30 August 2008

And I don't even eat mooseburgers

In case your local news hasn't picked up the story yet.

27 August 2008

A pop science book meme

Various book memes have come across my path, and they can be inspiring and interesting. Here's one I chose to pass along because it should result in the evolution of a pretty good list of recommended popular science books. (The originator calls it the "great pop-sci book project.")

If you choose to pass it on, follow the instructions and link to the source, which is Cocktail Party Physics. And thanks to Brian at Laelaps for the heads-up.

The instructions, from Cocktail Party Physics:
1. Highlight those you've read in full
2. Asterisk those you intend to read
3. Add any additional popular science books you think belong on the list
4. Link back to Cocktail Party Physics (leave links or suggested additions in the comments, if you prefer) so I can keep track of everyone's additions. Then we can compile it all into one giant "Top 100" popular science books list, with room for honorable mentions.
And here's the list:

1. Micrographia, Robert Hooke
2. The Origin of Species, Charles Darwin
3. Never at Rest, Richard Westfall
4. Surely You're Joking, Mr. Feynman, Richard Feynman
5. Tesla: Man Out of Time, Margaret Cheney
6. The Devil's Doctor, Philip Ball
7. The Making of the Atomic Bomb, Richard Rhodes
8. Lonely Hearts of the Cosmos, Dennis Overbye
9. Physics for Entertainment, Yakov Perelman
10. 1-2-3 Infinity, George Gamow
11. The Elegant Universe, Brian Greene
12. Warmth Disperses, Time Passes, Hans Christian von Bayer
13. Alice in Quantumland, Robert Gilmore
14. Where Does the Weirdness Go? David Lindley
15. A Short History of Nearly Everything, Bill Bryson
16. A Force of Nature, Richard Rhodes
17. Black Holes and Time Warps, Kip Thorne
18. A Brief History of Time, Stephen Hawking
19. Universal Foam, Sidney Perkowitz
20. Vermeer's Camera, Philip Steadman
21. The Code Book, Simon Singh
22. The Elements of Murder, John Emsley
23. *Soul Made Flesh, Carl Zimmer
24. Time's Arrow, Martin Amis
25. The Ten Most Beautiful Experiments, George Johnson
26. Einstein's Dreams, Alan Lightman
27. *Godel, Escher, Bach, Douglas Hofstadter
28. The Curious Life of Robert Hooke, Lisa Jardine
29. A Matter of Degrees, Gino Segre
30. The Physics of Star Trek, Lawrence Krauss
31. E=mc<2>, David Bodanis
32. Zero: The Biography of a Dangerous Idea, Charles Seife
33. Absolute Zero: The Conquest of Cold, Tom Shachtman
34. A Madman Dreams of Turing Machines, Janna Levin
35. Warped Passages, Lisa Randall
36. Apollo's Fire, Michael Sims
37. Flatland, Edward Abbott
38. Fermat's Last Theorem, Amir Aczel
39. Stiff, Mary Roach
40. Astroturf, M.G. Lord
41. The Periodic Table, Primo Levi
42. *Longitude, Dava Sobel
43. The First Three Minutes, Steven Weinberg
44. The Mummy Congress, Heather Pringle
45. The Accelerating Universe, Mario Livio
46. Math and the Mona Lisa, Bulent Atalay
47. This is Your Brain on Music, Daniel Levitin
48. The Executioner's Current, Richard Moran
49. Krakatoa, Simon Winchester
50. Pythagorus' Trousers, Margaret Wertheim
51. Neuromancer, William Gibson
52. The Physics of Superheroes, James Kakalios
53. The Strange Case of the Broad Street Pump, Sandra Hempel
54. Another Day in the Frontal Lobe, Katrina Firlik
55. Einstein's Clocks and Poincare's Maps, Peter Galison
56. The Demon-Haunted World, Carl Sagan [I've read parts]
57. The Blind Watchmaker, Richard Dawkins
58. *The Language Instinct, Steven Pinker
59. An Instance of the Fingerpost, Iain Pears
60. Consilience, E.O. Wilson
61. Wonderful Life, Stephen J. Gould [I've read most of it]
62. Teaching a Stone to Talk, Annie Dillard
63. Fire in the Brain, Ronald K. Siegel
64. *The Lives of a Cell, Lewis Thomas [I've read excerpts]
65. Coming of Age in the Milky Way, Timothy Ferris
66. Storm World, Chris Mooney
67. The Carbon Age, Eric Roston
68. The Black Hole Wars, Leonard Susskind
69. Copenhagen, Michael Frayn
70. From the Earth to the Moon, Jules Verne [a long, long time ago]
71. Gut Symmetries, Jeanette Winterson
72. *Chaos, James Gleick
73. Innumeracy, John Allen Paulos
74. The Physics of NASCAR, Diandra Leslie-Pelecky
75. Subtle is the Lord, Abraham Pais

