells), but that also doesn’t make it a deficient theory about life origins; you’d have to be a brutal and committed determinist to consider that everything we see in the natural world around us was effectively pre-determined in the early stages of life’s origins more than 4 billion years ago.

    In fact there’s a good bit of evidence in support of the “RNA world” and it’s also a testable theory. Together with the fact that the “RNA world” theory and its evidence can be stated and described very clearly in language that we all use to communicate with each other, the “RNA world” theory is an excellent theory, and it’s sad that Andrulis feels it appropriate to trash it so as to clear a little elbow room for his own effort.

    As for your description of Andrulis’s “explanation” for the precise explanation for translation apparatus, genetic code, and biometabolic pathways :

    Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system……and etc.

    That’s nonsense though isn’t it nettles? Systems don’t “organize” in units of three”. Some classes of systems (proteins) organize in units of: one (myoglobin); two (dimeric coiled-coil proteins; transcription factors; glycophorin); trimers (collagen); tetramers (hemoglobin; pyruvate kinase); hexamers (hsp90); heptamers (some chaperonins) and many other discrete states of organization.

    The beauty of proper scientific description and theory is that one can understand these different levels of self-organization in terms of simple knowledge of molecular structure and ideas about shape, electrostatics, and hydrophobicity that governs intermolecular interactions. This very hard-won knowledge can be explained in very simple terms in a way that allows the transmission of understanding from one individual to another. It doesn’t rest of obscurant gibberish, protected by claims of priviliged insight.

  261. says

    4. my response to the critic

    Wow! You asked one specific question. I answered it. And you didn’t respond to the substance of my answer! Amazingly, you don’t even /acknowledge/ that I responded to your question.

    You response is very visceral — not thoughtful — and very biased as to what a theory /should/ be.

    You don’t raise prior explanations about the genetic code like those from Jukes and Osawa or more modern explanation by Paul Higgs (no relation to Higgs boson).

    You didn’t notice that Erik in the paper says systems “tend” to emerge in units of threes — and then proceeds to focus on the available evidence proving the existence of these units of threes in all of those systems.

    You bizarrely (but conveniently) ignore “Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s).”

    Um, dude, a quarternary complex is /not/ a unit of three. Why did you not acknowledge that statement but go off on a list of things that organize as other numerical oligomers? Perhaps, you didn’t because to do so would be to admit that Erik DOES show an example here of a unit of four, and for some strange reason you want to trash the entire paper instead of doing the hard mental labor of trying to understand a radical new way of viewing present science. The paper fully acknowledges present science, but you knew that, because you read the paper, right?

    Continuing: In summarily rejecting the tri-quantal concept, you dismiss the blatantly obvious organization of units of threes creating high energy systems, to wit, ATP!

    Also, you didn’t acknowledge the theoretical profiling of oxaloacetic acid (a tetra-quantal system) in the paper (pp. 36-37, and in figure 3)

    You are clearly hard set on the idea of the status quo of ad hoc theories that to a large degree do not interlink and that have nothing to do with each other. Consider these “illogical and non-sequitur” questions that must be addressed when modeling life: What does the mitochondrion have to do with phospholipid bilayers? How did phospholipid bilayers come about? What drove their initial formation? WHY did they form? And what about the golgi body? WHY and HOW did that come about? What does a golgi body have to do with the initial formation of the ribosome? Why do the two have that relationship?

    You have no overarching explanation as to how all the organelles came about.

    Your response proves that you are very comfortable having no overarching explanation about how or WHY all biological processes and systems came to exist. And please, please don’t embarrass yourself by saying, “natural selection.”

    You are fixed on the idea that what we have “just works.” Yet, as an informed scientist, you should know our present understanding of biochemistry /alone/ is shot full of holes.

    I am not going to do your homework for you. I already did enough in giving you a studious response that you appear to have barely glossed over. Read the present literature to find the anomalies yourself. You do read other papers more carefully, I hope.

    Another point: You reject Erik’s neologisms when you know that science is full of them — and creates more of them all the time!

    Pick up any copy of Nature or Science. When you see that a new protein is discovered, it gets a new name! How is this naming of proteins (with associated alphabet soup acronyms) not obscurantist? Have you ever looked at the names of Drosophila proteins? How about “Mothers against decapentaplegic?” “Bicoid?” “Cheap date?” all of which have graced these and other scientific journals. Oh yea, sure those names explain /precisely/ what those proteins do to a layperson. Go ahead, tell yourself they’re not “obscurant gibberish, protected by claims of priviliged insight.”

    Here’s another question for ya: What is the inherent meaning of Neuropeptide Y? Neuro means we “know” (really should be “suspect”) that the protein has something to do with neurons or neurological activity, but what does it do? And how did it emerge in the evolution of multicellular eukaryotes? And why the “Y?”

    Also, the words purine and pyrimidine have no inherent meaning to a layperson. They are part of the cryptic (!) language of science. Obscurantist!

    Do you think you could chit-chat about nucleotides and their functions in a bar over beer with a stranger? Only if she or he was privy to science’s weird language — which largely bears as much resemblance to English as to Finnish.

    All the names for organelles I mentioned meant nothing until someone decided to make them up.
    All subatomic particles are made up words. All new pharmaceutical products have made up names. If you are consistent, I suppose you dismiss these neologisms, too.

    Tell me: Do you believe the meaning of finesteride to be obvious to any trained scientist because semantically it makes inherent sense? You don’t because it doesn’t.

    And, hey, while we’re at it, why should we have the word “finesteride?” We could just have the more explanatory (albeit prosaic) hyphenated word, “drug-that-restricts-and-shrinks-an-overgrown-prostate-with-the-positive-side-effect-of-inducing-the-growth-of-scalp-hair.”

    Using your phraseology and logic, that hyphenated name “can be explained in very simple terms in a way that allows the transmission of understanding from one individual to another. It doesn’t rest of obscurant gibberish, protected by claims of priviliged insight.”

    Summing up this part: What knuckle-dragging contradictory rubbish: defending the use of pharmacological, medical, and scientific obscurant-ish neologisms but attacking the use of theoretical neologisms.

    CONCLUSIONS:
    I conclude that you did not studiously read the paper or did not read the paper at all. Based upon our exchange, it appears you are unable or unwilling to do so. You like to argue talking points.

    The fact that you did not acknowledge or respond to my accurate, thorough, and sincere response to your question is clear indication that you did not read or understand what I wrote. This fact bespeaks to a greater intellectually laziness that one can intuit: you do not have the intellectual capacity that is beyond your little knowledge box.

    I conclude that you are unable to carry on conversations in a scholarly and respectable manner. This casts doubt on the scientific experience that you claim to have.

    You are welcome to respond. I have nothing further to say to you.

    Nonetheless, I wish you well.

  262. says

    Bonus comment — for those of you who made it this far (or who just blithely jumped to the end and ignored my other substative posts).

    “Any time an author needs to provide a new vocabulary for readers to understand a paper, something is seriously wrong.”

    Based on that statement, I presume you would, upon reading papers on pharmceuticals (and not being in the pharmaceutical industry), figure something is seriously wrong about the pharmaceutical industry — because its vocabulary is almost entirely based on the generation of new words. For example, Celebrex. Hunh? Where did that word come from. Ask any physician about his repertoire of drugs and he will rattle off pure gibberish. Or do you disagree?

    “That’s based on four decades of reading and translating scientific papers.”

    And there is your problem. You have spend forty years of your life understanding and studying the present paradigm You have way too much invested in “what we have now” to put in the effort to what we could have that is radically different.

    Einstein’s theory of general relativity met with a decade or so of resistance. Why? Because it was radically new and most scientists (with very notable exceptions) had far too much invested in the status quo to study and learn such “gibberish.” Is the theory of general relativity gibberish? It all depends on your point of view.

    “No, I haven’t read your posts. I tried to but found them ponderous and far from unemotional, as comments should be.” Your statement is demonstrably false as my first two posts were indeed unemotional. I find strange tha you find my second comment ponderous, as I am largely dealing with pretty basic biochemistry — and not some arcana.

    But, when people react with dismissiveness of something that has significance, I should not be frustrated but respond as an automaton? That seems silly, but ok.

    After forty years you appear not to realize that ALL of science is ponderous. Pick up a copy of JACS and give an article from it to a undergrad chemistry major. There is no way they will understand it.

    “My observation was that the institution, in spite of its reputation as a strong research university, failed in its responsibility to provide the public with understandable information about the research in question, and clearly showed systematic errors in their decision-making process about which research they decide to communicate about.”

    Do you know WHY the retraction occurred? Did you think for a moment that if CWRU made an error in putting out the publicity, they may have made an error in retracting it? Possible?

    Definite! CWRU was bullied by two physicists who were “embarrassed” (e.g. threatened) by the paper. Why the heck should they care? Well, for starters, they saw a molecular biologist not just trespassing on their sacred ground, but audaciously slaughtering one of their sacred cows.

    For instance that the photon resides within the electron. But we KNOW this arrangement to be true. Heck, when an electron and a position “annihilate” they release, whaddya know, photons. Photons are not nothing, so this occurance is not annihilation. For a molecular biologist to be even mentioning the properties of the electron in a fashion alien to physicists is simply unacceptable in the ivory tower.

    “I could care less what your opinion could be” It is apparent that my opinion is not the only idea about which you could care less. A radically new theory that is hard to grasp seems to be one two. Suspicion about political games at CWRU’s publicity office is another one.

  263. 'Tis Himself, OM says

    I have to call bullshit on Erik’s nettleingenting’s claim to have “have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). ” Because if xe did have such degrees, then xe’d understand the objections to Erik inventing new definitions for common chemical terms.

    Sorry Erik nettleingenting but I don’t believe any of your pretences.

  264. Nerd of Redhead, Dances OM Trolls says

    Yawn, fuckwit didn’t say anything new, same old boring drivel, and not one citation to the peer reviewed scienitific literature as evidence, so has nothing but same old blather.

    The new “idea” must prove itself by citing the peer reviewed scientiific literature that provide conclusive evidence for the inane and insipid claim, and it has failed that criteria. As it goes with science, the “idea” is wrong until it can show itself right. Which it hasn’t, Nettlesome’s claims to contrary. The burden of proof is on the “idea”, not those laughing at the “idea”.

  265. says

    You guys are too much fun to resist.

    “I have to call bullshit on Erik’s nettleingenting’s claim to have “have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.)”

    The paper is full of biochemistry.

    “The new “idea” must prove itself by citing the peer reviewed scientiific literature”

    The paper has 800(!) scientific references.

    You would know that if you cared to read the paper. But you didn’t because you are intellectually lazy — and meanspirited too.

    “Yawn, fuckwit didn’t say anything new, same old boring drivel”
    Of course, I said a /lot/ new, but it /intimidated/ you because you don’t and can’t understand it — and won’t even try.

    Of course, you can’t /admit/ to being intimidated, being incapable of comprehending biochemistry I wrote, and not looking at one of the 800 scientific references that you hypocritcally claim to want soooooooo badly. You are being dishonest. So, you call me “fuckwit” — such praise!

    “The burden of proof is on the “idea”, not those laughing at the “idea”.”

    Those laughing at the idea are not interested in understanding it, you know this, as you will continue laughing regardless. So your statement is not just silly, it’s a lie.

  266. says

    The paper is full of biochemistry.

    If you really want people to stop laughing, don’t write sentences like that.

    What mystifies me is why, if there is so much sound science behind this, and we’re so ignorant, you keep coming here and trying to sell the thing to us. Why are you focusing so much on convincing some random internet commenters?
    And you keep insisting that Einstein’s General Relativity was “resisted” for a decade or so. This is incorrect; it was developed mostly between 1905 and 1915 and published in 1916. Three years later, it was verified after observations of a solar eclipse–which you kind of have to wait for, and can’t just cook up in a laboratory. There was also a world war going on around that time. You may have heard of it–it was rather disruptive.
    I may not be a biochemist, but you’re talking history here, which means you’re wandering into my wheelhouse. And proving yourself ignorant there.
    Do gyres explain why you can’t stick the flounce?

  267. Nerd of Redhead, Dances OM Trolls says

    Do gyres explain why you can’t stick the flounce?No, it’s the irrational and unevidence belief in gyres that exlains why it can’t stick the flounce. Along with a lack of honety and integrity that is expected from a real scientist.

  268. Nerd of Redhead, Dances OM Trolls says

    Dang, blockquote fail #333. First sentence quotes feralboy12. The rest is my snark.

  269. says

    nettleingenting:

    With the possible exception of nigelTheBold, Abbot of the Hoppist Monks, you guys seem incapable of deep critical thinking but are very skilled with making irrelevant comments and hurling insults.

    Thanks for the possible compliment. Unfortunately, I really am quite as dull as I claim. I was a physics major who never made it to graduate school, and instead ended up programming computers. I am, in general, quite intellectually inferior to most folks here.

