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Behe’s (malevolent) intelligent designer is still at work

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Correction: See this comment and this one. Operating from memory, I mis-stated Behe’s argument below. According to Behe’s “CCC” criterion, chloroquine resistance is (barely) within the capabilities of evolution given the time and population size available. It’s the “double CCC” that’s unevolvable according to Behe. Malaria itself, however, was designed according to Behe, and the case of artemesinin resistance is still open.

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In “The Edge of Evolution”(reviewed here and here), Michael Behe argued explicitly that an intelligent agent is responsible for the evolution of chloroquine-resistant malaria, arguing that the necessary mutations are beyond the reach of chance and selection given the time and population sizes available. Therefore, he claimed, an intelligent designer is responsible for drug-resistant malaria. He wrote

Here’s something to ponder long and hard: Malaria was intentionally designed. The molecular machinery with which the parasite invades red blood cells is an exquisitely purposeful arrangement of parts. C-Eve’s children died in her arms partly because an intelligent agent deliberately made malaria, or at least something very similar to it. (p. 237)

Not only that, the purported intelligent agent is responsible for drug resistance in malaria. Behe claimed that because it requires multiple independent mutations, none adaptive by themselves, given the time and population sizes available malarial resistance to chloroquine must have been designed (and presumably manufactured) by an intelligent agent (see his Chapter 3 for elaborate probability calculations). And chloroquine resistance in malaria is now nearly universal.

The currently most effective first-choice treatment for otherwise drug-resistant malaria is artemisinin. Hailed in 2004 as a “magic bullet” against malaria, artemisinin is an extract of a plant grown mainly in Viet Nam. Just a few years later, an artemisinin-resistant strain of malaria appeared in southeast Asia. In fact, according to this paper in Science published yesterday, April 6, 2012, 33 regions on the falciparum malaria genome appear to be under strong selection for artemisinin resistance. (See a news story here.) 33 genome regions on chromosome 13 that are under selection for artemisinin resistance! Surely in Behe’s fantasy world that’s way beyond the capabilities of evolution, and his malevolent intelligent agent is working over-time in Cambodia and Thailand to kill people.

Behe also discussed the research of Barry Hall on a class of antibiotic drugs called carbapenems. He approvingly quoted Hall as writing

“The results predict, with 99.9% confidence, that even under intense selection the [enzyme] will not evolve to confer increased resistance to imipenem [a member of the carbapenems].” (p. 237)

Behe continued, in his own words,

In other words, more than two evolutionary steps would have to be skipped to achieve resistance, effectively ruling out Darwinian evolution. (p. 237).

So if resistance to carbapenems (of which imipenem is an instance) should appear, according to Behe it must have been due to an intelligent agent. But even before Behe published that (“Edge of Evolution” was published in 2007), carbamenem-resistant gram negative bacteria were being detected in 2005. Again, in Behe’s fantasy world, a malevolent intelligent agent is hard at work right now, designing (and manufacturing) pathogens to kill people.

Like I just said – as DI guy David Klinghoeffer posted yesterday, the origin of hundreds of new genes in Drosophila is just microevolution. This is a direct deduction from their own ID/creationist logic, where small amounts of change “within the kind” are no problem for normal evolutionary processes. Too bad for Behe, Luskin, etc. Here’s the full quote for when they realize the problem and take the post down:

Jerry Coyne reports on a new paper in Science by Manyuan Long and colleagues on the origin and history of new genes in a large group of Drosophila that have recently had their full genomes sequenced.

Having this much phylogenetic and genomic information allows researchers to estimate the phylogenetic position of the origin of a new gene (566 new genes amongst the group of 12 fully sequenced genomes, actually), and the periods of time in which directional selection, stabilizing selection, or drift were the dominant regime that the new genes were evolving under. In many cases, there is a period of high selection after the origin of the gene, which weakens later – which is just what you would expect if the well-known, standard model for the origin of new genes is correct.