Some suggestions and comments:
  • I would probably substitute The Selfish Gene or The Extended Phenotype for The Blind Watchmaker, but The Blind Watchmaker is still a fine choice.
  • Like others, I would include something by Oliver Sacks, probably The Man Who Mistook His Wife for a Hat.
  • I would ditch anything by Carl Sagan, and certainly wouldn't keep The Demon-Haunted World.
  • I wouldn't include two works by one author (e.g., Richard Rhodes) unless they were both surpassingly great.
  • Include The Song of the Dodo by David Quammen and The Beak of the Finch by Jonathan Weiner. Phantoms in the Brain by Ramachandran and Blakeslee gets honorable mention.
  • Any votes for The Fourth Day by Howard Van Till? The Double Helix by James Watson? I'm partial to What Mad Pursuit, Francis Crick's nice memoir. I haven't read Genome by Matt Ridley, but maybe one of his works belongs on the list.
Looking forward to other suggestions.

Add The Song of the Dodo, The Beak of the Finch (it won a Pulitzer, people) and The Man Who Mistook His Wife for a Hat. Delete The Demon-Haunted World.

24 August 2008

Should we expect design?

What kind of universe should one expect to see, as a Christian, or as an atheist, or whatever? Is design (conveniently defined by fellows of the Discovery Institute) something that a Christian should expect to see? That's the question I ask over at Clashing Culture, reflecting on some of the weird theological claims of some ID proponents (and of Richard Dawkins). Wander over and weigh in.

23 August 2008

Why I'm not a Behe fan, Part IIB: abusing genetics

In a previous post, I started to explain a fact that some people (who don't know me) seem to find surprising or noteworthy. Michael Behe is a Christian who accepts common ancestry and an ancient cosmos, so you'd think I would be excited about the work of a fellow "theistic evolutionist." But I'm not. Two overall problems come to mind. (Basically, I find his conduct as a scientist to be unacceptable, and I find his proposals to be laughable failures.) I'm addressing the second one here. The discussion is quite long, so I divided it into two sections, Part A and this post, Part B, which will have to be split up. I'm sorry about the length; it would really take a whole book to carefully explain how Behe has misused genetics and probability.

1. Behe's fans say that he's a nice guy, and that the evolutionists are "crucifying" him. Both claims seem to be true, but they can't hide some serious problems with his conduct as a scientist.

Those issues are the subject of the first post.

2. Some of Behe's defenders think that he has effectively answered his critics. He has not, nor has he understood or acknowledged the most important criticisms of his crude claims.

Behe's recent book The Edge of Evolution (henceforth EoE) is the focus of this series, and as I exlained in Part A:
EoE makes exactly one specific scientific claim, accompanied by simplistic genetic assumptions and supported by a "case study." The scientific claim is that the mutations that drive large-scale evolution, and that are thought to underlie all evolutionary change (past and present), are non-random. And the "case study" is a long-winded account of the adaptation of the malaria parasite in the face of drugs intended for its destruction.
Part A dealt with the laughable case study. But the heart of EoE is the claim that random mutation rates are insufficient – spectacularly insufficient – to support step-by-step evolution of complex features. The implication, then, is that the mutations that underlie major evolutionary change did not occur randomly.

