Pharyngula

There is a maddeningly vague press release floating around, and I think everybody has sent me a link to it now. It contains a claim by some chemists that they have discovered a new organizing principle in evolution.

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.

The researchers — Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon — made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

If true, this would be an extremely remarkable claim. An amazing claim. Something that would make all biologists sit up and take notice. Unfortunately, the puff piece writer and the scientists involved seem incapable of actually explaining what they found, which makes me extremely suspicious. This is just empty noise:

The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace’s idea. “What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,” said Rabitz, the Charles Phelps Smyth ’16 Professor of Chemistry. “The data just jumps off the page and implies we all have this wonderful piece of machinery inside that’s responding optimally to evolutionary pressure.”

How? What is the mechanism? What kind of data suggests this peculiar notion? I’m unimpressed, so far, and unfortunately, Physical Review Letters hasn’t yet put the paper online. I’ll also point out that the history of statistical claims for exceptional mechanisms that extend evolution is littered with “never mind” moments — some clever dick comes along and points out the ways in which the result is an epiphenomenon, a product of the same old rules all along.

The other problem that often occurs is that one of the investigators opens his mouth and reveals that he is completely out of his depth, and that the team has absolutely no conception of how evolution actually works. This time, there is no exception.

“The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. “Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”

Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank? That first sentence is not even wrong. Darwin answered the question of how complexity can arise, so no, we haven’t been puzzled by that general question; evolution is not completely random, so that part is a complete non sequitur; randomness easily generates lots of complexity, so even if we accept his premise, it invalidates his question; and how does he reconcile his assertion of “completely random” with his use of the simple metaphor of the “blind watchmaker”, which implies non-randomness? That’s a sentence that contradicts itself multiple times in paradoxical ways.

Anyway, I’ll be looking for the paper. My bet would be that it says nothing like the claims made for it by the press release, or that it will be an embarrassing error of interpretation by the authors.

Comments

  1. #1 Zeno
    November 12, 2008

    A hierarchy of information credibility (descending order):

    Research paper
    Abstract of research paper
    Article in Science
    Article in Science News
    Article in Scientific American
    Article in New York Times
    Press release
    Internet rumor
    Article in WorldNet Daily
    Article from Discovery Institute
    Article from Answers in Genesis

  2. #2 Brian
    November 12, 2008

    Predictably enough, the folks over at UD have been going gaa gaa over this one. Having seen enough of their claims get thoroughly refuted, I was wondering how long it would take before we would start seeing the refutations.

    Brian

  3. #3 Dave Wisker
    November 12, 2008

    Where, oh where, do these people get the idea that evolution is completely random? What is it about natural selection that is so difficult to understand? I’m beginning to think Richard Dawkins was right when he said the human mind seems almost wired to misunderstand evolution.

  4. #4 JakeS
    November 12, 2008

    My guess is that about 60% of the mainstream news articles will we worded in such a way as to imply “scientists disprove evolution!” and the creationists will pass out and wet themselves.

  5. #5 Nerd of Redhead
    November 12, 2008

    As soon as I hear of a MSM report of an article that scienists haven’t seen yet, my BS detector starts pegging out. Lets check the situation in 6 months. Probably another “never mind” moment.

  6. #6 Emma
    November 12, 2008

    That’s a normal fluff piece put up on the University home page: written by a non-science type, dumbed down as much as possible for non-science types. How much the actual paper resembles it is anyone’s guess.

  7. #7 minimalist
    November 12, 2008

    So… they found mutations in the proteins… statistically? Is this a clumsy reference to mass spec, or something completely underpants-on-the-head nutsoid?

    Smart money’s on the latter, for all the reasons PZ laid out, but I don’t know how that could get into any respectable peer-reviewed journal. How respectable is Physical Review Letters, anyway?

    (You know, I’m now remembering a bizarre article from a year or so back about potential ‘plasma-based genetic information’ for alien lifeforms in extreme conditions because, hey, those wisps of plasma kinda look like double helices! I think that might have been in this journal. Anyone remember this article, the details of which I’ve no doubt mangled a bit due to fuzzy memory?)

  8. #8 Vic
    November 12, 2008

    Reads like a bunch of ID’ers got loose in the lab.

  9. #9 Matt Heath
    November 12, 2008

    Zeno@#1: Modulo certain exceptions.

  10. #10 minimalist
    November 12, 2008

    Also, I wouldn’t say it reflects poorly on Princeton at all. I think every sizable university has cranks that get through somehow, and in many cases (like this one) it’s because the crank may be quite good in his chosen field, but extremely cranky the instant he dabbles in other fields.

  11. #11 David Marjanovi?, OM
    November 12, 2008
    A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

    Reverse translatase at last! Yeehaw!!!

    Ehem. Let me just say I… sorta kinda… doubt it. Reverse translatase wouldn’t quite be a perpetuum mobile, but…

    And what exactly is a biology paper doing in a physics journal…?

  12. #12 David Marjanovi?, OM
    November 12, 2008

    On the other hand, reverse translation (“the ability to control their own evolution”) would be great news. Every time she has problems with her teeth or rather the fact that her lower jaw is too small for them, my sister says “let’s convert to Lamarckism”…

  13. #13 Paha Arkkitehti
    November 12, 2008

    Well, I can’t say much without reading it.. But I had no problem finding it online..

  14. #14 Darby
    November 12, 2008

    It sounds like they’ve discovered another system that, if you screw with the pertinent genes, is more robust than they were expecting – it’s most likely an evolved redundancy mechanism, one of many already in place.

    Also, if it were directed evolution, wouldn’t these supposed adaptations be passed to offspring? What organisms were they working with?

  15. #15 Graculus
    November 12, 2008

    ?Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank?

    Not a native USian English speaker?

  16. #16 Jesse
    November 12, 2008

    @ Dave
    Evolution itself is not a random process……but the net directionality of evolution is random. There is no goal, there is no endpoint, there is no objective. Tracking environmental changes over long periods of time usually results in a random walking pattern.

  17. #17 TR Gregory
    November 12, 2008

    Got me too!

    A frustrating press release (or, adaptation is not random).

    The original paper is mostly equations, but it does at least articulate the claim less ambiguously than the story.

  18. #18 bsk
    November 12, 2008

    Hm… I’m quite interested to see how this turns out. Please update us when you know more, PZ.

  19. #19 katie
    November 12, 2008

    Gotta love chemists (hell, I’m dating one). But would I ever believe they have any idea how to use the word “fitness”, or “evolution”? Hell no.

  20. #20 Foggg
    November 12, 2008

    Three of the same authors have a related paper at arxiv, available to everyone
    http://arxiv.org/PS_cache/arxiv/pdf/0806/0806.2331v1.pdf

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  21. #21 frog
    November 12, 2008

    PZ — and some of the commenters — seem to be making a fundamental fallacy, of judging the paper by the press release.

    Why don’t we wait and see before going all ballistic over it? How can you possibly believe quotes coming out of some PR flack? Have none of you ever been interviewed by a newspaper and seen your words become gibberish? They’ll be the right words, in the right order, but they appear to say something completely different from what you were actually saying.

    PRL is very reputable. Maybe it’s crap — like half the stuff in Science or Nature — maybe it’s useless (different from crap) — or maybe they’ve developed some new analytic tool.

    It reads like they’ve discovered “generic homeostasis” — which isn’t going to get published anywhere. So patience.

  22. #22 hinschelwood
    November 12, 2008

    #7

    Phys Rev Letters is one of the most prestigious physics journals. All really eye-catching research goes in there.

  23. #23 Astrofys
    November 12, 2008

    I believe I have found the pre-print on ArXiv:

    http://arxiv.org/abs/0806.2331

    And Phys Rev is a good journal, but maybe this slipped through….

  24. #24 Reginald Selkirk
    November 12, 2008

    I’m unimpressed, so far, and unfortunately, Physical Review Letters hasn’t yet put the paper online.

    Because all the most important papers about evolutionary biology appear in Physical Review Letters. (roll-eyes)

  25. #25 TR Gregory
    November 12, 2008

    The paper is here

    Raj Chakrabarti, Herschel Rabitz, Stacey L. Springs, and George L. McLendon

    Mutagenic Evidence for the Optimal Control of Evolutionary Dynamics

    Phys. Rev. Lett. 100, 258103 (2008)

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  26. #26 wamba
    November 12, 2008

    On the other hand, reverse translation (“the ability to control their own evolution”) would be great news.

    Someone has actually looked into that. Some links in the comments here.

  27. #27 IST
    November 12, 2008

    perused rather than read in detail, but I’m not overly impressed at the moment, especially with the conclusion that control exerted by one protein on another implies the possibility of artificial control of the entire process. Seems to be a non sequitur, with no basis for the premise in the data.

  28. #28 Elin
    November 12, 2008

    Oh my. There is no science in that press release. At all.

    “Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank?”

    As a Dartmouth gal, I’ve gotta say this must be an indictment of Princeton. :)

  29. #29 Pierce R. Butler
    November 12, 2008

    Can someone more in touch with university protocols (than this humble non-academic) please explain what “an associate research scholar in the Department of Chemistry” means? Is this a regular formalized status like an associate professor, or a wordy way to describe somebody just sorta hanging around?

  30. #30 anon
    November 12, 2008

    i am a physicist and am aware of rabitz, but don’t have anything to do with him directly. as far as i know he has a good reputation. the paper doesn’t seem to make any outrageous claims, although i feel it’s a little light on data compared to the conclusions. it looks to me like the quotes attributed to chakrabarti are exaggerations or distortions of the claims made in the paper. having been through the p.r. wringer myself i would hesitate to pass judgment at this point…

  31. #31 Matt Heath
    November 12, 2008

    @Pierce: It sounds like a title for some kind of post-doc researcher

  32. #32 laserboy
    November 12, 2008

    The story to this work is that it can be difficult to define fitness, and therefore an optimization path at the molecular level. Their example is that the redox chain that leads to ATP exhibits extrema in redox potentials that are unlikely to be under direct selective pressure (witness that redox potential vary between extreme maxima and minima. Looked at from a purely statistical perspective, it is highly unlikely that this would occur without some sort of selective pressure. The authors show that control over the process is the selective pressure that drives redox potentials to their extrema, but which extrema they go to doesn’t matter.
    What the press release fails to convey (amongst its many mistakes) is that the authors are surprised to find a biological example of optimal control theory at work. Which just goes to show that they don’t get out much :)

  33. #33 minimalist
    November 12, 2008

    Yeah, I just perused the PRL article a bit, as well as the related Biochemistry articles from ’00 and ’02 (upon which the statistical analysis is based) and fortunately the authors aren’t even coming close to claiming that

    A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

    so that part, at least, is oversimplified dumbassery from the author of the press release.

