The Blind Locksmith Continued: An Update from Joe Thornton

By Carl Zimmer | October 15, 2009 6:56 pm

I’ve written a few times here about the ongoing work of Joe Thornton, a biologist at the University of Oregon and the Howard Hughes Medical Institute. Thornton studies how molecules evolve over hundreds of millions of years. He does so by figuring out what the molecules were like in the distant past and recreating those ancestral forms in his lab to see how they worked. I first wrote about his work looking at how one molecule in our cells evolved from one function to another (here, here, and here). [Update: These links are now fixed.]

Most recently, I wrote in the New York Times about his latest experiment, in which he and his colleagues found that the evolution from the old function to the new one has now made it very difficult for natural selection to drive the molecule back to its old form. Its evolution has moved forward like a ratchet.

Thornton’s new work turned up last week on a web site run by the Discovery Institute, a clearinghouse for all things intelligent design (a k a the progeny of creationism). Michael Behe, a fellow at the Institute, wrote three posts (here, here, and here) about the new research, which he pronounced “great.”

This is the same Michael Behe who, when Thornton published the first half of this research, declared it “piddling.”

Why the change of heart? Because Behe thinks that the new research shows that evolution cannot produce anything more than tiny changes. And if evolution can’t do it, intelligent design can. (Don’t ask how.)

I pointed out Behe’s posts to Thornton and asked him what he thought of them. Thornton sent me back a lengthy, enlightening reply. Since the Discovery Institute doesn’t allow people to comment on their site, I asked Thornton if I could reprint his message here.

You may want to revisit my posts I linked to above to get a more detailed description of Thornton’s work before delving into Thornton’s reply. And while his reply is quite clear, there are a few terms that may be confusing, so let me preface it with a quick and dirty glossary of terms:

Cortisol: A hormone

Genetic drift: the change in the frequency of an allele (a version of a gene) in a population thanks to chance, not natural selection. Genetic drift can spread an allele through an entire population even if it provides no boost to reproductive success. It can even spread some mildly harmful ones under the right conditions

Glucocorticoid receptor: A receptor that binds cortisol. This is the molecule Thornton has studied, documenting the series of mutations that transformed it from an ancestral receptor sensitive to another hormone.

GR: Glucocorticoid receptor

Steroid receptors: A class of receptors that can bind steroids (a group of molecules that includes hormones such as cortisol).

And without further ado, here’s Thornton’s message–

**************

Dear Carl,

Thanks for asking for my reaction to Behe’s post on our recent paper in Nature.   His interpretation of our work is incorrect.  He confuses “contingent” or “unlikely”  with “impossible.”  He ignores the key role of genetic drift in evolution.  And he erroneously concludes that because the probability is low that some specific biological form will evolve, it must be impossible for ANY form to evolve.

Behe contends that our findings support his argument that adaptations requiring more than one mutation cannot evolve by Darwinian processes.  The many errors in Behe’s Edge of Evolution — the book in which he makes this argument — have been discussed in numerous publications.

In his posts about our paper, Behe’s first error is to ignore the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates.  Behe says that if it takes more than one mutation to produce even a crude version of the new protein function, then selection cannot drive acquisition of the adaptive combination.

This does not mean, however, that the evolutionary path to the new function is blocked or that evolution runs into a “brick wall,” as Behe alleges.   If the initial mutations have no negative effect on the ancestral function, they can arise and hang around in populations for substantial periods of time due to genetic drift, creating the background in which an additional mutation can then yield the new function and be subject to selection.   This is precisely what we  observed in our studies of the evolution of the glucocorticoid receptor (GR).

In our 2007 paper in Science, we showed  that multiple mutations were indeed required for the GR to evolve its specificity for the hormone cortisol;  some of the mutations that trigger the change in function are deleterious if introduced in isolation, but others are “permissive”: they have no apparent effect on the function of the protein, but once they are in place the protein can tolerate the other mutations that shift and then optimize the new function.

By experimentally characterizing the functional effect of the key historical mutations in various combinations, we showed that there were indeed pathways from the ancestral protein to the new function that passed only through permissive and beneficial intermediate states.

A path to a new function that involves neutral intermediates is entirely accessible to the evolutionary processes of mutation, drift, and selection.  Our work showed that these classic neodarwinian processes are entirely adequate to explain the evolution of GR’s new function. (I should mention that pathways involving mildly deleterious intermediates are also accessible in reasonable time under some population genetic conditions; it’s just that their relative probability is lower than those involving neutral or beneficial intermediates.)

Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution.  We studied whether the key mutations that drove the “forward” evolution of GR’s new function could be reversed in a later version of the GR, restoring the ancestral conformation and function.  We found that the later version of the protein could no longer tolerate the ancestral amino acids at these key sites, despite the fact that they had been present in the protein at an earlier stage of evolution.

We identified the specific “restrictive” historical mutations, which occurred after the shift in function, that either clashed with or failed to support the ancestral conformation. If these mutations are reversed first before the key function-switching mutations, the ancestral structure and function can be restored.

Reversing the restrictive mutations alone does not enhance the ancestral function, but in some orders they have no effect on the GR’s function.  These restrictive mutations are simply the flip-side of permissive mutations: reversal of a restrictive mutation is a permissive mutation for reverse evolution.  As Fig. 4  in our paper shows, there are several pathways back to the ancestral sequence that pass only through steps that are neutral or beneficial with respect to the protein’s functions.

Thus, all pathways to the ancestral sequence and structure are not blocked, as Behe says they are.  The chance effects of genetic drift could allow the protein to “float” along such paths, producing the appropriate background in which the function-shifting mutations could be reversed. However, selection alone would not be sufficient to drive the protein deterministically through the neutral steps. If selection for the ancestral function were imposed, reversal to the same sequence and conformation as the ancestor would be unlikely, though not impossible.

Taken together, the existence of permissive and restrictive mutations indicates that neutral paths to specific adaptive combinations of mutations are opening and closing during evolution.  If the clock could be turned back and history allowed to run again, it’s likely that some different path would be followed, and different protein forms would evolve by the natural processes of evolution.

This brings us to Behe’s second error, which is to confuse reversal to the ancestral sequence and structure with re-acquisition of a similar function.  We showed that restrictive mutations make selection alone insufficient to drive the protein back to the same form as that found in the ancestor.  But nothing in our results implies that, if selection were to favor the ancestral function again, the protein could not adapt by evolving a different, convergent, underlying basis for the function.

Indeed, directed evolution experiments in the laboratory have shown that mutation and selection alone can cause steroid receptor proteins to rapidly evolve sensitivity to new hormones; some of the mutations involved are different from those that occurred during the historical evolution of ancient proteins.

Our paper shows that re-evolution of the underlying ancestral form is unlikely, but it says nothing about the re-evolution of the ancestral function.  We found that chance processes play a key role in determining which adaptive forms actually evolve under selection, but this does not mean, as Behe alleges, that no adaptive form can evolve.

Finally, Behe erroneously equates “evolving non-deterministically” with “impossible to evolve.”  He supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve.  This is like saying that, because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, the fact that all this occurred means it must have been willed by God.

Consider the future: there are countless possible that could emerge from our present state, making the probability of the one that actually does evolve extraordinarily  low.  Does this mean that the future state that will ultimately emerge is  impossible?  Obviously not.  To say that our present biology did not evolve  deterministically means simply that other states could have evolved instead; it does not imply that it did not evolve.

