Richard B. Hoppe posted Entry 3184 on June 13, 2007 07:40 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/3173

The iconic image of the Kitzmiller v. Dover trial in Pennsylvania was Michael Behe sitting on the witness stand, a pile of papers and book chapters on the evolution of the vertebrate immune system on his lap, steadfastly denying the existence of research on the evolution of the vertebrate immune system. In his new book, The Edge of Evolution, Behe continues his practiced denial, minimizing or ignoring a pile of research in order to maintain his claim that evolution can’t produce this or that biological structure because it is “irreducibly complex”. While I didn’t get a review copy, I know a friendly bookstore owner who encourages customers to read in the store.

I will leave it to others to evaluate Behe’s claims about the various specific biological systems (and many have: see Science after Sunclipse for a complete listing). I will return to a piece of research that demonstrates that Behe’s conception of how evolutionary processes produce complicated structures is amazingly over-simplified and empirically false, and that his conception of what evolutionary processes are capable of is pure caricature.

Mark Chu-Carroll has already dissected Behe’s misuse of probability and his utter ignorance of the properties of high-dimensioned and plastic fitness landscapes and ERV nicely illustrates the point. As Nick Matzke has remarked,

My first take is that The Edge of Evolution is basically an incompetent attempt to provide a biological foundation for the silly assumptions that were made in Behe and Snoke’s (2004) mathematical modeling paper in Protein Science.

Mark analyzed Behe’s argument from teeny-weeny numbers, showing that it is based on fundamentally flawed assumptions about the topography of fitness landscapes and the supposed inability of evolving populations to escape from local maxima. I’ll show that Mark’s analysis has empirical corroboration – Behe’s probability model generates wholly absurd results. In addition, I’ll describe data, some of it from new analyses, that flatly contradict Behe’s claims about what evolutionary mechanisms allegedly cannot do. To put it in the most direct terms possible, Behe is either ignorant or actively ignores evidence that contradicts his fundamental assumption about what evolutionary mechanisms can do. I’ll show that in addition to producing entities that are irreducibly complex by Behe’s original Darwin’s Black Box definition, computer models of evolution also produce those entities via evolutionary pathways that are irreducibly complex by Behe’s second so-called “evolutionary” definition, pathways that contain multiple unselected mutational steps. Neutrality lives! Then I’ll make a few remarks on Behe’s probability calculations in the light of computer evolutionary simulation runs, and make a few remarks on Behe’s notion of fitness landscapes.

More below the fold.

The research to which I return is Lenski, et al.‘s The Evolutionary Origin of Complex Features, the 2003 Nature paper that used Avida, an evolutionary simulator, to show the evolution of IC structures. I have previously written on that research (see here for one post). In that previous post I described how the Avida research showed that structures that meet Behe’s first definition of “irreducible complexity” evolve by standard Darwinian mechanisms – random mutations and selection. In the course of an interminable thread on Internet Infidels I did some additional analyses of the Lenski, et al., data to show that evolution can produce structures via pathways that are IC by Behe’s second definition.

I. Evolving irreducibly complex structures

Behe’s original definition of irreducible complexity in Darwin’s Black Box defined IC in terms of the structure of the object under analysis:

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning. (Darwin’s Black Box, 39)

That implies a simple operational procedure to determine whether a structure is IC: Do knockout experiments. Knock out components one by one and determine whether the structure retains its function. By that operational criterion, the evolution of Avida critters capable of performing EQU produced IC structures. See here for the results of Lenski, et al.‘s knockout analysis. Case closed on that version of IC.

II. Evolving irreducibly complex structures via irreducibly complex pathways

Following DBB, Behe later offered a second, “evolutionary” definition of irreducible complexity:

An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway. (p. 17)

Behe & Snoke’s 2004 Protein Science paper was an attempt to show that the time and population sizes required to produce structures via irreducibly complex evolutionary pathways are prohibitively huge. See here for a rebuttal.

