Mismatch of the decade: Thornton vs. Behe

| 220 Comments

One of my favorite examples of the step-by-step evolution of molecules has been the work coming out of Joe Thornton's lab on glucocorticoid receptors. It's marvelous stuff that nails down the changes, nucleotide by nucleotide.

It's also work that Michael Behe called "piddling", despite the fact that it directly addresses the claims of irreducible complexity. Have you ever noticed how the creationists will make grand demands (show me how a duck evolved from a crocodile!) and then reject every piece of fossil evidence you might show them because there are still "gaps"? This is the converse of that argument: when you've got a system where you can show each tiny molecular/genetic change, they dismiss that as trivial. You really can't win.

Well, Thornton has been working hard and coming up with more and more details, while Behe is still sitting there, eyes clamped shut and ears stoppered, insisting that IT CAN'T HAPPEN LALALALAALALALALAAAA. Behe threw together some dreck claiming that not only didn't Thornton's work demonstrate evolution, but it actually supported Intelligent Design creationism!

Boy, did he make a mistake.

Remember how when the creationists started playing games with his work, it roused Richard Lenski to slap down Conservapædia hard? We've got a similar situation here.

Joe Thornton has written a beautiful response to Michael Behe.

Read it. Really. It's a whole lesson in important principles in evolutionary theory all by itself. It exposes the ignorance of Behe through and through, and demolishes the premises of Behe's latest foolish book. And it made me feel soooo gooooood.

220 Comments

A level-headed response; Lenski’s was somewhat annoyed. Thornton did miss a slight bet on Behe’s Point #3, not labeling as the classic “lottery winner fallacy”: The odds of winning the lottery are so low that if you did, then somebody must have rigged it.

Somebody needs to ask Behe: When are you going to give it up? All this work and it’s just going to sink out of sight like a stone thrown in a pond.

Before this thread goes too far down the argumentative track let’s have a moment to appreciate the beauty of Joe’s work. Being able to actually do experiments this detailed to identify the more or less exact pathway that molecules evolved (or to within a small amount of uncertainty). That should be more than enough precision to give the physicists biology envy.

wile coyote Wrote:

Somebody needs to ask Behe: When are you going to give it up? All this work and it’s just going to sink out of sight like a stone thrown in a pond.

Why should he give it up? He has tenure at a university (practically a guaranteed job for life), is immune to embarrassment (his pathetic performance at Dover, public rejection of his ideas by his own dept. at Lehigh), moonlights at a pseudoscience outfit, and probably has more nonscientist fans than 99% of biochemists.

The questions that need to be asked, and are not asked nearly enough IMO, are not of Behe, but of his fans. Specifically whether they agree with him on the age of life (~4 billion years) and common descent (he accepts it). And if they disagree with either, why they haven’t challenged him directly.

Frank J said:

Why should he give it up?

Oh, I didn’t say he would. But we can drop a hint that he’s being a bore.

Sounds like more whining from the chance-in-the-gaps gallery.

Thornton:

“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”.

Isn’t this darwinian ‘philosophy in a nutshell? Even if the probability is next to nil, the fact that in ‘theory’ a nano-chance still exists, then evolution, with deep time on it’s side will ‘somehow’ eventually find it?

IOW, just wishful thinking on Thorton et al’s part. Science? Meh.

Thornton:

“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. “

No shit shirlock. If the mutation has not been fixed, of course the function will be restored. That is what the organism is trying to do, fight off the mutation. It is trying to preserve what is already adequate. If it can’t, and the mutation gets fixed, there is no reversal possible. So it deals with it to the best of its ability.

This is exactly Behe’s point. The organism is not building anything, it is fighting, then losing the mutation battle, then figuring out how to accomodate it without disrupting its normal operation.

What is observed is at best a renovation, at worst a repair job, but never a construction site.

Thornton:

“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.”

In other words, we ‘know’ organisms don’t re-evolve but we are still ‘hoping’ we will someday find some evidence that it ‘could’ happen.

Keep the faith, Thorton. Keep the faith.

Here’s another Thornton quote I just love (from the NYT article PZ courteously pointed out. Thx,PZ)

Thornton:

“It had a different function and was exploited to take part in a new complex system when the hormone came on the scene,” Dr. Thornton said.”

Now how in the hell does an organism ‘exploit’ a new part? And just how pray tell did the hormone ‘come on the scene’?

Really, this is more material than Stephen Colbert could ever hope for!

IOW, just wishful thinking on Thorton [sic] et al’s part. Science? Meh.