Consider your own life history as an analogy.  We can all look back at the road  we have traveled and identify chance events that had profound effects on how our lives turned out.  “If the movie I wanted to see that night when I was 25 hadn’t been sold out,  I never would have gone to that party at my friend’s house, where I met my future spouse….”  Everyone can tell a story like this.  The probability of the life we actually lead is extraordinarily small.  That obviously doesn’t mean that its historical unfolding was impossible.

That we inhabit an improbably reality requires a divine explanation only if we, like Behe, take the teleological view that this is the only reality that could exist.  But if we recognize that the present is one of  many possibilities, then there is no difficulty reconciling the nature of  evolutionary processes with the complexity of biological forms. As history unfolds, potential pathways to different futures are constantly opening and  closing. Darwinian processes are entirely adequate to move living forms  along these pathways to a remarkable realization – but just one realization out of many others that could have, but didn’t, take place.

I considered hard whether I should address Behe’s argument or ignore it.  I am well aware that Behe and his supporters might portray my response as an indication that there is scientific debate over the possibility of adaptive protein evolution: “Look, an evolutionary biologist who actually does scientific research is arguing with me; let’s teach this controversy in public schools!”   Because Behe has grossly misinterpreted the results of my research to support his position, however, I feel some responsibility to set the record straight.

Behe’s argument has no scientific merit.  It is based on a misunderstanding of the fundamental processes of molecular evolution and a failure to appreciate the nature of probability itself.  There is no scientific controversy about whether natural processes can drive the evolution of complex proteins.  The work of my research group should not be misintepreted by those who would like to pretend that there is.

Best regards,
Joe

CATEGORIZED UNDER: Evolution

Comments (83)

  1. Thanny

    This reminds me of Lenski’s response to the Conservapedia nutcase.

    The links at the top are broken, however – they contain today’s date embedded in the URL ahead of the actual dates, which makes the blog load a blank page (removing it produces the correct result).

  2. Drosera

    Another reason why a reversal to the ancestral condition may be unlikely is that the acquisition of a new function could well cause a change in the fitness landscape. This could trigger the evolution of still more new functions that may be incompatible with the ancestral condition and would effectively make the initial change irreversible.

    The function of chance in the evolutionary process is undoubtedly the most persistent source of misunderstanding among those who oppose the Theory of Evolution (or ‘darwinism’, as most of the religious opponents usually call it.)

  3. NewEnglandBob

    It is not surprising that Behe would misinterpret the work of others instead of actually doing science. He knows that what he does is malevolent but does not care when he is shown to be a fool.

  4. Thornton’s letter is one of the best explanations of modern evolutionary thought that I’ve seen in a long time. It should be required reading for everyone who wants to understand evolution.

    Thanks, Carl, for stimulating him to write it and thanks for posting it.

    Do I detect a tendency to become a little more sympathetic to random genetic drift and evolution by accident?

  5. Hey, if you can’t do the science, try to get credit for showing that the science can’t be done. That’s Behe in a nutshell.

    There’s something profoundly ironic about the Discovery Institute’s blog which expels all dissenting thought, while complaining about censorship whenever their lies and ignorance are accurately labeled as such.

    You know they’d whine piteously if matters were reversed, that our side didn’t allow comments, while theirs did. But they don’t dare allow free discussion just to look good, because the free market of ideas ruthlessly destroys anything as unintelligent as “Intelligent Design.”

    I appreciate Zimmer requesting Thornton’s response, and for Thornton writing such a great reply.

    Glen Davidson
    http://tinyurl.com/mxaa3p

  6. Brownian

    [quote]You know they’d whine piteously if matters were reversed, that our side didn’t allow comments, while theirs did. But they don’t dare allow free discussion just to look good, because the free market of ideas ruthlessly destroys anything as unintelligent as “Intelligent Design.”[/quote]

    But, but, there was that movie with that guy from [i]Ferris Bueller’s Day Off[/i] in it…

    Dr. Thornton’s response to the argument from probability is one of the most accessible I’ve ever seen. Even for a non-sports enthusiast like myself, the World Series analogy hits home better than the often-used poker hand ones.

  7. Ric

    Holy… crap. That last paragraph alone ought to crush Behe. Note that I said “ought to”; when one is impervious to logic, nothing can crush you.

  8. Mel N

    What I find amazing is that he was %95 correct in his analogy of meeting my spouse at a party. My friend didn’t want to go to the movies and I was 16 at the time.

    Where there be a follow up in the NYT?

  9. eric

    Brownian, just think of the lottery. In a typical “5 balls + superball” lottery the odds are ~80 million to 1 of any specific number coming up.

    But every time the lottery is held, you get some number. So every time the lottery is held, an event occurs that only had an 80 million to 1 chance of happening. If you hold two lotteries a week for 52 weeks, then the events of that year had an 80,000,000^104 to 1 chance of happening!

    The point being that, when the physical, chemical, or biological conditions are right, there is a near-100%* chance of something highly improbable happening.

  10. Holbach

    The obvious and overriding reason that Behe and his demented ilk consistently and vehemently deride science is the mental block of insane religion which will be impenetrable to anything that smacks of sound reason. We are indeed fortunate and needful of sound minds like Joe Thornton, Carl Zimmer, PZ Myers and assorted like minds.

  11. A very interesting exposition about the role of contingence in biological evolution. I very much like his analogy about our personal lives. As for the sentence: “That we inhabit an improbably reality requires a divine explanation only if we, like Behe, take the teleological view that this is the only reality that could exist. But if we recognize that the present is one of many possibilities, then there is no difficulty reconciling the nature of evolutionary processes with the complexity of biological forms.“, it has an interesting many-world flavour.

  12. Alcari

    I love the “finetuned hand of cards” counterargument. It’s a response to a creationist saying that because the odds are low for the current outcome, there must be a god steering his creation this way.

    I like the example of the game of bridge, where you are dealt a hand of 13 cards. The odds of you getting a specific hand are 8 * 10^67 (52!-39!), staggeringly low odds. The odds of any game playing out the way it does (assuming people randomly play cards) are 10^107 (52!*13!^4) for just a single hand. Surely, there must be a Bridge-hand dealing god, to ensure that a game played out just the way.

    Of course, the creationist will fail to realize that it’s not about a specific out, it’s about getting a outcome in the first place. In the case of Bridge that’s about 1 in 1.

    (I’d do the math for Poker, but it’s a lot more complicated)

  13. Alcari

    Hmm, the moment I hit submit I realized my math is off. Permutations vs. Combinations… Well, just fill in appropriately big numbers :p

  14. Brownian

    Thanks eric, but I wasn’t referring to myself. I work with stats on a daily basis and play poker in my spare time–not always that well, to the detriment of my wallet, hence the stats job–so those analogies aren’t lost on me. However, as someone who works with stats on a daily basis I well know how uncomfortable probability makes the general public, and I think the World Series analogy is better suited to explain the failings of the anthropic and probability arguments to the average person who breaks out in a cold sweat whenever numbers are mentioned. (Sports stats seem to be the exception to this rule.)

  15. Toni

    Looks like the key word here “probability.” Creationists–and even Christians who do not consider themselves Creationists–often spout such phrases as “it’s God’s will” or “it was meant to be” or (my least favorite) “everything happens for a reason.” When in this mindset, there is nothing you can show them that will make them believe anything different. Perhaps Biology isn’t the science to be using to counter them–it’s Probability Theory.

  16. Joe Thornton is as good a scientist as Michael Behe is not… an utterly sad disgrace to the profession. In this posting (via Carl Zimmer) Thornton not only exposes the bad faith of Michael Behe, but also the utter contempt he Behe must have for the audience Behe writes for.