    If you are friends with Erik, I presume you are possibly in the Cleveland area. If so, are you going to the Origins Institute public lecture at the Happy Dog this month?

  270. says

    nigelTheBold, Abbot of the Hoppist Monks

    As I understand the paper, a moon can perform a balancing function, but the paper does not say a moon is necessary — because it isn’t.

    Thus, Mercury and Venus having no (known) moon(s) is not a problem.

  271. Nerd of Redhead, Dances OM Trolls says

    As I understand the paper, a moon can perform a balancing function,

    Citation needed to back up the claim. Why not present the citation the paper uses here? That way we can have a good laugh as the citation probably doesn’t back up the claim….

  272. says

    nettleingenting:

    As I understand the paper, a moon can perform a balancing function, but the paper does not say a moon is necessary — because it isn’t.

    That’s what I gathered as well.

    It seems there was nothing in the paper that uses gyres to explain the origins of the moon, which was one of the claims (if I remember correctly). So this appears to be another case in which gyres appear to explain everything, but in reality, explain nothing.

    Our current best hypotheses about lunar genesis explain not only why we have a fairly large moon, but also explains why other similarly-sized planets (Mars and Venus) do not. I did not get that from the paper. I just wanted to make sure I wasn’t missing something.

  273. says

    Nerd of Redhead, Dances OM Trolls

    I will not give you any citation because 1. you don’t even try to understand anything I say 2. you are not a critical thinker and haven’t read the paper and 3. you are mean-spirited — like many folks here.

    The /only/ person here who merits respect is nigelTheBold, Abbot of the Hoppist Monks. Everyone else just wants to argue and insult.

    I guess such activity is fun for some people, but I debate. I won’t argue. And I don’t want to insult anyone.

    Mean-spirited is descriptive and /highly/ accurate, so it’s not an insult.

  274. says

    nigelTheBold, Abbot of the Hoppist Monks (only, the rest of you can ignore the following)

    I am far from cleveland, so no I won’t be attending “Origins Institute public lecture at the Happy Dog.”

    Also, Erik forwarded a supportive email to me. I give you an excerpt below.

    I have just spent the weekend reading your paper Theory of Origin, Evolution and Nature of Life and feel that I would like to thank you for the experience. I am not a scientist but for the last 20 years I have read all sorts of scientific papers and books that are, quite frankly, just beyond the range of my understanding. It has been a mystery why I get so much pleasure out of this activity. The only way I can describe it is by saying it feels very much like channelling, which is another activity I have encountered in the same 20 years. I would not do it if there wasn’t a pay-off, so I have accepted that I am drawn to anything that shows the scientific status quo to be a dogmatic dead end.

    So you will realise that I am broadminded and intuitive. These are the characteristics that led me to your paper. At first I thought that it was a clever and carefully orchestrated joke, the sort of satire a bored professor might come up with as he approaches retirement and has nothing to lose. But I soon realised that you are in fact a young man employed in a prestigious American University with everything to lose(including tenure) by kicking the can. So I figured that it was worth spending some time reading and one way or the other digesting what it is you have to say. I found it perplexing profound and very exciting. My intuitive response is that what you write is true.

    While reading it I wondered what is it that gives a young man the courage to take on the orthodoxy (and cyberspace)with this level of passion?

    Annie Smith
    Bristol, UK

    Broadminded and intuitive. Got that? Attributes that are lacking here.

  275. Corporal Ogvorbis (Would that be considered punishment?) says

    If gyretheory explain the moon, how does it explain the absence of a large moon around Mars or Venus?

    That would be erygtheory. Do try to keep up.

  276. Nerd of Redhead, Dances OM Trolls says

    I will not give you any citation because

    Ah, but I am a critical thinker and skeptic, along with being a career scientist. Which is why evidence, not claims, matter. Claims are worthless without evidence to back them up. All those “persecuted” scientists had the evidence or showed where to get the evidence for their claims.

    You don’t show the proper respect for evidence, which tells me you know the paper is light on evidence. You pretend that a critical thinker will agree with your fuckwittery (which is how you define critical thinker, their agreeing with you) without the proper evidence to back up inane claims. You are tacitly acknowledging that the paper is so much bullshit by failing to provide evidence when asked.

    Broadminded or freethinking does not mean swallowing bullshit without requiring evidence. But those words tend to be used by those, like yourself, who do swallow the unevidenced bullshit to ridicule those, like myself, who do require evidence. Extraordinary claims require extraordinary proof. That means a high bar is set for the evidence. And you have shown none here to date.

  277. says

    nettleingenting:

    Broadminded and intuitive. Got that? Attributes that are lacking here.

    I’ve read similar letters praising the electrical universe “theory” as well.

    Skepticism plays a very important part in science. It helps eliminate the worthwhile from the worthless. Without healthy skepticism (which is really all I see displayed here, save for some frustration in the inadequacy of some of your responses), everything becomes possible.

    The grander the claims, the more skepticism should be employed. The claims for this paper are very grand. The level of skepticism here is really quite in-line with the grandiose claims of the paper, I think.

    While intuition is important in science (especially in the hypothesis-building stage), reference to real substantiated evidence is far more important. So when people ask for references, they are asking for something vastly more important than simple intuition. They are asking for substantiated evidence to back up a claim. Substantiated evidence comes in the form of existing theories (meaning, hypotheses that have been validated by data), or by new data supporting the new hypothesis. The more controversial the new hypothesis, the more incontrovertible the reference required.

    There are two ways a new hypothesis can be controversial. Either it describes a new phenomena which is itself controversial (such as research into psychic phenomena, which haven’t even been established as real phenomena). Or, the new hypothesis can attempt to supplant an established theory. For an example of this, check out Joy Christianson’s disproof of Bell’s theorem.

    This paper attempts to do both. In fact, it attempts to replace not a single established theory, but many established theories, using a phenomena that hasn’t yet been established as real. So this paper isn’t just controversial. It’s controversial squared.

    Hopefully you can understand why people might be hesitant to accept it at all. It purports to be a framework for everything, but it’s not based on anything that has come before, so it doesn’t automatically have a basis in reality. In fact, it proposes a novel new process without any basis for supposing that process is real. Then it attempts to use that framework to explain, well, everything.

    Only in doing so, it really doesn’t really explain anything. At least, not that I can see. The example of the moon is just one instance. It doesn’t really explain the origins of the moon. It just describes how the moon and the earth interact in a gyresystem. I’d like to point out, we already had an decent description of the earth-moon system using standard physics, and an excellent description using general relativity.

    As for the claim that it explains the why of it, I think the fact it doesn’t explain why the earth has a large moon, but Venus does not, shows it is inadequate even in that regard.

    I love the various propositions that lie at the fringes of science (or way out past the neutral zone, sometimes). Some are just silly, like the electrical universe. Some are crazy and incoherent, like Timecube. Others are truly fascinating, like causal dynamical triangulations, which has at least predicted a universe of approximately three dimensions (a unique accomplishment, to the best of my knowledge).

    This is the only reason I’m taking this half-seriously. The fact that it’s a completely novel approach is honestly a strike against it — the greatest breakthroughs in science are almost always built on the works that precede them. The second fact that it is presented as a great breakthrough, rather than just a novel approach, is also a strike against it. It shows the people advocating this aren’t being skeptical of their own results. That shows they don’t take the scientific process seriously. Your comparisons upthread to Galileo furthers this impression, as that comparison is inapt and largely emotional.

    The effusive message you quoted talked about intuition. The scientific method is designed specifically to overcome the biases of intuition, because intuition leads to the wrong answer more often than not. This stripping away of intuition is the single most important tool at a scientist’s disposal.

    This paper seems based almost entirely on intuition. That is yet one more reason to suspect it is wrong.

    There are some things that can be done to support this new proposition, even without direct evidence. First thing, someone should be able to derive QM and general relativity. Do this, and the possible validity of the paper rises substantially. If it reconciles the two, then you have strong support. If it presents a way to test the reconciliation of general relativity and QM, then you are well on your way to advancing this proposition to a theory.

    Really, though, that’s about the only way I can see to vetting this proposition. It would take something as dramatic as this to really demonstrate this is anything more than another crackpot proposition.

    But if it is the fundamental explanation of everything, it shouldn’t be too hard to derive either QM or general relativity, complete with the mathematical rigor that is a hallmark of both.

  278. says

    nigelTheBold, Abbot of the Hoppist Monks (and to no one else),

    your conclusions are fair (as usual), and I agree with entirely, I think.

    I wish to clarify my reference to Galileo, which I agree appears overblown. I was not trying to say that Erik was being threatened with torture and then placed under lonely house arrest for having a heterodox idea.

    I am saying that Erik /is/ being persecuted for having a heterodox idea, though.

    According to my computer dictionary’s definition, persecuted means,
    1. To pursue in a manner to injure, grieve, or afflict; to
    beset with cruelty or malignity; to harass;

    Everyone is attacking the review process. CWRU, and Erik.

    Right now, I know of /one/ person in internet forums — other than you and me — who is at least trying to give the paper a critical reading with an open mind — giving criticism that shows he has at least read the paper — if not believed it.
    Just like Einstein’s theory of general relativity, you neither have to understand the paper nor believe it. Not understanding is not a good basis for criticism, as many theories are incomprehensible to those outside the field. Nor is it a reason for mockery.

    Heck, I know what the theory of general relativity means in a superficial way, but I am ignorant of its underpinnings, so I am in no position to criticize it. I will add modestly, I almost certainly lack the knowledge to even read Einstein’s papers. I admit my ignorance, and remain generally silent on Einstein’s work.

    As Wittgenstein said (more or less), “what we don’t understand, we must pass over in silence.”

    In this forum, the reverse dynamic is in /full effect/. I have no doubts that only you would not be making fun of Einstein for all his jargon and impenetrable math. Such fun. Such willful ignorance.

    Wittgenstein got it right.
    Others here wouldn’t even understand Wittgenstein, but that wouldn’t stop them from making fun of him too.
    With the exception of you, no one here has intellectual curiosity. They do have spite in good supply, though.

  279. hotshoe says

    Also, Erik forwarded a supportive email to me. I give you an excerpt below.

    Holy shit, the lurkers really DO support him in email.

  280. Corporal Ogvorbis (Would that be considered punishment?) says

    With the exception of you, no one here has intellectual curiosity. They do have spite in good supply, though.

    And you think that we have insulted you? I am a professional historian (kind of hard to do that with no intellectual curiousity) and read extensively in palaeontology (outside my field, so the only reason to do it is intellectual curiousity). There are many other people here who are also both well educated and intellectually curious. Very few here are limited to only their particular field in their intelletual curiousity.

    None of us, and I do mean none, need someone like you to come on here and insist that, because we ask for evidence, we have no intellectual curiousity. None of us need you to tell us that becaue we are skeptical about a paper that claims, with no actual evidence, to overturn the scientific theories of multiple disciplines, we are intellectually curious. I do not need your smug condescension. I do not need your sneers and putdowns. Seriously. I don’t immediately believe a paper with no citations given, no peer review, no outside evidence, and I am the one who is failing in my skepticism? Go fuck yourself, you condescending asshole.

    And you are, when it comes to your historical knowledge, full of shit. Before trotting out your idiocy about Galileo, you may want to read up on the details. They are very different in the historical record than in the popular culture.

  281. says

    nettleingenting:

    I have no doubts that only you would not be making fun of Einstein for all his jargon and impenetrable math. Such fun. Such willful ignorance.

    I know these folks here. There is a lot of intellectual curiosity. One of the things I love about this forum is the diversity of knowledge and interest, with experts on everything from history to economics to physics to philosophy. When a subject comes up, I am guaranteed to be outclassed by at least one of the commentators — and usually by many. So I tend to politeness when the subject isn’t about social issues.

    I’m being more polite than others, perhaps, but please don’t mistake politeness for acceptance. I’ve pointed out several reasons why others here ridicule the paper. It has all the hallmarks of a crackpot proposition. Every single one. And it has nothing to support it (as far as I can see, anyway), other than a certain internal consistency. This consistency makes it interesting for me, but only in the way I’m interested in other propositions that fall on the fringe-to-crackpot spectrum. People here have every reason to treat it like a crackpot proposition, and nothing except internal consistency (it seems, anyway) to recommend it.

    I tend less to the crackpot end, and more to the “interesting in an abstract way, but currently useless” end of the spectrum. It seems to me that Erik is very earnest, intelligent, not in the slightest bit crazy, but probably quite wrong. I’ve outlined a couple of ways to show he has something truly interesting, and I hope he pursues them if he intends to keep with this proposition. But really, I don’t hold out much hope. Note, though, that I don’t hold out much hope for string theory, either. (Which also isn’t a theory, due to the fact it has no supporting evidence yet. It is, however, falsifiable, so that at least makes string theory an hypothesis. But string hypothesis just doesn’t have a very good ring to it.)