The operational definition of an irreducibly complex evolutionary pathway is simple in principle: determine the “necessary-but-unselected” mutational steps in an evolutionary history and count them. Unfortunately, in biological systems we typically don’t know the actual evolutionary history nor the nature of the selective environments through that history at the level of detail necessary to determine whether a given mutation was selectively neutral or deleterious when it first occurred and hence was unselected. However, in the Avida evolutionary simulator it’s easy to do that: the selective environment is controlled by the experimenter and the complete evolutionary history of a lineage can be dumped to disk for analyses. In fact, Lenski, et al. made available the evolutionary history of one of the lineages that evolved to perform EQU and that was IC by the first definition. Since the knockout procedure tells us which instructions in the first EQU-performing critter were necessary, we can trace back every one of them through the evolutionary history to determine whether they were selected when they first occurred. The saved evolutionary history includes the fitness value of the critter associated with each mutational step. Hence one can classify every instruction in the final IC structure according to whether on its first appearance it was beneficial, neutral, or deleterious.

In the case study lineage there were 111 mutational steps leading to the first critter capable of performing EQU. That critter had a genome of 60 instructions. Of those 60 instructions, 28 were necessary to perform EQU. I traced back all of those 28 instructions in the evolutionary history of that critter, determining for each mutation whether on its first appearance it was selectively beneficial, neutral, or deleterious. Of the 28 essential instructions, 7 produced by insertion or substitution mutations were either neutral (6) or deleterious (1) on their first appearance. (It’s also noteworthy that three other EQU IC instructions were part of the original Ancestor’s replication code that acquired an additional role in performing EQU. Two simultaneously retained their original role in replication – knocking them out abolished both replication and EQU – but one was no longer used in replication but only in EQU, a nice example of change of function through evolution. Behe, of course, studiously ignores changes of function.)

III. How does Behe address Lenski, et al.? He doesn’t.

And how does Behe’s book actually address the Lenski, et al., paper? Behe’s initial 2003 reaction to the paper, quoted in the PT critique of Behe & Snoke, was

“There’s precious little real biology in this project,” Mr. Behe said. For example, he said, the results might be more persuasive if the simulations had operated on genetic sequences rather than fictitious computer programs.

This from a man whose iconic metaphor is a mousetrap, and who in Behe & Snoke constructed a computer model that eliminated virtually all evolutionary mechanisms and then imagined that he was testing an evolutionary hypothesis! In The Edge of Evolution Behe again declines to address the substance and specifics of the Lenski, et al. study, but instead focuses on an irrelevant side issue. In Appendix D he refers to the Avida experiments without describing them. Rather, he focuses on just one property of the simulation. In the Lenski, et al., study, genome length was rendered selectively neutral by apportioning computer cycles in proportion to length. The effect of that is to make genome length invisible to selection. Describing that, Behe wrote

Let’s look at just one example to illustrate the point. In Avida, acquiring new abilities is only one way for an organism to get computer food. Another way is by simply acquiring surplus instructions, whether or not they do anything. In fact, instructions that aren’t ever executed—making them utterly useless for performing tasks – are beneficial in Avida because they provide additional food without requiring any additional consumption. It’s survival of the fattest! (p. 276; italics original)

But it’s false that “instructions that aren’t ever executed … are beneficial“. They’re selectively neutral. Either Behe didn’t read the paper or he didn’t understand it or he consciously misrepresents it. Adding instructions does increase “food” consumption – it requires cycles to reproduce the added instructions. Hence, apportioning computer cycles in proportion to genome length neutralizes length.