    But I can’t say I’m especially impressed by the scientific articles themselves. Simplified, this is what the authors seem to have done/claim:

    1. In the Biochemistry articles, they artificially introduced mutations into the active sites of a cytochrome and watched the effects on the redox potential;

    2. Depending on the species, the mutations tended to push the redox potential generally in on direction; i.e. “nowhere to go but up” or “nowhere to go but down”; that is, they are (so the authors claim) already “extremized” in one direction or the other

    3. As organisms evolve, they bounce abruptly from one extreme to the other;

    4. The authors claim that “maximal fitness (ATP production)” of the electron transport chain arises from “maximization of the proton concentration gradient, which does not bear a direct physical relationship to the redox potentials”;

    5. Therefore there is no selective advantage for cytochromes to rapidly bounce between the extremes of redox-potential; quote from the authors: “Even if evolutionary selection did act directly on the redox potentials, it would be necessary to assume the selection pressure oscillates due to environmental dynamics that have no relation to the function of the ETC”

    6. The authors then contradict 4 by stating that “the efficiency of the proton pumps is a function of the redox potentials”

    Gotta go to a seminar so I’ll just sum up by saying that the authors seem to be sort of restating a common ID-creationist thing, which is claiming that a system requires multiple simultaneous mutations in multiple components. Not to say thay they are creationists themselves, but it’s close enough to that ID’ist claim that I’m not surprised that that crowd seized on this paper.

    The paper itself makes some rather trivial observations and unwarranted claims (not the least being its arbitrary ruling out of selective pressure on redox potential when they themselves give very good reasons for selection to apply!). But I’ll defer to someone who can actually crunch numbers to see if the stats hold up.

  34. #34 IST
    November 12, 2008

    Actually took the time to read through it:

    1. The modeling they use depends upon the assumption that the constituent pieces of the model coevolve.

    2. Based on the results of the model AND the above assumption, it appears that the proteins in the electron transport chain exert control over one another with regard to redox potential.

    3. The authors state that the “oservation that coevolving bipolymers may optimally control each other’s evolution raises the prospect of artificial optimal control of evolutionary dynamics”. In context, they are not stating that there IS an artificial control on these processes, rather that we COULD used the feedback mechanisms to control these processes for medical purposes.

    So while I’m not real impressed with the article, the summary has something dead wrong.

    Comment 34: You either have no grasp of how the review process works, you like to take argument from authority as valid because of its source rather than its merit, or you’re being sarcastic and I missed it. The last one is the only one that’s excusable as an argument.

  35. #35 Glen Davidson
    November 12, 2008

    #37 makes it sound like the paper is sound, but the whole “How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” makes me want to ask how the orbits of the planets can be so orderly and predictable (albeit with chaotic effects over the long run) when gravity is completely random and operates like a blind watchmaker (and of course random events do heavily play into the ultimate outcome of each0.

    Uh, yeah. That’s why we don’t say that gravity is completely random, and also why we don’t say that of evolution. The IDiots, on the other hand…

    Glen D
    http://tinyurl.com/2kxyc7

  36. #36 Sven DiMilo
    November 12, 2008

    Jules = Charlie Wagner. Again.

  37. #37 The Chemist
    November 12, 2008

    *Sniff*
    *Sniff*

    I smell cold fusion all over again.

    I’m going to give them the benefit of the doubt until Physical Review Letters publishes their research. However just based on the speed of the press release- it does suggest rather poor form from what I understand.

  38. #38 Liberal Atheist
    November 12, 2008

    As someone who is neither a chemist nor a biologist, the stuff about the proteins is beyond my understanding of it all. But I do understand that evolution is not a random process. I expected people who do research in this field to know that too.

  39. #39 Scott
    November 12, 2008

    I’d need to read the paper (and try to understand it, as it’s not my field) but the summary here reminds me a lot of Greg Bear’s novel “Darwin’s Radio”. Probably that’ll go away as I understand it better, but it makes sense to me now. :)

  40. #40 jj
    November 12, 2008

    I believe I have found the pre-print on ArXiv:

    http://arxiv.org/abs/0806.2331

    Good find. The complete PDF is available http://arxiv.org/PS_cache/arxiv/pdf/0806/0806.2331v1.pdf>Chakrabarti et al. Optimal control of evolutionary dynamics

  41. #41 rrt
    November 12, 2008

    Oh, wow, Charlie…there’s a blast from the past.

    My first impression from the press release was that they’d just gotten overheated over their “discovery” of redundancy in the system. Bit reading comments here I’m more confused. Are they saying they found proteins that interact to such a degree that one tends to “repair” the other? If so, that’s neat, bit I don’t see what the big deal is. Or are they saying the proteins do something else?

  42. #42 jj
    November 12, 2008

    Ooops, didn’t close tag properly. That link should’ve been

    Chakrabarti et al. Optimal control of evolutionary dynamics

  43. #43 rrt
    November 12, 2008

    Durn iphone. Bit = but.

  44. #44 Michael Johnson
    November 12, 2008

    Hi. I’m not a biologist (not even a scientist), but something seems straightforwardly logically amiss here. And that on top of the fact, as people have pointed out, that evolution is not “random.”

    That is, how could any non-sentient structure, be it a protein or whatever, “control its own fitness.” I mean, fitness is not an internal property: it depends on your environment. If predators live on the forest floor, better I live in the trees; if they live in the trees, better I live on the floor. So for something to control its own evolution, it would have to have a representation of its environment, and a decision procedure, yes? Otherwise it might change based on direct causal contact with its environment, but that’s hardly having control over anything, now, is it?

    Am I missing something? Sorry, I apologize again for not being a biologist.

  45. #45 IST
    November 12, 2008

    Jules Winnfield/Eric Williams/ Charlie Creotroll:
    So my 2nd assumption was correct, you’re taking it on authority simply because of the source (sort of like that Bronze Age text you’re trying to support?). Please demonstrate how a process that systematically weeds out characteristics that are unfit is not random? In fact, if you’d rather not explain for yourself, just find some peer reviewed literature that states that evolution IS random… and no quote mining, it’s cheating.

  46. #46 Michael Johnson
    November 12, 2008

    Whoa. Just read my post and realized it could be taken the wrong way.

    I’m *not* arguing that non-sentient things can’t control their own fitness; the paper is right; therefore ID.

    Instead, I was assuming we’re all rational, don’t think Jesus is fiddling around with our DNA on the weekends or whatever fundies have him doing, and we’re just trying to evaluate the claims of the paper as described in the press release. And from that perspective I’m having trouble wrapping my mind around how they could even *possibly* be true.

  47. #47 Peter Ashby
    November 12, 2008

    From the introduction to the paper at:
    http://arxiv.org/pdf/0806.2331v1

    Should the evolutionary dynamics of
    such a system demonstrate features indicative of optimal
    controls, this would constitute evidence that the
    system’s evolution has attained a sophisticated level of
    self-organization amounting to the solution of an OC
    problem. Here, we show that application of this theory
    to active site mutations in an enzyme network of central
    importance for metabolism-the electron transport chain
    (ETC)[7]-indicates that the redox potentials of electron
    transport proteins are controlling the evolutionary dynamics
    of this network in an optimal fashion, providing
    insight into the self-organization of this system.

    The problem seems to be that they have made the mistake of thinking that evolution seeks optimal solutions. Natural selection does nothing of the sort, it only measures variants that work well enough. The authors are showing a lack of imagination if they think the ETC is optimal. It was clearly designed by a series of harried ad hoc committees, half of which were high on something.

    It only appears to work optimally within its own parameters, the mistake is assuming that the extant parameters are the only possible solution.

  48. #48 jj
    November 12, 2008

    The introduction seems ridden with needless teleology:

    Evolution is guided by the optimization of fitness measures
    that balance functionally beneficial properties. In
    modern theories of evolutionary dynamics, such as the
    quasispecies model [2] and variants thereof, the fitness
    measure of a biological system plays a role analogous
    to that of the free energy of a mechanical system. The
    dynamics of the system, embodied through mutations,
    seeks to optimize this measure.

  49. #49 Xerxes
    November 12, 2008

    Without saying anything about the weird press release or conclusions of the paper, I think there’s something off about their statistical analysis of the “optimality” of the redox potential shown in Fig~1. They show distributions of redox potential for different mutations with the wild-type redox set to zero. Of the 6 proteins shown, 3 of the distributions fall roughly on 0, indicating (by eye) no optimization at all. The other three are kind of near optimal, but actually two of those have more extreme redox potentials available under the simple perturbations they made. Yet, they claim some absurd degree of confidence (one-in-ten-billion) that the redox potential was biased. Even if that were true (it’s hard to tell by eyeballing), finding statistically significant bias is nothing like demonstrating optimality.

    Also, I can’t figure why this was submitted to or accepted by PRL. Are they trying to cash in on the trend toward biophysics?

  50. #50 The Swiss
    November 12, 2008

    Matt Heath #9: That’s horrible! I also have an article published in an Elsevier journal, my first (and so far only) scientific publication. But “my” journal is more respectable, or at least so they tell me, and I know one editor is a very respected mathematician. Wait, no, that’s not me… I don’t even really know him…

    aargh!

  51. #51 minimalist
    November 12, 2008

    #45:

    Are they saying they found proteins that interact to such a degree that one tends to “repair” the other?

    Not necessarily, just that there would basically need to be coevolution of two components of the electron transport chain — that is, a mutation in one component alters the chemistry of the system to such an extent that there needs to be a compensatory mutation in a cytochrome in order to alter the redox potential, restoring the system to equilibrium and maximizing ATP efficiency once again.

    Problem is that the paper is not mechanistic, and the authors admit as much. There is no proposed mechanism for, say, one protein repairing other components or altering the gene, or whatever, nor is any evidence given for such — that’s entirely a fanciful fabrication by the writer of the press release.

    It does bring up a lot of questions about fitness landscapes and multiple targets, but doesn’t even come close to addressing them in any substantive way. Basically they only address a few molecular details of one component of this huge multiprotein system, and only make simplistic assumptions about the other components in order to make their model work.

    Not to say that the model can’t have value as far as it goes, and the paper, to its credit, is careful not to overreach. I doubt it would ever had been published anywhere except the crank journals if they’d tried to claim that this was evidence that ‘proteins cause their own evolution’ or whatever. Press releases, on the other hand, aren’t constrained by such concerns. The question is whether the authors actually hold with the nonsense interpretation of the PR, or if it was the result of an overzealous and undereducated writer.

  52. #52 Nick Gotts
    November 12, 2008

    Jules Winnfield@43,
    You’re a liar. Does the term “natural selection” suggest randomness? What gets naturally selected is what works best in the environment concerned – that is not random. Now troll off.

  53. #53 Matt Heath
    November 12, 2008

    The Swiss @#54: I don’t think there is any general problem with Elsevier’s journals; I think this is something of a one-off. If the editorial committee has integrity (and they mostly do) the journal will be respectable and if it has a good reputation it has probably earned it.

    Since you have mathematics published, I guess you know that in maths the publishers don’t actually do much. Reviewing and editing is all done by volunteer academics working for the prestige. Elsevier and Springer just lock up access and take a profit (and print paper versions of the journal that nobody really wants). You would think that at the least the publishers would at least be responsible for maintaining standards amongst editors; that they can’t do this convinces me that they serve no purpose.