    Anyway, my main point is, don’t mistake dismissal of this paper as a lack of intellectual curiosity. That’d be a huge mistake. Even if I fully understood the paper (which I won’t pretend I do), I do understand it enough I can see it lacks theoretical antecedents, and that it has no current supporting evidence. Those two problems alone make it easy to dismiss the proposition out-of-hand.

  282. Nerd of Redhead, Dances OM Trolls says

    I am saying that Erik /is/ being persecuted for having a heterodox idea, though.

    If you mean being laughed at for having a fuckwitted idea, then you are right. But nobody is persecuting him, they are merely putting distance between themselves and a public display of idiocy.

    Not understanding is not a good basis for criticism, as many theories are incomprehensible to those outside the field. Nor is it a reason for mockery.

    Yes there is. It is utter and total fuckwittery. It isn’t a case of not understanding on our part, but rather in Erik’s part. What part of science, like providing clear evidence for your claims, didn’t he (and you) understand? Apparently all of them.

    As Wittgenstein said (more or less), “what we don’t understand, we must pass over in silence.”

    Sorry, no appeal to inane and inapt authority will stop our mockery. Producing the evidence to back up all his claims would. And that isn’t there.

    I have no doubts that only you would not be making fun of Einstein for all his jargon and impenetrable math. Such fun. Such willful ignorance.

    No, science in action. Einstein provide ways to falsify his theory, and it put forward an explanation for Mercury’s precession. No such predictive power is in the paper. In fact, the claim was “unfalsifiable”. Crank territory.

    With the exception of you, no one here has intellectual curiosity. They do have spite in good supply, though.

    And you show a thorough misundrstanding of intellectual curiosity. You seem to imply that only the “intellectually curious” can understand the paper. Utter tripe. I’m intellectually curious, but not gullible. That is what is needed to think Erik’s paper is anything other than tripe, being gullible. Quit defining any term as implying that acceptance of the inane fuckwittery is required to be considered, like “openminded”, “intellectually curious”, “non-dogmatic”, or “freethinking”, which shows your ignorance and presupposition. Stop embarrassing yourself Erik. Lay low.

  283. says

    Corporal Ogvorbis (Would that be considered punishment?

    Why did you bother to read a post that was directed at someone else? Is it because you were simply looking for something to trash?

    “And you think that we have insulted you?”
    You are being fatuous and bizarre, as lower in your post you /try/ to insult me liberally. Dude, insults slide off me like water off a duck’s back.

    You conveniently ignore the /many/ other insults people have given me here. So, your question is based on a dishonest premise. You prove yourself to be amoral — if not immoral. Dishonesty is not a moral practice, but I suppose you don’t care.

    Moreover, I have no insults but rather praise for nigelTheBold, Abbot of the Hoppist Monks.

    Clearly, you lack the ability for balanced, inquisitive interpretation. I understand. Everyone has his limitations.

    “There are many other people here who are also both well educated and intellectually curious.”
    There may be well educated people here, but intellectual curiosity is clearly restricted to little boxes of knowledge that “fit” the present paradigm — which as a historian you /should/ know is broken. Why do we have all these wars if not because international relations (and sometimes relations within a nation) are in many places broken?

    Apparently, your little box is history and palaeontology. Full stop.

    “None of us need you to tell us that because we are skeptical about a paper that claims”
    More dishonesty. Once again, the /only/ person to show healthy, reasoned skepticism is nigelTheBold, Abbot of the Hoppist Monks. I have many issues with the paper, I admit.

    But you are being dishonest, and you know so — and you don’t care. What we have here is trashing and attacking, but you don’t know the difference between that and skepticism. You have reached your intellectual limits and are intimidated. That’s right. You are intellectually threatened by the abstruse nature of the paper (which you clearly have not read) — though of course you are too proud to admit to such.

    “I do not need your smug condescension.”
    You are right. You probably need a good spanking for your potty mouth and you gross insincerity, but I do not believe in corporal punishment, so I won’t administer the punishment.

    “I do not need your sneers and putdowns.”
    Correct. You need a more open mind.

    “Seriously. I don’t immediately believe a paper with no citations given.”
    800 citations. You clearly haven’t read the paper.
    So, you prove my statement of lack of intellectual curiosity. Thank you.

    “Go fuck yourself” Right-o. I will do so as soon as I figure out how.

    “you condescending asshole” You flatter me.

    You also prove my point of spite.

    I guess the bar is set too high for you. Some ideas are too tough for people to understand. I don’t understand more the the basics of General Relativity, and I readily admit my inability. Moreover, I highly doubt I could understand Einstein’s original papers. Radical new ideas (and many old ones — like quantum mechanics and physical chemistry) are hard to understand. Mockery is easy.

    Clearly, you have chosen the intellectual low road of knuckle dragging nonsense. Some ideas are just too tough. Pass over them in silence, dude.

    You seem like a fun person to watch at a bar. With your attitude, after a few beers, I’m sure you’d be in a fight in a jiffy.

    “And you are, when it comes to your historical knowledge, full of shit.”
    Of course I am. I digest my food. I may not be as knowledgeable as you when it comes to history, but I may be judging from you lack of historical facts — not even a link to an explanatory web site. Your intellectual laziness is impressive.

    Why do you lamely attempt to put me down instead of correct me? You make me doubt that you are truly a historian, since someone dedicated to his field would be eager to explain a historical figure. You are not eager to discuss your understanding of history — for reasons known only to yourself.

    “Before trotting out your idiocy about Galileo, you may want to read up on the details.”
    My details on Galileo are from the historian Professor Kors at the University of Pennsylvania. Why don’t you call him and help him out in the error of his understanding? Maybe a tenured and respected professor just makes stuff up. I dunno.

    You demonstrate yourself to be a dishonest, mean-spirited person — eager to make a fool of himself by making remarks on a comment not meant for him.

  284. Amphiox says

    A rare sight indeed, to see someone quote the correct dictionary definition of a word, and STILL, in the very same post, use the word wrong.

  285. says

    Nerd of Redhead, Dances OM Trolls

    Why did you bother to read a comment clearly not intended for you?
    Is it because you just like opportunities to make yourself look more foolish? If so, mission accomplished.

    On a different note, I challenge you to explain the math in a clear, simple way behind Einstein’s General Theory of Relativity.

    You won’t because you can’t, and you know so.
    It looks like gibberish to a non-physicist because it /is/ gibberish to a non-physicist. You know that, but you won’t admit it because to do so would be a concession that even some /old/ theories that are radical are impenetrable. Such hypocrisy would be breath taking were I not already exposed to so much of it.

    Conclusions:
    You are dishonest.
    You are intellectually lazy.
    You are a hostile person who feels the need to resort to profanity.

    You haven’t read the paper because it doesn’t fit into your little box of knowledge. You enjoy being ignorant of radically new ideas. To each his own.

  286. Corporal Ogvorbis (Would that be considered punishment?) says

    nattleingenting:

    First off, this is a public thread. Everyone reads all, or most, of the comments. Even the ones not directed at them. To imply that when you accused all but Nigel of lacking intellectual curiousity it was not aimed at me, or any other readers, is just flat out bullshit.

    PZ pointed out, up at the top, all of the things that made this look like a crackpot paper. When I, and others, asked where the supporting evidence was, when I, and others, asked about peer review or citations, we were told that it is hopelessly beyond out cabability and that we should stick to things we understand. All you have done in this thread is continuously lash out with thinly veiled insults, allusions to lack of intelligence or curiousity, and, basically, been an ass. When you have been asked for clarification, you have refused.

    You are correct, though. Someone is making an arse of hirself on this thread.

    And mockery is well deserved in some places.

    I heartily invite you to imbibe in that sweet nectar called reality. Or you can fornicate yourself and become biologically inert. Your choice.

  287. says

    Conclusions:
    You are dishonest.
    You are intellectually lazy.
    You are a hostile person who feels the need to resort to profanity.

    You haven’t read the paper because it doesn’t fit into your little box of knowledge. You enjoy being ignorant of radically new ideas. To each his own

    Do you know what an Ad Hom is?

    Keep repeating that so it’ll become true. Jackass.

    In case you forgot, I was 100% nice to you and you responded with insults. remove your head and shove your self righteous attitude up your ass instead.

  288. Corporal Ogvorbis (Would that be considered punishment?) says

    nettleingenting:

    How many more times are you going to use the Courtier’s Reply rather than actually answering valid questions (not mine because, as you said, I am ignorant, lazy, useless, and incapable of out thinking a Gephyrostegid)?

  289. says

    I have to admit, making comparison to Galileo, getting called on it, admitting it’s off base, and then making comparison to Einstein? Brilliant. That is a brilliant example. I’m not sure what it’s a brilliant example of, but whatever it is, it is all the way. It’s whatever-it-is goes to eleven.

  290. says

    We Are Ing,
    You were dismissive of me from the get-go,

    I think you mean ad hominem.
    Sure.

    But to call, say, Obama or Bush dishonest is correct.
    So ad hominem remarks can indeed be accurate, you see.

    I find it curious that you feel the need to resort to profanity.
    To each his own. I bear you no grudge.

  291. Corporal Ogvorbis (Would that be considered punishment?) says

    I find it curious that you feel the need to resort to profanity.
    To each his own. I bear you no grudge.

    [Yoda]The passive aggressive is strong in this one.[/Yoda]

  292. Nerd of Redhead, Dances OM Trolls says

    Why did you bother to read a comment clearly not intended for you?

    Who the fuck are you to tell me what I can read and respond to? Who gave you that authority? I know I didn’t idjit.

    I challenge you to explain the math in a clear, simple way behind Einstein’s General Theory of Relativity.

    The difference between a gravity well and acceleration can’t be determined, as they both behave the same. I actually read Einstein on relativity back when I took German in college. Still no proving your case, which requires you to supply evidence.

    You are dishonest.
    You are intellectually lazy.
    You are a hostile person who feels the need to resort to profanity.

    I just love the way trolls try to describe us, but describe themselves instead. You are intellectually lazy, or you would have provided the citations when asked. You are dishonest, trying to define terms to act like you are being persecuted, rather than ridiculed. You are being hostile by not providing the required evidence, and by not answering the skewering questions that put your intelligence where it belongs, in middle of pointed fingers with laughter.

    You haven’t read the paper because it doesn’t fit into your little box of knowledge. You enjoy being ignorant of radically new ideas.

    No, I haven’t read the paper as it is utter fuckwittery, from just the abstract and definitions. Bad ideas are obvious to an educated and skeptical person. I don’t argue his delusions, any more than I argue theology. I just challenge them, like you, to prove what they claim has solid evidence. And you don’t.

    please, educate me. How is what I said incorrect?

    Sorry, you must prove yourself correct. You are wrong until you do so. And you haven’t.

  293. says

    I find it curious that you feel the need to resort to profanity.
    To each his own. I bear you no grudge.

    Because the first response you gave when I explained to you why you were wrong about a core fundamental of the scientific method was to insult me…then you started ignoring me despite continuing a polite tone. Then I got mad and you paid attention to ask why I was so profane.

    Because you are ill mannered, rude, arrogant, vacuous, and shallow.

  294. says

    Oh and if I may add a personal opinion. I suspect the reason you’ve latched onto the ‘controversial new paradigm’ isn’t because of some genius or insight (you clearly show that you grapple with even the simplest concepts of chemistry and biology and physics and philosophy) but that you are of the ‘nonconformist niche’ that feels a pathological need to loudly challenge any authority they come across in an effort to mask internal insecurity.

  295. says

    (you clearly show that you grapple with even the simplest concepts of chemistry and biology and physics and philosophy)

    Or language for that matter.

  296. says

    nettleingenting:

    On a different note, I challenge you to explain the math in a clear, simple way behind Einstein’s General Theory of Relativity.

    Einstein’s general relativity came inexorably from the math of other theories. Einstein didn’t just make it up. He was following the work of Lorentz, Maxwell, and Poincare. He took their equations and synthesized them using pure mathematics.

    It’s the results of those maths that were staggering, and took even Einstein years to decode. But make no mistake: Einstein did not just make it up wholecloth.

    As for the simple explanation, those are fairly common. Motion is frame-dependent. You can’t really say you are going a specific speed. You have to describe your velocity with a frame of reference. However, in all frames of reference, the speed of light does not change. As you increase your velocity with respect to a light-emitting body, the velocity of light remains the same. However, the energy of the light changes by shifting its frequency up or down, depending on whether you are accelerating toward or away from the light-emitting body.

    Further, as you accelerate toward a body, and your relative velocities approach that of light, the energy you use to accelerate will not appreciably change. However, the apparent mass of the objects will change, maintaining the basic energy, E = (mv^2)/2. (This looks suspiciously like the derivative of something, doesn’t it?)

    This is all pretty much explicit in the basic formulation of the now-familiar e=mc^2. (This is special relativity, rather than general relativity, but general relativity includes quite a bit more math, and would take a book to explain.)