Now it’s still worth asking whether making genome length selectively neutral invalidates the simulation. Several lines of research are relevant. Genomes in biological critters vary enormously in length. For example, in animals the C-values (on present data) vary by 5 orders of magnitude. In Archea and Bacteria the number of protein-coding genes varies by at least an order of magnitude. The major metabolic cost of DNA apparently lies in its expression – transcription and translation – and not in its reproduction during cell division. Added DNA that is not expressed is apparently not strongly selected against; the metabolic cost of replicating DNA during cell division appears to be down in the noise in a cell’s energy budget. Corroboration comes from the persistence of pseudogenes and other non-coding DNA in genomes. Their ubiquity argues against strong selective pressures to slim down the genome. Also note T. Ryan Gregory’s remark here:

I make this statement because there are several different sorts of DNA sequences in the genome whose presence can be explained even if they do not benefit (and indeed, even if they slightly harm) the organism carrying them. Pseudogenes, satellite DNA, transposable elements (45% of our genome), and other non-coding sequences may or may not be functional – that requires evidence – and some may exist as a result of accidental duplication or even due to selection at the level of the elements themselves (by “intragenomic selection”). The old assumption that all non-coding DNA must be beneficial to the organism or it would have been deleted by now ignores genome-specific processes by which non-coding DNA evolves.

As a consequence, Behe’s claim that

It’s also very unrealistic. Biological organisms show the opposite behavior—genes that are useless in the real world are not rewarded; the genes are rapidly lost or degraded by mutation.

is false. Degraded, yes, but “rapidly lost” in the sense of disappearing altogether? The data argue that’s not the case. So rendering genome length selectively neutral is not a disabling flaw in the Avida work, and the results stand as refutations of Behe’s claims.

IV. Calculating Behe’s probabilities for an Avida run

One can use Behe’s probability model in Chapter 3, “The Mathematical Limits of Darwinism” to analyze the Lenski, et al. data. Behe treats the initial appearance of components of a structure as statistically independent and calculates the probability of occurrence of the necessary mutations as the product of the probabilities of occurrence of each mutation individually:

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. (italics added; p. 62-63)

So for Behe it’s simple: Multiple the probabilities of the (allegedly) independent events to get the probability of the joint event. Let’s do that for the Avida case study lineage. Again, seven of the mutations that produced components of the final irreducibly complex structure were unselected when they first appeared.

There are 26 instructions in the Avida instruction set, so the probability of any given instruction occurring via a random insertion or substitution mutation is 1/25. On average the genome of the lineage that produced the first critter to perform EQU had fewer than 60 instructions through the course of most of its history – it started at 50 instructions in the Ancestor, increased to 61 instructions by step 92, and then shrank back to 60 at step 111 when the EQU-performing critter appeared. Call it an average of 55 instructions. Since sequence is important in the Avida genome – it is after all an opcode program – the probability that a given mutation will appear via insertion or substitution in a given position is then about 1/55 * 1/25, or 0.000727. On Behe’s assumptions (mainly independence), the probability that the seven specific unselected mutations would occur in the specific positions in which they did is 0.0007277, or 1.076x10-22.

Now, 1.076x10-22 is a pretty small probability, but it gets worse. Critters capable of performing EQU evolved in 23 of the 50 runs in Lenski, et al.‘s main experiment. If the other 22 lineages were comparable to the case study run (and there’s no reason to suppose they weren’t), then the joint probability of all 23 runs evolving via pathways including seven unselected mutations is (1.076x10-22)23, or a number so small (on the order of 10-506) that Excel calls it zero. Excel poops out at (1.076x10-22),14. Clearly it couldn’t have happened.

Of course, that’s a ridiculous set of numbers, since the probability calculations do not veridically map the phenomena. Behe’s calculations are directly parallel to those of young-earth creationist Henry Morris in his 1974 Scientific Creationism and they are equally ludicrous. Unfortunately for Behe, they are informative only about the ignorance of the person doing the calculating. They ignore the role of neutral mutations in making multiple potential evolutionary pathways available and the probability amplification of cumulative selection – see Jerry Coyne’s review and ths recent Nature brief review of the reconstruction of selectable pathways in molecular evolution. Of particular interest in the latter review is a description of one study in which 120 potential evolutionary pathways from a precursor to a ‘final’ structure were identified. Of the 120 potential pathways, 18 were composed of selectable steps all the way. Now, if one picked out one of the pathways with unselectable steps, one could marvel at how an intelligent designer was necessary to bridge the gaps. On the other hand, if one knows there are pathways in which all steps are selectable, no designer is necessary. Behe consistently picks out just one path and marvels at the gaps.