  54. #54 WRMartin
    November 12, 2008

    But ionically enough, it is true if you accept intelligent input!

    Please enlighten us as to this intelligent input you speak of.

  55. #55 Johnny Vector
    November 12, 2008

    Ah yes, Hersch “baud-rate-too-high” Rabitz, the guy who didn’t understand the difference between “Physical Chemistry” and “Badly-taught Quantum Mechanics”.

    Not that I’m bitter.

  56. #56 ChemBob
    November 12, 2008

    Without having read all the prior comments (will do that next), please allow me to scream that this is not an indictment of ALL chemists at the very least.

  57. #57 Liberal Atheist
    November 12, 2008

    Jules, how is natural selection a random process, then? If evolution was entirely random, how would we have ended up like this? And where does it leave chemistry as a science, if reactions apparently occur randomly?

  58. #58 dc-agape
    November 12, 2008

    Hey, I’m a PhD candidate in chemist at UT-Knoxville and I know that it can’t be an indictment on chemists! Most of us understand that evolution is more complex than random selection! But do sure hope that it’s not an indictment on Princeton! So, I guess it must be just Chakrabarti or bad press.

  59. #59 Sili
    November 12, 2008

    Friggin’ PR department. One thing the uni introduced before I left in disgrace was that all ph.d. students had to write a one page popular summary of their thesis before they could have their viva. Dunno if that was in any way helpful – I had given up by then.

    Speaking as a (failed) chemist I had absolutely no interest in bio-stuff till I started reading Pharyngula. Not that I’ll hold myself up as an exemplar of the field.

  60. #60 Theodore
    November 12, 2008

    I once sent an email to PZ about this topic. Unfortunately he didn’t reply. I asked him how science knows genetic mutations are “random”. And I don’t mean “God did it”. What I mean is, is there something naturally inherit in cells to push them to mutate.

    I was wondering if science has actually answered that question already or is someone currently looking at it. The theory of evolution states “random” mutation. Is it “random” because science just doesn’t yet know why cells mutate?

    If anyone can respond with more reading on this subject that would be great.

    Thanks

  61. #61 Glen Davidson
    November 12, 2008

    I asked him how science knows genetic mutations are “random”. And I don’t mean “God did it”. What I mean is, is there something naturally inherit in cells to push them to mutate.

    These are not mutually exclusive matters. Indeed, many genes appear to be set to mutate, so that genes encoding cone snail venom mutate much faster than, say, Hox genes tyically do. Nevertheless, there is nothing in HIV mutation (another very fast mutating organism) or in cone snail mutation that suggests that it is not “random” (in this case “random” doesn’t mean “without chemical bias,” it just means “without direction”).

    Is it “random” because science just doesn’t yet know why cells mutate?

    No, a good deal is known about why cells mutate, from chemicals to radiation. And within that context, it has been observed that such mutations are “randomly produced”. Also, the organisms with high rates of mutations appear to have that capability simply in order to “try out” many combinations, and not in order to settle in any fixed, “optimal” position in the “fitness landscape.”

    Glen D
    http://tinyurl.com/2kxyc7

  62. #62 Noah
    November 12, 2008

    A caution for those of you looking at the arxiv preprint: it is quite different from the paper published in PRL (the PRL paper even adds another author). It appears that the authors took significant feedback from the peer review process; it’s impossible to tell whether they still stand behind the preprint.

    Which is the problem with preprint servers, isn’t it?

  63. #63 ScienceTim
    November 12, 2008

    At 9:19 AM, Emma said: “That’s a normal fluff piece put up on the University home page: written by a non-science type, dumbed down as much as possible for non-science types. How much the actual paper resembles it is anyone’s guess.”

    (Item 1) Being a non-scientist does not make one stupid. Dumbing-down is done by those who think so. Alternatively, scientists who think that non-scientists are stupid, think that the public should be taught specialist jargon in order to understand an idea. Neither notion is correct.

    (Item 2) *Our* public affairs department works with the scientists to create a press release, and discourages us from an excess of incremental releases. I doubt that the standards are any more lax at Princeton. Scientists have no excuse for press releases that are stupid or misinformed or that misinterpret their own results. They have chosen to commit one or the other (or both!) of the intellectual sins mentioned in item #1.

  64. #64 Former PZ Student
    November 12, 2008

    “But ionically enough, it is true if you accept intelligent input!”

    Here we go……

    “Evolution is guided by the information (intelligence) in the genome and the effect of environment.”

    Wow…… I don’t even know where to begin…..I have no words.

  65. #65 The Chemist
    November 12, 2008

    @ Jules Winnfield #35

    Please. Don’t. Seriously.

    (See here).

  66. #66 Steve_C
    November 12, 2008

    Jules continues to fail. Do try to understand how dna, reproduction and natural selection work together.

  67. #67 Former PZ Student
    November 12, 2008

    I got it!! Jules, please read a biology textbook.

  68. #68 Vic Stenger
    November 12, 2008

    Independent of the merits of this paper, don’t dogmatically dismiss the possibility of self organization playing some role in evolution. Physical systems of all sorts exhibit self organization or, more generally, simplicity -> complexity. Think of a snowflake. And we may need something beyond natural selection to explain the origin of life.

  69. #69 Nerd of Redhead
    November 12, 2008

    JW is just a troll. His use of “darwinism” is evidence of that. As a working scientist, I just don’t understand what darwinism is. Sure, Darwin first described evolution, but he lacked information that was discovered after his death. As a result, he made some mistakes. As a result, while scientists acknowledge he was first, his ideas are not the sum of evolution. By now, 150 years later, they are just a part of the whole. So evolution is what the theory is called today. “Darwinism” sounds like a cult, made up to ridicule science, but merely shows the ignorance of those who try to imply that it is a cult. At no point has another theory of how life diversified been presented in the scientific literature, even though there would be a Nobel prize for anyone who did so and was found to be right.
    So JW, instead of questioning us, start citing the literature to back your arguments, if you have any. Attacking evolution proves no other theory right. That theory needs positive evidence, which is lacking.

  70. #70 Former PZ Student
    November 12, 2008

    Jules, please read this information from talk.origins.

    http://www.talkorigins.org/indexcc/CB/CB940.html

  71. #71 Midnight Rambler
    November 12, 2008

    Johnny Vector | November 12, 2008 12:50 PM #59:

    Ah yes, Hersch “baud-rate-too-high” Rabitz, the guy who didn’t understand the difference between “Physical Chemistry” and “Badly-taught Quantum Mechanics”.

    Interesting angle; I noticed on his web page he gives 680 publications in a 37 year career, or an average of 18 per year. Somewhat suspicious.

    As for this one, I’m a biologist with a decent understanding of genetics, evolution, and some biochem, and I have no idea WTH they are talking about. As someone pointed out, Fig. 1 is baloney; all it shows is that mutations change the potential, which is unsurprising, but it doesn’t support their conclusion that it can be only changed in one direction. And can someone tell me what a “quasispecies” is?

  72. #72 Sven DIMilo
    November 12, 2008

    JW is just a troll.

    Charlie. Wagner.
    See the “Dungeon” tab up top. Smart people have been talking sense to Charlie for many years without evidence of effect. He’s just not worth feeding.

  73. #73 Nerd of Redhead
    November 12, 2008

    JW, still no citation of the scientific literature to back your ideas. That is a great indication that you don’t know what you blather about. So either cite some proof from the scietific literature, or crawl back under your rock. Your ignorance is showing. And you will disappear again when PZ gets around to it.

  74. #74 Tulse
    November 12, 2008

    At no point has another theory of how life diversified been presented in the scientific literature

    Historically that’s not true — Lamarckism, saltationism and even Mendelism were seen in their day as counters to Darwin’s assertions that characteristics were not acquired (Lamarckism) and that evolutionary changes were graduated (saltationism/Mendelism). (And of course Lysenkoism was also presented in the Soviet literature in opposition to Darwinism.) These were considered scientific theories, and certainly expressed in the scientific literature of their day.

    It’s a testament to the strength of the theory of natural selection that none of these challengers could provide a base of compelling evidence, unlike “Darwinism”.

    (And yes, I’m reading a rather interesting book by a historian of biology called Genesis: The Evolution of Biology. It’s especially interesting to see how some of the current fundie arguments against natural selection are echoed in some of the early scientific literature, e.g., claims in the 19th century that the protoplasm must be the source of major developmental guidance and species change, because changes to the chromosomes could not produce large enough differences to give rise to new species, just alterations of existing species.)

  75. #75 frog
    November 12, 2008

    ScienceTim: Scientists have no excuse for press releases that are stupid or misinformed or that misinterpret their own results. They have chosen to commit one or the other (or both!) of the intellectual sins mentioned in item #1.

    That’s what we need, scientists who are trained primarily as spokespeople! Gah, what idiocy — one reason people get into science is to get away from being salespeople.

    Are we to judge every PR flack on their grasp of science to the level of a full professor? No — we have specialization to avoid that — PR flacks are experts at selling, and it’s their job to understand salesmanship, while it’s the scientists jobs to do science.

    I reserve my right (and of my colleagues) to be semi-autistic, cranky and asocial — that kind of honesty and sincerity is exactly what good science is about, and the opposite of what a good press release is about. Feynmann got 4F’d because he was “nuts” on that basis — he wrote hilarious books, but you could never have gotten a reasonable press release out of him. Fortunately, he had the guts to send PR types to hell (unless he found them attractive, in which case he’d get them drunk instead).

  76. #76 Nerd of Redhead
    November 12, 2008

    Tulse, I stand corrected. Our troll kept mentioning ID, so I was trying to point out it isn’t an idea in the scientific literature. Anyway, our troll will be gone when PZ gets done with classes.

  77. #77 The Chemist
    November 12, 2008

    @Sven DIMilo

    Thanks for the heads up about the Charlie Wagner thing.

    Still, anyone who argues cold fusion is pretty much shouting their stupidity from the rooftops. I just wanted to see how zealous about his belief in No Neutrons this particular person is.

  78. #78 Katkinkate
    November 12, 2008

    Posted by: Jules Winnfield @ 32 “BTW, you were wrong about cold fusion too…

    “Against a monumental backdrop of bad publicity for cold fusion since 1989, researchers in Japan on May 22 demonstrated the production of excess heat and helium-4, the results of an historic low-energy nuclear reaction experiment.”

    Has it been replicated and confirmed yet? I’ll be more positive when the process is repeated in a few other labs.

  79. #79 Tulse
    November 12, 2008

    Tulse, I stand corrected. Our troll kept mentioning ID, so I was trying to point out it isn’t an idea in the scientific literature.

    I didn’t mean to come off as tutorial — you’re absolutely right that ID is a complete scientific nonstarter. I just find it interesting that, contrary to the claim that there is some big “Darwinian conspiracy”, natural selection actually had several purely scientific competitors, which were weeded out by the time of the Modern Synthesis.