First, some important points of clarification:
  • Behe is not denying that common descent is true, or that evolutionary change results from mutation. He acknowledges both. He is saying that the most important mutations – those that led to, say, new cell types – could not have been random.
  • Behe is not saying that the combination of random mutation and natural selection (the "darwinian" mechanism) is not a driving force in evolutionary change. He acknowledges the efficacy of the process in explaining "a number of important details of life," such as drug resistance in bacteria or pesticide resistance in insects, and is willing to attribute the differences between widely divergent organisms to the workings of "randomness." Specifically, he writes that "explicit design appears to reach into biology to a certain level, to the level of the vertebrate class, but not necessarily further." (p. 220) This means that Behe claims to be certain that the major distinctions between goldfish and bats are non-random, but that the major distinctions between bats and people could be accounted for by random mechanisms. (He asserts the "edge of evolution" to lie somewhere between the species level and the class level. [p. 201])
  • Behe does not commit himself to a particular mode of divine intervention whereby the supposedly non-random mutations came about, and in fact he seems to favor a front-loading scenario in which God "was able to specify from the start not only laws, but much more." (p. 231)
These clarifications are important, because much of the criticism of EoE has been botched significantly. The book is bad, really bad, but it can't be honestly characterized as an anti-evolution argument. Ultimately, Behe seeks to prove that evolution had to be guided. That's the way to understand EoE, and as Joan Roughgarden wisely noted in her review, there are some "constructive" aspects of the book, including the abandonment of opposition to – or even ambivalence about – common descent.

So what's so wrong with Behe's argument in EoE? Well, first, here's the argument summarized:
  1. Evolutionary changes in the features of organisms require changes in genomes, changes which occur by mutation.
  2. Many of the most interesting evolutionary changes require multiple changes in the same genome, often in the same gene.
  3. Mutation rates, in terms of number of mutations per generation, are known to be on the order of 1 in 100 million.
  4. Based on this mutation rate, the probability of occurrence of an evolutionary change requiring several mutations is vanishingly small, such that the whole of life's history is not nearly long enough for the change to occur via random mutation.
And here are some ways in which Behe's argument is wrong and/or misleading.

I. Behe's assumption of a particular mutation rate is both absurdly oversimplified and inappropriately extrapolated into the entire tree of life.

The basis of all of Behe's calculations is a mutation rate of 1 in 100 million. This is the estimated rate at which misspelling-type mutation occurs in each generation, averaged over the entire genome, in humans. (The number doesn't consider other types of mutation, now known to be more common than previously thought.) Behe uses this number in all of his (flawed) probability calculations. Even if we knew nothing about mutation rates, the notion of extrapolating from an human (or even mammalian) characteristic to the whole of the biosphere (past and present) is ludicrous enough that it would by itself cast doubt on the credibility of the author.

Rates and characteristics of mutation are the focus of active current research, and many important questions remain unanswered. But we know that there is no such thing as "the mutation rate," in the biosphere or even in particular species. In fact, mutation rates can vary significantly, between types of organisms, between organisms in different states of health, in individual subpopulations of organisms, even between regions of the genome of a particular organism.

More importantly, it is ridiculous to assume that "the mutation rate" has always been the same. Consider a flowchart outlining mutation and its effects, taken from a recent review of the evolution of mutation rates:

Image from "Mutation rate variation in multicellular eukaryotes: causes and consequences," by C.F. Baer et al., Nature Reviews Genetics, August 2007. Click to enlarge (opens in new window/tab).

The idea is that mutations are created in at least two ways: 1) damage to DNA from external influences such as radiation; and 2) errors in the replication process. During the evolution of early life, neither of these influences would be expected to be the same as – or even comparable to – similar influences today. And that's just the beginning of the flowchart. There are error-correction systems that erase mutations before they can be passed on to the cell's descendants; again, only a fool would suppose that these systems have been present throughout life's history; indeed, bursts of mutation that occur today are usually caused by deficiencies in DNA repair and the appearance of "mutator lines" is thought to be an accelerating force in adaptation.

My point is not that we know what the genetic landscape was like during the early evolution of life's toolkit, nor am I claiming that we know whether or not certain mutations were "nonrandom." My point is that the extrapolation of estimated mutation rates in modern humans into the deep past is clearly unjustified, a move so foolish that it can only be the product of folk science.

II. Behe's treatment of adaptation always ignores existing genetic variation, and his arguments seem to assume that multiple mutations must occur simultaneously.

I've mentioned these problems before, and they constitute some of Behe's biggest errors. When he envisions the process of adaptation, in which several genetic changes separate one state from another, he automatically assumes that none of the changes exists at the beginning. Yet even Darwin knew that populations of organisms harbor huge amounts of genetic variation, as evidenced by the profound success of domestication (of plants and animals) by human selection. Most of Behe's critics have noted this, and Behe's response was a lame dodge. But perhaps the critics haven't been clear about why superfast evolution under human selection is such a problem for his ideas. Here's why: since organisms are so profoundly diverse genetically, many of the genetic changes that could be exploited by selection already exist. In fact, current theory predicts that rapid evolution, such as that required after significant environmental change, is much more likely in populations with significant standing variation.