V. The topography of fitness landscapes

As noted above, Mark Chu-Carroll analyzed Behe’s argument from teeny-weeny numbers, showing that it is based on fundamentally flawed assumptions about the topography of fitness landscapes and the notion that evolving populations cannot escape from local maxima. Mark and ERV have already done the heavy lifting on the fitness landscape issue. My remarks corroborate theirs.

That 25% of the mutational steps in the Lenski, et al. case study lineage were unselected when they occurred is consistent with the dispersal of populations along selectively nearly-equal ‘ridges’ in fitness space. Those ridges enable subpopulations to escape apparent local maxima, especially in high-dimensioned genotype spaces where ‘local’ maxima are maxima only in a subset of the dimensions. That’s an empirical demonstration of Gavrilets’ argument that the topography of fitness landscapes in high-dimensioned spaces is akin to a highly interconnected network with genotypes connected by traversable ‘ridges’ of nearly-equal fitness, rather than like a one- or two-dimension surface with inescapable local maxima as in Behe’s conception. As John Wilkins described it,

Gavrilets uses a different metaphor, and I must point out that it is indeed a metaphor not a model, of a holey landscape, in which there is a high region of fitness in the landscape, interspersed with regions of low fitness (see figure). In the high fitness region, a random walk can take you all over the place. Of course, one thing Gavrilets insists upon is the high dimensionality of the space of fitness combinations - the 2-dimensional space here is a necessary limitation of paper.

Put differently, high-dimensioned fitness spaces are like Swiss cheese, with the (relatively) high fitness cheese surrounding local low-fitness ‘holes’. Behe actually used a figure from Gavrilets’ book, but as Mark Chu-Carroll pointed out, Behe confines his consideration to low-dimensioned spaces. Even worse, Behe footnotes Gavrilets’ book in his discussion of rugged fitness landscapes, but completely ignores Gavrilets’ main argument! Thus while Behe is demonstrably aware of Gavrilets’ work (after all, he uses Gavrilets’ figure), he ignores Gavrilets’ analysis. Maybe he just looked at the pictures.

VI. From dogs to cats?

Finally, I can’t resist quoting from a radio interview Behe recently gave plugging his book. On Michael Medved’s program there was this interchange at about 23:30:

Medved: “What you’re talking about really is the leaps, aren’t you. I mean the kind of random mutations, or allegedly random mutations, who (sic) create a new species.”

Behe: “Yeah, well I wouldn’t call it species. I’d go a little higher, maybe genus or something in biology. Biology has a number of levels and you might be able to get, say, from a wolf to a dog using random mutation and natural selection. But I don’t think you can get from a dog to a cat or a precursor organism and get from a dog to a cat or certainly to an elephant.”

That’s pure creationist drivel. I half expected Behe to start telling us about how all those kinds fit on the ark.

VII. Take-home summary

Behe studiously ignores contradictory data, is ignorant of relevant properties of fitness landscapes, misrepresents evolutionary processes and research, and misuses probabilities in exactly the fashion of young-earth creationists. His book is an extended sham and will appeal only to a pre-committed and biologically ignorant audience. It’s a damn shame that its appeal depends on such egregiously poor scholarship, flat ignorance, and apparently purposeful misrepresentations.

RBH

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Comment #183069

Posted by Roy on June 13, 2007 6:02 PM (e)

Nice work.