    “I considered hard whether I should address Behe’s argument or ignore it. I am well aware that Behe and his supporters might portray my response as an indication that there is scientific debate over the possibility of adaptive protein evolution: “Look, an evolutionary biologist who actually does scientific research is arguing with me; let’s teach this controversy in public schools!” Because Behe has grossly misinterpreted the results of my research to support his position, however, I feel some responsibility to set the record straight.”

    The late Dominican Herbert McCabe once wrote that people who live in fear are the most susceptible to swallowing lies. These are the people– worried about what their children are learning in public school, worried and concerned about what science is discovering about the human body, the climate, our future –these are the people that the Discovery Institute and their pack of liars-for-hire target with their intellectual dishonesty–to exploit that fear for their own misguided political and ideological purposes.

    When a fat man who calls himself a Christian can take the stand in a courtroom and lie under oath because he’s been persuaded that what’s wrong with the American classroom is that “Jesus” isn’t part of the course on biology and that Darwin leads to Hitler, and that Michael Behe is happy to perpetuate his ignorance–we can see how those lies work.

    The corrupt ideologues of the Discovery Institute don’t realize… it’s not Darwin that makes Christians atheists. It’s self-described Christians who are shown up as liars, shills and perjurers who inspire other Christians to discard their faith.

    [Carl: Commented edited after John sent in a clarification.]

  17. MadScientist

    “Does this mean that the future state that will ultimately emerge is impossible? ”

    Behe would say “of course not, the one preordained by my fickle malicious sadistic skyfairy will prevail” and we’ll all laugh and point at Behe and tell the kids “you’d better pay attention in school or you’ll turn out like THAT moron.”

  18. Jud

    Another lovely extreme-unlikelihood-doesn’t-mean-impossibility example comes from one of Sean B. Carroll’s books, where he points out that although the odds against winning the lottery are utterly astronomical, within a few weeks at most someone always does win.

  19. shonny

    I presume Behe’s willful misrepresentations are attempts to win appraisal and admiration from the IDiots, because surely no self-respecting real scientist would make such efforts to make an ass of him- or herself.

  20. Mike from Ottawa

    I walked across the parking lot from my car to my office this morning. It will be extremely unlikely I could retrace my path on the way home, placing my feet exactly where I placed them earlier today (and doing it exactly would require walking backwards!). Only a prize fool, though, would think that means I couldn’t get back to my car or that I had to have had my steps divinely guided in order to get from my car to office in the first place.

    How can Behe get such simple stuff wrong?

  21. Carlos

    This is just great, I love these back and forth debates. Thanks, Carl.

    When is Behe’s rebuttal due to be posted?

    [Carl: Beats me.]

  22. Sili

    “Look, an evolutionary biologist who actually does scientific research is arguing with me; let’s teach this controversy in public schools!”

    That Wee Willie says “does not” to his fifth grade teacher, when she tells him that 2 and 2 makes 4, does not mean that she is then required to teach that some people insist it’s 5.

  23. YetAnotherKevin

    This is like saying that, because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, the fact that all this occurred means it must have been willed by God.

    I think there’s also the corollary, “because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, _no team could win the world series, ever_.” In their view, the baseball season never happened, only the final statistics.

  24. Bruce

    Behe’s argument is like saying the big odds against any single set of poker hands being dealt must prove that God deals out every hand in every poker game. So, does he believe in the church of Texas Hold ‘em?

  25. Robert

    > “Another lovely extreme-unlikelihood-doesn’t-mean-impossibility example comes from one of
    > Sean B. Carroll’s books, where he points out that although the odds against winning the lottery are
    > utterly astronomical, within a few weeks at most someone always does win.”

    The creationist argument, of course, is that when someone does win the lottery they must have cheated. Arrest them!

  26. Jim Patten

    I learned a great deal reading this article, thanks for posting. I was pleased to see that Joe Thornton is a Yankee fan! Yankees leading the Angels 4-1 top of the ninth, game 1 of the ALCS in the Bronx!

  27. Thornton’s use of the “condition” of genetic drift is much in line with the selfish gene. And in certain instances, as Thornton outlines, the selfish gene (ie. a gene that cares only about its own replication, not so much about the long-term fitness of the organism) is what pushes a phenotypic modification, even though it doesn’t actually mean to.

  28. Svammelman

    Thanks for posting that. Brilliant stuff. Very clear and accessible, even to a lay person like me. Behe should get some educational award for playing the Simplicio.

  29. An

    Thornston wrote:

    “Finally, Behe erroneously equates “evolving non-deterministically” with “impossible to evolve.” He supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve. ”

    I tried to read Behe’s comments, but he didn’t claim so. Behe is a ID evolutionist, who believes in common descent. And he would not ever claim, that none evolutionary outcome is possible. He has also many times emphasized that he is not claiming any logical impossibility.

    As I see it, Behe’s point was (not that “evolving non-deterministically” is the same than “impossible to evolve”, but that there actually are also other possibilities than just chance and determinism):
    “Bridgham et al (2009) aimed to test “the importance of contingency and determinism in evolution”. But chance and necessity are not the only things that exist. There are also mind and plan. In fact, in their own work the authors themselves reconstructed the ancestral protein from the descendant protein, easily overcoming the hurdle that they realized would block a Darwinian process. Their own minds directed events that chance and necessity never could.”

  30. An 1

    Thornston:

    “If selection for the ancestral function were imposed, reversal to the same sequence and conformation as the ancestor would be unlikely, though not impossible.”

    “Thanks for asking for my reaction to Behe’s post on our recent paper in Nature. His interpretation of our work is incorrect. He confuses “contingent” or “unlikely” with “impossible.” He ignores the key role of genetic drift in evolution. And he erroneously concludes that because the probability is low that some specific biological form will evolve, it must be impossible for ANY form to evolve.”

    “The probability of the life we actually lead is extraordinarily small. That obviously doesn’t mean that its historical unfolding was impossible.”

    “Finally, Behe erroneously equates “evolving non-deterministically” with “impossible to evolve.” He supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve.”

    and what Behe wrote was:

    “Thus the work strongly supports the conclusion of Edge that Darwinian processes are highly UNLIKELY to have built the complex molecular machinery of the cell.”

    and Behe summarized Thornston works as:
    “GR-like protein would be very UNLIKELY to revert to an MR-like ancestral form by Darwinian means”

    So Thornston mispresented Behe’s argument. And because he didn’t tell that Behe actually wrote about likelyness, not logical possibilities, Thornston made also a straw man argument. Arguments should be adressed in their strongest form, not in mispresented forms.

  31. John Kwok

    Carl,

    Thanks for asking Joe Thornton for his comments and for posting it. Behe’s inane reasoning is exactly the same – which Joe has alluded to – as his explanation that it was either “all or none” with regards to the point mutations he refers to in the Plasmodium malarial parasite in his “The Edge of Evolution”. Using similar, almost identical, logic as Joe Thornton’s, a few critics, like for example, Ken Miller, have demonstrated why Behe is so egregiously wrong in his absurd misinterpretation of Plasmodium’s mutations.
    Moreover, as some others, myself included, have observed, Behe’s “book” displays his gross ignorance and understanding of evolutionary ecology, especially from the context of co-evolutionary arms races.

    Appreciatively yours,

    John

    P. S. @ Jim, I too second your endorsement of Joe Thonton’s enthusiasm for my beloved Bronx Bombers. That was a great game last night. Only three more wins (I hope) till the World Series.