With his simplistic view of genetics and variation in mind, Behe then describes how an adaptation that requires two different changes will be extraordinary unlikely, because the probability of each change is one in 100 million, and the probability of each occurring together is one in 100 million times 100 million. His critics argue, correctly, that his calculations assume that the mutations must occur simultaneously, and that is indeed very improbable. (Although maybe not nearly as improbable as we used to think.) In some of the discussions in EoE, he describes sequential acquisition of mutations (e.g., p. 111), but he calculates probabilities according to simultaneous occurrence (e.g., p. 63). Jerry Coyne explains why this is a gigantic error, and Behe seems unable to understand why.

I've written a separate post about Behe's mishandling of probability. It shows that he is not someone to consult when the subject is population genetics.

III. Behe claims that huge population sizes automatically generate more evolutionary opportunity than smaller ones do. This is incorrect.

It seems so obvious. More organisms means more mutations means more beneficial mutations means more and faster evolution. It's the kind of obvious, simplistic, intuitive claim that forms the bedrock of any folk science. But it's wrong.

On the contrary, very large population sizes lead to a so-called "speed limit" on adaptation that results from competition among beneficial mutations. The phenomenon is called clonal interference and it's particularly well understood in asexual organisms such as bacteria. The basic idea has been around for decades, but measurement and modeling of the phenomenon has been increasing in the last ten years. A very recent report, the subject of an upcoming post here, showed that the beneficial mutation rate in bacteria is 1000 times higher than previously thought – and the underestimation is due entirely to clonal interference.

The effect is not limited to asexual organisms; in fact, the problem of clonal interference is thought to constitute one of the major driving forces behind the evolutionary development and maintenance of sexual reproduction. The idea is that the genetic shuffling that accompanies sexual reproduction can bring beneficial mutations together and increase the effectiveness of selection. One of the few studies to examine this experimentally led to the conclusion that clonal interference is a problem for sexual organisms, and that sex reduces the impact of clonal interference and lowers the evolutionary "speed limit." (Interestingly, the malaria parasite is partly asexual, and reproduction inside a human is completely asexual, so clonal interference is probably a very significant "speed limit" on the evolution of P. falciparum – another reason not to use malaria as a benchmark "case study" for the understanding of all of evolutionary genetics.)

In summary, I find Behe's handling of genetics in EoE to be unacceptable. He seems ignorant of basic evolutionary genetics, and is clearly content to create a folk science alternative to modern evolutionary biology. No one has proven that random mutation generated the wonders of biology, to be sure, and so I'm not saying that Behe's conclusion is known to be false. I'm saying that his attempts to establish his conclusion have failed miserably, as have his responses to his critics, and the result is that he cannot be trusted as a careful, thoughtful, knowledgeable critic of evolutionary science. EoE is folk science, nothing more.

My final post in the series will have closing comments and some ideas for how we might go about posing questions about the processes that yield biological design.

Behe botches basic probability...how likely is that?

In The Edge of Evolution, Michael Behe presents arguments against the role of random mutation in large-scale evolutionary change, using probability calculations that are so utterly mishandled that they call into question his scientific credibility and integrity. To present evolutionary genetics in this way, one must be possessed of both ignorance and arrogance (a nasty combination) and/or of the kind of compromised scientific integrity that gives rise to folk science. The issue I raise here is independent of Behe's many errors regarding the biology of genetics and adaptation. It's all about misusing probability, and it looks suspiciously like a bait-and-switch. Here is one of many places in EoE where Behe makes a very basic mistake in the presentation of probabilities:
Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose during the course of life on earth that required a cluster of mutations that was twice as complex as a CCC? (Let's call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 1020 cells to solve the evolutionary problem, we would need 1040 cells. (pp. 62-63)
What Behe is saying is this: if event A has probability a, and event B has probability b, then the probability of both events happening is a times b. But that is only true if the events must happen simultaneously. That's the only time you multiply two probabilities. And to make matters worse, Behe is confusing two very different probabilities: the probability that the event will happen in any given attempt, and the probability that it will occur at all.

Consider the following example to see how these mistakes (if that's what they are) are so tremendously misleading. Suppose I hand you a pair of dice and ask you: "What is the probability that you will roll snake eyes?" You might immediately ask: "In how many rolls?" And that is quite an important question. The probability that you will roll snake eyes on any given roll is 1/36, which is the probability of getting a 1 on the first die (1/6) times the probability that you will get a 1 on the second die. Because the two events must happen together, we multiply the probabilities of the separate events. And that probability, 1/36, is pretty small.