(And I don’t mean travail)

Comment #183070

Posted by SteveF on June 13, 2007 6:04 PM (e)

Cue Lee Merrill (IIDB members will understand this reference)

Comment #183071

Posted by CJO on June 13, 2007 6:13 PM (e)

Behe studiously ignores contradictory data, is ignorant of relevant properties of fitness landscapes, misrepresents evolutionary processes and research, and misuses probabilities in exactly the fashion of young-earth creationists. His book is an extended sham and will appeal only to a pre-committed and biologically ignorant audience. It’s a damn shame that its appeal depends on such egregiously poor scholarship, flat ignorance, and apparently purposeful misrepresentations.

Give the guy a break. He writes about ID. How would you even know, if he didn’t do all that stuff?

Comment #183074

Posted by Flint on June 13, 2007 7:08 PM (e)

On another site, someone has already attempted to mock my efforts to explain how evolution works, by saying “Here a real biologist has disproved evolution using actual, verifiable experimental evidence. He’s a full professor. What are YOU?” I’ve showed this guy Coyne’s review, and the one in Science, and a couple others. Which only “proves” that the Establishment conspiracy has been caught with their pants down, and is desperate to attack the person because they can’t contest his DATA!

This is all they know, and all they need to know. I doubt the comments I’ve seen about Behe undermining the DI by conceding common ancestry and the like are very much on target. Nobody reads the book, nobody understands the science. Behe’s latest book, in at least this one instance, is presented as incontrovertible, and I’m asked either to admit I’m wrong, or show that I can’t admit error. Behe has found a career-quality schtick for Lying For Jesus. In the larger battle, neither Behe nor any of his reviewers has changed a single mind that I can find.

Comment #183095

Posted by JohnK on June 13, 2007 11:52 PM (e)

Michael Behe, 2007:
“Yeah, well I wouldn’t call it species. I’d go a little higher, maybe genus or something in biology…. I don’t think you can get from a dog to a cat…”

Henry Morris, That You Might Believe, pp. 48,49, 1946:
“…the Bible does not teach the fixity of species or even genera in some instances,… Thus, it is probable that the original Genesis “kind” is closely akin to what the modern systematist calls a “family” (dogs, cats, horses, etc.).”

Modern creationism anticipates another 60 wonderful years.

Comment #183096

Posted by SWT on June 13, 2007 11:56 PM (e)

Flint wrote:

On another site, someone has already attempted to mock my efforts to explain how evolution works, by saying “Here a real biologist has disproved evolution using actual, verifiable experimental evidence. He’s a full professor. What are YOU?” I’ve showed this guy Coyne’s review, and the one in Science, and a couple others. Which only “proves” that the Establishment conspiracy has been caught with their pants down, and is desperate to attack the person because they can’t contest his DATA!

Actually, Behe is not a biologist. His BS is in chemistry, his PhD is is biochemistry, his postdoctoral work at NIH was on DNA structure. He moved on to be an assistant professor of chemistry at Queens College in NYC, then moved on to Lehigh, where he a professor of biochemistry.

(All this is from Wikipedia, except for a quick peek at his page at Lehigh which shows him to be a professor of biochemistry.)

Comment #183097

Posted by Douglas Watts on June 14, 2007 12:01 AM (e)

I’m more of a geologist than a molecular biochemist, but the analogy Behe is trying to use is straight from late 18th century geology, ie. uniformitarianism vs. catastrophism. He’s 200 years too late and at least in 1800 there was not much data to constrain the speculative hypotheses.

Comment #183101

Posted by Torbjörn Larsson, OM on June 14, 2007 12:18 AM (e)

Congratulations, it was a long time time since I’ve seen the creationists mismodeling turned around in terms of concrete predictions from them. More the joy, since Behe apparently has used mathematical models himself and can’t pretend the methodology is inapplicable.

Richard B. Hoppe wrote:

Maybe he just looked at the pictures.

I bet he did, since pictures are irreducible complex (because omitting a point divides any line into two :-) and thus can’t lie for him. While words in english can be reordered, or in english words can be reordered, or reordered words can in english be, or words reordered in english can be (at least Yoda seems to think so), which must give him an uneasy feeling of variation and selection.