  80. #80 frog
    November 12, 2008

    Xerxes: Yet, they claim some absurd degree of confidence (one-in-ten-billion) that the redox potential was biased. Even if that were true (it’s hard to tell by eyeballing), finding statistically significant bias is nothing like demonstrating optimality.
    Also, I can’t figure why this was submitted to or accepted by PRL. Are they trying to cash in on the trend toward biophysics?

    Hmm, the 4 left-most look like extremely low probability distributions, applying an ordering test. The last two in the opposite direction.

    But it’s not clear to me what they’re assumed distribution is that they’re testing against. I’d hope that the PRL reviewers were sharp about that, particularly since it’s the base of the paper.

    But why PRL? Because a lot of interesting biological work that is heavily mathematical isn’t interesting in bulk to many biologists. They dismiss it as “methodology” papers, and the journals actually suggest that you should go try physical chemistry — not because they find the papers weak, but because it doesn’t speak to their market.

    They publish a lot of biophysics, since the biophysical journals are strong on the “bio” part, but weak on the “physics” part. If your a biophysicists, besides trolling BJ and such standards, PRL and associated journals are troll-worthy.

  81. #81 Nerd of Redhead
    November 12, 2008

    Tulse, don’t worry. I had a *headdesk* moment when I read your post. I have heard of Lamarckism, and always thought Mendel proved Darwin right at the end of the day (most of my biology comes from reading Asimov).

  82. #82 Dutch Delight
    November 12, 2008

    This idea that publishing papers is similar to preaching the truth would be funny, if it was put forth by a child.

  83. #83 travc
    November 12, 2008

    The actual work seems just to show that certain proteins are robust somewhat surprisingly (if you are a noob IMO) robust to mutations. Of course, to anyone who understands molecular evolution this is a “no duh”, but nice confirming evidence. It is still just canonization and phenotypic pasticity.

    To plug a friend’s paper, “Survival of the flattest” showed this totally predictable result.
    http://www.nature.com/nature/links/010719/010719-4.html

  84. #84 The Swiss
    November 12, 2008

    (slightly off-topic and rather specialized, so sorry y’all)

    Matt Heath #57: yeah I know, I was being overly dramatic. I agree with you that publishers (for what concerns mathematical journals at least) are becoming obsolete: they don’t do much (other than uselessly mess around with the author’s painstakingly and lovingly typed preprints, that is!) but they still take money from universities for printing papers with their name on them.
    Witnessed what happened with Springer’s K-theory. If I got that correctly, Springer kept too high a price without any apparent reason, so the editorial board resigned en masse and founded elsewhere a new journal, the… “Journal of K-theory”. Problem solved.

    That way lies the future. And in online publishing, of course.

  85. #85 Blake Stacey
    November 12, 2008

    A caution for those of you looking at the arxiv preprint: it is quite different from the paper published in PRL (the PRL paper even adds another author). It appears that the authors took significant feedback from the peer review process; it’s impossible to tell whether they still stand behind the preprint.

    Which is the problem with preprint servers, isn’t it?

    Which is why papers on the arXiv are typically updated to reflect the versions which are published! The fact that these authors did not do so is more than a little irresponsible.

  86. #86 Tulse
    November 12, 2008

    I [...] always thought Mendel proved Darwin right at the end of the day

    Mendelism was definitely part of the “Modern Synthesis”, but as I understand it, initially many saw Mendelism as an alternative to Darwinism. The issue at contention was the nature of the mechanism of heredity. Some critics aregued that Darwinism implied that characteristics shaded imperceptibly from one form to another. The critics thought that this would lead to an averaging out of all characteristics, and thus no variation would be available for selection to work on — all individuals in a species would tend toward the same average. In contrast, Mendelism thought that heredity was more discrete, or to put it in modern terms, “digital”, and that characteristics varied in specified ways with specified values. For an analogy, it is like creating a colour by mixing various paints versus using a variety of different coloured pixels — the paint can’t be separated out into its components, but the discrete pixels can.

    Of course, this entire issue disappeared once we understood the genetic basis of heredity (and it turned out that Mendelism was largely right), and once we realized that this issue wasn’t really central to the insights that Darwin had regarding natural selection.

  87. #87 Wayne Robinson
    November 12, 2008

    I think Jules Winfield’s (comment #78) vague ideas about genetics are about 30 years old. My own personal vague recollections of genetics are much more up to date, and I have some vague idea that there are these toolbox genes which are important in evo/devo biology, in determining which genes, when and where, are turned on and off, to change structure during embryological development. I have this vague idea Sean B. Carroll wrote this book “Endless Forms Most Beautiful” discussing this, but I could be wrong.

  88. #88 Arnosium Upinarum
    November 12, 2008

    “…proteins…possessing the ability to control their own evolution.”

    “Ability”? “Control”?

    Towards what goal?

    That in the opening line of the press release is all anyone needs to know that

    this

    is

    pure

    bunk.

    They only go about proving it.

  89. #89 Anton Mates
    November 12, 2008

    I was wondering if science has actually answered that question already or is someone currently looking at it. The theory of evolution states “random” mutation. Is it “random” because science just doesn’t yet know why cells mutate?

    Mutations are random in two senses. Most importantly, they are random with respect to fitness. A given mutation isn’t any more likely to occur just because it would, in the current environment, benefit its carrier.

    Luria and Delbruck designed an experiment to test this in bacteria, for which they got a Nobel. Some scientists have claimed to find evidence for directed mutations, but so far, this hasn’t ever panned out.

    http://en.wikipedia.org/wiki/Luria-Delbr%C3%BCck_experiment

    The other and less important sense in which mutations are random is that they are, literally, unpredictable. This is because they are caused by unpredictable phenomena–radiation happening to strike a DNA strand in one particular place, or interaction with one particular molecule of a chemical mutagen. Events on this scale are governed by quantum theory, and to our knowledge are non-deterministic.

  90. #90 frog
    November 12, 2008

    Tulse: Some critics aregued that Darwinism implied that characteristics shaded imperceptibly from one form to another. The critics thought that this would lead to an averaging out of all characteristics, and thus no variation would be available for selection to work on — all individuals in a species would tend toward the same average.

    I thought that wasn’t a “some critics thought” thing, but a “Darwin was wrong about it” thing — he did think that inheritance was blended, which would have made his essential insights incorrect — but fortunately he was wrong about the right thing, and wasn’t a strong enough theoretician to cause him to abandon where he was right due to where he was wrong.

    There was also orthogenesis — which formed a strong element of Gould’s thinking — aka, evolution by the inter-fitting of the pieces rather than external fitness. People just confuse the two. Folks in the early 20th century — important folks like Bateson — thought that was the dominant force, but unfortunately it’s analytically less than helpful because topology is a much harder problem than functional minimization.

  91. #91 Kel
    November 12, 2008

    If evolution was entirely random, we would NOT have ended up like this.

    The false dichotomy between randomness and intelligence. Who is to say evolution is for us any more than it is for the fruit fly, or the mangrove, or the lichin? We are just one of millions of known working configurations, we are born out of natural selection. Yes change was there, but it wasn’t completely random. The environment crafted us through natural selection, our configuration has come from 3.5 billion years of our ancestors being crafted by a changing environment. Just like every other organism on this planet.

  92. #92 Anton Mates
    November 12, 2008

    In contrast, Mendelism thought that heredity was more discrete, or to put it in modern terms, “digital”, and that characteristics varied in specified ways with specified values.

    It’s interesting to note that Darwin himself speculated that inheritance might be discrete, and even did experiments similar to Mendel’s on sweetpeas. I believe he also noticed the 3:1 ratio in–was it primroses? But he never put that ratio together with the observation of discrete inheritance.

    So close….

    http://www.guardian.co.uk/books/2003/feb/08/peopleinscience.evolution

  93. #93 Jadehawk
    November 12, 2008

    Natural selection is a trivial
    effect that has nowhere near the power vested in it by evolutionists.
    True, it can change the frequency of alleles in populations under
    selection pressure, but no evolutionist has ever demonstrated that these
    changes in gene frequency can ever lead to new processes, structures or
    organisms.

    Yes, i know we’re not supposed to feed the trolls, but this line made me think. Why do creationists always think that science hasn’t proven something-or-other, when in reality it seems that they’re merely unaware of the fact that it HAS?

    I remember an article about e-coli that evolved the ability to feed of citrate. this was caused by mutation(the e-coli have been mutating happily and randomly for the entire course of the experiment)and natural selection (the medium in which they were growing had citrate in it, which e-coli can’t usually process. this originally limited the growth of the colonies. the new mutation allowed better feeding, thus resulting in a growth explosion).

    do we need to start announcing scientific discoveries on billboards? because apparently, to creationists, what they don’t know about doesn’t exist

  94. #94 Former PZ Student
    November 12, 2008

    @ JW 101

    “Huh?

    What is your area of expertise?”

    Completely irrelevant. Darwinism is merely a term coined by creationists used by creationists to describe scientists who disagree with creation.

    Go away

  95. #95 Angel Kaida
    November 12, 2008

    I believe what Nerd of Redhead is getting at is that “Darwinism” is the name of a set of ideas about evolution that have been replaced by the modern evolutionary synthesis. The way you ID’ers throw the word around, it certainly looks like you’re talking about a theory that’s still in use, and hence you can’t possibly be talking about the set of ideas we’d define as “Darwinism.” So we’re not sure what this thing you’re calling “Darwinism” is.

  96. #96 Kel
    November 12, 2008
  97. #97 Nerd of Redhead
    November 12, 2008

    Huh?
    What is your area of expertise?

    PhD with thirty years academic/industry. What is yours?

  98. #98 CJO
    November 12, 2008

    counters to Darwin’s assertions that characteristics were not acquired (Lamarckism)

    Acquired characteristics isn’t the primary clash between Darwinian theories and Lamarckian ideas; since, as you note, the mechanism of heredity was unknown to Darwin, acquired characteristics was a live option for him. He understood that his theory wouldn’t be nearly as compelling if inheritance weren’t particulate, though, so you’re right as far as Mendelism eventually supporting Darwin in the synthesis, even if it seemed like a challenge to traditional Darwinian thought in 1900.

    But the real divide with Lamarckism is common descent. Rather than the tree of life, as in Darwinian explanations where all life shares a ‘root,’ presumably in a single abiogenesis event, Lamarckism posits something more like parallel ladders, where ‘lower’ forms are continually arising via abiogenesis, and ascending the ‘ladder’ via acquired characteristics.

  99. #99 Kel
    November 12, 2008

    We are no more Darwinists than we are Einsteinists, Newtonists, Faradayists, Hubbleists, Bohrists, or Crick & Watsonists. What we believe about evolution comes from observation and testing, it comes from over a century of falsifiable testing in which some of Darwin’s ideas have been validated and others have been either shown to be wrong or have been expanded upon. There would not be a single person here who would refer to Origin Of The Species over more recent experiments that disagree with the book.

  100. #100 Nerd of Redhead
    November 12, 2008

    JW, you are a biologist and use the term “Darwinism”? I just don’t believe you. No self respecting biologist would use that term, if they aren’t a godbot creobot/IDer.