  32. DaveG

    John Farrell,

    I don’t understand why you call Thornton a disgrace. If he treats Behe’s audience with contempt, it’s because their attitudes (specifically, treating ID as “science” and wanting to inflict it on schoolchildren) are contemptible. Yet you are clearly anti-ID.

    On re-reading your post, you’re suggesting that Scientists should condescend to ignorant (i.e. religious) people as if faith somehow makes them less able to think critically. That’s called the bigotry of low expectations. Contempt, at least, indicates that Thornton expects more from his audience.

  33. Pierce R. Butler

    John Farrell @ # 18: Joe Thornton is … an utterly sad disgrace to the profession. In this posting … Thornton … exposes … the utter contempt he must have for the audience Behe writes for.

    I hope I’m misinterpreting your comment, but that first paragraph comes across the way I’ve abridged it above. Since the excoriation which follows addresses only Behe & his fellow Discotutes, I’m assuming you’re not intending to assail Dr. Thornton – but a clarification, either of intent or of syntax, does seem to be called for.

  34. Drosera

    An 1 @ 33 cites Behe:

    “Thus the work strongly supports the conclusion of Edge that Darwinian processes are highly UNLIKELY to have built the complex molecular machinery of the cell.”

    I interpret this to mean that Behe thinks that it is highly unlikely that the process of evolution builds anything complex at all. This is clearly refuted by Thornton, so he is not using a straw man argument at all.

  35. Michael

    And what the fundees will take away from this is that god’s a Yankees fan. *Sighs*. You just can’t argue someone out of a position they were not argued into in the first place unfortunately.

  36. “There is no scientific controversy about whether natural processes can drive the evolution of complex proteins. ” Dr Thorton

    Design is a natural process, evolution is not being debated- designed to evolve/ evolved by design- and what about the origin of complex proteins- or just functional proteins?

    It would be interesting if Dr Behe reads Dr Thorton’s critique and responds to it.

    I remeber when David Berlinski wrote about the Nilson Pelger paper on the eye and people attacked him only to have their attacks exposed as childish tantrums.

  37. John Farrell

    Pierce and Dave G–sorry, if it was misleading. What I wrote was:
    “Joe Thornton is as good a scientist as Michael Behe is… an utterly sad disgrace to the profession.”

    Meaning Thornton is as good as Behe is not.

    I should have rewritten the next sentence like this:

    “In this posting (via Carl Zimmer) Thornton not only exposes the bad faith of Michael Behe, but also the utter contempt BEHE must have for the audience he writes for.”

    Sorry for the confusion!

    [Carl: I've edited the original comment to reflect John's clarification]

  38. Thanks, Carl! Much appreciated.

  39. DGS

    @32 An, you and Behe are both committing a very grand logical fallacy. You are claiming that the Thornton lab “mind and plan” somehow automatically invalidates their results. Your argument is, in other words, “If humans can logically think through it, humans can’t use it as evidence for evolution.”

    Try again.

    RT @32. An Says:
    I tried to read Behe’s comments, but he didn’t claim so. Behe is a ID evolutionist, who believes in common descent. And he would not ever claim, that none evolutionary outcome is possible. He has also many times emphasized that he is not claiming any logical impossibility.

    But chance and necessity are not the only things that exist. There are also mind and plan. In fact, in their own work the authors themselves reconstructed the ancestral protein from the descendant protein, easily overcoming the hurdle that they realized would block a Darwinian process. Their own minds directed events that chance and necessity never could.”

  40. Mr_Man

    Carl,

    Please add the attribute rel=”nofollow” to your links to creationist websites (unless you don’t mind boosting their PageRank). http://skeptools.wordpress.com/2008/09/03/not-just-for-spam-anymore-nofollow-for-skepticism/

  41. hackenslash

    Beautiful! ‘Nuff said.

  42. Michael D. Houst

    Wonderful article.

    I’d overlooked the point about non-detrimental, or only mildly mutations accumulating and hanging around in the gene pool providing material for later mutations; and had only considered duplications, and subtractions of beneficial genes to provide variability.

    It would partially explain all the “junk” DNA we carry. That junk represents accumulated raw material that once changed, may contribute to changes in our species in the future.

    All it takes is a single, self-sufficient, self-replicating cell to start the ball rolling. With a planetary-scale bio-reactor, and a billion years to make the attempt, small wonder that we achieved living cells as “early” in the Earth’s history as we did.

  43. Martin

    <>

    Is that all? Boy, I didn’t think it would be so easy.

  44. Michael Heath

    Here’s a ScienceDaily Article from three years ago where Thornton falsified Behe’s notion of IC prevented natural selection through random mutation by replicating such: http://www.sciencedaily.com/releases/2006/04/060406231032.htm

  45. Martin

    Here’s Behe’s rebuttal.

    C:UsersMartinDesktopDocumentsIntelligent Design the Future The Lamest Attempt Yet to Answer the Challenge Irreducible Complexity Poses for Darwinian Evolution.mht

  46. Apparently Martin doesn’t know how to post a hyperlink….

  47. Drosera

    Anyone who bothers to look at Behe’s replies will see that he still doesn’t understand the basics of the evolutionary process. The man is clueless and hopeless.

  48. David

    Hi Drosera,
    You wrote: “Anyone who bothers to look at Behe’s replies will see that he still doesn’t understand the basics of the evolutionary process.”

    Would you mind saying a bit more about some of the problems you detect with Behe’s reply? I am pretty new to this discussion and I am still trying to naviage my way through it. I (perhaps mistakenly) thought that Behe’s reply had some merit, but again I’m a novice.

    Thanks in advance

  49. Drosera

    David,

    Basically, what Behe is saying is this: Given that an organism is already able to produce a certain set of proteins, the probability that it is able to produce, through random mutations, a new, functional protein (let’s call it protein X) with a certain pre-specified function is too small to be realistic.

    There are three problems with this:

    1. Behe is not able to actually calculate that probability, so he is just guessing that it is vanishingly small. Depending on the property in question, it may actually be very small for some proteins, but not so small for others.

    2. More important, mutations are undirected. It is not that the evolutionary process is actively trying to find protein X: any mutation, or combination of mutations that leads to a new type of protein that is useful (improves fitness) will be selected for in the offspring (because the offspring carrying this mutation tend to have a higher survival rate). So, instead of finding protein X the organism ends up with protein Z, which has a completely different function. Again, Behe is not able to prove that the probability for this happening is too small to be realistically possible; he just asserts it is. Empirical work (real science), such as that by Thornton, shows that Behe is simply wrong.

    3. If mutations can not produce new proteins, then where do they come from? Behe will surely avoid trying to answer this question, mumbling something about an ‘intelligent designer’. But if he is honest he will say that it is his Christian god who now and then tinkers with his creation.

    In the end, Behe is not motivated by science but by religion. As has often been said, Intelligent Design is creationism in a cheap suit. It is all smoke and mirrors; it has not produced a single fruitful theory, a single prediction, a single new technology. Nothing. It is intellectually sterile because it can not propose a mechanism beyond invoking miracles. Behe is selling snake oil and tries to make you believe that it will cure cancer.

  50. Drosera

    Just to clarify: the word ‘organism’ in the first sentence of my previous post should be understood as kind of organism, not as individual organism.

  51. Julian

    Drosera wrote: “Basically, what Behe is saying is this: Given that an organism is already able to produce a certain set of proteins, the probability that it is able to produce, through random mutations, a new, functional protein (let’s call it protein X) with a certain pre-specified function is too small to be realistic.