But what is the probability that you will get snake eyes in, say, 12 rolls? It is in considering the second question that you can begin to see how Behe went badly wrong in his arguments in EoE. When Behe reports on the likelihood of occurrence of a "double CCC," he reports its probability of occurring in a single attempt. That's what the simple multiplication assumes, and Behe knows that this is nonsense.

The real question, then, is this one: what is the likelihood that a certain event will occur given a certain number of attempts? Behe is happy to calculate probabilities based on crude estimates of certain events in a certain organism, but he never takes a whack at the only interesting question: assuming a certain mutation rate, and a certain number of effective generations, what are the probabilities involved in particular mutational trajectories that have led to adaptation? What, for that matter, is the probability of a particular pair of mutations occurring in a human gene over a certain number of generations?

Back to our example of dice rolling. Behe's suggestion that we multiply the probabilities of "independent mutations" assumes that the two mutations occur simultaneously. Using his assumption of 1 in 100 million (108) as the probability of occurrence of a given point mutation, then we would conclude that the probability of a double mutant is 108 times 108, or 1016. But how many attempts do we get? It matters a lot. If you have 12 tries to get snake eyes, your odds improve dramatically – the probability is now 0.29. Not bad, but things get even better when we correct Behe's other colossal error, which was assuming that the mutations must happen at the same time in the same organism. We know that's not true – even Behe knows that's not true (p. 111). This makes the game entirely different. Now I give you the dice and say, "How many rolls do you think it will take till you have a 1 on each die? The 1's don't have to appear together." Well, I did the calculations for one example scenario:
  • You're trying to get two 1's, either together or sequentially.
  • You get 6 rolls, if necessary, to get the first 1.
  • After you get a 1, you get 6 rolls (if necessary) of the remaining die to get the second 1.
The probability that you will get snake eyes in this scenario is 0.60, and note that 12 is the maximum number of rolls here; many of the successes come in far fewer attempts.

It's hard for me to understand why Behe is so careless with such an important aspect of his argument. His whole case depends on probability, and yet the two weakest aspects of his story are his ludicrous extrapolations and his mishandling of probability. Perhaps he's just not a very careful thinker. Or perhaps we're seeing a sophisticated version of old-fashioned folk science, which typically depends on the kind of obfuscation that the EoE bait-and-switch suggests.

16 August 2008

Does religion deserve respect from atheists?

Check out a renewed discussion of PZ Myers' Crackergate stunt and the concept of showing respect for religion, over at Clashing Culture. Mike makes an interesting point about "respect" for Muhammad and Islam in the context of outrage over the desecration of a Eucharistic host, and I've responded with some scenarios aimed at distinguishing respect for religion from respect for other people. Please chime in!

12 August 2008

First blogiversary for Quintessence of Dust

Actually, my first post went up 3 August 2007, a little more than a year ago, but my first real article wasn't posted till 19 August, so I guess today is as good a day as any to celebrate. It's been a fun year, coinciding with my sabbatical, which ends [sniff] in 3 weeks. Once I'm back in my professor routine, I expect that my posting will be less erratic, especially since I requested a new office that's a bit removed from the beaten track. We'll see.

Thanks to all for reading and commenting. (I think I'll do better at responding to comments when my schedule calms down.) I'm especially thankful to Steve Martin at An Evangelical Dialogue on Evolution for being the first to find me and welcome me to the blogosphere. John Farrell was an early encouragement, and Panda's Thumb linked to one of my first journal club articles. The high point was the teosinte article, which was linked at ERV, Pharyngula and PT and which was honored with a place in The Open Laboratory 2007. The blog has about 240 subscribers and gets roughly 100 hits a day. Room to grow, but it's nice to have enthusiastic readers.

To Mike Beidler: thanks for the compliment; it's my favorite link in the one-year life of the project. To Gordon Glover: keep up the fantastic work; your book is a precious gift.

Here's to Year 2 of Quintessence of Dust. More journal clubs, more developmental biology, a little less bitching about lame creationist claptrap. Or your money back.