Thornton has the experimental evidence that supports his statements while Behe has insisted over and over that the things Thornton observed must be impossible. The only wishful thinking going on is in Behe’s head.

Now how in the hell does an organism ‘exploit’ a new part? And just how pray tell did the hormone ‘come on the scene’?

Thornton’s work was a step-by-step description of how the hormone “came on the scene.” You are a living example of the Kruger-Dunning Effect.

Steve P. said:

Isn’t this darwinian ‘philosophy in a nutshell? Even if the probability is next to nil, the fact that in ‘theory’ a nano-chance still exists, then evolution, with deep time on it’s side will ‘somehow’ eventually find it?

This is what I usually refer to as a “wrong end of the telescope” argument. Thornton’s point, and also that of evolutionary theory–as I understand it–is that while a *specific* outcome is unlikely, *some* outcome is highly probable. And, of course, the probability of anything that actually does happen is 1.000.

If there are enough tickets in a lottery, one of them *will* win. You just can’t predict which one before the winning numbers are selected. What’s so difficult to understand?

Chris Lawson said: You are a living example of the Kruger-Dunning Effect.

While I agree with that assessment, isn’t every example of the K-D Effect a living example?

Steve P. said:

What is observed is at best a renovation, at worst a repair job, but never a construction site.

As opposed to all the details we have observed about the Mysterious Alien Designers (or Functional Equivalent) who supposedly can account for it all. Y’know, like who they were, what they did, when they did it … little things like that.

Oh, I know, we’re going to get the “pseudoskeptic” response: “Well, I’m just an impartial skeptic. Modern evolutionary science is on the wrong track. There’s [ahem] SOME OTHER THEORY [if pigs had wings!] out there that could do a better job … “

wile coyote Wrote:

Oh, I know, we’re going to get the “pseudoskeptic” response: “Well, I’m just an impartial skeptic. Modern evolutionary science is on the wrong track. There’s [ahem] SOME OTHER THEORY [if pigs had wings!] out there that could do a better job … “

Or as recent PT regular “Mr. G” would put it, the pseudoskeptic would say “I have no dog in the fight.” To which the reply would be “So that explains why you keep attacking the black dog while ignoring the white one.”

Quick every adult who had a dairy product this week we need to get some gene therapy so we can fight off this horrible mutation that allows us to still digest lactose into adulthood! It is an unexpected bonus in this day and age of horrible conflation of terms and ideas in pretty sciency sounding language when someone comes out, Steve P., with a conception so wrong I could easily explain why it’s wrong to a 5th grader.

Steve P. said:

Isn’t this darwinian ‘philosophy in a nutshell? Even if the probability is next to nil, the fact that in ‘theory’ a nano-chance still exists, then evolution, with deep time on it’s side will ‘somehow’ eventually find it?

IOW, just wishful thinking on Thorton et al’s part. Science? Meh.

Is Steve P. really this stupid, or is he lying for Jeebus? The whole point of the essay, IDiot, is that evolution isn’t searching for “it”. “It” just happens to be the reality we live in, out of the innumerable potential realities which could have existed. Each possibility is highly improbable, but one has to exist. You write well enough to show you aren’t retarded, so if you refuse to concede this simple point, you are clearly lying. Just like Behe.

Steve P. said:

Thornton:

“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. “

No shit sherlock. If the mutation has not been fixed, of course the function will be restored. That is what the organism is trying to do, fight off the mutation. It is trying to preserve what is already adequate. If it can’t, and the mutation gets fixed, there is no reversal possible. So it deals with it to the best of its ability.

This is exactly Behe’s point. The organism is not building anything, it is fighting, then losing the mutation battle, then figuring out how to accomodate it without disrupting its normal operation.

What is observed is at best a renovation, at worst a repair job, but never a construction site.

Exactly! Evolution usually doesn’t begin from a new “construction site”, but proceeds in a series of “renovations”! Each “renovation” adding to or subtracting from the “house” until it is different from it was originally!

The whole point of the essay, IDiot, is that evolution isn’t searching for “it”.

How is it that even the densest IDiot can understand that water doesn’t need to be “searching” the bucket to find the pinhole, yet they can’t fathom the fact that biology does the same thing, constantly trying random little steps over the whole solution space to find any working solution?

… 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”

Isn’t this darwinian ‘philosophy in a nutshell? Even if the probability is next to nil, the fact that in ‘theory’ a nano-chance still exists, then evolution, with deep time on it’s side will ‘somehow’ eventually find it?

Err, Steve, you don’t understand. Remember the Lottery illustration just before yours? The odds of any given person winning the lottery are next to nil, but the odds of someone winning are 100%, that was Thornton’s point.

Don’t let this embarrassing mistake discourage you, keep on learning!

Steve P. said:

Thornton:

“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.”

In other words, we ‘know’ organisms don’t re-evolve but we are still ‘hoping’ we will someday find some evidence that it ‘could’ happen.

Keep the faith, Thorton. Keep the faith.

I was about to reply to this, after I replied to the block above, but then I realized that Steve P. has completely FAILED to grasp the meaning of that last paragraph he quoted, thus rendering any reply useless.

The creationist argument from probability is the very definition of question-begging–an argument that assumes its own conclusion. The fact the Steve P., et al either don’t understand this, or do understand it and use the argument anyway, tells us all we need to know about them.

woodchuck64 said:

Remember the Lottery illustration just before yours? The odds of any given person winning the lottery are next to nil, but the odds of someone winning are 100%, that was Thornton’s point.

I’m very fond of the “lottery winner” fallacy concept and I like to push it, but it does have a slight weakness in that it suggests a “winning” solution, which is misleading. The subtle reality is that there is merely a “solution” – any one that works.

Another analogy is a robot car that cruises the freeways and takes freeway interchanges at random. How could it POSSIBLY navigate from New York City to Los Angeles? It can’t – but it might end up there. It might end up in Miami. It might end up in Albuquerque. It might end up in Des Moines. It might end up in Toronto. But it’s going to end up SOMEWHERE.

And of course, it won’t end up in Paris. If it is impossible for it to get from here to there … it WON’T.

It is interesting that this notion of “destiny” is so hard for humans to drop. Like Dawkins more or less said, it’s like our brains are not wired to understand a process that isn’t under long-range direction – not following a road map, just taking any interchange that seems handy.

Steve P -

I don’t mean to be rude, but you really don’t have a clue what you are talking about.

Isn’t this darwinian ‘philosophy in a nutshell? Even if the probability is next to nil, the fact that in ‘theory’ a nano-chance still exists, then evolution, with deep time on it’s side will ‘somehow’ eventually find it? IOW, just wishful thinking on Thorton et al’s part. Science? Meh.

You didn’t understand what you read. Thornton was not describing the theory of evolution, but rather, correcting a very stupid mistake that Behe made about probability. What Thornton pointed out is that if a large number of future outcomes are possible on a probabilistic basis - for example suppose I’m going to draw a single card at random from a shuffled deck - then each could be said to have a low initial probability, but, as Behe claims not to understand, something will occur.

In my example, for each card, the probability of it being chosen 1/52. However, if I draw a card and stand there with the three of diamonds in my hand, it doesn’t mean that magic was required because “there was only one chance in 52 that it would be the three of diamonds”.

Also, in your mis-statement, you have made a stupid mistake about probability. If something occurs at a low frequency, but you do enough trials, you will indeed encounter it at about that frequency.

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

None of this is directly about biological evolution. It’s about Behe and you not understanding basic probability.

No shit shirlock.

That’s “Sherlock”. I notice that you try to bolster your arguments with exaggerated expressions of scorn. This tactic backfires when your arguments are transparently wrong, however.

If the mutation has not been fixed, of course the function will be restored.

Incorrect, in a way that suggests that you don’t know what a mutation actually is in any sort of detail. Simply because a mutation is not fixed in a population does not mean that the mutant allele will mutate again in a way that restores function.

That is what the organism is trying to do, fight off the mutation. It is trying to preserve what is already adequate. If it can’t, and the mutation gets fixed, there is no reversal possible. So it deals with it to the best of its ability.

There are imperfect DNA repair mechanisms, which I know quite a bit about and you know nothing about, but this is not an accurate description of how they work.

This is exactly Behe’s point. The organism is not building anything, it is fighting, then losing the mutation battle, then figuring out how to accomodate it without disrupting its normal operation.

No, that is not Behe’s point. Behe’s point was completely different (his basic point, to paraphrase fairly, was that evolution can never occur through the sequential accumulation of mutations, which is nonsense). I honestly don’t understand what you are saying. You haven’t provided sufficient detail.

You shouldn’t misrepresent Behe’s arguments.

What is observed is at best a renovation, at worst a repair job, but never a construction site.

I notice that you are using evasive, highly metaphorical language. However, if you are trying to say that mutations never lead to new functions, you are wrong.

In other words, we ‘know’ organisms don’t re-evolve but we are still ‘hoping’ we will someday find some evidence that it ‘could’ happen.

What Thornton said was something completely different from this. What he said, to paraphrase accurately, was that it is highly improbable that the exact original form of the ancestor allele (implicitly, nucleic acid sequence) will re-evolve, but that equivalent function to the ancestor allele may more easily re-evolve (because more than one sequence may lead to the same function).

Keep the faith, Thorton. Keep the faith.

Your sarcasm is embarrassing, given that you are completely mistaken and ill-informed on all topics which you discuss.

I tried the deck-of-cards analogy with a creationist acquaintance once, pointing out to him that the order of a shuffled deck must be impossible because there’s just a one-in-52! chance that the cards could be in that particular order. It went something like this:

Creationist(C): But they have to be in *some* order.

Me: That’s my point.

C: But the order is meaningless.

Me: That’s also my point.

C: Well, that doesn’t make any sense.

Me: If you keep shuffling the deck long enough, you’ll get to an order that you *do* recognize.

C: That could take thousands, maybe millions of years.

Me: Exactly.

C: So what’s your point?

Me: Never mind.

James Grover -

The other thing that is difficult for people to grasp - even non-creationists - is that of course, every particular order is exactly as likely as every other order.

Another point that is tricky to some is that whether or not an order has “meaning” is entirely defined by the observer.

Of course, these are arguments about probability.

They are relevant to the extent that the theory of biological evolution is entirely compatible with probability theory (and indeed, population genetics draws heavily on probability), and to the extent that, if a creationist argument is grounded in a wrong idea about probability, it is wrong on the face of it, with no further analysis needed.

However, we should also be careful to note that creationists sometimes use arguments related to probability that are not wrong about probability, but are dishonest misrepresentations of the theory of evolution.

Wile Coyote -

By the way, I agreed with you point that, among peripheral arguments, creationists are especially likely to make peripheral arguments about “information theory” - usually in a completely uninformed way - for the reasons you described.

It is interesting that this notion of “destiny” is so hard for humans to drop. Like Dawkins more or less said, it’s like our brains are not wired to understand a process that isn’t under long-range direction – not following a road map, just taking any interchange that seems handy.

Yes, this is pretty deep stuff even for non-creationists.

One sort of related thing I find interesting is that humans evolved brains with a high capacity for learning and modifying behavior (although this capacity may not be expressed much in the modern United States).

The implication is that the conscious ability to choose between two or more potential behaviors has been selected for.

That may suggest that conscious choice of a behavior, from among potential alternatives, impacts on the way that the universe unfolds. Otherwise, why would it have been selected for?

This is not intended to endorse any philosophical or spiritual stance whatsoever, it’s just a point that I find interesting.

Harold wrote

What Thornton said was something completely different from this. What he said, to paraphrase accurately, was that it is highly improbable that the exact original form of the ancestor allele (implicitly, nucleic acid sequence) will re-evolve, but that equivalent function to the ancestor allele may more easily re-evolve (because more than one sequence may lead to the same function).

That’s why I like the Lenski, et al., 2003 Nature paper. It shows 23 different evolutionary histories that produce 23 different evolved programs that all perform the same complex function. There are many different roads to adaptation. Which road is taken is a contingent matter depending on the particular chance events that generate population variability for selection and genetic drift to work on.

Steve P makes a diagnostic error, too. He wrote

The organism is not building anything, it is fighting, then losing the mutation battle, then figuring out how to accomodate it without disrupting its normal operation.

“The” organism is not doing anything at all. Populations of organisms do stuff – they vary and differentially reproduce as a function of fitness, and as a consequence the succeeding populations differ from their ancestors, being better adapted to their selective environments. Evolution is a phenomenon of populations, not individuals, and the essentialist notion implicit in Steve P’s remark leads him badly astray.

Indeed, Steve P seems to be suggesting that an individual creature’s somatic cells are mutating one by one and the creature is trying to fight off the invasion like an infection.

Steve P, here’s a hint: In multicellular organisms, only mutations (copy errors) that appear in the gametes (sperm and eggs) get passed on. The new mix of genes either works better, the same, or not as well as the previous mix in surviving to reproduce.

Simple, really.

harold said:

What is observed is at best a renovation, at worst a repair job, but never a construction site.

I notice that you are using evasive, highly metaphorical language. However, if you are trying to say that mutations never lead to new functions, you are wrong.

Ironically enough, his metaphorical use of the word “renovation” describing a mutation is actually pretty good. A “renovated” object is altered but doesn’t lose functionality.

harold said:

By the way, I agreed with you point that, among peripheral arguments, creationists are especially likely to make peripheral arguments about “information theory” - usually in a completely uninformed way - for the reasons you described.

Thanks. I have to grin a bit at the use of the word “peripheral” … hmm, does that read to “red herring”?

There’s a saying that applies to evobasher information theory argument: There is no THERE there.

fnxtr -

Steve P, here’s a hint: In multicellular organisms, only mutations (copy errors) that appear in the gametes (sperm and eggs) get passed on. The new mix of genes either works better, the same, or not as well as the previous mix in surviving to reproduce.

What’s interesting is that somatic mutations (mutations not in germ cells) are equally likely to occur, relative to the rate of transcription of DNA (usually related to cell division). Mutations can occur when DNA is not being replicated, as well, but they’re much more likely to occur during replication.

Of course, somatic mutations can’t be passed on to another organism through sexual reproduction (that’s what the term “somatic” means in this context), but they can have consequences that are highly related to evolution.

One potential result of accumulated somatic mutations is cancer. A clone of cells may end up becoming relatively independent of the regulatory signals that direct their appropriate behavior within the context of their environment.

Such a clone of cells may begin to reproduce excessively and/or fail to differentiate properly, invade inappropriate anatomic spaces, and make excessive use of common resources.

That clone, in fact, be strongly selected for, relative to the normal cells of the organism.

But eventually, if not treated, this process will kill the organism, including the cancer cells themselves.

Grishan -

Ironically enough, his metaphorical use of the word “renovation” describing a mutation is actually pretty good. A “renovated” object is altered but doesn’t lose functionality.

This would be true for that subset of mutations that doesn’t result in change in functionality in the phenotype.

However, many mutations do result in a loss or harmful in function in the phenotype.

Some mutations of accumulations of mutations result in completely novel function in the phenotype. It is this latter point which Steve P was attempting to deny with his vague analogy.

wile coyote: the classic “lottery winner fallacy”: The odds of winning the lottery are so low that if you did, then somebody must have rigged it.

There was, I am led to believe, a German man in the 1970s who was charged with fraud because he won the lottery twice. The only evidence against him was statistical: the chances of him winning twice were so astronomically small that he must have cheated. Apparently it took a couple of mathematicians testifying for the defence to show that while the chances of this particular man winning twice were very small, the chance of *someone* winning twice was quite feasible. Unfortunately my Google-fu is weak today and I can find no link to the actual story. But the principle is still correct. Michael Behe and Steve P. are behaving like the (possibly apocryphal) prosecutors in the German lottery case. They are sticking to their prosecution despite a complete lack of evidence and a false understanding of probability theory.

george babbled:

if scientists are on the same trend of thought as you guys are, the world will evolve to “perfection” and bliss …

go with your gibberish to some other planet…

So says the arrogant moron who is too lazy to learn elementary school level grammar skills.

Why don’t you take your own advice and leave, then?

I think George’s comments should be left up. People who stumble over this thread in years to come will be struck by the intellectual calibre of his remarks.

This comment has been moved to The Bathroom Wall.

george,

youre leavin.….

good ridance.….

why would anyone ever considered, reading anything you wroted?????

you are the morons.….

Man, this is easy.

This comment has been moved to The Bathroom Wall.

This comment has been moved to The Bathroom Wall.

george babbled:

you are all pathetic…

evolution is worse than a 6 day creation…

and that means, illogical, brainless, the worst science ever humans have ever accepted in ACADEMIA…

Then how come Evolutionary Biology is taught in universities around the world, while you are forced to babble incoherently on a website, and lie about leaving?

This comment has been moved to The Bathroom Wall.

george babbled:

evolution is taught in universities around the world, because it must be a global conspiracy

Got evidence?

or they like showing publicly, and for that matter, legally, how stupid they are…

The grammar-challenged troll is projecting again.

Have a look at the book. I hope Authorhouse got full payment in cash before they printed a word.

It would appear that george’s first language is Spanish, which may account for his epic struggles with English grammar; but that hardly conveys the full flavour of his magnum opus. As a work of imagination his “Book of Pure Logic” is up there with “Atlanta Nights” or “Naked Came the Stranger”, but where in those great epics can we find the value of pi to a thousand decimal places? What more could anyone ask? Other than coherence, that is.

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This page contains a single entry by PZ Myers published on October 16, 2009 11:59 AM.

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