    There are three problems with this:

    1. Behe is not able to actually calculate that probability, so he is just guessing that it is vanishingly small. Depending on the property in question, it may actually be very small for some proteins, but not so small for others.”

    No, Behe is using the probability calculations of Thornton, who said that they were vanishingly small. And yes, maybe they are vanishingly small for some proteins, but not for others. But their work suggests that this may be a very wide problem.

    Drosera continues: “2. More important, mutations are undirected. It is not that the evolutionary process is actively trying to find protein X: any mutation, or combination of mutations that leads to a new type of protein that is useful (improves fitness) will be selected for in the offspring (because the offspring carrying this mutation tend to have a higher survival rate). So, instead of finding protein X the organism ends up with protein Z, which has a completely different function. Again, Behe is not able to prove that the probability for this happening is too small to be realistically possible; he just asserts it is. Empirical work (real science), such as that by Thornton, shows that Behe is simply wrong.

    No Thornton’s work supported Behe’s assertion. And Behe does offer what appears to be a fairly strong argument for his position in his book, The Edge of Evolution, in the chapter on “The Two-binding Sites Rule.” So he doesn’t just “assert” it.

    Drosera continues: “3. If mutations can not produce new proteins, then where do they come from? Behe will surely avoid trying to answer this question, mumbling something about an ‘intelligent designer’. But if he is honest he will say that it is his Christian god who now and then tinkers with his creation.

    First, regardless of whether or not Behe offers a plausible alternative theory, the point is that he has offered a very good refutation of the current theory, and Thornton’s work supports Behe’s case. Second, Behe’s alternative theory is that the designer — if you read his book you’ll know — designed a universe that had all the future specified events needed to take place loaded into it. So he doesn’t just “mumble something.”

    Drosera continues: “In the end, Behe is not motivated by science but by religion. As has often been said, Intelligent Design is creationism in a cheap suit. It is all smoke and mirrors; it has not produced a single fruitful theory, a single prediction, a single new technology. Nothing. It is intellectually sterile because it can not propose a mechanism beyond invoking miracles. Behe is selling snake oil and tries to make you believe that it will cure cancer.

    Behe was a happy theistic evolutionist, until he started investigating the problems with neo-Darwinism. He’s pointed out how sterile a theory it is in accounting for the history of evolution. He’s not trying to sell a “cure for cancer.” He’s trying to answer the question, How did we get here?

  52. Drosera

    Julian,

    Can you or your friend Behe please show me where Thornton (or any other respected scientist) calculates the probabilities that I mentioned? Hint: it is not equivalent to calculating the probability that a hurricane will turn a scrap yard into a Boeing 747.

    You claim that Thornton’s work supports Behe’s assertions. Thornton himself says it doesn’t. Considering the evidence presented by Thornton in Carl Zimmer’s piece above, I am with Thornton. What he has shown is that a product of evolution, once it has occurred, may become effectively irreversible, for reasons that thanks to his work are well understood. This is no problem at all for evolutionary theory. And Thornton also shows that this product actually evolved, so Behe is simply deluded (or deliberately obfuscating) when he asserts that Thornton’s work undermines the theory of evolution.

    Behe’s alternative theory is that the designer — if you read his book you’ll know — designed a universe that had all the future specified events needed to take place loaded into it. So he doesn’t just “mumble something.”

    Do you really think this ‘theory’ is anything else than silly mumbo-jumbo? Well, perhaps you could say it’s Calvinist mumbo-jumbo. At least, it smacks of predestination to me. Nice evasion to talk of ‘the designer’, when we all know that he’s talking about the father of Jesus Christ (who is also Jesus Christ and the Holy Spirit, but never mind the details).

    Behe was a happy theistic evolutionist, until he started investigating the problems with neo-Darwinism. He’s pointed out how sterile a theory it is in accounting for the history of evolution. He’s not trying to sell a “cure for cancer.” He’s trying to answer the question, How did we get here?

    A sterile theory doesn’t produce hundreds of thousands of scientific articles in the peer reviewed literature (compare that with the pathetic record of ID). Behe and his cronies are just trying to find ways to defame certain parts of science that they think threaten their religion. They will do anything to accomplish that. Having visited his website I have to conclude that I was far too mild in my assessment. He isn’t a quack trying to sell a cure for cancer; it’s much worse. He is actively spreading a form of intellectual cancer. Do you really want to help him with that?

  53. Julian

    Hi Drosera,

    You ask: “Can you or your friend Behe please show me where Thornton (or any other respected scientist) calculates the probabilities that I mentioned?

    First, though I wish I could call Behe my friend, unfortunately the two of us have never met. Next, as you point out later on, Thornton “has shown is that a product of evolution, once it has occurred, may become effectively irreversible….” In other words, the probability is much too small for it to happen.

    Then you wrote: “ This is no problem at all for evolutionary theory. And Thornton also shows that this product actually evolved….

    But it is a problem for evolutionary. It’s not clear that Thornton has shown that the product actually evolved, but let’s assume he has. So what he has shown is that product B evolved by Darwinian processes from product A. Then he shows that the probability of product B being able to evolve back to product A is much too small. From what I can tell, Thornton showed that product B evolved from product A by a process of product A losing function (it went from being able to bind to numerous hormones to binding to only one or two hormones). If I understand Thornton (I may not), it sounds like he’s saying that product A evolved (or devolved) into a less complex product B. In other words, it was easier for B to evolve from A, because B was simpler than A. It would be much more difficult for B to evolve back into A, because A is more complex than B.

    If my understanding of Thornton’s work is correct, then we must ask, “So how did A come to be in the first place?” If it came from a protein similar to B, then it would face the same brick wall that B would face — unless it was more complex than B or A. In that case, A could have devolved from this even more complex protein. But then we need to ask how this more complex protein came to be?

    In fact, it begins to look like Dollo’s (Dolo’s) Law, which Thornton’s work supports, is another way of stating the principle of the conservation of information.

    I wrote: “ Behe’s alternative theory is that the designer — if you read his book you’ll know — designed a universe that had all the future specified events needed to take place loaded into it. So he doesn’t just “mumble something.”

    You replied: “Do you really think this ‘theory’ is anything else than silly mumbo-jumbo? Well, perhaps you could say it’s Calvinist mumbo-jumbo. At least, it smacks of predestination to me.

    I agree that if the laws of physics aren’t completely deterministic then Behe’s theory has problems, but I wouldn’t call it “mumbo-jumbo.” So if the laws are not deterministic, then the designer (assuming it is “outside” of the universe) would occasionally need to intervene in the universe. But I don’t see that as an overwhelming problem.

    Then you wrote: “ Nice evasion to talk of ‘the designer’, when we all know that he’s talking about the father of Jesus Christ (who is also Jesus Christ and the Holy Spirit, but never mind the details).” Actually Behe doesn’t evade who he thinks the designer is. He thinks it’s God. However, Behe, as do most of the proponents of ID, admits that the evidence is insufficient to prove that God is the designer. Sir Fred Hoyle, for example, was an atheist, who believed in ID. But he didn’t think the designer was God. He was rather fuzzy on who he thought it was.

    Then you wrote: “ A sterile theory doesn’t produce hundreds of thousands of scientific articles in the peer reviewed literature (compare that with the pathetic record of ID).

    Well, actually, the papers don’t explain how life came into existence, or how Irreducibly Complex systems came into existence, or even how Thornton’s original hormone receptor came into existence. They do tend to show that natural selection and common descent are very probably true. Unfortunately, they don’t show that random mutation was the cause of most of the variations or novelty that natural selection works upon. Behe’s argument says that whatever the cause was, it wasn’t random mutation. But you don’t need Behe to tell you that. Lynn Margulis has been preaching it for years.