11 August 2008

Why I'm not a Behe fan, Part IIA: the malaria scam

In my previous post, I started to explain a fact that some people (who don't know me) seem to find surprising or noteworthy. Michael Behe is a Christian who accepts common ancestry and an ancient cosmos, so you'd think I would be excited about the work of a fellow "theistic evolutionist." But I'm not. Two overall problems come to mind. (Basically, I find his conduct as a scientist to be unacceptable, and I find his proposals to be laughable failures.) I'm addressing the second one here. The discussion is quite long, so I'm dividing it into two parts, A and B.

1. Behe's fans say that he's a nice guy, and that the evolutionists are "crucifying" him. Both claims seem to be true, but they can't hide some serious problems with his conduct as a scientist. First, he showed contempt for his (former) colleagues when he avoided the process of peer review. Second, his comment-free blog is lamentably characterized by misleading and disingenuous "responses" to criticism that look to be calculated attempts to protect what is nothing more than folk science.

Those issues are the subject of the first post.

2. Some of Behe's defenders think that he has effectively answered his critics. He has not, nor has he understood or acknowledged the most important criticisms of his crude claims.

There's something interesting about the ID community's response to Jerry Coyne's review of The Edge of Evolution (henceforth EoE). Thomas Cudworth referred to it as "nasty" and Behe dismissed it as just so much ad hominem and "question-begging." Meanwhile, Bilbo (regular commenter here and contributor at Telic Thoughts) thinks that Behe is "carrying the day" on his comment-free Amazon blog.com, where he has responded to critiques by Ken Miller, Richard Dawkins, Sean Carroll and others.

Well, in fact the review is a piece of crap, as is much of what Jerry Coyne has produced lately. (He's an equal opportunity thug, attacking his scientific colleagues with the same lack of grace and intelligence that he displayed in his recent diatribe against faith.) The piece represents at best a missed opportunity (to address Behe's claims in detail for a lay audience) and at worst a windfall for Behe and the ID movement, focused as they are on convincing the public that they are a persecuted scholarly minority. I'm not the only one who was horrified by Coyne's brainless screed; Jason Rosenhouse blasted it for all the same reasons.

As Rosenhouse predicted, the shoddy nature of Coyne's review enabled Behe to avoid a full-scale defense of his folk science. Behe has never bothered to rigorously justify his claims, and has never carefully engaged existing evolutionary data or theory, so Coyne's shallow account gave him a perfect opportunity to continue to pretend that his ideas can withstand real scientific scrutiny. And so we have ID propagandists whining about Behe's mistreatment, and laypersons reading ID blogs and concluding that EoE has sounded an unanswered challenge to evolutionary theory. It's a boon for ID.

The truth is that Jerry Coyne did identify the errors in the book. EoE makes exactly one specific scientific claim, accompanied by simplistic genetic assumptions and supported by a "case study." The scientific claim is that the mutations that drive large-scale evolution, and that are thought to underlie all evolutionary change (past and present), are non-random. And the "case study" is a long-winded account of the adaptation of the malaria parasite in the face of drugs intended for its destruction. Coyne's review addresses both, and Behe's responses failed to defend either.

The scientific claim is unsupported, and all available evidence contradicts it. And the "case study" is laughably misused in a ploy that a high school sophomore could see through. Let's look at the malaria ploy first, then examine Behe's central scientific claim and its implications in the second half of this article (part B, to be posted later this week).

EoE is actually a very small book, with very little to say. Most of the book is devoted to a recounting of the biology of the malaria parasite, Plasmodium falciparum, and the "trench warfare" between the parasite and its host, Homo sapiens. The outcome of the struggle between the parasite and its host has provided a useful case study of evolutionary change, and specifically of the power of natural selection. Behe grants this readily; indeed, he concludes that random mutation and natural selection can account for the divergence of organisms at the species level (at least). In other words, Behe does not deny the reality of common descent, and acknowledges some role in evolution for natural selection acting on random mutation. (He uses the divergence of dog breeds as an example of what random mutation & selection can do (p. 200), leaving one to wonder why Richard Dawkins chose dogs as an example of why Behe is wrong. I'm guessing Dawkins didn't read the book too carefully, what with all his important work as a scholar.) But Behe's reasoning is stunningly dumb. It goes like this.
  • In the fifty years since antimalarial drugs were brought to bear on P. falciparum, more than 1020 (that's 10 to the 20th power, if the superscript isn't working) of the parasites have been born.
  • In that time, the parasite has adapted to the drugs, through selection acting on random genetic variation, but hasn't developed any completely new proteins or biochemical functions.
  • This means that the Darwinian process is unable to generate significant novelty in fewer than 1020 tries.
That's the argument. And Behe uses it to identify the "edge of evolution."