    What’s important to note here is that Einstein derived his work from the vetted, accepted works of others. His results weren’t heterodox at all. In fact, they were perfectly within the framework that was already emerging. His work was generally accepted almost immediately on publication. There was some discussion, yes, and some of it heated. However, there was little doubt that his work was solid. And all debate was put to rest when the real-world predictions of his theories were put to the test.

    Therein lies the epistemological differences between Einstein and Erik. The theories of special and general relativity were derived from what came before. They made real-world predictions that were later supported by real-world observation. All of that is the very essence of good science.

    I suspect most folks here would’ve been very accepting of the possibility that Einstein was correct. It smelled solid, from the derivation from solid previous research to the humble publication to the following scrutiny to the final vindication. All of it worked just as science is supposed to work.

    It seems Erik is trying to take a shortcut by ignoring all the work that came before, all the theories that have predicted real-world phenomena. This is quite different from what Einstein did, and is part of the reason I don’t hold out much hope his ideas will prove out.

    But in any case, the comparison to Einstein really isn’t that apt.

  297. Ogvorbis: Now With 98% Less Intellectual Curiousity! says

    I actually started reading the paper… It makes even less sense to me now… Impressive, I’ll give him that.

    You are reading the paper? That shows intellectual curiousity. You don’t understand it? That shows lack of intellectual curiousity.

  298. Rev. BigDumbChimp says

    I look forward to the wide acceptance of this study along with biophotons, ley lines, steady state theory, and the time cube.

  299. says

    pentatomid:

    I actually started reading the paper… It makes even less sense to me now… Impressive, I’ll give him that.

    What’s weird is, there’s a general consistency throughout. And I don’t mean in just the obfuscating and confusing language. (I still make glarey-eyes every time I see “amino” in that paper.) It’s in the strange diversity of the application of gyres. It’s like, everything that has spin can be considered a gyre. And everything has spin. Voilà!

    I’ll have to go back to check this out, but it seems he has a 1-to-1 correspondence between different types of gyres and different quark flavors. It seems gyres are a drop-in replacement for quarks. I have to do some math to verify parity, but it seems that way on the second read-through (which is probably about as far as I’ll go).

    Not that it means anything. That’s just symbol replacement. Replacing an up quark with a dextragyre (for example) is really just a nomenclature substitution, and doesn’t affect the model at all.

    Anyway, I think there are far better models. Hell, the simple model of everything I linked earlier (the one with the E8 lie group model) has a lot more going for it. I just like that, even after all I’ve seen, someone can come up with something new.

    None of this has anything to do with correspondence to reality. It just gives me a weird kind of hope, that we really are still inventive.

  300. Ogvorbis: Now With 98% Less Intellectual Curiousity! says

    I look forward to the wide acceptance of this study along with biophotons, ley lines, steady state theory, and the time cube.

    But where does the FSM (blessed be His giant balls) and his daughter fettucine (and her husband, Alfredo) fit into all of this?

  301. says

    pentatomid:

    Funny little quote from the article:

    I also mean to emphasize, up front, that this manuscript is dense.

    Y’know, that reminds me of a quote from the book Scientology, by L. Ron Hubbard. (Yeah, I picked it up for a $1.50 at a used book store. I was doing research for a story I wanted to write in which Scientologists were a strange cult. In spite of that, it was fiction.)

    He said in the preface (and I paraphrase), “If you find you don’t understand something, it means you don’t really know the meaning of a word used earlier. Go back, find that word, and work out your misunderstanding.” Yeah. ‘Cause if something doesn’t make sense, it means the reader is at fault, not the author. It sure as fuck does not mean the basic concept is incorrect, incoherent, or just plain stupid.

    It’s a kind of literary “blame the victim” device, I think, used as prior restraint against valid criticism.

  302. says

    “You are reading the paper? That shows intellectual curiousity. You don’t understand it? That shows lack of intellectual curiousity.”
    I never said or even implied that. In fact, I explicitly said that reading the paper is a hard slog.

    nigelTheBold, Abbot of the Hoppist Monks,
    Erik’s theory is based on the work of many other scientists — and includes loads of science. I explicitly stated so in a previous post, which I reproduce below. But first, a list of explicit examples of Erik’s referring to the work of other scientists (which he backs up in his 800 references).

    Note all of the following is contemporary science, so just as Einstein based his theories on existing science so has Erik.
    1. translation apparatus, genetic code, and biometabolic pathways
    2. the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code
    3. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems
    4. Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide.
    5. to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins
    6. The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA
    7. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.
    8. Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.)

    My full comment (which I already posted but I reproduce for your convenience).
    The criticism:
    you seem to be playing the “I can understand Andrulis’s paper because I have advanced degrees in science” ploy. But I (and lots of others too) have advanced degrees and quite a few years of research into relevant subjects (Chemistry, Biochemistry, Mol. Biol.). Of course that doesn’t rule out the possibility that I can’t recognize paradigm-shifting brilliance when I see it, but it’s usually the case that remarkable insights in molecular life sciences are amenable to rather simple explanations (by far the hardest part of obtaining astonishing insight in molecular biology in its broadest sense is in overcoming experimental/technical issues).
    So Andrulis’ states (using straw-man, and non-sequitur type illogic) in his introduction : “Finally, the RNA (ribonucleic acid) world hypothesis posits that ribonucleotide-based genetic systems evolved prior to protein and deoxyribonucleic acid (DNA). This hypothesis does not fit well with the central dogma and is unable to resolve precisely how the translation apparatus, genetic code, and biometabolic pathways evolved [7-9].”
    Yor task, nettle, (since you understand Andrulis’ paper very well), is to explain to us in simple terms how Andrulis’s hypothesis “resolves precisely how the translation apparatus, genetic code, and biometabolic pathways evolved”.

    My reply:
    Nice, you and I both have similar experience, as I have worked in chemistry, biochemistry in molecular biology laboratories in Cambridge and Southern California. I didn’t mean it as a “ploy.” I meant it to be genuine. But I digress.

    Frankly, I don’t see the illogic nor do I see the non-sequitur nature of that quote you gave. Perhaps that’s because I can see quite clearly that the RNA world hypothesis says nothing about the flow of genetic information in an extant cell (central dogma) and the central dogma says nothing about the origin and evolution of RNA. The point Erik was trying to make is that current models/theories/hypotheses/ideas are ad hoc and thus should be considered provisional at best and wrong at worst. Could you point out the illogic there?

    As for how theory treats those three problems (translation apparatus, genetic code, and biometabolic pathways), I would call your attention to where these problems are treated:

    – p. 43 Origin of the genetic code

    Erik’s core model shows that systems organize in units of threes, creating a system that has high potential energy but less exergy than the evolutionarily prior system. The tri-quantal system (as he calls it) is the tri-nucleotide, with each component of the system having a relative amount of energy (see section 2.4.5, pp. 13-14), “(i) a high energy (exergic), unstable, excited form; (ii) an intermediate energy, quasi-stable, transition form; and (iii) a low energy, stable, ground form.” My read of this is that the first nucleotide is the most stable, the second is the quasi-stable, and the third position of the codon is the least stable. His model echoes what I know about the wobble hypothesis and the variability of the genetic code. Is there a problem with the interpretation that I am missing?

    Erik has proposed that the code evolved autocatalytically, from the metabolism of the orthophosphate bonds between the 2nd and/or 3rd nucleotides. Perhaps the reason why I don’t find Erik’s proposal so outlandish is that it is fully consistent with mainstream scientific ideas: both the Nobelist Eigen and complexity theorist Kauffmann argue that the origin of RNA involved autocatalytic systems. I assume you are familiar with their work.

    – pp. 45-48 Specificity of genetic code; origin of translation apparatus.

    Three RNA classes (mRNA, tRNA, rRNA) are required for the formation of a polypeptide. Erik models these RNAs as being the tri-quantal state that drives the emergence of and exists in a quarternary complex with one or more amino acid(s). Again, points for Erik, as this is, in fact, what one observes in existing cells (in fact, to the best of my knowledge, RNA scientists have shown that the peptide bond can form sans accessory ribosomal proteins; more points). The cycling of one RNA (the rRNA) leaves a ternary complex of the amino acid (linked to the tRNA, Erik calls it aa-tRNA) and the mRNA. And, just as the rRNA can cycle in and out of the quarternary complex, Erik models the mRNA cycling in and out that previously mentioned ternary complex. Both cycling phenomena are depicted accurately by the gyre and the latter of the two reveals a co-adaptational relationship between the aa-tRNA and the mRNA.

    My only problem in understanding is how the genetic information of RNA is transferred to the link between the amino acids that make up the polypeptide chain. Erik points out that the formation of the amide bond is, first, a consequence of loss of mRNA and rRNA relationships with the aa-tRNA. (I think he means after the tRNA passes from the A site to the P site in the ribosome.) Next, the nitrogen link imports information from the tRNA into the amide bond as is subsequently cycled out, too. (I think he means after the tRNA passes from the P site to the E site in the ribosome.) He relies on an axiom (the tenth one) to take this position. Seeing as this axiom applies to all systems in his theory, and finding no experimental evidence to refute it, I cannot dismiss it outright as wrong.

  303. says

    He said in the preface (and I paraphrase), “If you find you don’t understand something, it means you don’t really know the meaning of a word used earlier. Go back, find that word, and work out your misunderstanding.” Yeah. ‘Cause if something doesn’t make sense, it means the reader is at fault, not the author. It sure as fuck does not mean the basic concept is incorrect, incoherent, or just plain stupid.

    That is exactly what’s going on here.

    Regarding the paper, though, I was wondering: the introduction opens with:

    How life abides by the second law of thermodynamics yet evolutionarily complexifies and maintains
    its intrinsic order is a fundamental mystery in physics, chemistry, and biology

    Which seems to me to be hinting at a conflict between thermodynamics and evolution of the kind creationists like to invoke. Am I misreading here, because this bothers me.

  304. Nerd of Redhead, Dances OM Trolls says

    And not one citation to back up the claims from neettlesome the vapid. Ergo, nettlesome the vapid wasted a post for nothing, as it said nothing scientific without the evidence to back it up. Welcome to real science, where evidence trumps ideas every day of the week and twice when Nettlelsome the vapid ignores it.

  305. says

    @Pentatomid

    You’re not wrong. It seems to be saying it answers a question that doesn’t exist. We KNOW that answer already. It’s rather fundamental to cell biology.

  306. Ogvorbis: Now With 98% Less Intellectual Curiousity! says

    You are reading the paper? That shows intellectual curiousity. You don’t understand it? That shows lack of intellectual curiousity.

    I never said or even implied that. In fact, I explicitly said that reading the paper is a hard slog.

    First, am I allowed to read that part of your comment? After all, it was not addressed to me.

    Second, do you grok sarcasm?

  307. says

    nettleingenting:

    Erik’s theory is based on the work of many other scientists — and includes loads of science.

    I think you misunderstand. Yes, Erik has a lot of references to other research. But his basic axioms, his basic model, are not based on prior scientific antecedents. His references are quite detailed, but they are secondary. They are the effects which he is trying to model, many of which are already understood in terms of other models.

    Einstein’s model, for instance, was derived from prior research. The effects of his model were the interesting bit. It wasn’t that it explained anything known. It’s that it explained something new and unforeseen.

    Erik’s model seems too adaptable, in fact. The ability to model (only in a general way, not in specifics) both quarks and the moon indicates it might be too general (as in, “God did it” general). If it is adaptable to any proposed process, real or imagined, it has no explanatory powers, no predictive powers. Even if it were right, it wouldn’t really help us to understand anything.

    That’s all I’m saying with that.

  308. says

    Note all of the following is contemporary science, so just as Einstein based his theories on existing science so has Erik.

    The difference is that while Einstein built on the existing science directly, thus coming to a conclusion which was, in a way, a synthesis of existing science, Andrulis seems to make a load of things up and then gives examples from contemporary science which are supposedly consistent with his ‘theory’. Yet the links are, more often than not, far from obvious and it is unclear to me how he has come to the gyre model as a conclusion of the observations he notes.
    Mind, I haven’t made it through the entire paper yet, so maybe my perception will change…

  309. Nerd of Redhead, Dances OM Trolls says

    How life abides by the second law of thermodynamics yet evolutionarily complexifies and maintains
    its intrinsic order is a fundamental mystery in physics, chemistry, and biology

    Nope, not a mystery at all. Good old thermodyanmics in an open system, where the input of energy from the sun gives the energy that allows the appearance of entropy breaking by life. Life actually follows all the laws of thermo as expected.

  310. says

    You’re not wrong. It seems to be saying it answers a question that doesn’t exist. We KNOW that answer already. It’s rather fundamental to cell biology.

    As I thought… Which means that from the very first sentence of the introduction, the paper already shows it’s ridiculous.