    You write: “Behe and his cronies are just trying to find ways to defame certain parts of science that they think threaten their religion. They will do anything to accomplish that. Having visited his website I have to conclude that I was far too mild in my assessment. He isn’t a quack trying to sell a cure for cancer; it’s much worse. He is actively spreading a form of intellectual cancer. Do you really want to help him with that?

    My goodness, Drosera! All Behe has done is put meat on the bones of Margulis’s criticism — that neo-Darwinism can’t explain most of evolution. My chief criticism of Behe’s book is that he neglected to deal with Margulis’s own theory — symbiogenesis. I’m not sure how good the evidence for her theory is, but Behe should at least have addressed it. But meanwhile, he’s offered a fairly strong argument against neo-Darwinism. And Thornton’s work, as far as I can tell, supports it.

  54. Drosera

    Julian,

    As used by Intelligent Design adepts and acolytes, complexity and information are ill-defined terms that are mainly used to create confusion. As a result, ‘conservation of information’ is a completely spurious concept. Would you say that in Thornton’s work there is evidence of conservation of information? Judging from what you write it looks as if you think there has been a loss of information, rather than conservation.

    Thornton has shown that it is highly unlikely that protein B will evolve back into protein A. But this doesn’t say anything about how protein A evolved in the first place (probably from protein C), nor does it say anything about the probabilty that protein B may evolve into yet another useful protein D. Complexity and information are pretty useless concepts in this context. We assume that the evolution of proteins involved a large number of very unlikely events, just as your existence is the result of a long sequence of almost impossibly unlikely coincidences. And yet you exist, or so it seems to me.

    So if the laws are not deterministic, then the designer (assuming it is “outside” of the universe) would occasionally need to intervene in the universe. But I don’t see that as an overwhelming problem.

    The nice thing about the Theory of Evolution is that a designer is not needed. What an immense simplification! That is of course the reason why many religious people don’t like it at all.

    Well, actually, the papers don’t explain how life came into existence, or how Irreducibly Complex systems came into existence, or even how Thornton’s original hormone receptor came into existence.

    First of all, the Theory of Evolution is not a theory about the origin of life (or the origin of gravity, or whatever shifting goalpost you may want to insert). Second, there is no proof that Irreducibly Complex systems exist in nature, so there is not much reason to explain them. Third, how any particular protein evolved is necessarily guesswork, since in most cases this would have happened millions of years ago over a very long stretch of time, involving huge populations of unicellular organisms.

    All Behe has done is put meat on the bones of Margulis’s criticism — that neo-Darwinism can’t explain most of evolution.

    Margulis once had the happy insight that certain organelles must have resulted from symbiosis. In her later work she has taken the importance of symbiosis and hybridisation to extremes that few modern biologists would consider credible. But at least, unlike Behe, she has made a major contribution to real science, and one which is not at all in conflict with the Theory of Evolution. I am not sure in which way Behe has put meat on Margulis’s criticism, as you claim; their ideas seem totally unrelated to me (intelligent design versus ubiquitous symbiosis). But while Margulis is most probably wrong in her extreme views, Behe, to borrow a famous put down from Wolfgang Pauli, is not even wrong.

  55. Julian

    Hi Drosera,

    You wrote: “Judging from what you write it looks as if you think there has been a loss of information, rather than conservation.

    Yes, I’m not sure why they call it conservation of information, when the idea is that information is easily lost, but very hard to create or regain.

    “AThornton has shown that it is highly unlikely that protein B will evolve back into protein A. But this doesn’t say anything about how protein A evolved in the first place (probably from protein C), nor does it say anything about the probabilty that protein B may evolve into yet another useful protein D.

    What Thornton’s work did was show that if multiple unselected mutations are necessary in order to gain function, then it won’t happen. That is exactly what Behe has been saying.

    Complexity and information are pretty useless concepts in this context.

    I disagree. Protein A had more information — the ability to bind with more proteins than protein B. So there was a loss of information in the evolution from A to B. In order to evolve from B back to A, there would be a gain of information.

    We assume that the evolution of proteins involved a large number of very unlikely events, just as your existence is the result of a long sequence of almost impossibly unlikely coincidences. And yet you exist, or so it seems to me.

    Yes, and it seems like you exist, also. But let’s compare our existence with the reverse evolution of protein B bact to A. According to Thornton, this would require a “large number of very unlikely events.” So large and unlikely, in fact, that it wouldn’t happen. Perhaps the assumption that most of evolution happened this way is just plain wrong.

    The nice thing about the Theory of Evolution is that a designer is not needed. What an immense simplification! That is of course the reason why many religious people don’t like it at all.

    I like simplicity, when it’s believable. Here we have two homologous proteins A and B. If we had thought that B existed before protein A, then the Theory of Evolution would have told us that B evolved into A. Simple! No need for a designer! But according to Thornton, that would have been wrong. So now, I’m supposed to believe that Theory of Evolution is correct about all those other homologous proteins and systems. I’m supposed to believe that the T3SS randomly evolved into a flagellum, because it has so many homologous proteins. Simple! But if B couldn’t even evolve into A, then why should I believe that the T3SS randomly evolved into the flagellum?

    First of all, the Theory of Evolution is not a theory about the origin of life (or the origin of gravity, or whatever shifting goalpost you may want to insert).

    Technically, no. But if Darwin had known that even the simplest cells resemble highly advanced nanaotechnology, he would have reconsidered his theory.

    Second, there is no proof that Irreducibly Complex systems exist in nature, so there is not much reason to explain them.

    Behe’s definition of an Irreducibly Complex system is (if I remember correctly), a single system, composed of multiple interacting parts, where the removal of anyone causes the system to cease functioning. Based on that definition, there are very many such systems in nature.

    Third, how any particular protein evolved is necessarily guesswork, since in most cases this would have happened millions of years ago over a very long stretch of time, involving huge populations of unicellular organisms.

    Yes, but Thornton’s work should make us wonder, if B couldn’t evolve into A, what would C have to be like? It sounds like C had to have even more functions that A.

    I am not sure in which way Behe has put meat on Margulis’s criticism, as you claim; their ideas seem totally unrelated to me (intelligent design versus ubiquitous symbiosis). But while Margulis is most probably wrong in her extreme views, Behe, to borrow a famous put down from Wolfgang Pauli, is not even wrong.

    Both Margulis and Behe thinks that neo-Darwinism cannot explain most of evolution. And according to Margulis, so does Francisco Ayala. And it sounds like Carl Woese has joined the list, also. None of them think Behe’s solution is correct. But if they weren’t worried about being categorized with a ID whacko, they would admit his argument against neo-Darwinism is right.

  56. Drosera

    Julian,

    Yes, I’m not sure why they call it conservation of information, when the idea is that information is easily lost, but very hard to create or regain.

    That’s precisely why conservation of information is a nonsensical idea.

    What Thornton’s work did was show that if multiple unselected mutations are necessary in order to gain function, then it won’t happen. That is exactly what Behe has been saying.

    What you don’t seem willing to understand is that all proteins keep on mutating, possibly accumulating dozens of minor, largely neutral mutations. Very occasionally, one or two additional, non-neutral mutations will then produce a new protein with a different function. It’s like the probability of finding a very rare species of insect. While it is highly unlikely that you will find any particular rare species during a field trip, there are so many rare species, that you are bound to discover at least a few.