Now, I hope it's already clear to most readers why the argument is spectacularly bad, but here are some comments.
  • Most basically, it should be obvious that demonstrating the failure of X to happen in one particular situation is hardly proof that X cannot happen. To extrapolate from a single negative observation (even if it were representative of the scenario in question) to the blanket impossibility of the phenomenon is a foolish mistake.
  • More specifically, it should be obvious that we need not expect dramatic new functions to appear during adaptation, since we need not even expect adaptation to occur at all. If functional innovation were as inevitable as adaptation, the dinosaurs would not merely have survived, they would have mastered apparation in additional to intergalactic travel (and world peace). Behe wants you to believe that evolutionary biologists expect dramatic evolutionary innovation to occur, at the level of molecular machinery, whenever selection is applied to a population. That's nonsense, and I think he must know that.
  • It is important to keep in mind that Behe solidly affirms common ancestry, and knows that mutations account for the differences between lineages. This means that he acknowledges the existence of a continuous genetic tree of life, which means that he should be able to formulate scientifically credible approaches to his hypothesis. Pointing to the lack of innovation in one special (parasitic) scenario is hardly a substitute for a direct examination of the myriad exemplars of evolutionary novelty. In other words, the way to determine whether gigantic population sizes are needed for the stepwise generation of novel functions via random mutation is to: a) identify examples of such evolutionary innovations and to work on elucidating the genetic trajectories that could have led to their development; then b) work on determining the population sizes, mutation frequencies, and other parameters that apply to the trajectory. (I like to call this "science.")
The questions that I have after reading EoE (besides the disturbing question raised also by Dennis in a comment here) are these: does Mike Behe really think that evolutionary biologists expect P. falciparum to develop new molecular machines while adapting to antimalarial drug assault? Does he really think that the struggle between a primate and one of its parasites is a model for the generation of evolutionary novelty, of whole gene families whose origins often predate the Cambrian? Does he really believe that the failure of P. falciparum to give rise to a magic drug-dodging charm, or a microscopic invisibility cloak, is an argument against random mutation and natural selection in the evolution of biological novelty?

Probably not. He has another really bad idea: that random mutation doesn't provide enough variation for natural selection to generate novelty. And the mistakes are typical for him: sloppy (or non-existent) examination of the facts, and wild extrapolation from those he carefully selects. Part IIB will look at the rest of the mess.

06 August 2008

Why I'm not a Behe fan, Part I

Michael Behe's name has come up around here a lot lately. During the lovefest over on Uncommon Descent, they mentioned him both as a scientist and as a Martyr, and here on QoD, a regular commenter named Bilbo has mentioned Behe a few times, noting that he finds Behe's argument in The Edge of Evolution compelling. Michael Behe is a Christian who accepts common ancestry and an ancient cosmos, so you'd think I would be excited about the work of a fellow "theistic evolutionist." But I'm not. There are two issues I'd like to address here, both raised in the UD discussion or by Bilbo or both. I'll tackle them in two separate posts.

1. Behe's fans say that he's a nice guy, and that the evolutionists are "crucifying" him. Both claims seem to be true, but they can't hide some serious problems with his conduct as a scientist. First, he showed contempt for his (former) colleagues when he avoided the process of peer review. Second, his comment-free blog is lamentably characterized by misleading and disingenuous "responses" to criticism that look to be calculated attempts to protect what is nothing more than folk science.

a. Behe exudes an arrogant contempt for the scientific community, exemplified by his neglect of peer review.

Michael Behe, I'm told, is quite a decent gentleman. I don't doubt this at all. He even seems to be a smart gentleman, and I gather that he's a gifted teacher based on his excellent writing. He doesn't tend to directly attack other people (though he can be pretty obnoxious), and he seems uninterested (in general) in Culture War. He doesn't deserve to be mocked, and I think he was treated somewhat unfairly by many critics of ID after the run-in with Abbie Smith at ERV. Mike Behe, it seems to me, is worthy of far more respect than are many of his fellow ID proponents.