  101. #101 Sven DiMilo
    November 12, 2008

    Jules’s Charlie’s area of expertise is saying the same thing over and over and over. Brick-wall city.

  102. #102 Kel
    November 12, 2008

    No self respecting biologist would use that term

    Well there is one… Dawkins uses the term.

  103. #103 Nerd of Redhead
    November 12, 2008

    Kel, you are right in that some old school biologists like Dawkins in the UK use that term, but that is changing.

    Our troll uses it to try to pretend a cult of personality. What a twit. Next he needs to show his evidence for what he believes by citing the scientific literature. I’ll not stay up waiting for that answer.

  104. #104 Nerd of Redhead
    November 12, 2008

    What’s the matter Charlie, afraid PZ might ban you for the umpteeth time if post your real URL?

  105. #105 Kel
    November 12, 2008

    Kel, you are right in that some old school biologists like Dawkins in the UK use that term, but that is changing.

    Fair enough. I always found his use a little odd, but that’s mostly because I’m a young’un so the only time I’ve really seen the use is when creationists try to characterise evolution as a religion. (then comes the “Darwin repented on his death bed” comment that is wrong on so many levels)

    Now with Charlie Wagner, why isn’t he submitting his ideas for peer review? Why isn’t he fighting in academic circles for his ideas to be accepted? Why is he taking this fight public? Why is he deliberately misrepresenting biologists by using terms like Darwinism instead of trying to fight the good fight and just look at evidence? This to me suggests that he’s not really interested in being right; just that people believe he is right. His use of the word Darwinism is just an ad hominem attack. Bring on the peer-reviewed science Mr Wagner.

  106. #106 Pete Rooke
    November 12, 2008

    Now it would be interesting to see if you would all be so sceptical about a paper affirming the status quo in biology. Closed minds are not something scientists should aspire to.

  107. #107 JJ
    November 12, 2008

    Oh, so its teleogical again? Toward the goal of better functioning?

  108. #108 Nerd of Redhead
    November 12, 2008

    Pete “well meaning fool” Rooke. How open is your mind to god not existing? If it isn’t open to that idea, stop criticizing others. Get it?

  109. #109 Kel
    November 12, 2008

    Now it would be interesting to see if you would all be so sceptical about a paper affirming the status quo in biology. Closed minds are not something scientists should aspire to.

    There you go being gravely insulting again. Do you find it funny to be so insulting, do you get a kick out of offending others?

    Scientists always have been and always will be sceptical to new ideas. it’s a good thing too, that scepticism is needed to filter the good ideas from the bad.

  110. #110 Jadehawk
    November 12, 2008

    Now it would be interesting to see if you would all be so sceptical about a paper affirming the status quo in biology

    again, for those who missed it the first time: just because you don’t know about something happening, doesn’t mean it isn’t happening. there have been several reviews of research papers on this blog could in no way, shape or form be considered contrary to the evolutionary framework… and the more sloppy of them have been similarly ripped to shreds.

  111. #111 Wowbagger
    November 12, 2008

    Now it would be interesting to see if you would all be so sceptical about a paper affirming the status quo in biology. Closed minds are not something scientists should aspire to.

    Pete, reports like this are the equivalent of a scientist claiming to have found a cow whose udders squirt, say, Bailey’s Irish Cream, rather than milk. Just because something can be dismissed out-of-hand does not mean those doing so are closeminded. There’s not enough time in the world to dismiss each claim some god-fuelled crank vomits forth.

  112. #112 jt512
    November 12, 2008

    Zeno, #1:

    A hierarchy of information credibility (descending order):
    Research paper
    Abstract of research paper
    Article in Science
    .
    .
    .

    Science, as in the journal Science, the most prestigious scientific journal on the planet? And you put it third?

  113. #113 rrt
    November 12, 2008

    I think “Article in Science” means “news article,” no?

  114. #114 JD
    November 13, 2008

    Science, as in the journal Science, ONE OF the most prestigious scientific journal

    FIXED.

  115. #115 jt512
    November 13, 2008

    JD, thanks for not attaching my name to your “fixed” (ie, fabricated) quote of mine. Nice to know that the ethics of commentators at this blog are at least infinitesimally better than average.

    As to what other journals could be considered as prestigious as Science, I’d like to see you defend any other journal besides Nature. These are the only two major international journals that I am aware of that restrict publication to papers that are either groundbreaking in a field or are so fundamental to science that there is a need for scientists outside the authors’ field to be aware of the research. Any respectable scientist can get published in the top journal in their field. But to get published in one of these two major interdisciplinary journals is a rare and coveted honor.

  116. #116 Wayne Robinson
    November 13, 2008

    I’ve spent some time reading some of Charlie Wagner’s entries on his blog. I think he is confusing the origin of life with evolution, doesn’t understand evolution itself because he states that; “While evolution is now accepted as a fact by science and is becoming accepted by the Catholic Church, the mechanism underlying its most important aspect, macroevolutionary progress, is not clearly established. Even science acknowledges that the mechanism depends on very long streaks of luck. The evidence for it is thin, a working model has not been demonstrated, and consensus within science has not been reached”, and seems to think that panspermia is a scientific method of resolving any problems with evolution. Evolution doesn’t depend on long streaks of luck, just each small change being a little better. Panspermia doesn’t solve any problems, it just moves the problem elsewhere, and anyway is impossible to test.

  117. #117 Kanaio
    November 13, 2008

    If only I had a self-actualized existence. < (.)(.)>

    A bit off topic, but at what age do you think Evolution should be taught to children? After reviewing the Department of Education’s science content standards for Evolution taught in elementary schools where I live, I was appalled to see how watered down the subject is — almost to the point of irrelevance. If we want to make real headway toward reaching people, before they are indoctrinated into creationism, we would do well to initiate reform in elementary school science content standards covering Evolution.

    Children are skeptical of anything which refutes the biblical presentation, which they learn first. This is a lot bigger deal than Santa Clause. Teachers don’t like teaching subjects that parents will take issue with. Elementary education teachers need good direction on how to navigate through this quagmire, or they will simply not teach evolution. The local science teachers associations would be a good place to start; unfortunately few elementary school teachers are members.

    I get a kick at the surprised look on children’s faces when they hear about evolution for the first time. The later they hear about it, the more amazed they are. It is critical that children start getting higher quality science instruction at an early age.

    BTW, I would add peer review to the top of Zeno’s hierarchy.

  118. #118 JD
    November 13, 2008

    jt512 wrote,

    JD, thanks for not attaching my name to your “fixed” (ie, fabricated corrected) quote of mine.

    FIXED AGAIN.

    As to what other journals could be considered as prestigious as Science, I’d like to see you defend any other journal besides Nature.

    Oh, so you concede there is more than one. Good. I’m glad that little ol’ Journal Nature that’s been around for nearly 140 years wasn’t completely forgotten. Publishing P.N.A.S. is also good for the ol’ CV as well.

  119. #119 LwPhD
    November 13, 2008

    @jt512 #126

    Science and Nature are pretty much crap shoots. Sure, they’re prestigious, but so are Academy Awards (of the Hollywood variety, not the NAS variety). I can quite unambiguously from my own personal experience say, that, were it not for the prestige and high circulation of Science and Nature papers, I would vastly prefer to publish in a good solid journal like Genome Research, Genetics, [fill in the blank with your own favorite field-specific jounral].

    What they (Science and Nature) have going on is a racket that consistently churns out a reliable minority of high profile papers that are very sexy and also very wrong. I say this having been first author in 2 Science papers and a contributor to 2 Nature papers. The constraints the authors are forced into because of the format is almost as bad as the editorial process that frequently elevates crap to conventional wisdom. Even when a paper is correct, it is hard to show it convincingly in the straightjacket that is forced upon those who publish in such “rarefied” journals.

    That being said, it is hard to be heard over the din without publishing in such journals, and excellent science is usually the majority of such journals. And until suitable alternatives emerge, it is definitely worth publishing in and reading Science and Nature. But remember, you don’t have to look very far before you find real shit in those journals.

  120. #120 jt512
    November 13, 2008

    Since JD obviously has no scruples, allow me to appeal directly to the moderator: I’m not sure exactly what you’re moderating, if you allow someone to write: “XYZ wrote” and then allow them to write anything other than what XYZ wrote. Back in the days of Usenet, that sort of intentional misquoting was a capital offense, and it should be now as well. I’m more than happy to stand by what I wrote, but the door has to swing both ways: no immature child should be permitted to attribute something to me that I did not write.

  121. #121 LwPhD
    November 13, 2008

    @JD #130

    Don’t even get me started on PNAS. The contributed (Track I) and communicated (Track III) tracks are corruptions of what may originally have been a good idea when publishing was substantially harder than it is now. Track II has excellent work, but still, it is hard to read a PNAS paper without first confirming its submission history before proceeding.

  122. #122 LwPhD
    November 13, 2008

    @jt512 #131

    What in the heck are you talking about? Search on “by: JD” and you’ll find only two comments. The first comment (at #125) takes exception to your exclusive declaration that Science is the best journal.

    I hesitate to continue, as this must be blindingly obvious to anyone who has spent anytime in any discussion forum from usenet ’til now. Perhaps you are trolling for obvious answers? Anyway, throwing caution to the wind, here is the answer: Editing your comments with his/her own point of view is a snarky way of disagreeing with you, more or less the equivalent of saying “No, Science isn’t the best journal, it is ONE OF the best journals.” There was no fabrication, and to suggest otherwise is silly. Where did “JD” put words into your virtual mouth?

  123. #123 jt512
    November 13, 2008

    In #130, LwPhD wrote

    Science and Nature are pretty much crap shoots.

    In my albeit limited experience, all the top journals are crap shoots. For example, I used to do nutrition research. We did a clinical trial to test the effect of the consumption of a particular nut on serum cholesterol. The result was that consuming this nut lowered cholesterol by a clinically significant amount. The paper was rejected by the top clinical nutritional journal, and we published elsewhere.

    A year later we repeated the trial, with the exact same protocol, except that we used a different nut, and the results were identical. The PI wanted to submit to the journal that rejected us the last time. I (being rational) said, “why waste our time?” but the PI said we should give it a shot.

    Guess what. The paper was accepted — despite the fact that it wasn’t groundbreaking this time around; it was just a replication of the previous trial (which, then, really was novel) using a slightly different intervention.

    What they (Science and Nature) have going on is a racket that consistently churns out a reliable minority of high profile papers that are very sexy and also very wrong.

    I’m kind of curious what you mean by “wrong.” In science, we use observations to model the truth. Every model is “wrong” by definition of “model.” But that’s the way science works. The models keep getting closer to the truth. Newton was “wrong” insofar as his models didn’t hold up to very large or small scale systems. It now appears that Watson and Crick were “wrong” insofar as RNA may make an important contribution to heredity independent of DNA. I don’t know where Newton or Watson/Crick published, but I suspect that Science or Nature would not have minded publishing these “wrong” findings.

    I say this having been first author in 2 Science papers and a contributor to 2 Nature papers. The constraints the authors are forced into because of the format is almost as bad as the editorial process that frequently elevates crap to conventional wisdom.