    Protein A had more information — the ability to bind with more proteins than protein B. So there was a loss of information in the evolution from A to B. In order to evolve from B back to A, there would be a gain of information.

    Protein A was more general, if you like. But to say that it contained more information is not the same thing. Does a protein with function X contain more information than a protein with function Y? I am fairly sure that you have no way of measuring the difference, if any, in information content in a non-trivial way (of course, there are measures based on string length and algorithmic complexity, but these are trivial). I maintain that the concept of information does not add anything useful here. It is only a smoke screen.

    why should I believe that the T3SS randomly evolved into the flagellum?

    Because the components for the flagellum were already there. And the evolution was not entirely random, but guided, as it were, by natural selection. It was not inevitable that the flagellum evolved from these components, but any structure that improved the mobility of the cell would have had enormous benefit, and therefore would have been strongly selected for. If you look at unicellular organisms and consider the many widely different ways that they have of moving about, then you will see that there are many solutions to the same problem.

    Behe’s definition of an Irreducibly Complex system is (if I remember correctly), a single system, composed of multiple interacting parts, where the removal of anyone causes the system to cease functioning. Based on that definition, there are very many such systems in nature.

    The definition, as I recall it, also postulates that the individual parts of the system would have been useless, so the system could not have evolved in small steps. It’s either all or nothing. This has simply not been demonstrated to occur. The bacterial flagellum is a case in point. See this lecture by Ken Miller (who is not an atheist, by the way).

    But if they weren’t worried about being categorized with a ID whacko, they would admit his argument against neo-Darwinism is right.

    If they thought Behe was right then they wouldn’t think he was a wacko. By the way, seeing that Margulis has some very strange ideas, for example about 9/11, she is not exactly a beacon of rationality. As for Ayala and Woese, I am not aware that either of them claims to have refuted the Theory of Evolution. Citations needed here.

  57. Julian

    Drosera,

    I wrote: ” Yes, I’m not sure why they call it conservation of information, when the idea is that information is easily lost, but very hard to create or regain.”

    You responded: “That’s precisely why conservation of information is a nonsensical idea.

    Calling it “conservation” when it’s really about dissipation is what is nonsensical.

    What you don’t seem willing to understand is that all proteins keep on mutating, possibly accumulating dozens of minor, largely neutral mutations. Very occasionally, one or two additional, non-neutral mutations will then produce a new protein with a different function.

    I’m willing to understand it. I’m not willing to buy it. In his book, The Edge of Evolution, Behe claims that at least 5 0r 6 amino acid changes are needed to create a new binding site in a protein. He allows that 1/3 of these will be neutral. That still means that 3 or 4 non-neutral mutations are needed. Apparently you would dispute his claim. I imagine this can be decided by a comparison of your studies with the ones that Behe cites.

    Protein A was more general, if you like. But to say that it contained more information is not the same thing. Does a protein with function X contain more information than a protein with function Y? I am fairly sure that you have no way of measuring the difference, if any, in information content in a non-trivial way (of course, there are measures based on string length and algorithmic complexity, but these are trivial). I maintain that the concept of information does not add anything useful here. It is only a smoke screen.

    I’ll admit that I’m out of my element here. But the fact that A could bind with three hormones, while B could only bind to one of them suggests that A has more useful information than B.

    I asked: ” why should I believe that the T3SS randomly evolved into the flagellum?”

    Because the components for the flagellum were already there.

    If we assume that the T3SS existed before the flagellum, which is disputed, not only by ID people, but by neutral scientists.

    And the evolution was not entirely random, but guided, as it were, by natural selection. It was not inevitable that the flagellum evolved from these components, but any structure that improved the mobility of the cell would have had enormous benefit, and therefore would have been strongly selected for.

    I’ll grant you that mobility would have been selected for. However, it would take very many changes to the T3SS before it had mobility to be selected for.

    I wrote: ” Behe’s definition of an Irreducibly Complex system is (if I remember correctly), a single system, composed of multiple interacting parts, where the removal of anyone causes the system to cease functioning. Based on that definition, there are very many such systems in nature.”

    The definition, as I recall it, also postulates that the individual parts of the system would have been useless, so the system could not have evolved in small steps. It’s either all or nothing. This has simply not been demonstrated to occur. The bacterial flagellum is a case in point. See this lecture by Ken Miller (who is not an atheist, by the way).

    I’m in my element on this one. In Darwin’s Black Box Behe points out that the parts of one system may also exist in other systems. Ken Miller misconstrues Behe’s definition.

    If they thought Behe was right then they wouldn’t think he was a wacko.

    They think his solution to the problem — Intelligent Design — is wrong. But they his argument against neo-Darwinism is right. Or so it seems to me.

    By the way, seeing that Margulis has some very strange ideas, for example about 9/11, she is not exactly a beacon of rationality.

    She and over 950 architects and engineers, so far: check out ae911truth.org

    As for Ayala and Woese, I am not aware that either of them claims to have refuted the Theory of Evolution. Citations needed here.

    You keep calling neo-Darwinism “the Theory of Evolution,” as if there are no other theories of evolution. Here’s Woese’s proclamation (I hope I did the link correctly. I’m computer illiterate):

    Woese

    I’ll see what I can find on Ayala.

  58. Julian

    Woese link didn’t work. I’ll try again later.

  59. Julian

    One last time, then I give up:

    Woese

  60. Drosera

    Julian,

    Thanks for trying. I have now seen Woese’s article that you wanted to link to. In a way, Woese’s case resembles that of Margulis. Both made important discoveries that were initially met with scepticism (it seems that Margulis’s theory of symbiogenesis had been anticipated by Russian scientists, by the way). Both now use rather strong language, exaggerating the importance of some aspect of the hereditary mechanism, that may seem to you as if they oppose the Darwinian theory of evolution. Woese sees horizontal gene transfer everywhere. Fine. Even if it were true, so what? He doesn’t say that these genes did not evolve in the first place through the standard mechanism of mutations and natural selection, or that they will cease to evolve after they have been incorporated into a different genome.

    There is a reason why I use the term Theory of Evolution, instead of neo-darwinism, as you noted. The Theory of Evolution states that there is descent with modification, with differential survival rates due to natural selection. Note that this definition is silent about the exact hereditary mechanism. In other words, symbiogenesis and horizontal gene transfer, as well as neutral mutations and punctuated equilibria, are entirely compatible with the theory. We still have a lot to learn about the specific mechanisms, but as far as I can see, there has been no serious challenge to the basic tenets of the Theory of Evolution.

    The term neo-darwinism is mainly used by creationists who apply it to a straw man
    version of the Theory of Evolution, which allows them to suggest that criticisms like those of Margulis and Woese are attacks on some kind of dogma. This is a typical case of projection. While individual scientist may well have personal convictions that amount to dogma, science itself is free from dogmas. Darwin is not a god. So far there is no evidence that he was wrong about the basic principles of evolution, but if real evidence is found his theory will have to be abandoned. I doubt that this will happen, but even if it does, I doubt even more that the alternative will turn out to be Intelligent Design.

    You say:

    In Darwin’s Black Box Behe points out that the parts of one system may also exist in other systems. Ken Miller misconstrues Behe’s definition.

    If Behe did point this out, then he just undermined his own concept of irreducible complexity. In that case it all boils down to the argument from personal incredulity.