  311. says

    nigelTheBold, Abbot of the Hoppist Monks
    I largely agree with you again.

    The entire point of the paper is to show how processes from the photon to the cell are interlinked. The paper merits much skepticism for such an ambitious goal. Such a goal must include modern science but does not necessarily have to resemble modern science. In fact, such an overarching theory will highly likely /not/ resemble science.

    Similar to Einstein’s model, Erik’s paper does describe something new and unforseen: the relationship of various systems from the electron all the way up to the cell. That is an accomplishment. Before the paper, we had /no/ explanation of how water related to molecules containing only carbon, oxygen, and hydrogen. Now we do.

    Is the explanation right? I believe so, but (as clearly shown here) I honestly admit that my interpretation is not particularly important. Until some recognized scholar proclaims his work to be true, most people will find it to be a creative fiction — at best — despite the paper being loaded with science. But scholars have been /entirely/ silent.

    “If it is adaptable to any proposed process, real or imagined, it has no explanatory powers, no predictive powers. Even if it were right, it wouldn’t really help us to understand anything.”

    I understand this position very well, as one belief is that a theory that explains everything explains nothing.
    I disagree that “it has no explanatory powers” as it clearly explains how processes from the photon to the cell are interlinked. That’s explanatory powers.

    Processes from the photon to the cell must be interlinked somehow. The universe holds together by some universal, unifying law. Before Erik’s paper all we had we ad hoc theories — i.e. theories that did not interlink. Goodness, we had no overarching theory of biochemistry — though we knew a lot about a lot of interacting processes. The paper now provides us with the basis (much more is needed, but you have to stop somewhere with your first paper on a subject) for an overarching, unifying theory of all these processes.

    No one has to agree with Erik — or even read the paper for that matter. I am just decribing what the paper states.

  312. says

    nettleingenting:

    There are two very important things you address. One is the essence of what science is. The other is the essence of what science does.

    The first is in this quote:

    Such a goal must include modern science but does not necessarily have to resemble modern science. In fact, such an overarching theory will highly likely /not/ resemble science.

    Science is one of two ways of knowing things. The other is logic (including math). We have no other way of knowing things. Logic by itself does not reveal anything about the way the world really works. All it can do is assure us that our conclusions stand, based on our suppositions. For logic to work, for it to be effective, the results must be compared against reality, the way the world really works.

    Near as I can tell, Erik’s paper relies entirely on logic for its core propositions. It compares itself to the known real world, in the bits that are referenced; but that isn’t a very good metric by itself. To demonstrate it isn’t merely a set of axioms that can describe anything whatsoever, it must predict something knew and unique. It must have a test of some sort.

    This is science.

    So, declaring something this overarching, this powerful, will not resemble science is basically saying, “There’s no way to compare it to reality.” Either it’s tractable to the observation of reality, or there’s no way to use it in any kind of meaningful sense. It’s essentially useless.

    I disagree that “it has no explanatory powers” as it clearly explains how processes from the photon to the cell are interlinked. That’s explanatory powers.

    But that really isn’t even a question. It presents an explanation for something that hasn’t been a mystery. It’s attempting to impose an order top-down, based on a set of axioms that seem applicable to any imaginable scenario. Need to explain why the Earth has a large moon? Done. Need to explain why Venus, a planet very similar to the Earth, does not? Done. But there’s no way to predict in advance which will have a moon and which will not. It seems to be very useful for providing a post hoc rationalization, but not so good for describing what must be.

    And that’s what science does. It works from the bottom up, from observation. It doesn’t just explain what we observe. If we wanted that, we could stick with gods. It helps us predict what we don’t know. It demonstrates our ignorance even as it gains us knowledge.

    Maybe I’ve missed something, but I can’t figure out what new territory Erik’s proposal illuminates. I’m not sure what vast new swath of ignorance it reveals. Einstein’s paper on special relativity revealed with a single formula not only the equivalence of mass and energy, but also the relativity of frame of reference for motion. It illuminated one thing we’d speculated on (relativity), and showed us something we didn’t even know we didn’t know: that mass and energy are transmutable to each other.

    I don’t see the revelation of ignorance in this paper. I see a complex, jargon-laden system for post-hoc rationalization.

    Again, I suspect I’m missing something. Well, I know i’m missing something. There are entire sections of the paper I don’t get. But I understand enough to realize those bits aren’t showing us an area of knowledge of which we were previously unaware.

    And one thing I know for sure. If we are to accept it as something true, if we are to make use of it, it’ll only be with the application of science, with the comparison of its predictive powers against the objective nature of reality.

  313. says

    I disagree that “it has no explanatory powers” as it clearly explains how processes from the photon to the cell are interlinked. That’s explanatory powers.

    I just realized what this really is.

    Erik shouldn’t’ve named them gyres. If he really wanted buy-in on this, he should’ve called them midichlorians.

  314. dontpanic says

    I have to admit, making comparison to Galileo, getting called on it, admitting it’s off base, and then making comparison to Einstein? Brilliant. That is a brilliant example. I’m not sure what it’s a brilliant example of, but whatever it is, it is all the way. It’s whatever-it-is goes to eleven.

    Oooh, I haven’t been following this thread (as a physicist I just rolled my eyes and moved on) but could you score him on John Baez’s A simple method for rating potentially revolutionary contributions to physics scale for us. Rough numbers, doesn’t have to be exact.

  315. says

    nigelTheBold, Abbot of the Hoppist Monks

    “Science is one of two ways of knowing things. The other is logic (including math). We have no other way of knowing things.”
    No. We now have a third way of knowing things: the gyre model.

    Again, I believe it to be correct, but that’s just one man’s interpretation.

    “To demonstrate it isn’t merely a set of axioms that can describe anything whatsoever, it must predict something knew and unique. It must have a test of some sort.”
    It has plenty of tests — but they are hard to see because the paper is full of neologisms and odd forms of describing science.
    For example, the cellulogyre is testable by simply looking at a single cell go through its cell cycle. The cell is oscillating just a gyre does. A very simple test given just as an easy to explain example.

    I’m sure Erik could give you endless tests. He’s demonstated them to me, but I was at /my/ limits, so I can’t remember them. I could probable deduce more, but as you know, this new theory is hard for /me/ to understand. I admit, I am still trying to figure it out, and I’ve been exposed to this theory (in its full form which is /much/ larger than a mere 65 pages.

    “So, declaring something this overarching, this powerful, will not resemble science is basically saying, “There’s no way to compare it to reality.” Either it’s tractable to the observation of reality, or there’s no way to use it in any kind of meaningful sense. It’s essentially useless.”
    You’ve missed the point here. The paper models reality. What is a cell if not a body in oscillation? What is the weather (and seasons) if not an oscillation of environment? What are /you/ if not a body in oscillation: wakefulness, sleep; hunger, satiety; ingestion, excretion.

    You should be freaked out by the following statement.
    The paper models /you/.
    You do oscillate as I indicated, right?
    Pretty funky for /you/ to be described in a publication.

    “I don’t see the revelation of ignorance in this paper.”
    Ironically, the paper has revealed the ignorance of a lot of people, but I know that’s not what you mean.
    The paper unifies many ad hoc theories.
    Prior to the release of the paper, we had no overarching theory of how an electron was related to water or how water was related to the cell. Now we have one.

    I accept the paper as correct (albeit extremely weird), but of course I could be wrong. The paper claims to be unfalsifiable, but of course that’s just a claim. It could indeed somehow be falsifiable. I do hold that the paper is unfalsifiable, though.

    Thus, though the paper includes a lot of science, it is /not/ science. It does not claim to be science. It is underscience — as in under-standing. It stands under science.

    “I see a complex, jargon-laden system for post-hoc rationalization.”
    I hear ya. The paper is “a complex, jargon-laden system.”

    “Maybe I’ve missed something, but I can’t figure out what new territory Erik’s proposal illuminates”

    Yeah, you’ve missed a lot, but I don’t blame you. I blame the paper for using neologisms mixed with an odd way of describing contemporary science. Erik is, paradoxically, not to blame as a unifying theory does not resemble contemporary science.

    Necessarily, just as Kuhn wrote in (I believe) his Scientific Revolutions, paradigm shifts are greatly resisted as are revolutions.

    This link may interest you (it’s not about Kuhn)
    http://en.wikipedia.org/wiki/Scientific_revolution

    “Again, I suspect I’m missing something. Well, I know i’m missing something. There are entire sections of the paper I don’t get. But I understand enough to realize those bits aren’t showing us an area of knowledge of which we were previously unaware.”
    I am /very/ impressed that you had the mental tenacity and intellectual curiosity to make it so far. Good man!

    “And one thing I know for sure. If we are to accept it as something true, if we are to make use of it, it’ll only be with the application of science, with the comparison of its predictive powers against the objective nature of reality.”
    I think you meant to say the predictive powers of ideas in the paper. It already is predictive in that it predicts the formation of life /as a necessity/ as long as you have CHNOPS and an environment conducive to life (e.g. you must have liquid water for starters). Thus, we now have a logical conclusion that, based on statistics, there /must/ be life elsewhere, and it /must/ form just as it has on Earth.

    That is one hell of a prediction.

  316. says

    I missed something.
    “But I understand enough to realize those bits aren’t showing us an area of knowledge of which we were previously unaware.”
    You mean we were aware of what drove the initial formation of molecules containing only oxygen, hydrogen, and carbon? Of what drove the formation of phospholipids? RNA? Amino acids? DNA?

    Come on, dude. We had /no/ theory that not only explained the initial formation of these molecules but also unified them in a cascade of formation.

    Those explanations are /definitely/ “showing us an area of knowledge of which we were previously unaware.”

  317. says

    nettleingenting #395

    (nigelTheBold)
    “Science is one of two ways of knowing things. The other is logic (including math). We have no other way of knowing things.”

    No. We now have a third way of knowing things: the gyre model.

    Folks, he’s not even trying any more. Time to call it.

  318. says

    Come on, dude. We had /no/ theory that not only explained the initial formation of these molecules but also unified them in a cascade of formation.

    Bullshit. Hypothesises on abiogenesis frequently deal with this. Your ignorance is not universal.

  319. says

    “Science is one of two ways of knowing things. The other is logic (including math). We have no other way of knowing things.”
    No. We now have a third way of knowing things: the gyre model.

    Which is neither science nor logic?

  320. Nerd of Redhead, Dances OM Trolls says

    Please, allow me to express myself in a way you want to hear.

    kvaaak, kvak, kvak, kvak!

    I see our troll is attempting to describe one of the regulars again, but is actually describing itself and the fuckwitted idjit it is irrationally defending. The only quacks seen on this page are Erik and Nettlesome. Both flaming evidenceless idjits without any cogency, rationality, or basis in reality..

  321. Ariaflame, BSc, BF, PhD says

    Ariaflame, BSc, BF, PhD

    In any case, unless Erik provides some indication of what it would take to prove his hypothesis or idea wrong it can be safely put on the shelf with the other interesting, or in this case baffling ideas about the universe. If the is no way to test it, then we have no obligation to take it seriously.

    Nettle:
    A fair criticism.

    Arguing about minutiae and his misappropriation of scientific terms doesn’t address this.

    Ditto

    So now my feefees are hurt, not because Nettle subsequently claims that nigelthebold is the only one arguing sensibly with him, but because he here acknowledged my point as a fair criticism and then completely failed to address it. If this hypothesis doesn’t explain anything that current theories don’t (and it doesn’t appear to) and doesn’t predict anything that can be tested, then I have no incentive whatsoever in my busy academic life to slog through pages of it. It is not useful. ‘Everything is gyres’ is no more helpful in my life nor useful in my career than ‘Goddidit’

    It’s not even elegant like the twisted photon theory of electrons I came across in my student days (it was pretty, and elegant, but it wasn’t falsifiable, and thus only an elegant idea, not a theory).

  322. says

    Science is one of two ways of knowing things. The other is logic (including math). We have no other way of knowing things.”
    No. We now have a third way of knowing things: the gyre model.

    At least he admits the gyre model isn’t science. That’s a start, right?

  323. says

    Here’s a summary of the paper:

    There’s all this stuff, right, which doesn’t have an explanation and is all mysterious and stuff (well actually, a lot of this stuff does have an explanation, but I’ll ignore that). So… Gyres. Lots and lots of gyres.
    Demonstrate these gyres? Testing this hypothesis? Explanatory power? Uhm… Right… Look, it’s a cell cycle! Woop woop woop woop woop… (Scuttles away)

  324. Rev. BigDumbChimp says

    Rev. BigDumbChimp
    Yours is an apt nick.
    Please, allow me to express myself in a way you want to hear.

    kvaaak, kvak, kvak, kvak!

    Especially for you.

    You do realize that you’ve successfully filled the crank bingo cards of every watchign or participating in this thread, right? The coup de grâce of your battle to the top of the crank heap was your claim of other ways of knowing here:

    No. We now have a third way of knowing things: the gyre model.