Comment #183114

Posted by Nigel Depledge on June 14, 2007 6:39 AM (e)

SWT wrote:

Actually, Behe is not a biologist. His BS is in chemistry, his PhD is is biochemistry, his postdoctoral work at NIH was on DNA structure. He moved on to be an assistant professor of chemistry at Queens College in NYC, then moved on to Lehigh, where he a professor of biochemistry

Well, when I was taking my BSc in Biochemistry with Chemistry, the faculty insisted that I also had to take at least some physiology. Heck, I even took some real biology too (a module in Population Genetics). So there’s no excuse for a biochemist to not know at least some biology.

What particularly gets my goat about Behe is that biochemistry (his area of expertise, allegedly) is overflowing with evidence that supports evolution. All you have to do is line up the sequences of the same protein from ten different organisms to see it.

I get that he accepts (or has at least given up arguing against) common descent and natural selection, but as someone with some alleged knowledge of biochemistry and chemistry, he should be aware of the mechanisms that create mutation. Thus, he should also be aware that they are not regarded by biologists and biochemists as random (in the sense of having equal probability).

Comment #183115

Posted by Richard Wein on June 14, 2007 6:43 AM (e)

I have a question for those who’ve read The Edge of Evolution. How does Behe now define IC? Does he even give (or cite) a specific definition?

Comment #183118

Posted by SWT on June 14, 2007 7:55 AM (e)

Nigel Depledge –

My comment was focused more on the claim Flint quoted about Behe being a “real biologist.” He’s not a real biologist, although as a biochemist, he should still know better.

Comment #183119

Posted by Jon Fleming on June 14, 2007 8:09 AM (e)

SteveF wrote:

Cue Lee Merrill

Yup, I figure he’s gotta love the new book.

Comment #183121

Posted by Flint on June 14, 2007 8:25 AM (e)

SWT:

My comment was focused more on the claim Flint quoted about Behe being a “real biologist.” He’s not a real biologist

Yes, I know this as well as you do. You have missed the point: Behe is being touted in creationist circles as a genuine biologist, and by denying this Truth, the atheists are splitting hairs because they must attack the person, having no defense against the TRUTH.

My larger point is, creationists want the scientific stamp of approval for their doctrines. The claim that creation myths are based on scientific research is important for them, and Behe’s books serve to reinforce it. Behe is positioned as a genuine scientist, publishing creationism in peer-reviewed literature, a full tenured professor of biology (or close enough), who has “proved” that goddidit after all.

His target audience is being stroked with great skill. They don’t know about any contradictory data, they’ve never heard of a fitness landscape, they’re not familiar with the theory, processes, research, probability, or anything resembling the merits. They have no need to read the book anyway; the fact that it exists and was written by a “real scientist” is sufficient.

I think RBH is a little too polite in saying the book consists of “apparently purposeful misrepresentations”, but I hope his message reaches a wide audience.

Comment #183122

Posted by Flint on June 14, 2007 8:25 AM (e)

SWT:

My comment was focused more on the claim Flint quoted about Behe being a “real biologist.” He’s not a real biologist

Yes, I know this as well as you do. You have missed the point: Behe is being touted in creationist circles as a genuine biologist, and by denying this Truth, the atheists are splitting hairs because they must attack the person, having no defense against the TRUTH.

My larger point is, creationists want the scientific stamp of approval for their doctrines. The claim that creation myths are based on scientific research is important for them, and Behe’s books serve to reinforce it. Behe is positioned as a genuine scientist, publishing creationism in peer-reviewed literature, a full tenured professor of biology (or close enough), who has “proved” that goddidit after all.

His target audience is being stroked with great skill. They don’t know about any contradictory data, they’ve never heard of a fitness landscape, they’re not familiar with the theory, processes, research, probability, or anything resembling the merits. They have no need to read the book anyway; the fact that it exists and was written by a “real scientist” is sufficient.

I think RBH is a little too polite in saying the book consists of “apparently purposeful misrepresentations”, but I hope his message reaches a wide audience.