    I have no idea what “constraints” you are talking about. I’ve never published in either of those journals, but my girlfriend recently had a second paper published in Science. The article required a substantial rewrite in order to be understandable by scientists outside my girlfriend’s area of expertise — but that’s the whole point of publishing in a major interdisciplinary journal. If your work is important enough to bring to the attention of scientists outside your field, the technical level of the article has to be written at their level. The journal editor and my girlfriend had a mutual understanding that a more technical paper would need to be published in a specialist journal. Thus, publishing in Science imposed no constraint, except that it necessitated publishing a second, more technical article elsewhere.

  124. #124 Tualha
    November 13, 2008

    #134: Crick & Watson published in Nature. Interestingly, Nature didn’t subject the paper to peer review. (Source: http://en.wikipedia.org/wiki/Nature_(journal) )

  125. #125 IST
    November 13, 2008

    Jules> nice.. a response… perhaps we can actually have a conversation here.

    You accuse my reply of being a red herring, when in fact it is a direct response to your query. If you’re referring to the origin of life in general ,then you don’t want to use the words natural selection, evolution, or Darwinism because none of those explain the origin of life, nor are they INTENDED to do so. You show a misconception that is common among opponents of natural selection as a theory.
    You also pulled another Behe argument out of your hind end with the “macroevolution can’t be proven” bollocks. I suggest you have a look at something having to do with transitional fossils, preferably not put out by DI, and come back to us on that. I’d start with the progression from fish to amphibians, perhaps something off of Ken Miller’s website? You may find his easier for you to swallow being that he’s also a theist.

    http://www.millerandlevine.com/km/evol/

    That you were a science teacher for that period of time and with those credentials, yet fail to comprehend natural selection, is completely incongruous. There is clearly a high level of mendacity occuring here… care to enlighten us on which of the two it is?

  126. #126 IST
    November 13, 2008

    My fault Charlie, I actually took the time to read your website… perhaps you need to read a few things before there can be any sort of discussion, as the arguments you’re likely to use (unless you’ve come up with some new ones) all have gaping holes in them. There are fundamental misunderstandings in your reasoning, starting with the VERY large one that not ruling out a supernatural creator as a source for life is still scientific. The inability to prove or disprove something removes it from the realm of science, period. You’re entitled to your views, we’re entitled to scorn them as we do the rest of the religite nonsense that we’re fed, and neither aspect of that qualifies what you have to say as a legitimate scientific argument. The entire premise for ID is an argument from personal incredulity without an attempt whatsoever to formulate evidence for its postulates. Rather, you seek to kick holes in natural selection with updates to Paley’s argument from nearly two centuries ago. WHEN you actually have something to support YOUR point of view that is more substantial than “I just can’t see how it happened”, let me know and there may be a discussion to be had. Until then, perhaps you should examine: Carl Sagan -Demon Haunted World (for an evaluation of what is actually science), and any 3 or so books by Dawkins, Gould, Miller, etc for a critical examination of natural selection. It might help fill in the gaps in your understanding.

    I’m simply not going through the same tired arguments over and over when it’s been better done before this. The transcript from the Dover trial demonstrates that your ideoology hasn’t a leg to stand on in the scientific community, even among those who share your religious beliefs.

  127. #127 Tualha
    November 13, 2008

    Re #100, a good summary of the citrate adaptation result is here:

    http://scienceblogs.com/grrlscientist/2008/06/evolving_without_gods_permissi.php

  128. #128 Emmet Caulfield
    November 13, 2008

    Thus spake Wowbagger:

    a cow whose udders squirt, say, Bailey’s Irish Cream, rather than milk.

    Fantastic! I definitely want one of those cows and I have three magic beans to trade.

  129. #129 Marios
    November 13, 2008

    It sounds like they’ve discovered an example adaptive phenotypic plasticity – even toy evolution simulations show evolution for developmental robustness. Off the top of my head: ” Plasticity, Evolvability, and Modularity in RNA ”
    http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.31.6447

  130. #130 Larry Boy
    November 13, 2008

    “I was wondering if science has actually answered that question already or is someone currently looking at it. The theory of evolution states “random” mutation. Is it “random” because science just doesn’t yet know why cells mutate?”

    First, for evolution to proceed by natural selection, ‘random’ mutations are not required. Instead, it is only necessary that mutation can produce variation in all relevant directions of the phenotype.

    Mutations arise from various process acting on DNA. However, fitness is essential a property of proteins (and regulatory elements). Since there is an arbitrary mapping from DNA to proteins, mutations to DNA cannot predispose DNA to create particular kinds of proteins.

  131. #131 minimalist
    November 13, 2008

    jt512 @ 134:

    I have no idea what “constraints” you are talking about. I’ve never published in either of those journals, but my girlfriend recently had a second paper published in Science. The article required a substantial rewrite in order to be understandable by scientists outside my girlfriend’s area of expertise — but that’s the whole point of publishing in a major interdisciplinary journal. If your work is important enough to bring to the attention of scientists outside your field, the technical level of the article has to be written at their level. The journal editor and my girlfriend had a mutual understanding that a more technical paper would need to be published in a specialist journal. Thus, publishing in Science imposed no constraint, except that it necessitated publishing a second, more technical article elsewhere.

    The constraints are definitely there because some concepts are subtle and require a lot of explanation and thorough experimentation to demonstrate. These journals, by their nature, favor articles that are punchy, “big”, and easily explainable. It also favors more conservative modes of experimentation, relying on standard techniques that people outside the field are probably familiar with.

    I submitted to Nature recently, and found this to be the case. My paper really couldn’t be subdivided into “general audience” and “more technical” publications, because the big insight was so difficult to demonstrate that it required a lot of thorough testing and extensive controls. But the implications were pretty big for a variety of subfields in biology, so we (and the editor who sent it out for review) felt that the “big insight” of the paper was important enough to consider.

    The problem was, it required a lot of figures, a lot of subtle and novel experiments that needed to be explained, and a lot of words in general. Even though I ran over the word limit, I had to delete a lot of stuff that I knew was going to trip up the reviewers and readers, and hey presto, it did.

    We ended up resubmitting to another high-impact journal, one with a more generous word count, and judging from the reviews we got back (asking mostly for stuff we’ve already done or know we can do), we’re pretty much in. And I’m much happier knowing our intent was generally more clear.

  132. #132 North of 49
    November 13, 2008

    Way upthread were a few predictions that IDers would seize (have seized?) on the press release that prompted this post and this fascinating thread.

    I’m no biologist so I can’t follow all of what’s been discussed here, but I can think of one other group that will pounce on this news with great excitement, once they hear of it: New Agers.

    It’s this bit from the press release that will get them all quivering and sweaty:

    “A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

    Really, they’ll swoon. We knew it, we knew it, we knew it! Proteins can THINK!!!11!!! Proteins are conscious!!! Proteins have will!!!1!

    Perhaps none of you have had the pleasure of talking biology with a New Ager? If you discussed, say, that experiment with E. coli and the citrate medium with such an intellect, you’d quickly hear some comment like “Isn’t it amazing how they know what to do,” the subtext being that these bacteria have consciousness and will, make decisions about which genetic material to keep and which to discard, like a person deciding which clothes to put in the wash. When you try to explain that it’s really just a function of the (complex) properties of the (complex) chemicals of which the E. coli are made, (keeping it as simple as possible, you see) you get a blank stare — they simply don’t have the mental reference points to connect to the concept. In their world view consciousness pervades everything; they’re like animists in that respect.

    To my mind it’s a little like saying “Isn’t it amazing how water always knows how to run downhill”, but that argument doesn’t fly too well either. Their minds seem impervious.

    Anyway, wrapping up, I predict with 100% confidence that as soon as some New Ager somewhere comes across this press release, there will be a spate of postings in the usual places like Whale.to, which will take this theme and run with it to places you may have trouble imagining: “proof” of a cosmic consciousness, “proof” that consciousness creates reality, “proof” that prayer can heal, “proof” that “spiritual energy” can connect living beings across interstellar distances, “proof” that water has memory (and feelings!) — so homeopathy is too real, and those are just off the top of my head.

    Orac, if you happen to be reading this, I predict a flood of new woo based on this misconception, along with a lot of old woo reconfigured to take advantage of the New Hot Thing. For example, I think we’ll see the “vibrational energy” pitch replaced with something along the lines of “vibrational consciousness”, as in “the proteins in your cells know what their optimum vibrational frequency should be, but are forced into non-optimal frequencies because of toxins in the body. Our quantum-frequency wave generator bypasses the toxins’ distortional heterodyning and ‘shines a light’ that the body’s proteins ‘see’ and ‘follow’ toward their natural healthy frequency of vibration.”

    Or some such.

    Those Princeton PR people may have a lot to answer for, though in their defense I’ll admit it’s not possible to inoculate against stupidity; still, perhaps they and those in similar jobs should think carefully about how their words could be twisted and misinterpreted, and choose them more judiciously.

    Thanks PZ and all the (sane) commenters. Great thread.

  133. #133 David Marjanovi?, OM
    November 13, 2008

    I asked him how science knows genetic mutations are “random”. And I don’t mean “God did it”. What I mean is, is there something naturally inherit in cells to push them to mutate.

    I was wondering if science has actually answered that question already or is someone currently looking at it. The theory of evolution states “random” mutation. Is it “random” because science just doesn’t yet know why cells mutate?

    Cells don’t mutate, DNA does.

    Off the top of my head, there are the following kinds of mutations:
    - Copying mistakes. When a base flips around — I mean physically turns over, rotates on its chemical bond to the deoxyribose –, it often has the same shape as a correctly oriented other base, so DNA polymerase (the enzyme that copies DNA) puts the wrong base into the copy.
    - Damage to DNA. Plenty of sources for that: radiation, a large array of chemicals, and the simple instability of DNA at reasonable temperatures in water. DNA falls apart when stored in water — we spend lots of energy constantly repairing our DNA.
    - Mistakes in repair of damage — see copying mistakes.
    - Duplications, losses or inversions of parts of chromosomes. In other words, mistakes in the repair of double-strand breaks.

    And, well, all of these are observably random, as we’d expect from our knowledge of chemistry. Plus, while not all mutations are equally probable — an A is more likely to be miscopied as a G than as a C or T, and the probabilities have been measured from observations –, the effect of any such mutation on how the resulting protein works is different for every single position in the genome.

    Indeed, many genes appear to be set to mutate, so that genes encoding cone snail venom mutate much faster than, say, Hox genes tyically do.

    This is completely wrong.

    What’s going on is that most mutations in a Hox gene are lethal. A zygote with a broken Hox gene doesn’t get far. Mutations in Hox genes are selected against, in other words. Snail venom protein genes have much more freedom to change without having detrimental effects on the snail — so that’s what we see happening! The DNA repair apparatus is equally active all over the genome; it doesn’t even distinguish genes from junk DNA, because it can’t.