    This is a prime indicator of a crank.

    That one being you.

    Congrats.

  325. KG says

    nettlecrank,

    The paper claims to be unfalsifiable, but of course that’s just a claim. It could indeed somehow be falsifiable. I do hold that the paper is unfalsifiable, though.

    As has already been pointed out to you, that it is unfalsifiable is precisely what is wrong with it. It is such a vague mishmash that no conceivable empirical finding could show it to be wrong, nor is there any clear way it could be developed to produce falsifiable hypotheses – so it is not science. But nor does it provide any new mathematics – which, of course, is the real foundation of scientific theory. Incidentally, I see you’re now back to coining stupid neologisms, e.g. “underscience”, and have filled yet another box in the crank bingo card: attempting to use etymology, or more usually, as in this case, pseudo-etymology, to prop up your nonsensical claims. Here is what the Online Etymological Dictionary has to say about “understand”:

    O.E. understandan “comprehend, grasp the idea of,” probably lit. “stand in the midst of,” from under + standan “to stand” (see stand). If this is the meaning, the under is not the usual word meaning “beneath,” but from O.E. under, from PIE *nter- “between, among” (cf. Skt. antar “among, between,” L. inter “between, among,” Gk. entera “intestines;” see inter-).

    To continue:

    For example, the cellulogyre is testable by simply looking at a single cell go through its cell cycle. The cell is oscillating just a gyre does. A very simple test given just as an easy to explain example.

    No, to test a theory requires that it predict something that is not already known.

    You should be freaked out by the following statement.
    The paper models /you/.
    You do oscillate as I indicated, right?
    Pretty funky for /you/ to be described in a publication.

    Freaked out? Funky? The 1960s were, like, a long time ago, man. Also, see above. Lots of things oscillate; that is not a novel insight into the nature of reality, and only an ignorant idiot such as yourself could think it was.

    We had /no/ theory that not only explained the initial formation of these molecules but also unified them in a cascade of formation.

    See the first two chapters of Nick Lane’s Life Acending for a popular treatment of current scientific thinking on these issues.

    It already is predictive in that it predicts the formation of life /as a necessity/ as long as you have CHNOPS and an environment conducive to life (e.g. you must have liquid water for starters).

    Until you specify properly what “an environment conducive to life” is, this is not a falsifiable prediction at all. Whenever we examined an environment and found no life there, you could just add another condition to what is required for an environment to be “conducive to life”.

    I’m sure Erik could give you endless tests. He’s demonstated them to me, but I was at /my/ limits, so I can’t remember them.

    *Guffaw*
    So why are we talking to the monkey, not the organ-grinder?

    Necessarily, just as Kuhn wrote in (I believe) his Scientific Revolutions, paradigm shifts are greatly resisted as are revolutions.

    As is worthless garbage.

  326. Antiochus Epiphanes says

    The RNA world hypothesis is not intended to explain the evolution of the central dogma so much as the abiogenic origin of replicator/metabolic systems. While there are massive black boxes needing explanation (how might early RNA systems have incorporated DNA/protein?), I don’t think that the gyre model provides a plausible, or even coherent explanation.

    A long ways upthread, it was indicated that one of the so-called “predictions” of this “theory” is the ubiquity of annotated RNA…RNA that has no DNA precursor. So I’ll ask again; where is this annotated RNA? Thousands of transcriptomes have been sequenced and analyzed, and no such evidence exists. This seems to provide an easy enough evaluation of Andrulis’ “theory”. Yet this seems to have been ignored.

    It is very possible that I am simply too stupid to understand Andrulis’ paper. However, if that is true, many people are. I suspect however, that in this instance, a high-tech Gish Gallop is taking place. Every purported attempt to clarify seems only to muddy the waters. These seems purposeful. I have spent far more time with the paper than it has been worth. Should I be wrong in my perception of it, I will take my place in the shamed throngs of ignorant scoffers.

  327. says

    Antiochus Epiphanes

    “I don’t think that the gyre model provides a plausible, or even coherent explanation. ”
    I partially support you in having your opinion here. I readily admit that, were I simple shown the math for General Relativity without being told what it was, I would be totally lost.

    I would /not/ jump to a conclusion that it did not provide “a plausible, or even coherent explanation.”

    I would simply say I don’t understand it, so I have no idea what it is or if it is right or wrong.

    For some strange reason, you draw conclusions on that which you understand. For the most part, I support you.

    Unannoted RNA has no DNA precursor.

    You clearly don’t understand basic biochemistry.

    For you to make such a mistake shows restricted reasoning skills because clearly “a note” as in annoted, means that there’s a note for the RNA in question, namely in DNA.

    You don’t stand a chance of understanding the paper.

    “Should I be wrong in my perception of it, I will take my place in the shamed throngs of ignorant scoffers.”

    Yep. By the way, I don’t have a problem with people not understanding.

    The scoffing just makes people look foolish, and I, trying to be a sympathetic person, urge you not to scoff at the paper and make yourself look like a fool.

  328. says

    To those of you enamored with science, consider the following if you care. If you don’t, don’t.

    In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    Intellectual dishonesty is rampant in science.

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

  329. says

    In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of how a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    Intellectual dishonesty is rampant in science.

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

  330. says

    Second sentence corrected.

    In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of how a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    Intellectual dishonesty is rampant in science.

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

  331. Ariaflame, BSc, BF, PhD says

    No, when a scientist gets 6 results and three make sense, one is a little off and two are anomalous a good scientist goes back and does more experiments around the areas where the results are strange. They check that their controls are good. That they’ve limited as many variables as possible. They do statistics to evaluate the significance of these results. That’s what good scientists do. If that is not what you do then I can only conclude that you are NOT a good scientist.

    And I see that you still fail to address my criticism. If a hypothesis produces nothing testable, then it is worthless.

  332. Nerd of Redhead, Dances OM Trolls says

    Intellectual dishonesty is rampant in science me.

    FIFY. YOu are dishonest. You fail to have scientific perspective. You presuppoose without evidence That isn’t scientific. Due to your lies and bullshit, every allegation, like the above, you make must be backed up third party evidence. Or you are wrong.

  333. Ariaflame, BSc, BF, PhD says

    Also, a good scientist frequently loves results they weren’t expecting.

    The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…’–Isaac Asimov.

  334. KG says

    Nettlecrank@444/5 ticks a space on the crank bingo card again (he’s ticked this one before, presumably he’s just making assurance doubly sure): generalised and evidence-free denigration of “present science”.

  335. says

    Oh, FFS

    The paper claims to be unfalsifiable, but of course that’s just a claim. It could indeed somehow be falsifiable. I do hold that the paper is unfalsifiable, though.

    How many times do we have to explain falsifiability to you. Seriously, you still have no idea what falsifiability even means. I don’t believe for one second you hold any degree whatsoever.

    And this:

    In present science, when a scientist gets a six results, and three make sense, one is a little off, and two are anomalous, scientists keep the three results that make sense and simply throw the other three away.

    Thus, science gains only a partial understanding of a system works.

    You can’t have data points that you don’t understand and throw away, and claim to have a complete understanding of a system, yet scientists do this /all. the. time./

    No… That’s just… No! That is absolutely not how science works!

  336. Rev. BigDumbChimp says

    Intellectual dishonesty is rampant in science.

    Lots of problems here

    Define rampant in a measurable way.

    Provide citations supporting that, but please make sure they are citations where the dishonesty wasn’t corrected because if not this…

    It is not looked upon as intellectual dishonesty because of the imprimatur of the peer review system.

    becomes you just making shit up.

  337. says

    Ariaflame, BSc, BF, PhD

    “No, when a scientist gets 6 results and three make sense, one is a little off and two are anomalous a good scientist goes back and does more experiments around the areas where the results are strange.”

    Sure, you’re right, and in an ideal world we would only have good scientists.

    Even so, they may not find the answer.

    They may not necessarily have a good explanation for the two anomalies.

    They may have /one/ explanation but is it the right explanation? Hard to tell at least sometimes.

    Is their explanation the only answer?

    Could their explanation be a biased explanation that supports the purpose of their grant?

    Let’s be honest here, most scientists are simply defending their thesis.

    Also, the hypothetico-deductive approach has failed.

    We should see that a scientist is that a scientist is looking for data that falsifies their ideas, but the status quo is that a scientist is looking for data that supports their ideas.

    “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’ but ‘That’s funny…’–Isaac Asimov.”

    A famous quote by a privileged scientist with the status to defend a /really/ strange anomaly.

    That’s funny, but I don’t have time to address funny, I have to spend time defending my thesis project (e.g.), is more typical.

    For the typical scientist, that’s funny, but it challenges the major conclusions in the field, is not fun at all.

    Erik’s having providing a overarching “overscience” in his paper is no fun for him at all.

  338. Nerd of Redhead, Dances OM Trolls says

    Nettlesome is still lyin, bullshitting, and making shit up. He wouldn’t know how to use a map and GPS to escape from a torn wet paper bag.

  339. says

    Here’s what you need to be doing to prove the proposed ‘theory’ has any scientific merrit whatsoever:
    1) Show how this ‘theory’ was derived from actual observations. This is completely unclear from the paper.
    2) Give a way to falsify the gyromodel. Since I know you have problems understanding falsifiability. How can we test it? What observations would prove the gyromodel wrong?
    3)Give us any new predictions made by the gyromodel and show these are correct.
    4) Explain why the gyromodel explains things better than our current scientific understanding about these things. Feel free to use any example you wish.

    In other words you need to demonstrate the model’s falsifiability and its explanatory power.

    So far, you, and the paper for that matter, have failed to do any of these things.

  340. Ariaflame, BSc, BF, PhD says

    Perhaps nettle is spending more time marking high school lab write ups than actually associating with scientists. I don’t deny that there are occasionally bad apples. But to suggest that scientific malpractice is the norm? No. That is not my experience.

  341. says

    Seriously, nettles – just STOP. You are convincing NO ONE. All you are doing is demonstrating that you are a crank, peddling bullshit.

    Do you really think you can possibly accomplish something with this pathetic display?

  342. Rev. BigDumbChimp says

    Erik’s having providing a overarching “overscience” in his paper is no fun for him at all

    /headdesk

    Erik is providing double plus extra good science.

  343. KG says

    nettlecrank,

    Let’s be honest here, most scientists are simply defending their thesis.

    Duh! That’s why we have the institutional systems of science, which largely ensure that for every scientist defending a thesis, there is (if the thesis is a matter of current scientific interest) another interested in attacking it. You just show once more that you have absolutely no idea how and why science works.

    Also, the hypothetico-deductive approach has failed.

    You’ve repeatedly demonstrated that you don’t understand that approach, by boasting about unfalsifiability as if it was a badge of merit. You are also putting out your idiotic bilge using machines that have been designed using scientific findings resulting from that approach; and one only has to look at the scientific progress over just the past decade to see that your claim is utter crap.

    None of the above means that there are no problems with how science currently operates; but stupid nonsense like yours, and empty windbaggery like Andrulis’, are of no benefit whatever in addressing them.

  344. says

    pentatomid
    Most of your points I’ve already addressed, so you can just search through my posts.

    For example, #4 I answered in #395 and #396.

    #2 is worth a response vis-a-vis falsifiability.

    We can’t disprove String Theory. Not falsifiable.

    We can’t disprove Natural Selections. Not falsifiable.
    If were true, then it would explain the origins of life, and it does not.

    It does not explain evolutionary saltations (jumps).
    By the way, the idea of Punctuated Evolution was (and to a certain degree still is) extremely controversal because it is not explained by Darwinism

    Massive changes are not explained by Darwinism.

    So, if you are consistent, you are up in arms with regard to String Theory and Darwinism. Right?

    Ariaflame, BSc, BF, PhD
    Your previous comment was so intelligent. I’m disappointed in you.

    Scientific malpractice is hard to pin down and highly subjective.

    Is throwing out a lone anomaly malpractice? Depends.

    Without someone being in the laboratory to witness the behavior, you don’t have the proof all the time — if even much of the time.

  345. Brownian says

    Since it’s Friday, I propose we create a drinking game based on nettleingenting’s posts. I’ve got three rules so far:

    Take a drink whenever:

    a) nettleingenting praising shkler own kindness immediately before delivering an insult: 1 drink
    b) nettleingenting using partial data (i.e. a few blog comments) to form a conclusion about an individual’s intelligence or knowlege: 1 drink (2 drinks if shklee does so in a comment in which shklee also criticises another commenter of doing same; 3 drinks if shklee criticises scientists or science in general of doing same)
    c) nettleingenting uses the common creationist tactic of declaring that because theory/idea/concept A is incomplete, therefore theory B: 1 drink

  346. says

    Brownian,
    A fantastic idea!

    I suspect all participants will black out — just as they have blacked out any reasonable consideration of the paper.

    Gee whiz, reading it is hard. Understanding it is harder.