    “By the way, seeing that Margulis has some very strange ideas, for example about 9/11, she is not exactly a beacon of rationality.”
    She and over 950 architects and engineers, so far: check out ae911truth.org

    Then you probably also agree with Margulis that HIV doesn’t cause AIDS, and that the Gaia hypothesis is not a crackpot idea. It’s an interesting phenomenon that people who believe one strange thing for which there is no evidence (say, Intelligent Design) are bound to believe other strange things for which there is no evidence. The key word here is evidence. Maybe I should repeat it a few times. Evidence. Evidence.

  61. Julian

    Hi Drosera,

    You wrote:
    The term neo-darwinism is mainly used by creationists who apply it to a straw man version of the Theory of Evolution, which allows them to suggest that criticisms like those of Margulis and Woese are attacks on some kind of dogma.

    Margulis specifically uses the term “neo-Darwinism,” and Woese uses the term “the Modern Synthesis,” which refers to the same thing: Variation or novelty is supplied mostly by the accumulation of random genetic mutations, which are passed on either by being naturally selected or by genetic drift. Margulis definitely says, and Woese seems to say that this is not the case. Margulis thinks it’s symbiogenesis, and Woese thinks its HGT. But I think both would offer an argument similar to Behe’s as to why neo-Darwinism (or the Modern Synthesis) is wrong.

    By the way, I found the place where Margulis claims that Ayala confided to her that he believes that neo-Darwinism is dead. But I found another place where he certainly seems to endorse it. So until I find differently, I would strike Ayala off the anti-neo-Darwinism list.

    I wrote: “In Darwin’s Black Box Behe points out that the parts of one system may also exist in other systems. Ken Miller misconstrues Behe’s definition.”

    If Behe did point this out, then he just undermined his own concept of irreducible complexity.

    Not at all. Behe’s claim is that Irreducibly Complex (IC) systems cannot evolve directly. For example, the flagellum could not have evolved from a simpler system that performed the exact same function, since it would mean that the flagellum was not IC to begin with, but the simpler system was. But Behe does admit that IC systems can evolve indirectly. For example, the flagellum could evolved from the T3SS, which has a different function, through cooptation. But the more mutations it would take to achieve this, the more improbable that it could happen.

    I wrote: “She [Margulis] and over 950 architects and engineers, so far: check out ae911truth.org

    Then you probably also agree with Margulis that HIV doesn’t cause AIDS, and that the Gaia hypothesis is not a crackpot idea.

    I didn’t know she believed that HIV doesn’t cause AIDS. And I read somewhere that she was careful not to attribute mystical powers to Gaia.

    It’s an interesting phenomenon that people who believe one strange thing for which there is no evidence (say, Intelligent Design) are bound to believe other strange things for which there is no evidence.

    Most ID proponents I know reject alternative 9/11 theories. And most 9/11 truthers I know reject ID. I seem to be about the only double whacko around. :) But then I think there’s good evidence for both.

  62. Drosera

    Julian,

    Margulis specifically uses the term “neo-Darwinism,” and Woese uses the term “the Modern Synthesis,” which refers to the same thing: Variation or novelty is supplied mostly by the accumulation of random genetic mutations, which are passed on either by being naturally selected or by genetic drift. Margulis definitely says, and Woese seems to say that this is not the case. Margulis thinks it’s symbiogenesis, and Woese thinks its HGT. But I think both would offer an argument similar to Behe’s as to why neo-Darwinism (or the Modern Synthesis) is wrong.

    I don’t think so. Both still have to explain where the genes originally come from. They have offered no alternative to the standard explanation for that (the modern synthesis), and I am sure that they will not endorse any hypothesis involving the supernatural. Their work does not support Behe in any way.

    Most ID proponents I know reject alternative 9/11 theories. And most 9/11 truthers I know reject ID. I seem to be about the only double whacko around. But then I think there’s good evidence for both.

    Let’s conclude then by admitting that we have different standards of evidence. And if you can recognize yourself that you are a wacko then there is still hope for you ;)

  63. Julian

    Hi Drosera,

    You wrote: “ Both [Margulis and Woese] still have to explain where the genes originally come from. They have offered no alternative to the standard explanation for that (the modern synthesis), and I am sure that they will not endorse any hypothesis involving the supernatural. Their work does not support Behe in any way.

    I agree that they have not offered an explanation of where the genes originally came from, and I consider that a serious problem for them and for all non-ID theories. And I agree that they will not endorse any hypothesis involving the supernatural. But though they would not agree with Behe’s solution — ID — I still think they would agree with his criticism of neo-Darwinism.

    Let’s conclude then by admitting that we have different standards of evidence. And if you can recognize yourself that you are a wacko then there is still hope for you ;)

    My guess is that our standards of evidence are pretty much the same. I recognize that most people would consider me a whacko, for one reason or another. And I can live with that.

    Leave a Reply

  64. Martin

    Michael Houst said:

    Well, I didn’t realise it was that easy. What’s all the fuss about then?

  65. Martin

    Sorry, post number 76 didn’t copy what Michael Houst said. As follows:

    All it takes is a single, self-sufficient, self-replicating cell to start the ball rolling.

  66. peter

    What is boring about the whole ID issue it is the old supernatural explanation in new clothes.

    If one proposes an intelligent designer, one has to admit that by denying evolution as the mechanism of developing biological complexity, that designer in turn needs a designer, who must have then again created a space (universe?) where that designer could have operated in.

    And so the regression of a succession of designers continues …

    Evolution works, all agriculture of today is based on random mutations selected for – by humans. There alone the evidence for beneficial mutations (not necessarily beneficial for the species) exposing as a lie the claimed improbability of those mutations. Now we have genetic engineering as a tool, enhancing the speed of mutations by gene transfer.
    Nature just does the same for much longer. What is there not to understand?

  67. Buho

    Behe’s responses to Thornton’s reply above are linked below. I enjoyed reading the back and forth between Behe and Thornton, and between Drosera and Julian above. All-in-all, it seems Thornton’s work supports Behe, and this really shouldn’t be a big deal, but there’s a patina of culture that makes getting to this truth difficult.

    Part 1: http://www.evolutionnews.org/2009/10/the_science_writer_carl_zimmer027301.html
    Part 2: http://www.evolutionnews.org/2009/10/not_so_many_pathways_response027361.html
    Part 3: http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo027401.html
    Part 4: http://www.evolutionnews.org/2009/10/probability_and_controversy_re027491.html

  68. Daniel J. Andrews

    So the guy who did the research and wrote the paper thinks Behe’s reading of his paper is wrong, and you (Buho) think the work does support Behe. Even if I hadn’t read the work (and the reply) I know which scientist to bet on (i.e. it wouldn’t “be he” who didn’t do the research).

  69. Stuart Poss

    I am struck that the mistake Behe and other make regarding low probability events is in many ways remarkably similar to Zeno’s paradox in which Achilles couldn’t possibly win a race with a turtle that started out ahead of him, because to do so he would have to travel half way of the distance to the turtle and by then the turtle would have advanced, etc., etc. (also told by noting that Achilles could never reach a wall because to do so he would first have to travel half way and then again half way ad infinitum.

    The probabilities of events can be exceedingly small, but if these probabilities are even only slightly more likely than others, quite a few extraordinarily highly improbable events will necessarily occur with near certainty. In many cases, its just a question of time. With enough time even near random events can appear as though “designed” to come out that way.

    It is remarkable that even though the concept of limits is extremely well known and has been for 400 years (or longer if one recognizes the method of exhaustion of Archimedes as being sufficiently close to count), not to mention the the obvious fact that most can readily recognize that they can outrun a turtle, folks like Mr. Behe seem still unable to grasp the consequences.

NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

ADVERTISEMENT

See More

ADVERTISEMENT
Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »