To Jerry @68:
Thanks for the words of welcome. I need to be relatively brief now, especially on Behe's work, but I'm happy to discuss biology and evolution with anyone anytime, and I welcome questions, the more specific the better. I hope you and the others here will be patient with me: I work full time in the lab, run a blog of my own, and juggle several additional writing projects among my time with my wife and four kids. When/if there's a question you really want me to address, make it clear.
First, re banning on this site, I've heard from too many decent people on this topic to believe that the policy here is a good one. And the claim that people are banned due to "ad hominems" is laughable, as anyone who reads this blog knows all too well. I've been warmly welcomed, and that's all that matters in this conversation, but please don't ask me to defend your venue. It is what it is, and I happen to think it's a mess -- let's leave it at that.
"I think design is the question, and you think it's the answer." Here, basically, is what I mean. In your first paragraph, you note that you and others here "do not believe there is any naturalistic mechanism that can explain macro evolution or the origin of life," and so you "opt for design events as the only answer." Design, for you, is the answer, and the question was how did these biological systems come about? In between, we find your conclusion that the phenomena in question cannot be explained naturalistically.
I start with the same question: how did these biological systems come about? At the same time, I notice design, "purposeful arrangement of parts," even "prodigies of nature." As I already mentioned in my first post here, I'm quite happy discussing design, and completely reject the suggestion that design has no place in science. Baloney! Design is what we're trying to understand. Design is the question. Here is this biosphere, filled with mind-blowing nanomachines and indescribably intricate processes. Do we need a mathematically-inclined philosopher to coax the specter of "design" out of modern probabilistic theories? Do we need an underinformed biochemist to locate "design" through analysis of mutation rates in Plasmodium falciparum? Good heavens, no. It's right there; it's everywhere. Detecting design, for me, is almost effortless, natural, automatic. (Consider the vocabulary of cell biology, which we can further discuss later.) And so I identify "design" as the very thing I'm trying to understand. My question becomes how did all of this design come about?
I think, then, that we can identify at least two crucial ways in which our thinking diverges. First, design for you is the stuff you use to fill explanatory gaps -- it's the answer. For me, it's the thing we seek to understand -- it's the question. Second, you are convinced that "naturalistic" explanation of natural history is not possible. I'm not at all convinced of this, and in fact I expect God's world to be largely amenable to natural explanation. In other words, I expect that naturalistic mechanisms can account for biological evolution, just as I expect that they can account for embryonic development and for, say, autism. Did that answer your question?
And what about Behe's The Edge of Evolution? Writing carefully about his errors is not easy; evolutionary genetics is challenging under the best of conditions, and laypersons are understandably poorly-equipped to grasp the necessary details. I have been planning a series on my blog, and this conversation might get that project moved up on the to-do list. I've explained some of the most dramatic errors on my blog, and I'll add three further comments here.
1. In TEoE and elsewhere, Behe presents a highly simplified vision of adaptation and microevolution, in which only beneficial mutations are maintained in populations. He gives the impression that a population would only harbor a given mutation or polymorphism if that change had been specifically favored by selection. This is a substantial mischaracterization of evolutionary genetics, overlooking some very important aspects of eukaryotic genetics. There are several mechanisms, well-known to geneticists but almost universally neglected in popular discussions of evolution and inheritance, that can lead to the maintenance of a non-adaptive or "non-beneficial" allele in a population, especially in a sexually-reproducing diploid population (like, say, Plasmodium falciparum). Moreover, during evolutionary and/or environmental change, the beneficial-ness of a particular allele can change completely. Beware of simple evolutionary stories in which adaptation can only proceed in happy little steps from good to better to best. Genetics is more complicated (and interesting) than that.
2. The book's central argument is based fundamentally on population genetics, but ignores the work of the world's most prominent and accomplished geneticists. Allen Orr, for example, is precisely the kind of expert whose work should be the focus of Behe's analysis, but Behe's references to Orr's work are minimal. He leaves untouched the entire field of evolutionary genetics, merely cherry-picking two of Orr's papers. The point is this: a serious consideration of evolutionary genetics -- never mind a complete rewriting of the entire field -- should show marks of serious engagement with existing ideas. TEoE doesn't even try to do this. And most tellingly, Behe hasn't been able to get population geneticists to endorse his book, or to follow up on his assertions. Did he even ask Allen Orr to read the manuscript before going to press? Has he asked Allen Orr to critically review the book, the way any real scientist would seek critical feedback before (or after) advancing a big new idea?
3. If Behe's claims in TEoE are correct, he will soon be the most celebrated biologist since Watson and Crick, and perhaps of all time, for he will have shown conclusively that essentially everything in the biosphere has arisen through mechanisms unknown to science. It is impossible to exaggerate the magnitude of the impact of such discoveries, and I assure you that if I thought there was anything there at all, I would hasten to follow up on Behe's skeletal introduction, devising bioinformatic analyses to bolster his hypothesis and working hard to establish myself as a part of this historic sea change in science. I would achieve scientific "immortality" for myself, worldwide acclaim for Calvin College, and maybe enough of a raise to retire my student loan debt while paying for Christian school education for my kids. Guys, if Allen Orr or Michael Lynch or Sean Carroll or Francis Collins or Craig Venter thought there was anything even remotely plausible about Behe's analysis, they would marshal resources of every kind to pursue the question, and some of them would gather investors and start an institute, bearing the name of some benefactor eager to have his/her name associated with the most momentous discovery of the 20th century and with the Nobel Laureate who made it happen.
Wake up, people. There's nothing there.
20 comments:
Good stuff. Reading tEoE was the final nail in the already well-nailed ID coffin for me. As a geneticist it was painful to read, it was so flawed - and it left me to wonder if (a) Behe was really that poor of a scholar or (b) that he knew what he was doing but that he was deliberately trying to deceive his audience. Neither option was appealing.
You realize, of course, that your time on UD is limited...
Limited? I'm amazed (and grateful) they allowed Steve to comment to this extent.
What's astonishing is that the ID folks don't even recognize that methodological naturalism has its roots in medieval universities--where folks like Jean Buridan and Adelard etc all insisted that the best way forward for natural philosophy was to study nature by looking for natural causes--not supernatural ones.
Hi Steve,
Writing as a layperson, I'm certainly in no position to dispute what you have written about Behe's TEoE. However, a number of scientists (including Ken Miller, Richard Dawkins, and Jerry Coyne) have offered similar criticisms of Behe, and he has responded to them at his blog at amazon.com. So far, his critics have failed to further respond. Perhaps they are just frustrated with Behe's failure to adequately answer their critiques. Or perhaps they don't have adequate replies to his answers. As a layperson, I stand on the sidelines and try to determine which side is winning. So far, it looks like Behe is carrying the day. I look forward to a more detailed critique from you. If it's written in a non-hostile tone, perhaps Behe will respond, and then you can point out on your blog why his answers are inadequate.
Or you could just ignore Behe's book and read Mike Gene's book, The Design Matrix. Behe's approach in both of his books has been trying to prove what Darwinian evolution can't do. Proving a negative is a very difficult, if not impossible task. What usually happens is the other side says, "It's still possible." Then the first side says, "No it's not." Then the second side says, "Yes it is," ad nauseam.
Mike Gene's approach is to sidestep the question of what Darwinian evolution can or can not do, and concentrate on clues that intelligent design may have been involved. So instead of trying to prove Darwinian evolution wrong, he's trying to build a positive case for intelligent design. His first book is laying the conceptual ground work for how such a research program could be carried out. It will be interesting to see where he goes with this.
Bilbo,
Have you seen this yet? It was one of Steve's first posts, and nicely deals with the very claims that Behe makes.
Thanks, John. I just now looked it over. If Steve thinks this is how to explain Irreducible Complexity, hey, go for it. Or even Behe's "two binding site rule." It's clear that Steve doesn't think it answers either one of Behe's claims, yet.
And again, one can either get in a tit-for-tat debate over what Darwinian evolution can or can not do. Or one can try Mike Gene's approach, viewing evolution teleologically. I find that approach much more refreshing.
No problem, Bilbo. It was meant as a place to start. Hopefully you'll look over some of the other posts here as well.
BTW, since Behe has disabled comments on his Amazon blog, it hardly strikes me as evident that he is really interested in hearing from people who disagree with him.
"since Behe has disabled comments on his Amazon blog, it hardly strikes me as evident that he is really interested in hearing from people who disagree with him."
Maybe. Or maybe he only wants to engage with serious arguments from competent scientists, instead of the constant sniping that one encounters on blogs from day to day.
One could find many examples: Behe has never responded to computer scientist Mark Chu Carroll, who pointed out some basic problems with Behe's mathematical assumptions in TEoE:
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The part of the book that is most annoying to me, and thus the part that I'll focus the rest of this review on, is chapter three, "The Mathematical Limits of Darwinism". This is, basically, the real heart of the book, and for obvious reasons, it seriously ticks me off. Behe's math is atrociously bad, pig-ignorant garbage - but he presents it seriously, as if it's a real argument, and as if he has the slightest clue what he's talking about.
The basic argument in this chapter is the good old "fitness landscape" argument. And Behe makes the classic mistakes. His entire argument really comes down to the following points:
1. Evolution can be modeled in terms of a static, unchanging fitness landscape.
2. The fitness landscape is a smooth, surface made up of hills and valleys, where a local minimum or maximum in any dimension is a local minimum or maximum in all dimensions.
3. The fitness function mapping from a genome to a point of the fitness landscape is monotonically increasing.
4. The fitness function is smoothly continuous, with infinitessimally small changes (single-point base chanages) mapping to infinitessimally small changes in position on the fitness landscape.
Of course, Behe doesn't phrase it like that; in fact, I doubt that he even understands that he's making those assumptions: His grasp of math is extremely shallow, and his mathematical reasoning is glib at best.
First, I'll repeat what I've said in the past about what's wrong with each of these assumptions. Then I'll put out a couple of examples in the text of how Behe attemps to refute these criticisms, and show what's wrong with them.
Behe uses these assumptions about the fitness landscape, and the search process which is his model of evolution, to build his argument. He frequently talks about how things can get trapped at a local maximum. By Behe's reasoning, once a species reaches a local maximum of a fitness landscape, that's the end of any process of change in that species. When he talks about a limit of what can be done by mutation+selection, that's what he's talking about: the idea that local maxima are traps.
This is one of the oldest canards of the IDists: the mis-modeling of evolution as a search process over a static landscape. The problems with this are quite simple:
First, It assumes that the fitness landscape is fundamentally low-dimensional. If the fitness landscape truly has many independent dimensions, then there are very few (if any) true local maxima. To assume that local maxima are common requires assuming that when moving through one dimension brings you to a local maximum, moving through any other dimension will also bring you to a local maximum at the same point - which is really another way of saying that the dimensions are not independent - they all reach maxima and minima at the same places.
The idea of local maxima and minima being common comes from thinking of things in terms of low-dimensional surfaces. A fitness landscape with two variables forms a three dimensional graph - and in three dimensions, we do frequently see things like hills and valleys. But that's because a local minima is the result of an interaction between only two variables. In a landscape with 100 dimensions, you don't expect to see such uniformity. You may reach a local maxima in one dimension - but by switching direction, you can find another uphill slope to climb; and when that reaches a maximum, you can find an uphill slope in some other direction. High dimensionality means that there are numerous directions that you can move within the landscape; and a maximum means that there's no level or uphill slope in any direction.
(As an interesting aside, IDists, when they're quoting Dembski, like to talk about the No Free Lunch theorems. The NFL theorems are based on the idea that landscapes really aren't smooth - that they don't have uniform properties that permit a search strategy to work. Behe's argument totally contradicts that - the kinds of landscapes that must be considered to make NFL work totally devastate Behe's idea. )
Second, Behe assumes that the landscape can't change. If it's a local maximum today, it's a local maximum tomorrow. The reason that he needs this is obvious: if todays local maximum can stop being a maximum, then it's not any kind of a barrier. The argument requires that the landscape never change.
This is the biggest problem with the whole idea of modeling evolution as search over a fitness landscape: landscape search generally assumes a static landscape. But this doesn't match reality at all. Just consider a simple example. Suppose you've got a local maximum in the landscape, and that that maximum represents a fitness point for a plant-eater: that point represents an adaptation to a diet that's based on some kind of vegetation, and a behavior that protects it from predation. Because it's a maximum, things that get anywhere near it end up climbing the slope to that maximum. The local maximum becomes a clustering point for plant-eating species. The fact of that clustering means that the population at that point is going to grow.
The growing population means that you'll be creating another fitness point on the landscape: a point for a predator. That point didn't exist before: when there wasn't a population of plant-eaters for a predator to consume, there would be no advantage to evolving to fit the niche of eating the creatures that eat the vegetation; once there is a population of plant-eaters there, then you've got a new fitness point.
The growing population also means that the fitness of that point may start to decline: too much competition for the resources. Too many creatures trying to eat the same limited food source.
This is the reality of the "fitness landscape": the landscape is shaped from the species that inhabit it; as the species change, the landscape changes. Those traps that Behe keeps talking about only exist if the landscape doesn't change. But the only way that the landscape doesn't change is if the species in it don't change. The moment any species starts climbing a hill in the fitness landscape, the landscape must change to describe the new circumstances.
Third, Behe, as in his IC gibberish, insists on a monotonically increasing fitness function, and he insists on mutation behaving as a continuous function. According to Behe, the only changes are changes that produce an immediate increase in fitness. So if you're at a local maximum, there's no way to escape it, because you can't go downhill. There are two problems here: one is that it's possible for a species to become less fit; the other is the continuity assumption.
With respect to that first issue, it's possible in many circumstances, for a population to become less fit. When a species is not under strong selective pressure, it's possible for numerous neutral or even slightly negative mutations to accumulate in the population. There's nothing in reality preventing that: mildly negative mutations do occur in reality. In Behe's model, that means that in reality, evolution isn't a strict hill-climber; crossing a valley to get to a higher fitness summit is not impossible.
The second part if this is a huge problem for Behe's argument. Behe wants to be able to argue that local maxima are traps. A local maxima is only a trap for a search process if the search has certain strict limitations: the search needs to behave as an almost continuous function. This is a bit messy, because we're straddling the line between continuous math and discrete math here. But the idea is that Behe's model is that there's a function from a species genome to a point in the fitness landscape; and that mutation makes an small change to the genome, and that that small change to the genome must correspond to a proportionately small change in the mapped location on the landscape. So mutations can only produce small changes; and small changes can only result in small motions on the landscape. That means that the evolutionary search process can't jump valleys in the landscape.
The problem is, that doesn't correspond to reality. There are times when a small change can have a huge impact. The classic textbook example of this is the Panda's thumb: a very small genetic change caused a change in the developmental process in the wrist of the panda, which produced what is effectively an extra thumb. The genetic change that produced this is tiny; the effect is huge. This is not an unusual thing: small changes can have huge effects. But small changes with large impacts totally blow Behe's argument out of the water: they mean that Behe's barriers aren't barriers at all.
So Behe's argument fails miserably, because it's built on a pile of obviously invalid, long-discredited assumptions. And yet he builds his entire book around them - and just acts as if the assumptions were obviously correct, and no one has ever refuted them. Even when the sources that he cites contradict him, he acts as if there's nothing wrong: he cites several papers about modeling evolution with a fitness landscape that specifically discuss the dimensionality issues, and then in the same paragraph as the citation, talks about the fitness landscape as a surface in three dimensions. The only explanation I can find for his is that he really doesn't understand most of the math that he's talking about. (I don't think that Behe is above deliberately lying; but I think he's smart enough that he wouldn't cite things that contradict him so blatantly if he understood what they really said.)
Behe isn't entirely ignorant of the criticisms of the landscape arguments - he does devote some space to arguing around them. Anyone care to guess what kind of argument he uses? Anyone?
What's the favorite bullshit mathematical argument of creationist assholes worldwide? Why big numbers, of course! He starts to slap together some sloppy probabilities to argue how unlikely it is for a mutation to jump valleys in a fitness landscape. He goes through a really sloppy argument about how unlikely it is for malaria to evolve chloroquine resistance, arguing that the odds of evolved resistance are one it 1020. Now, when you realize that each person infected with Malaria has billions of malaria cells in their bodies, and that number starts to not look so scary anymore: billions of cells reproducing daily in millions of individuals, which has been going on for decades of chloroquine use, and you start to realize that that's not such a big number after all. But even so - it's a deliberately inflated number, relying on things like the monotonicity assumption, and the assumption that resistance is all-or-nothing. But even with those sleazy assumptions, that number just isn't compelling when it comes to malaria. So, he tries to take the inflated malaria number, and wave his hands around by applying it to human beings, because we reproduce so slowly compared to malaria:
If all of these huge numbers make your head spin, think of it this
way. The likelihood that Homo sapiens achieved any single mutation
of the kind required for malaria to become resistant to chloro-
quine--not the easiest mutation, to be sure, but still only a shift of two amino acids--the likelihood that such a mutation could arise just
once in the entire course of the human lineage in the past ten million
years, is minuscule--of the same order as, say, the likelihood of
you personally winning the Powerball lottery by buying a single ticket.
What's particularly astonishing about this is that even this rotten argument - taking an artifically inflated probability number based on the peculiarities of the biochemistry of one specific organism, and applying it to a completely different organism (waving hands furiously to try to distract from the fact that it's just nonsensical to cross that way), contains its own refutation. Yes, perhaps the odds of this happening are similar to the odds of winning at powerball. But the fact is someone wins the powerball lottery. He wants to pretend that it's unlikely by pointing at you specifically, and saying that it's like you winning the lottery. But in fact, the power of evolution is that it doesn't just try one thing. It's not a process of one mutation, wait and see if it works out and fixes in the population; it's not a process with a predetermined destination. It's a process of countless mutations happening at the some time - some propagate, some don't - and if any of them work, then they take over. The real chance of evolution producing something are like the chances of someone winning the lottery. The chances of them producing humanity taken a priori are like the chances of you winning the lottery; but since humanity was not a predestined result, the chances of the evolutionary sweepstakes producing something is like the chances of someone winning the lottery - i.e., virtually inevitable.
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Can you point me to a link or evidence that Behe has ever responded to Chu_Carroll's points?
Wow! Long post, John. I try to limit my time on the computer, and I was busy putting out a fire at telicthoughts.com and putting up a new post. I'll try to read your comment tomorrow. Sorry.
Not at all. I apologize for the length, but Chu-Carroll I thought was making some long points, and I didn't want to edit them/botch them myself.
BTW--I like Mike's site; even though I don't agree with all his posts, he has a great sense of humor. (I still keep a copy of his post on testing God by seeing if water will turn into wine in the lab...)
Hi John,
I wrote a reply earlier, but the time on my computer at the library ran out before I could post it, and it got sucked out of existence like a watermelon seed....sigh. So I'm at another computer, where I'll try again.
Haven't looked at Chu-Carroll's stuff, and I'm not sure if Behe has tried to answer it.
Yes, a 100 dimensional fitness landscape would provide many more alternatives than a 2 or 3 dimensional one. Still, it's finite, so there could still be dead-ends. Nevertheless, Behe's proving his point would be much more daunting, which is why proving a negative is probably impossible. Which is why I prefer Mike Gene's approach.
Nevertheless, I think Behe has provided an additional challenge to non-teleologists: Not only is IC a challenge, but showing that non-teleological evolution that requres at least two mutations has occurred in multicellular organisms.
Your example of the panda's thumb doesn't refute Behe. As you noted, it required only one mutation. And Behe emphasizes in his book and in his blog that there is contingency in biology to at least the species level.
So has Behe proved his point? No. Has he provided an additional challenge (besides IC)? Yes.
I just looked over Chu-Carroll's entry. It seems to be what you posted, verbatim. Are you Chu-Carroll? I can see why Behe wouldn't answer it. It's rather insulting and derogatory in tone. Typical blog stuff.
Oops. I see you were just quoting Chu-Carroll. Sorry about that.
Hi Bilbo,
I should've demarcated the line between my intro and Chu-Carroll's more boldly.
I'm definitely not Chu-Carroll.
:)
That said, it's easy to let tone get in the way of substance, and I think his points good.
If I understand Behe's position (and I'm not sure I do), it's this: Given the current length of natural history (3.5 billion years or so):
1) Unicellular life reproduces quickly enough that it could achieve selective changes that required 3 random mutations or less.
2) Multicellular life reproduces much more slowly, and can only achieve selective changes that only required 1 random mutation.
3) There have been changes in unicellular life that required more than 3 random mutations, and changes in multicellular life that required more than 1 random mutation.
It seems to me that it would be difficult to prove or disprove this.
If people like Chu-Carroll want someone like Behe to respond to them, common everyday manners would help. Perhaps his parents failed to teach him that.
Well, on number pt. # three Lenski has evolved in his own lab a citrate eating form of e-coli that required more than one mutation. Zimmer's take on Lenski is here.
As for the tone--I can't that worked up about it, Bilbo.
If you or Behe are going to avoid discussing substantive points because of the tone of the one making the case, I don't know what to tell you, except that, had they been put off by St. Jerome's tone (and by all accounts he was a monumental asshole to everyone he knew, including his friends), people would've stopped being Christians back in the 4th century.
On a more serious note, it's worth recalling that Behe himself admitted under oath on the stand during the Dover trial that, even by the standards of his own paper (which he co-wrote with Snopes in 2004), an irreducibly complex trait could evolve within 20,000 years.
I can see why his book influences lay people. I liked Darwin's Black Box when it first came out. But when I started querying biologist I soon realized why they didn't take it seriously.
For what it's worth. You can't learn science just by reading the pop-science books. At some point, if you want to get down to it, you need to make a few calls, bug a few researchers and hang out with them for a while.
The reason why I don't take Behe or ID seriously is I know they're counting on the fact that most of their readers won't.
Right, E-coli, unicellular organism, according to Behe, could have as many as 3 mutations. Your point?
Curious about that 20,000 year thing with IC. Do you have a reference.
I read the objections to Behe, then read Behe's responses. He seems to answer his critics adequately. Could you show me where he doesn't?
Behe isn't trying to be an apostle to the skeptics. He's trying to do science. If people want him to respond to their criticism, common good manners are in order.
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