Two additional points are worth mentioning: (1) in some cases (about 30%, 59 out of the 195 they targeted for knockout studies), these new genes have become essential to viability for the species in question – even though they are totally absent in other, basically similar, flies that do just fine without them! This is strong support for the notion that one way “irreducible” systems evolve is by evolving parts that are helpful at first, but later become essential as other parts coadapt to become dependent on them. (2) I’m sure Luskin, Ewert, and other DI people would like to dismiss this as just another case of evolutionists “illegitimately” inferring common ancestry from “mere” sequence similarity, and that “common design” could be the explanation. However, in any other context, these creationists, and virtually any creationists including the young-earthers, would easily say that all of these Drosophila are just different varieties of the Drosophila kind, and that whatever variety exists between them (minor, in the grand scheme of biology) is “merely” “microevolution within the kind!” (And in the Edge of Evolution, Behe clearly puts his estimated “edge” well above the genus level.)

What’s that? Standard boring microevolutionary processes can produce new genes with modified sequences and new functions, which is clearly new information on anyone’s definition, even the creationists’ and even (explicitly so) Michael Behe’s definition? Oh my goodness, someone better call the DI news blog to put out this fire and reassure the faithful!

References

Chen, S., E. Zhang, and M. Long. 2010. New genes in Drosophila quickly become essential. Science 330:1682-1685.

A previous bit of ranting on this topic by me (responding to Luskin’s ridiculous critique of another famous paper by Manyuan Long, entered into evidence in the Kitzmiller case as exhibit P-245, actually: Long et al. (2003), Nature Reviews Genetics, “The origin of new genes” (free online in many places).

I don’t have time to do a serious blog entry, but I would just note that Jerry Coyne has been blogging Behe’s QRB paper, and the scandalous abuse of it by ID proponents (well, I’m sure the abuse was intended by Behe, but what he could actually establish in a peer-reviewed paper does not support even a smidgen the claims that Behe and other ID fans are making about the paper on the blogs).

In the latest thread, Paul Nelson popped up with another promise for another piece explaining why something that’s obviously wrong is actually reasonable (in this case, why ID advocates are allowed to disdainfully ignore the massive evidence that gene duplication + divergence is the main source of new genes with new functions, and why they are allowed to claim that the origin of new functional sequence is a big problem, when in fact it’s basically a solved problem, with the answer – gene duplication + divergence – known across biology, tested and verified in numerous different ways, and written down for beginners in the textbooks). We’ll see if he ever comes up with it. But in the meantime, here are a few irate comments from me:

Apparently Behe has been mentioning this in his England tour:

Volume 85 Number 4 December 2010 Major Articles

Current Perspectives on the Biological Study of Play: Signs of Progress Kerrie Lewis Graham and Gordon M. Burghardt

Experimental Evolution, Loss-of-Function Mutations, and “The First Rule of Adaptive Evolution” Michael J. Behe

What is an Individual Organism?: A Multilevel Selection Perspective Henri J. Folse III and Joan Roughgarden

Irreducible Incoherence and Intelligent Design: A Look into the Conceptual Toolbox of a Pseudoscience Maarten Boudry, Stefaan Blancke, and Johan Braeckman

The Boudry article is online here and is quite good, catching points that most commentators on the IC argument miss. (Part of the goodness is that it cites Pete Dunkleberg’s 2003 “IC Demystified” at talkdesign.org, which is one of the better discussions out there.)

If past experience is any guide, Behe’s article will make abstract arguments about the improbability of adaptations *if* many simultaneous events are required, but will present no evidence that many simultaneous events are likely to be necessary for the sorts of adaptations we actually see in biology. Positive evidence for ID will not be provided at all, but the article will be trumpeted as such by the usual ID propagandists. But the article isn’t out yet, so we’ll see, I suppose.

flunked.jpgOn Evolution News Luskin claims, quoting Behe, that the number to establish probabilities of fixation of a mutation is not a calculation but rather statistical data:

The number of one in 1020 is not a probability calculation. Rather, it is statistical data.