But I have written before that Behe is properly an object of scorn in evolutionary biology. What I mean is that while I don't think he should be ridiculed or taunted, I do think he is mostly unworthy of professional scientific respect. Mike Behe has shown contempt for the scientific community in his writing on evolution, especially in The Edge of Evolution. This stance has quite appropriately alienated him from science and led scientists in relevant fields to view him, rightly, with suspicion and to dismiss him as ignorant and/or disingenuous. Behe has excused himself from the company of those who seriously study evolutionary science, and has done this by approaching the complex and fascinating analysis of evolutionary genetics with a malignant combination of arrogant condescension and pitiful ignorance. (Or, alternatively, his integrity has been somehow compromised.) You see, it actually doesn't matter how you couch your words when the message to an entire field of science (about which you know relatively little) is: "Hey, guys, give it up; I just figgered the whole thing out." In fact, in my opinion, there's something pretty creepy about a bland smile on the face of an undistinguished biochemist who claims to have overturned a century of work by some of the best minds in the history of biology.

There is only one new scientific idea in TEoE: Behe claims that random mutation rates are insufficient to generate the genetic diversity that is necessary for evolutionary change. That's it. That is an empirical claim, one that leads to some clear predictions. The claim is, at least in principle, testable. It's not theology, it's not metaphysics, and it doesn't have anything specific to do with "complexity" or any other doctrine of Intelligent Design. Behe's hypothesis, that random mutation cannot drive evolutionary change, is a scientific hypothesis of significant import that should have been carefully constructed and vetted by the professional scientific community. But as near as I can tell, the claim was never subjected to peer review. As far as I know, Behe has not completely formulated his hypothesis (by, for example, analyzing actual measurements of genetic variation in living organisms), and has not attempted to publish it in the professional literature or even to present it to a gathering of scientific experts. Instead, he wrote a popular book, aimed at a lay audience. His ideas are, in fact, almost completely without merit, but even if his radical hypothesis were worthy of scientific consideration, his choice to abandon the scientific community – and to eschew even the most basic review of his proposals by known experts – is an expression of arrogance and contempt that is difficult to overstate.

Richard Dawkins' New York Times review of The Edge of Evolution is pretty crappy; it's really not a review at all, and the hysterical Culture Warriors at the Discovery Intitute are right about that much. But one of Dawkins' final comments on the book summarizes why it is not a worthy contribution to science and why its author deserves to be dismissed as a critic of evolution:
If correct, Behe’s calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation. Single-handedly, Behe is taking on Ronald Fisher, Sewall Wright, J. B. S. Haldane, Theodosius Dobzhansky, Richard Lewontin, John Maynard Smith and hundreds of their talented co-workers and intellectual descendants. Notwithstanding the inconvenient existence of dogs, cabbages and pouter pigeons, the entire corpus of mathematical genetics, from 1930 to today, is flat wrong. Michael Behe, the disowned biochemist of Lehigh University, is the only one who has done his sums right. You think?
If you don't find the preceding to be a devastatingly damning criticism of Behe's project, then you either don't understand what those scientists actually did (and you're in good company), or you actually do believe that Michael Behe is the architect of the most cataclysmic scientific paradigm shift since Copernicus. The point is that a person (like me) who knows some evolutionary genetics is left with a more difficult choice: whether to believe that Behe is really that ignorant and arrogant, or to believe that he lacks a full commitment to scientific integrity. While considering those options, one tends not to dwell so much on etiquette and gentility.

b. I find many of Behe's responses to his critics to be suspiciously misleading, and I believe this provides a clue as to why he does not allow comments on his blog or participate in professional discussion of his proposals.
  • When challenged by Richard Dawkins on his failure to have his hypothesis subjected to peer review, he redirected the discussion to a consideration of his publication record in general, and compared it to Dawkins' nonexistent contributions.
  • Confronted with the reality of superfast evolution of domesticated organisms, he redirected the discussion to an irrelevant (but technical-sounding) consideration of "developmental plasticity."
  • He mocked Sean Carroll's accurate claim that Behe's ideas (and errors) involve technically-challenging concepts and theories, obnoxiously implying that it is Carroll who is hiding indefensible claims behind difficult math and biology.
  • Confronted with evidence that, at least in bacteria, beneficial mutation rates are a thousand times more likely than previously thought, he redirected the discussion to the irrelevant consideration of whether many or most beneficial mutations "break things" or not, and concluded (based on no evidence at all) that the report in question most likely involves "degradatory mutations."
Behe's critics make many mistakes. But his responses are indicative of a defender of folk science, not of a serious scientist in a rigorous debate.

In part II, I'll deal with the second issue raised by Behe's admirers:

2. Some of Behe's defenders think that he has effectively answered his critics. He has not, nor has he understood or acknowledged the most important criticisms of his crude claims.