Comment #183140

Posted by jasonmitchell on June 14, 2007 11:26 AM (e)

re comment 183097 (uniformitarianism vs. catastrophism)

actually a facinating debate in an of itself - how long until the fudies hijack that?

see http://www.pbs.org/wgbh/nova/megaflood/about.htm…

example of how SCIENCE WORKS. J Harlen Bretz’s hypothesis wasn’t widely accepted until a MECHANISM for the catastophic “megafloods” was worked out (testable models)- contrast this to the yahoos that claim the Grand Canyon was formed by “THE” flood and then just make stuff up as their “evidence”

Comment #183141

Posted by PoxyHowzes on June 14, 2007 11:29 AM (e)

“I’ll see your Biologist and raise you one Mathematician.” While I agree with Flint (Comment #183074) that the argument is often not about right versus wrong, but about TRUTH versus [something-too-scary-to-contemplate], It seems that one counter to the statement that a “real biologist has proven evolution wrong” is “Oh, no, a real mathematician has shown that Dr. Behe made a mathematical error early in his book, so the proof is invalid.”

Since the listener presumably understands neither bio nor math, you’ve reduced the exchange to a pi**ing contest between appealed-to authorities.

Comment #183149

Posted by Science Avenger on June 14, 2007 12:27 PM (e)

Nigel Depledge said:

What particularly gets my goat about Behe is that biochemistry (his area of expertise, allegedly) is overflowing with evidence that supports evolution. All you have to do is line up the sequences of the same protein from ten different organisms to see it.

A little OT, but this ties into a point I thought of when Mark Hausam asked for evolutionary charts showing the transitional forms. IMO those of you with the ability to create such visual representations of evolutionary science would greatly benefit the cause if you did so. Graphics of the kinds of sequences described above, and similar ways of looking at it, would be a great PR weapon to counter IDer/creationist nonsense. In the way Behe is a man of the people, because people love pictures.

Comment #183152

Posted by Flint on June 14, 2007 1:16 PM (e)

Since the listener presumably understands neither bio nor math, you’ve reduced the exchange to a pi**ing contest between appealed-to authorities.

Sigh. As I wrote, I already pointed to several IMO devastating reviews of Behe’s drivel, written by no-doubt-about-it genuine authorities. But the decision as to which authority to accept can hardly be based on merits WAY beyond the knowledge base of the evaluator. So the decision is made on religious grounds entirely - critiques of Behe are characterized as caught-with-pants-down defenses of anti_Jeezus territory by atheists.

As the notorious lee_merrill has made endlessly obvious, no amount of education or intelligence is sufficient to even *understand* merits contradictory to faith-based convictions. Fortunately, no understanding of the merits is required. You’re either for Jeezus or against him. For=honest, against=atheist (these are opposites).

Comment #183165

Posted by harold on June 14, 2007 4:03 PM (e)

Flint -

It’s an absolute guarantee that you will very rarely convince the “pre-committed, biologically ignorant” audience that now consumes Behe’s books. When you’re dealing with people who already bought Henry Morris books before “ID” was even invented, prepare to be frustrated.

I’ve often stated my personal opinion, that this group of people, that is, not necessarily everyone who follows a religious tradition that overlaps with YEC, but the aggressive, obsessive ones who focus on public school curricula and other political issues, are as much motivated by an unhealthy, authoritarian social and political agenda, as they are by sincere religious belief.

However, criticism of Behe does a huge amount of good.

ID was hardly invented to sell a few more books to a relatively small number of hard core, right wing “creationists”, through the means of Regnery Press and similarly limited outlets, nor generate a few more frenzied right wing editorials, letters to editors, and comically crackpot web sites, which is effectively what it does now. Nor to generate one unsuccessful attempt to jam it into one single deeply rural school district, with ill-effects for all who made that dishonest effort.