    So, don’t bother.

  347. Brownian says

    So, you prove my statement of lack of intellectual curiosity. Thank you.

    Thank you for the intelligent and balanced criticism.

    Your previous comment was so intelligent. I’m disappointed in you.

    d) nettleingenting uses strategic praise (disingenuous or not) as an emotional debate tactic: 1 drink

    Without someone being in the laboratory to witness the behavior, you don’t have the proof all the time — if even much of the time.

    e) nettleingenting implies a conspiracy: 1 drink (2 if shklee points to lack of evidence as evidence)

  348. Nerd of Redhead, Dances OM Trolls says

    Yawn, still nothing but lies, bullshit and bombast from nettlesome. Not one iota of evidence from the peer reviewed scientific literature to show that gyres explain squat. What a fuckwitted bullshitter.

  349. Brownian says

    Brownian,
    A fantastic idea!

    [Takes a drink according to d).]

    I suspect all participants will black out — just as they have blacked out any reasonable consideration of the paper.

    f) Holy fucking awkwardly spliced non sequitur!: 2 drinks

  350. says

    Nettleface,
    You still don’t get falsifiability.
    While I don’t know enough about string theory, I’m guessing it is falsifiable in some way. Natural selection definitely IS falsifiable. That’s what makes it good science.
    And punctuated equilibrium was only made to sound controversial by the way it was originally presented (Gould and Eldredge, in their original publication, contrasted the punctuated equilibrium idea with what was basically a strawman version of gradualistic evolution), which was picked up my non-scientific media. In reality it is just the punctuated equilibrium is just Darwinian evolution + peripatric speciation leading to what may be perceived as evolutionary ‘jumps’ in the fossil record. It doesn’t contrast with Darwinian evolution, but follows diractly from it.In fact, in The origin of species, Darwin already hinted at something similar to PE(without elaborating on it).
    Again, you show no understanding whatsoever about any of the concepts given.

    Furthermore:

    Most of your points I’ve already addressed, so you can just search through my posts.

    While you may be under the impression that you have adequately adressed these issues, you have not. All you’ve done is borrow some of Andrulis’ baseless assertions.

    I’m done with you, nettletroll. Go pull your cephalogyre out of your proctogyre.

  351. says

    Since it’s Friday, I propose we create a drinking game based on nettleingenting’s posts. I’ve got three rules so far:

    Take a drink whenever:

    a) nettleingenting praising shkler own kindness immediately before delivering an insult: 1 drink
    b) nettleingenting using partial data (i.e. a few blog comments) to form a conclusion about an individual’s intelligence or knowlege: 1 drink (2 drinks if shklee does so in a comment in which shklee also criticises another commenter of doing same; 3 drinks if shklee criticises scientists or science in general of doing same)
    c) nettleingenting uses the common creationist tactic of declaring that because theory/idea/concept A is incomplete, therefore theory B: 1 drink

    Hmmm… I would so do this… Except, just looking at the rules, I don’t think I have enough beer at the moment.

  352. says

    pentatomid,

    “While I don’t know enough about string theory, I’m guessing it is falsifiable in some way.”

    So, let me see, you admit ignorance, but that won’t stop you from speculating.

    I laughed hard.

  353. Antiochus Epiphanes says

    Nettleingenting: Pardon my previous spelling error; I meant “unannoted” rather than “annotated”…I’m not sure where the latter came from.
    Previously, you wrote

    One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement.

    Again, we don’t find that. How do you explain the discrepancy?

    The scoffing just makes people look foolish, and I, trying to be a sympathetic person, urge you not to scoff at the paper and make yourself look like a fool.

    Worse things have happened.

    Intellectual dishonesty is rampant in science.

    Intellectual dishonesty is rampant in people. This is why science has safe guard like repeatability, publication, and peer-review.

    Also, the hypothetico-deductive approach has failed.

    Then we are indeed fucked.
    As you also seem to eschew an inductive approach, I would guess that in your view empiricism has also failed?

    We can’t disprove Natural Selections. Not falsifiable. If were true, then it would explain the origins of life, and it does not.

    I may be quite unlearned regarding biochemistry, but you need remediation as well. This is apparent by your use of the term “Darwinism”. No one has been a “Darwinist” since the 1930s.
    The tenets of natural selection are simple enough, and completely falsifiable.
    -Organisms produce more offspring than can be sustained by the environment, and yet population sizes tend toward equilibrium. This indicates that some organisms in a population are more successful than others in producing offspring.
    -Heritable variation is correlated with differential reproductive success.
    Ta da.

    Of course natural selection doesn’t explain the origins of life (I guess that’s where your biochem comes in), but works pretty well on any replicator system in which the above tenets hold.

    It does not explain evolutionary saltations (jumps).

    Evolutionary theory certainly does, and in excruciating mathematical detail. In fact, models explaining genetic revolution have been in existence since the 1940s. Empirically, speciation has been shown to be replicable in the span of a few generations.

    Without someone being in the laboratory to witness the behavior, you don’t have the proof all the time — if even much of the time.

    Is this the basis of your dismissal of empiricism?

  354. says

    So, let me see, you admit ignorance, but that won’t stop you from speculating.

    I laughed hard.

    Stop being dishonest. Me admitting ignorance is me being honest. You could learn a bit about that. When I say I’m guessing it is falsifiable, what I’m saying is that, since string theory is being taken seriously by scientists, there is probably at least exist some way of verifying/debunking it. However, I can’t be sure, as I don’t know enough about it and don’t even know if it actually has the status of ‘theory’ yet.
    My point about evolution still stands.

  355. Antiochus Epiphanes says

    Also:

    String theory therefore gyromodel?

    Most of what I have heard about string theory indicates that it isn’t falsifiable, and this is largely interpreted as a bug, not a feature.

  356. Dhorvath, OM says

    String theory suffers from many bugs, but the broad applicability is likely it’s greatest one. Imagine saying that you have figured out a theory pertaining to a constant and then saying, well, my theory says it lies on the real number line somewhere. It’s just too big.

  357. says

    pentatomid:

    While I don’t know enough about string theory, I’m guessing it is falsifiable in some way.

    Yep. It is. If space has a positive curvature, rather than 0 or negative curvature, it cannot be true.

    There are several other ways to falsify string theory, but it’s technologically difficult at the moment, due to the small scale — we’re talking planck length and below here. But string theory definitely makes positive claims about stuff we don’t know about yet, and gives us areas to investigate.

    That doesn’t mean string theory is a very good model. A coherent, complete model has in fact been a bit evasive. I’m not even sure it’s the best option we have. Loop quantum gravity seems to be a simpler, more coherent approach. It’s still too early to tell, though, as LQG isn’t nearly as mature as ST.

    In any case, both string theory and evolution through natural selection (“Darwinism,” indeed) are falsifiable. Evolution through natural selection is one of the best-supported theories in existence.

  358. Dhorvath, OM says

    Nigel,
    I wonder where LQG would be if it had the same resources to draw upon as string theory has enjoyed the past twenty five years.

  359. Antiochus Epiphanes says

    pentatomid:
    You must surely imagine that English is not my first language either. I’m not going to challenge that illusion.

    And btw: “shkler” and “shklee” are apt and mellifluous. Can I cite this thread as the source of coinage when I make my next OED entry?

  360. says

    Dhorvath:

    I wonder where LQG would be if it had the same resources to draw upon as string theory has enjoyed the past twenty five years.

    That was Lee Smolin’s premise in The Trouble With Physics. He made a good case that we should’ve spent some of that money on other ideas (his favorite is, of course, loop quantum gravity). Basically, we put all our research dollars in one path, and now we seem stuck on that path. Really, we should’ve been researching other, more tractable ideas.

  361. says

    nigelTheBold, Abbot of the Hoppist Monks

    As always, you make an intelligent comment.

    A scientific theory is by definition empirically observed.

    You are making a mathematical abstraction which is an abstraction — not empirical observation.

    String theory is not empirical.

    “If space has a positive curvature, rather than 0 or negative curvature, it cannot be true.”

    We can not test the curvature of space empirically.

  362. says

    I have to say, I spend a few hours replacing a hot water heater, and this thread’s turned into a drinking game. It’s a good thing I’m heading over to my brother’s tonight for Rifftrax and far too much beer. I’m gonna be perusing this thread with the official Brownian Rules.

    It’ll be painful, but fun.

  363. Dhorvath, OM says

    Nigel,
    Smolin is why I asked, I have read that book too.

    Nettle,
    Curvature is measurable, and our best measures place it quite close to zero.

  364. Antiochus Epiphanes says

    A scientific theory is by definition empirically observed.

    No, no, no. A fact is empirically observable. A hypothesis is an explanation of facts that predicts some other set of facts and excludes another non-overlapping set. A theory is a hypothesis that explains a general phenomenon ( a large set of related facts), has been tested many times without being falsified, and is the only explanation yet articulated that hasn’t been falsified.
    Or maybe you mean theory as a neologism meaning a fact or a compound with a sulfhydryl group.

  365. says

    Or maybe you mean theory as a neologism meaning a fact or a compound with a sulfhydryl group.

    That must be it! He’s talking in neologisms! Maybe his arguments actually make sence if we replace everything he’s said by different words in different sentences!

  366. Nerd of Redhead, Dances OM Trolls says

    We can not test the curvature of space empirically.

    What was that? You’re wrong of course. Nothing but liar and bullshitter..

  367. says

    I do know a little about string theory.
    I’m no expert, but I’ve managed to work my way through a few books and grasp, I think, the basic concepts. Which is a lot more than I can say about this gyre thing. String theory doesn’t require a glossary with 70,000 new terms; it does, however, require some math.
    Actually, a lot.
    It’s an attempt to create a theory that ties together quantum mechanics and relativity, both of which make specific predictions that have been repeatedly verified for roughly the last century. And string theory itself makes some predictions–for a start, the existence of some number of extra dimensions curled up on themselves so tightly as to be, at present, undetectable. Currently we have no idea how to look for these dimensions; they were not, however, pulled out of anyone’s ass. They are mathematically necessary for the model to work.
    Essentially, the extra dimensions are necessary to constrain the possible ways that the tiny loops of “string” can vibrate; the idea is for the possible ways they can vibrate to correspond with the known subatomic particles.
    To see the strings directly would require an accelerator the size of a galaxy, and maybe the size of the universe.
    The need for such a new theory is the long-noted failure of quantum theory and relativity to mesh; Einstein spent his last few decades looking at the problem.
    Not everyone regards string theory as science, but part of the problem with falsifying it is that the math hasn’t been entirely worked out–really, the theory isn’t done. There’s some very difficult topology required in order to specify the complex shape of the extra-dimensional space required (it’s what is known as a Calabi-Yau space, and last I read, they’re still trying to work out which one is required by the equations). Specific predictions could be forthcoming once this is done.
    I find the theory interesting, if not really compelling. It’s also entirely possible that I’m not up-to-date on this. But the concepts aren’t really that hard, and the mathematical nature of it (notably lacking in the gyre paper) could at least potentially give us more verifiable information. More than “wow, fingerprints, tornadoes!” anyway.

  368. says

    nettleingenting:

    We can not test the curvature of space empirically.

    And at one time we couldn’t measure the speed of light empirically.

    At the moment, string theory is falsifiable but not testable. The practical fact that it is currently not possible to test string theory does not negate the epistemological fact that it is falsifiable.

    As Dhorvath pointed out, string theory in its current form is too general anyway. Most of the problems its had have been reconciling the different parts to create something more specific. That lack of specificity, and the fact that theorists have not been able to create something more specific, hints at one of two things: either string theory just isn’t viable, or that the different models of string theory are really just part of a larger whole (M-theory, as all the cool kids call it these days).

    But that’s all beside the point. None of that negates the fact that string theory makes positive claims, very specific and unique positive claims, even in its general form. As far as I can tell, the gyre proposition doesn’t make specific, unique testable claims, of a practical or even impractical nature.

    This is an epistemological problem, not a practical one.

  369. Antiochus Epiphanes says

    As far as I can tell, the gyre proposition doesn’t make specific, unique testable claims, of a practical or even impractical nature.

    Except for this one upthread:

    One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement.

    Which seems to have been falsified.

  370. says

    One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement.

    Which seems to have been falsified.

    Yeah, but I bet the gyromodel can explain the situation as it is in reality as well… As has been pointed out with the earth’s moon vs. venus lacking a moon, this theory can apparantly mean whatever one wants it to mean.