    Natural selection is a trivial
    effect that has nowhere near the power vested in it by evolutionists.
    True, it can change the frequency of alleles in populations under
    selection pressure, but no evolutionist has ever demonstrated that these
    changes in gene frequency can ever lead to new processes, structures or
    organisms.

    Define “new”.

    I know this sounds silly, but it isn’t. Fingers and toes are not new, lungfish have plenty in their pectoral and pelvic fins (well, OK, among the living that’s only the Australian lungfish, the others have lost them). Vertebrate extremities are not new, they’re just ordinary outgrowths of the body wall (like scales, teeth, or taste buds) with a copy of the body axis inside. The Hox genes (which pattern the body axis and the limb axes) are all mutated copies of each other, and the ParaHox genes (which pattern the gut) are mutated copies of the Hox genes. The microtubuli in the cytoskeleton are mutated copies of a protein that bacteria and archaea use for cell division. And so on. I submit that nothing is ever new. You’re welcome to offer examples.

    Mendelism was definitely part of the “Modern Synthesis”, but as I understand it, initially many saw Mendelism as an alternative to Darwinism.

    Some think this includes Mendel himself.

    Science, as in the journal Science, the most prestigious scientific journal on the planet [after Nature of course ;-) ]? And you put it third?

    Of course.

    Nature and Science are extended-abstract publications. For the real papers to come out, you typically have to wait a year or three more, and that invariably happens in a much less prestigious journal that doesn’t restrict submissions to three fucking pages and small, coarse-grained photos.

    (The situation is improving now that people publish 95-page papers as online “supplementary information” to their extended abstracts, but…)

    Seen the Epidexipteryx paper in Nature? It has two or three glaring failures of peer-review. And Science used to publish one egnorant birds-are-not-dinosaurs paper after another in the late 90s.

    Scientists have a love-hate affair with Nature and Science (and, I hear, in big fields this continues to the top journals in those fields, like Cell). For the hate, see above. For the love, the worth of a scientist is judged, nay, calculated by their impact factor, and Nature had an impact factor of 27 last time I checked.

  134. #134 Jules Winnfield
    November 13, 2008

    “Define “new”.

    structures, processes and systems that did not exist in the past but exist now in the present.

    For example, in the cambrian period camera-lens eyes did not exist. Today they do. How did we get from “no eyes” to “eyes”?

    If all new forms “evolve” from previously existing forms then we must face the prospect of an “infinite regression of pre-existing forms.

  135. #135 Tualha
    November 13, 2008

    I forwarded the paper to a friend who does physics and bio, and she thinks the paper itself is basically ok, it’s just that the press release blew the actual claims way out of proportion, and possibly the authors, being from different disciplines, had terminology troubles.

    I have no opinion on the paper myself, it being rather over my head.

  136. #136 Nerd of Redhead
    November 13, 2008

    Charlie, either cite the scientific literature to back up your claims or shut up. Anything else is a dishonest liar at work.

  137. #137 Tualha
    November 13, 2008

    A modest proposal:

    Why don’t we all simply completely ignore all the creationist trolls? We all have better things to do than argue with someone whose mind is made up and who will ignore all evidence and reason.

    A counterargument to my proposal:

    On the other hand, the practice might come in useful if we ever want to argue against creationism to those whose minds aren’t made up, in circumstances where it matters. A school board, for example.

    Thoughts?

  138. #138 Tulse
    November 13, 2008

    How did we get from “no eyes” to “eyes”?

    By going from “light-sensitive patches” to “light-sensitive patches in pits that help to sharpen the incoming light” to “deep pits that have a very small opening like a pinhole camera” to “rounded pits where the opening is covered with transparent tissue” to “vision organs with lenses”, i.e., “eyes”.

    All of these steps are seen in various current organisms.

    But of course, if you had done only a modicum of reading on this matter, you’d realize that.

  139. #139 Jules Winnfield
    November 13, 2008

    “By going from “light-sensitive patches” to “light-sensitive patches in pits…”

    And where did the “light-sensitive patches” come from?

    Magic?

  140. #140 Nerd of Redhead
    November 13, 2008

    Charlie, still won’t cite any scientific literature to back up your points. What’s the matter, there isn’t any?

  141. #141 jt512
    November 13, 2008

    David Marjanovi?, #133:

    Nature and Science are extended-abstract publications. For the real papers to come out, you typically have to wait a year or three more, and that invariably happens in a much less prestigious journal that doesn’t restrict submissions to three fucking pages and small, coarse-grained photos.

    My girlfriend’s last paper in Science was 6 pages long and contained 6 full-color figures. Plus Science published an additional 21 pages of supplemental material online. So, either your facts are wrong, or Science is willing to make exceptions.

    Jay

  142. #142 IST
    November 13, 2008

    Tuala> I ignore the ones that can’t manage to write in something resembling English or become rapidly abusive. I engaged in a conversation with Charlie at first because he appeared to be more open to rational arguments than the typical troll, although his persistence in using refuted arguments makes me regret this assessment. If someone is rational enough to at least present points to be debated, it serves as decent practice, up to a point.

  143. #143 IST
    November 13, 2008

    getting tired of the same arguments… Charlie: http://www.youtube.com/watch?v=ieKDLtrBXs0

    Ken Miller answered your question better than we could hope to do.

  144. #144 Sven DIMilo
    November 13, 2008

    Science publishes both “Research articles,” which are typically 5-6 pages long and maybe one or two per issue, and “Reports,” which are far more numerous (maybe 12-20 per issue) and limited to 2500 words (about 3 journal pages).

  145. #145 Jules Winnfield
    November 13, 2008

    “getting tired of the same arguments… Charlie: http://www.youtube.com/watch?v=ieKDLtrBXs0

    Ken Miller answered your question better than we could hope to do.”

    I’m NOT arguing the case for irreducible complexity. I don’t believe it’s a compelling argument.

    The important point is that the adaptation of means to ends, the adaptation of structure and process to function requires insight. Behe’s mousetrap is unevolvable, not because you can’t take it apart without it losing it’s function, it’s unevolvable because you can’t put it together in the first place using only random, non-directed, accidental occurrences. The selection of the parts, the configuration in which they’re aligned, the assembly into one unit all require intelligent decisions at every step of the way. Similarly, living organisms show the same characteristics. It’s not that you can’t remove parts and lose total function, it’s that you can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

  146. #146 Nerd of Redhead
    November 13, 2008

    Charlie, still not citing the scientific literature. TSK, TSK.

  147. #147 Tulse
    November 13, 2008

    Similarly, living organisms show the same characteristics. It’s not that you can’t remove parts and lose total function, it’s that you can’t explain why these particular parts were selected

    Because in the population of organisms, those individuals that had those parts generally produced more offspring than those who didn’t (or, more technically, they had better inclusive fitness). What’s so hard about this?

  148. #148 Tualha
    November 13, 2008

    Please. Stop feeding the troll. It’s so fucking pointless.

  149. #149 Jadehawk
    November 13, 2008

    Charlie, your basic knowledge of chemistry clearly sucks. let me guess, you’ve never used a non-digital, old-fashioned b/w camera. otherwise, you’d know that there’s basic chemicals that are sensitive to light.

    a single-celled critter that has internalized a bunch of chemicals like that would be sensitive to light. a critter that concentrated that photo-sensitivity in one spot would be even more effective… and so on.

    also, you’re still arguing out of ignorance. ALL previous forms had a function, just not necessarily the same as the organ that evolved out of it. proto-bones were nothing but excess calcium deposits, which helped critters survive calcium-shortages. as the deposits got bigger for that reason, they incidentally started providing other benefits (size, strength, protection etc.)which in certain environments would have provided adaptive advantages… and so skeletons came into being. but the “point” of calcium deposits was never to develop into a skeleton. that’s arguing backwards. evolution says that nature can only work with what’s already there. of all the fossils we’ve ever found, we’ve never found a fossil that had something that couldn’t have somehow developed out of something else, similar to it. and if you get an extremely long progression of small changes, you’ll eventually end up with big changes.

    and if i remember correctly, some smart-ass actually found independent functions for the parts of a mouse-trap… can’t find it right now though.

  150. #150 David Marjanovi?, OM
    November 13, 2008

    And where did the “light-sensitive patches” come from?

    Magic?

    I don’t know how retinal is produced and what the enzymes in this pathway are most closely related to, but I wouldn’t be surprised if retinal were ultimately the product of, say, a slightly messed-up enzyme that used to be involved in unsaturated fatty acid metabolism. Gene duplication and mutation — as usual.

    Incidentally, IIRC, one of the crystallins (lens proteins) found in chickens is a broken version of lysozyme (an enzyme that is secreted through the skin and destroys the cell walls of bacteria). Apparently lysozyme is transparent. Yet another case of gene duplication and mutation.

    And gene duplication — or rather the duplication of random long stretches of the genome by means of a copying mistake — is common, and genome duplication (mitosis failure) is known to happen from time to time, too.

    But note what you’re doing: you are implying that just because we here happen not to know yet, science will never find it out (if it hasn’t already). You are implying that everyone is just as ignorant as you are, and that everyone will forever stay that ignorant. That’s silly of you.

    My girlfriend’s last paper in Science was 6 pages long and contained 6 full-color figures. Plus Science published an additional 21 pages of supplemental material online. So, either your facts are wrong, or Science is willing to make exceptions.

    That’s evidently a Research Paper as opposed to a Report (or, in Nature terminology, an Article as opposed to a Letter to Nature). Very few papers are allowed that special treatment; congratulations to your girlfriend! On the other hand, I did mention that there are now Nature papers with 95 pages of supplementary material (in other words, the paper got published online and the extended abstract got printed).

    Behe’s mousetrap is unevolvable [...] because you can’t put it together in the first place using only random, non-directed, accidental occurrences.

    What? Of course you can! How do you think your first and your second gill arch ended up forming the three ossicles in your middle ear, to take an example where physical proximity is involved?

    The selection of the parts, the configuration in which they’re aligned, the assembly into one unit all require intelligent decisions at every step of the way.

    Show us.

    you can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

    Give us an example so we can try!

    and if i remember correctly, some smart-ass actually found independent functions for the parts of a mouse-trap…

    Cutting board, paper clip…

  151. #151 David Marjanovi?, OM
    November 13, 2008

    Charlie reminds me of a biology teacher I once had in school. Around 60 years ago, she seems to have learned everything she was supposed to teach by heart, and then she regurgitated it each and every year. She never learned anything throughout her career. She tried to teach me that fungi are plants — the actual botanists and mycologists had stopped that nonsense 50 years ago. She taught my brother’s class that sponge fishing is an important branch of the economy in Mediterranean countries — yes, present tense.

    I bet Charlie has done the same: said the same words in every one of 33 years, and never learned a thing once he had his MSc in his pocket. That’s why he sounds like a random teenager on the net, so much so that I used to think he was one.

    Just for comparison: to get my MSc (two years ago), I had to sign an oath that I would always keep my knowledge up to date, as one should expect of a scientist.