ID was invented with the vain hope that courts would be bamboozled, creationism could be snuck into schools, and vast numbers of people would be convinced of that the DI had proven the existence of a “designer”. Which was presumably, if not logically, the first step to convincing them to conclude some but not all “Biblical Law” from Leviticus - that is, harsh execution for various now-legal private sexual behaviors, but complete lack of concern for dietary law and a variety of other important “laws” from the same source - should be the law of the land. The possibility that the “designer” might be a Hindu deity, for example, was not intended.

In fact, the Wedge Document states that the goal of the DI is that mainstream science use the “intelligent design paradigm”, rather than the “materialism paradigm”, in twenty years - and it was written in 1995, so they haven’t got much time left.

I suppose the odds were against them from day one, but healthy, honest, vocal criticism has been critical to isolating and exposing them.

Comment #183170

Posted by RBH on June 14, 2007 5:45 PM (e)

Richard Wein asked

I have a question for those who’ve read The Edge of Evolution. How does Behe now define IC? Does he even give (or cite) a specific definition?

Behe talks about it, using his original DBB structural definition. His new term, though, is “coherence”. Coherence takes up the theme of his later “evolutionary” definition of IC, packing together the steps required to build an IC structure and his notion of parts interacting, with some probabilistic baggage and ‘no direct routes’ business thrown in. I lost count of the number of times Behe used “coherence” in the book. I was making notes on its various usages, but lost interest after a while.

Comment #183225

Posted by Torbjörn Larsson, OM on June 15, 2007 6:35 AM (e)

jasonmitchell wrote:

J Harlen Bretz’s hypothesis

Interesting. There are places in the mountains here [Sweden] where the geography can be explained by the same phenomena on much smaller scales. (Or so the local maps tells you.) Ice lakes have been breached at the end of the ice age, so the retreating ice didn’t scour away the traces.

It can be quite impressive on some places. The ice has eaten away on our mountain sides so V valleys that I believe you expect in plate tectonic mountain terrain have become U valleys with a flat floor. (Which are easy to travel in, btw.) But in places the relatively naked valley floor is deposited with impressively thick beds of gravel and deep flood scars running through.

Comment #183226

Posted by Nigel Depledge on June 15, 2007 6:36 AM (e)

RBH wrote:

I lost count of the number of times Behe used “coherence” in the book. I was making notes on its various usages, but lost interest after a while.

An example of decoherence, or incoherence? :)

Comment #183227

Posted by Nigel Depledge on June 15, 2007 6:38 AM (e)

SWT wrote:

My comment was focused more on the claim Flint quoted about Behe being a “real biologist.” He’s not a real biologist, although as a biochemist, he should still know better.

It’s possible that I was reacting to the discomfort of discovering that Behe’s educational background is similar to my own.

Comment #183240

Posted by FastEddie on June 15, 2007 8:39 AM (e)

I wonder if this Behe book was “peer-reviewed” as rigorously as the last one?

Comment #183526

Posted by William E Emba on June 17, 2007 1:41 PM (e)

Another example of real science is Mwangi et al “Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing” PNAS 5/29/2007 v104,n22,pp9451-9456.

In summary, a patient had a staph infection that grew increasingly drug resistant. After 12 weeks, the patient died. S. aureus were isolated from multiple blood samples taken during the course of the patient’s treatment, and subjected to whole-genome sequencing. 35 point mutations were found between the earliest and latest isolates. That’s approximately 3 mutations per week.

Any doctor who does not understand how extremely rapid evolution can happen ought to have his license removed. Anyone who teaches medical students or even premedical students nonsense about the eons needed for just one lucky mutation to happen should be fired. It’s a critical matter of life and death.

Trackback: Chu-Carroll on Behe’s The Edge of Evolution

Posted by Science After Sunclipse on June 13, 2007 6:17 PM

Dear Gentle Readers: At the bottom of this essay, I’m collecting links to reviews of Behe’s book The Edge of Evolution, replies to reviews and so forth. Well, now the burden is off me, and I can devote my book-reviewing time to good books,...