  371. KG says

    We can’t disprove Natural Selections. Not falsifiable. If were true, then it would explain the origins of life, and it does not. – nettlecrank

    I think nettlecrank’s trying to pack as much stupid into a single sentence as possible. In the first place “natural selection” (no, nettlecrank, it doesn’t need initial upper-case letters) is a concept, not a theory. The theory of evolution by natural selection is that it is the operation of natural selection that is primarily responsible for evolutionary change, and specifically for the adaptive features of organisms, and for speciation. This is eminently falsifiable and indeed, has had to be modified to account for the prevalence of genetic drift, and for mechanisms of speciation such as polyploidy in plants, which can produce a new species in a single generation, without a role for natural selection (although whether the new species then survives does involve natural selection). Natural selection can only come into operation once there are populations of entities which show multiplication and heritable variation – that is, of organisms or artifacts possessing some of the properties of organisms. It therefore could not – logically could not – explain the origin of life.

  372. Brownian says

    We can’t disprove String Theory. Not falsifiable.

    …becomes…

    String theory is not empirical.

    g) nettleingenting moves goalposts: 1 drink

  373. Brownian says

    We can not test the curvature of space empirically.

    What was that? You’re wrong of course.

    h) nettleingenting makes a claim disproved by the most cursory knowledge of the subject at hand: 1 drink
    i) nettleingenting makes a claim disproved by a simple Google search: 2 drinks

    I’m gonna be perusing this thread with the official Brownian Rules.

    To recap, while reading nettleingenting’s comments, take a drink whenever:

    a) nettleingenting praising shkler own kindness immediately before delivering an insult: 1 drink
    b) nettleingenting using partial data (i.e. a few blog comments) to form a conclusion about an individual’s intelligence or knowlege: 1 drink (2 drinks if shklee does so in a comment in which shklee also criticises another commenter of doing same; 3 drinks if shklee criticises scientists or science in general of doing same)
    c) nettleingenting uses the common creationist tactic of declaring that because theory/idea/concept A is incomplete, therefore theory B: 1 drink
    d) nettleingenting uses strategic praise (disingenuous or not) as an emotional debate tactic: 1 drink
    e) nettleingenting implies a conspiracy: 1 drink (2 if shklee points to lack of evidence as evidence)
    f) nettleingenting uses a non sequitur: 1 drink (2 drinks if Holy fucking awkwardly spliced non sequitur!)
    g) nettleingenting moves goalposts: 1 drink
    h) nettleingenting makes a claim disproved by the most cursory knowledge of the subject at hand: 1 drink
    i) nettleingenting makes a claim disproved by a simple Google search: 2 drinks

  374. says

    Nerd of Redhead, Dances OM Trolls

    I guess I was wrong about testing the curvature of space.

    I am able to admit error. I would appreciate any one else’s ability to do so, but as with a decades-long good friend of mine, you can’t. (By the way, he has never admitted he was wrong to me. Ever. The man is either God, or just can’t admit mistakes. I suspect the latter but for all I know he may be God. He certainly acts as if he were God sometimes.)

    You make no comment about string theory being unfalsifiable.

    Can you offer a link that shows I am in error about string theory being empirically observed too?

    If I am wrong about sting theory?

    You were kind enough to offer a link to prove me wrong. Below, I return the favor.

    http://www.math.columbia.edu/~woit/wordpress/?p=468

    An excerpt:
    “The paper was entitled Falsifying String Theory Through WW Scattering…I had heard that this paper was going to be refereed, and was wondering whether a referee would really let the authors get away with the outrageous claim of their title. Well, it appears that the answer is no.”

  375. says

    Antiochus Epiphanes

    “One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement.

    Which seems to have been falsified.”

    Oh really?
    Seems?
    How?

  376. Brownian says

    I am able to admit error. I would appreciate any one else’s ability to do so, but as with a decades-long good friend of mine, you can’t.

    j) nettleingenting petulantly whines: 2 drinks (1 for the drinking game, the second to drown out the childishly manipulative appeal to shame)

    So, to recap (again): while reading nettleingenting’s comments, take a drink whenever:

    a) nettleingenting praising shkler own kindness immediately before delivering an insult: 1 drink
    b) nettleingenting using partial data (i.e. a few blog comments) to form a conclusion about an individual’s intelligence or knowlege: 1 drink (2 drinks if shklee does so in a comment in which shklee also criticises another commenter of doing same; 3 drinks if shklee criticises scientists or science in general of doing same)
    c) nettleingenting uses the common creationist tactic of declaring that because theory/idea/concept A is incomplete, therefore theory B: 1 drink
    d) nettleingenting uses strategic praise (disingenuous or not) as an emotional debate tactic: 1 drink
    e) nettleingenting implies a conspiracy: 1 drink (2 if shklee points to lack of evidence as evidence)
    f) nettleingenting uses a non sequitur: 1 drink (2 drinks if Holy fucking awkwardly spliced non sequitur!)
    g) nettleingenting moves goalposts: 1 drink
    h) nettleingenting makes a claim disproved by the most cursory knowledge of the subject at hand: 1 drink
    i) nettleingenting makes a claim disproved by a simple Google search: 2 drinks
    j) nettleingenting petulantly whines: 2 drinks (1 for the drinking game, the second to drown out the childishly manipulative appeal to shame)

  377. A. R says

    nettleingenting: Please, explain how the paper Andrulis et. al explains any natural phenomenon better than scientifically established physics.

  378. Nerd of Redhead, Dances OM Trolls says

    Can you offer a link that shows I am in error about string theory being empirically observed too?

    Illiterate fuckwit, who here said string theory (a mathematical theory, not a scientific theory), is falsifiable at the moment? I would never say that, as it hasn’t progressed to that point yet. Just as the Higg’s boson hasn’t been shown definitively to exist (probably next year, only 3.5 sigma confidence at the moment, 5.0 is needed). I do have a reference showing that natural selction does work at home. I’ll post it when I get there.

    Nettlesome, you need to stop bullshitting us. You are dealing with some real science professionals here, and you will lose bigtime any argument with us over scientific facts. Time to fade into the bandwidth, as you have lost any respect we might hae had for you with your inane bullshitting and trolling. At the moment, you are just trolling.

  379. says

    Antiochus Epiphanes:

    Except for this one upthread:

    Damn! I keep forgetting about that. I have to admit, I focussed on the physics aspects of the gyre proposition, as I’m a bit stronger in physics than biology. I reckon I’ll have to go back and re-read the biology sections to see if I can understand this prediction.

    Sigh

    I’m gonna need more beer.

  380. says

    Nerd of Redhead:

    Illiterate fuckwit, who here said string theory (a mathematical theory, not a scientific theory), is falsifiable at the moment?

    Well, I did, actually — though I also said it’s not currently testable (though as it turns out, I was wrong about that, as it seems we can measure the curvature of space). There are also some predictions about the force of gravity at the planck scale that could falsify it — if only we could measure the force of gravity at the planck scale.

    Here’s a list of positive, testable predictions made by string theory.

    Most of these would be really, really hard to test at the moment. And it would have to pass pretty much all the tests to have a chance at being accepted as “right.”

  381. Dhorvath, OM says

    Testing gravity at the sub mm scale is hard enough, Planck scale? I won’t hold my breath.

  382. says

    nigelTheBold, Abbot of the Hoppist Monks

    “At the moment, string theory is falsifiable but not testable. The practical fact that it is currently not possible to test string theory does not negate the epistemological fact that it is falsifiable.”

    A very good point, I do concede.

    On the other hand, I do not concede to the idea that natural selection can be disproven. It is descriptive. I see no way to disprove it.

    Someone gave a response (if I recall correctly) that claimed a way to attempt to disprove it, but I was not convinced.

  383. A. R says

    nettleingenting: Disproving natural selection would be quite simple, you could do it yourself. Get sick, only take half of your course of antibiotics, wait until you get sick again, take the same antibiotics. If you die from septic shock, you’ve failed to disprove natural selection.

  384. Antiochus Epiphanes says

    “One positive prediction one would would make would be that unannoted RNA should exist in ALL life forms, and one should be able to identify RNAs in organisms that have no genetic complement.
    Which seems to have been falsified.”
    Oh really?
    Seems?
    How?

    Every completely annotated transcriptome is a falsifier.

  385. A. R says

    nettleingenting: The idea isn’t that you have to actually disprove natural selection, but that there are ways that it could be falsified if it were not a valid hypothesis.

  386. Dhorvath, OM says

    We have seen that NS is insufficient in itself to describe the development of our life system. It was falsified, or at least rendered as a subset description of evolution, years ago. KG at 468 brought this up already.

  387. says

    Oy, nettleface, read this:

    A. R

    “you’ve failed to disprove natural selection.”

    Fine.

    How about disproving it?

    I know of no way to falsify natural selection.

    Perhaps you do

    now reread this:

    nettleingenting: Disproving natural selection would be quite simple, you could do it yourself. Get sick, only take half of your course of antibiotics, wait until you get sick again, take the same antibiotics. If you die from septic shock, you’ve failed to disprove natural selection.

    Now tell me: are you being dishonest or just very stupid? you keep demonstrating that you haven’t the faintest idea what falsifiability is. Falsifiable means that there is a way to potentially disprove a theory WHEN THAT THEORY HAPPENS TO BE WRONG!

  388. says

    And besides, as has been said before (again, you really should read what people are saying) it has already been shown that natural selection alone isn’t enough to explain current patterns of biodiversity. In a way, this was a falsification (though not to the extent that it has become a completely invalid concept).

  389. Antiochus Epiphanes says

    “On the other hand, I do not concede to the idea that natural selection can be disproven. It is descriptive. I see no way to disprove it.
    Someone gave a response (if I recall correctly) that claimed a way to attempt to disprove it, but I was not convinced.

    No one claims that selection operates on all traits simultaneously, but in any instance where selection is used to explain variation in a trait, one must attempt to falsify the following:
    Organisms X in population Y exhibit differential reproductive success that is correlated with heritable variation.
    That’s all it takes.
    The mathematical basis of this was first laid out in R.A. Fisher’s Genetical Theory of Natural Selection published in 1930. The entire version is available online. Since you like sloggy reads, this one will suit you well.

  390. A. R says

    nettleingenting: You are truly one of the more half-witted, unintelligent trolls I have had the displeasure to encounter. Alternatively, you are amongst the most prevaricatave, deceptive trolls I’ve had the displeasure to encounter.

  391. says

    Dhorvath, OM
    A fair enough statement. I did not completely consider this point.

    A.R
    “If you die from septic shock, you’ve failed to disprove natural selection.”

    “Now tell me: are you being dishonest or just very stupid? ”

    Neither.

    You simply lack the ability to understand what “test for falseness” means.

    Seeing a supporting piece of data is not a test for falseness.

    I would say that such a fact is obvious — were it not for your bizarre conclusion.

  392. says

    No one claims that selection operates on all traits simultaneously, but in any instance where selection is used to explain variation in a trait, one must attempt to falsify the following:
    Organisms X in population Y exhibit differential reproductive success that is correlated with heritable variation.
    That’s all it takes.

    Yes, exactly. But I think his problem isn’t just that he can’t think of a way to approach the issue. I think he just still doesn’t get that ‘falsifiable’ doesn’t equal ‘wrong’. It seems as though in his mind, a correct statement is always unfalsifiable.

  393. says

    You simply lack the ability to understand what “test for falseness” means.

    Seeing a supporting piece of data is not a test for falseness.

    I would say that such a fact is obvious — were it not for your bizarre conclusion.

    Jesus Fucking Christ, make him stop!!!

    Nettleface, have you not understood a single thing that has been said to you? Seriously? What you’ve just said is so… HEADDESK!

  394. A. R says

    You simply lack the ability to understand what “test for falseness” means.

    Seeing a supporting piece of data is not a test for falseness.

    *Headdesk*, rinse, lather, repeat.

  395. says

    pentatomid
    “It seems as though in his mind, a correct statement is always unfalsifiable.”

    Right.

    You are being illogical.

    Something that is correct can not be proven false.

    For example, you can not prove that, at the moment and with this post on this site, my nick is /not/ nettleingenting.

    The only exception would be if you pretended that my nick was not such.

    Such a belief /is/ valid (in a absurd kind of way), but only for you if you are pretending my nick was not, at the moment and with this post on this site, nettleingenting.

  396. Brownian says

    there are not enough heads or desks in the universe for this.

    thas’t why Mw drinkin gaem iss such more funner.

    You simply lack the ability to understand what “test for falseness” means.

    Tha’s another b)—drawing a conclusion from partial data (how could the fucking asshole possabl conclude that someone lacks the ablility to unnerstand, rathar than simpley misunmisunderstanding,. but shklee doesw anyway becuase the fucker aappears to eschew slef-reflecton like shklee’s a vamprie.

    Frink up, duckers!

    [Passes out.]

    [Comes to.]

    nettleingenting, is your inconsistency due to your mother being an idiot, your father, both, or are you just a fucking embarrassment to them?

  397. Nerd of Redhead, Dances OM Trolls says

    As promised, an article showing mathematically why natural selection works. Natural selection in action, Lenski, where e-coli became able to metabolize citrate instead of just glucose after three mutations occurred.

    And that nettlesome, is the type of evidence you keep avoiding for your posts. Which makes them inane and insipid.