  152. #152 Jules Winnfield
    November 13, 2008

    “a single-celled critter that has internalized a bunch of chemicals like that would be sensitive to light. a critter that concentrated that photo-sensitivity in one spot would be even more effective… and so on.”

    OK…

    So it IS magic.

  153. #153 Kel
    November 13, 2008

    There’s plenty of light-sensitive cells, it’s hardly surprising that it eventually became an eye. But of course that won’t suit you charlie. If we don’t know the exact mutation that led to light-sensitive cells, then despite knowing how to build an eye from a flat section of light-sensitive cells, it must all be invalid.

    Why don’t you send articles to Nature to get peer-reviewed Charlie? Why troll here when you have the ability to be the next Darwin?

  154. #154 Jules Winnfield
    November 13, 2008

    “Give us an example so we can try!

    Here’s your challenge:

    Build a trap to catch a live squirrel…

    Without using intelligent input!

  155. #155 Nerd of Redhead
    November 13, 2008

    Charlie, still no science literature citations.

    Why don’t you write up your brilliant observations and send them off to a nice, cozy, peer reviewed scientific journal for publication, so all the other scientists out there can admire your brilliance.

    Oh, yes, you are just sprouting nonsense.

  156. #156 CJO
    November 13, 2008

    Seems pretty simple.

    Charlie, will you please build me a trap to catch a live squirrel?

    What do I win?

  157. #157 Kel
    November 13, 2008

    Build a trap to catch a live squirrel…

    Without using intelligent input!

    No contest, rednecks do this all the time.

    Now surely you see the error of asking a human to perform a task without using intelligence. It’s like asking someone to breathe without using their lungs. If you are going to say stupid shit to make a point, at least be honest with yourself that it’s a stupid comparison.

  158. #158 Jules Winnfield
    November 13, 2008

    “I bet Charlie has done the same: said the same words in every one of 33 years, and never learned a thing once he had his MSc in his pocket. That’s why he sounds like a random teenager on the net, so much so that I used to think he was one.”

    HaHa!

    If you only knew ;-)

  159. #159 Nerd of Redhead
    November 13, 2008

    Charlie, still no journal citation? What are you, scientifically illiterate?
    Why waste your time on us. Just think of all those scientists missing your brilliance. But you have to publish in a peer reviewed journal. Shucks. There goes your Nobel prize, since your ideas don’t follow the rules of science.

  160. #160 Tualha
    November 13, 2008

    Re #154: It’s called a cat. Duh. =^..^=

  161. #161 Jules Winnfield
    November 13, 2008

    “I’m finished…” – Daniel Plainview

    http://www.youtube.com/watch?v=Ri33bydAavI

  162. #162 Nerd of Redhead
    November 13, 2008

    Still no journal citations, but a YT video. Do you think we are amused you fraud?

  163. #163 Jadehawk
    November 13, 2008

    OK…

    So it IS magic.

    just because you don’t understand it, doesn’t make it magic. do you need me to draw pictures or something?

  164. #164 LwPhD
    November 13, 2008

    jt512 sez:

    I’m kind of curious what you mean by “wrong.” In science, we use observations to model the truth. Every model is “wrong” by definition of “model.” But that’s the way science works.

    Hmm. So, by your definition, either every scientific publication is right under some model, or you are committing a “no true Scotsman” fallacy. I guess you wouldn’t call the bulk of ID “research” or young earth creationism “research” “true science”. But where do you stop? Ultimately, there are many game attempts at doing good science by honest and smart people that just fail. There are also many attempts by shameless self-promoters who have a good sense of a sexy topic. They far too frequently sneak into Nature and Science.

    For concrete examples of “wrong” science, think “cold fusion” wrong. Think “fraudulent human stem cells” wrong. Think “codon volatility” wrong. In the first two examples, it is unarguably the case that they hinder scientific progress. In the latter case, it is unarguably the case that the peer review did not reflect the expert evaluation of the community and that its sexiness won out despite an overwhelming lack of support from the first day of publication.

    I stand by my statement. Much of all published research is simply wrong (whether fraudulent, incompetent, counter-productive, a result of unintentional human error, a lack of understanding when first making a interdisciplinary change, etc). And furthermore, if these “wrong” findings happen also to be surprising and sexy, then they have a disproportionate chance to end up in a top tier journal.

  165. #165 LwPhD
    November 13, 2008

    jt512 sez

    My girlfriend’s last paper in Science was 6 pages long and contained 6 full-color figures. Plus Science published an additional 21 pages of supplemental material online. So, either your facts are wrong, or Science is willing to make exceptions.

    It sounds like she got a research article, which is very rare, even in Science or Nature. Most Science and Nature papers are about half that size. But to put this in perspective, a paper in Genetics can easily go to 20 pages, and frequently are over 10 pages, with no limits on the number of display items, like there are for Science and Nature. (Go read their instructions to authors.) Also, ask yourself, is science really best served by copious supplemental online material? It is most definitely not peer-reviewed to the same standards as the main manuscript, and the copy-editing is non-existent. And authors of Nature and Science papers are told this up front. So, I think you should question your understanding of the constraints placed upon authors and their readership by publishing in these high-profile journals. They offer advantages, no question about it. But there are very significant tradeoffs.

  166. #166 sloppy secondhand
    November 14, 2008

    hi boss!

    you know what Team Franken says about the biases in news. it’s not left/right, the stronger biases point at lazy+sensationalist. I see a ‘/news’ in the url. case solved.

  167. #167 jt512
    November 14, 2008

    Lw, I think this whole “right” and “wrong” issue is a red herring. A journal cannot judge submissions on the basis of their correctness. The journal has to judge the research on its methodological rigor and its potential importance to the field. Especially for novel findings, often time is required to tell whether the research turns out to be “wrong.” (You misinterpreted my earlier comment: it’s not that every finding is right under some model, it’s that every model is wrong to some extent, and hence is every research finding.)

  168. #168 LwPhD
    November 14, 2008

    Ultimately, I contend that the useful shelf-life in terms of practical research of far too many Nature and Science papers is far shorter than they should be in these premier journals. If a paper written in 2004 has 15 debunking citations less than 2 years after it is written, then that was a waste of everyone’s time. And while many papers aren’t quite so eye-poppingly bereft of utility for your average researcher, there are many papers out there that do little but pad resumes, and occupy brainspace for a year or two before being forgotten.

    And I think this limited shelf life is a direct result of elevating “breakthroughs” at the expense of rigor. There are always tradeoffs, and requiring high rigor would of course decrease the number of both real and false “breakthroughs” published. But on the balance, muting the spectacular claims in favor of more thorough peer-review would serve the consumers of Science and Nature more. Again, on the major issue, I stand by my previous claim. Science and Nature publish too many “wrong” papers (call them papers with “limited utility” or “short shelf lives” if you want) and that this problem could be fairly easily corrected if the offending journals were willing to tone down the “sensational” nature of their articles just a tad and be willing to ratchet up the rigor of peer review just a tad.

    To go back to the origin of this line of argumentation (back to the very first comment) I agree, that on average you would be better served trusting field-specific journal articles more than Nature or Science articles. In specific circumstances of course, this could be completely reversed. I don’t think that ranking the credibility of Science and Nature-type journals as 3rd is out of line at all.

  169. #169 Jeanette
    November 14, 2008

    PZ is so prolific, I had totally missed this post.

    Yeah, I was wondering if it was as exciting as it sounds in those articles going around.

    PZ if you bump into this very late post, I’m looking forward to your explanation of what’s really up with this story.

  170. #170 David Marjanovi?, OM
    November 15, 2008
    you can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

    Give us an example so we can try!

    Here’s your challenge:

    Build a trap to catch a live squirrel…

    Without using intelligent input!

    You completely misunderstood my question.

    But I can answer your challenge anyway. Give me raw materials that reproduce themselves using good but not perfect inheritance, and I can probably arrange selection pressures so that the materials — after many generations — end up forming a trap capable of catching live squirrels.

    Only organisms, languages, and computer simulations evolve. I just explained why.

    HaHa!

    If you only knew ;-)

    Sounds like I hit a nerve. :-)

  171. #171 Nick Gotts
    November 15, 2008

    Reading backward through the comments, I thought it was Charlie’s girlfriend who had a 6-page article published in Nature! “What’s wrong with the woman?”, I was thinking!

  172. #172 Stanton
    November 15, 2008
    you can’t explain why these particular parts were selected, why they’re integrated together in just such a way and how they were assembled from raw materials without invoking an intelligent agent.

    Give us an example so we can try!

    Here’s your challenge:

    Build a trap to catch a live squirrel…

    Without using intelligent input!

    Some of the Nepenthes pitcherplant species in Borneo, especially N. rajah, are extremely large, and have been observed to drown rats. Of course, the squirrels of Borneo are either much much larger than rats (being the size of cats), or do not come down to the ground where the pitcher plants lair for any circumstance at all, save for being on a tree that’s falling to the ground. Although, do the Borneo pitcherplants get any points for having some species develop spines to deter rats and tarsiers from poking their heads in?

    Hmm. So, by your definition, either every scientific publication is right under some model, or you are committing a “no true Scotsman” fallacy. I guess you wouldn’t call the bulk of ID “research” or young earth creationism “research” “true science”. But where do you stop? Ultimately, there are many game attempts at doing good science by honest and smart people that just fail. There are also many attempts by shameless self-promoters who have a good sense of a sexy topic. They far too frequently sneak into Nature and Science.

    A) A person can point out that Creationism and Intelligent Design “research” is not “true science” without resorting to the “no true Scotsman” fallacy in the exact same way one can point out that an orange with paper ears glued to its surface is not an actual rodent without resorting to the “no true Scotsman” fallacy. Creationism “research” comprises of numerous, illogical, repeatedly debunked assertions that evolutionism/Darwinism is both wrong and evil, and fanatical assertions that the events that occurred in the Book of Genesis are literally true and occurred as detailed in the King James’ translation. Intelligent Design “research” comprises of armchair philosophizing about how biological systems are too complicated to ever understand, and therefore, are evidence of an unknowable, inscrutable “Intelligent Designer” who may be God as described in the Bible, and the use of many, if not all of the numerous, illogical, repeatedly debunked assertions that evolutionism/Darwinism is both wrong and evil.

    B) It would help tremendously if either Creationists or Intelligent Design produced any “research” to begin with, but, both have demonstrated that they are vehemently against doing any research of any kind to begin with, preferring, instead, to peddling their toxic nonsense and perpetuate the idea that Evolutionists/Darwinists persecute them.

  173. #173 Jamie
    December 19, 2008

    Just some comments.

    I think people are too harsh on the authors based on the press release.
    It is one thing to be wrong or make mistakes in the calculations, and quite another to have falsified/fabricated the data although the distinction can be blurred. I think the former is actually quite common even amongst the best scientists; we’re not perfect!
    I don’t think the authors intentionally made anything up.

    I will probably get flamed for this, but I think evolution is not strictly deterministic. Even when environmental conditions are stable, there will be some individuals that die just by chance even if their “fitness” is high. As another poster pointed out, the end goal or directionality of evolution is not known.

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