But if Behe had read White’s 2003 paper (table 1) “The de novo selection of drug-resistant malaria parasites.” N J White and W Pongtavornpinyo Proc Biol Sci. 2003 March 7; 270(1514): 545–554. he would have read that

The estimates for chloroquine and artemisinin are speculative. In the former case, this assumes two events in 10 years of use with exposure of 10% of the world’s falciparum malaria (Burgess &Young 1959; Martin&Arnold1968; Looareesuwan et al. 1996; Su et al. 1997

Luskin is correct, the number is not a “mere guess”, it’s a speculative estimate. Glad we got that right. Why Luskin failed to mention this is beyond me since he does seem to quote the paper in question. Perhaps if Luskin had spent more time on reading the papers and less on emphasizing the academic achievements of White, he might have found the error in Behe’s claim himself.

What Behe meant when he said that

the 1020 statistic is an empirically derived fact

is less clear. Surely since ID proponents are so critical of evolutionary scientists when it comes to confusing fact and fiction, Behe may wants to revise his statement.

In the post about my review of Behe’s The Edge of Evolution, many complained that they couldn’t access the full text without a university subscription or paying a huge fee. I have checked Elsevier’s policies on this. Authors are not allowed to post the published PDF to their websites (you have to get that from Elsevier), but they can put up the unformatted, submitted preprint version of their articles, as long as they include the reference and DOI to the published version. So here is the reference: Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, doi: 10.1016/j.tree.2007.09.004.

…and the full text is below the fold. Note that the unpublished version has a few minor differences from the published version. For example, it has more emphases which were kind of my way of jumping up and down on the smoking ruins of Behe’s core arguments in The Edge of Evolution.

On Amazon Behe admits that Intelligent Design is nothing more than a code word for Christian faith.

Behe Wrote:
Miller Wrote:

Behe happily notes, as I would, that we live in a universe whose fundamental physical constants are remarkably hospitable to life. To me, and apparently to Behe, these constants may well reflect the will of a creator we would both identify as the God of Abraham.

So let me emphasize: Kenneth Miller is an intelligent design proponent. He believes that the laws of the universe were purposely set up to permit life to develop. Miller thinks that, to accomplish the goal of life, the universe had to be designed to the depth of its fundamental physical constants. I agree with him as far as he goes, but, on the other hand, as I write in The Edge of Evolution, I think design extends further into the universe, past physical constants, past anthropic coincidences, and well into biology. Yet, with respect to design, he and I differ only on degree, not on principle.

Behe review in TREE

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I am pleased to announce that Trends in Ecology and Evolution (TREE) has just put up the article-in-press version of my book review of Michael Behe’s The Edge of Evolution. Here is the reference and link:

Nicholas J. Matzke (2007). “The edge of creationism.” Trends In Ecology and Evolution, In Press, Corrected Proof, Available online 24 October 2007. ScienceDirect, DOI.

The DOI link doesn’t seem to be working just yet, presumably that is temporary. And the other link is one of those nasty superlong ones, so if nothing works, go to the TREE website and click on “Articles in Press” to see it (you will have to have a subscription or university access to get the article; I will provide a partial quote below).

Writing this review was challenging. There are a great many things wrong with Behe’s book, and attempting to hit the most important points effectively, with just 750 words to work with, was quite a challenge. For example, there was no way to fit in anything about HIV, even though some really good points have emerged on that front in the last few months. Thanks to the PT crew for a great many helpful discussions, comments, etc. I also had Cavalier-Smith’s (1997) TREE review of Darwin’s Black Box, literally the article that got me into ID criticism in a serious way, to inspire me (despite some flaws in that review).

I tried to make every word count, so it is hard to pick a summary quote, but here is a bit from the middle:

by Abbie Smith

Editor’s Note: This is a guest post by Abbie Smith, the blogger behind the Endogenous Retrovirus (ERV) blog (original post), who we marked early as having a special talent for this creationism-rebutting stuff. Abbie works in an HIV lab and has a few things to say about Behe’s argument in The Edge of Evolution that evolution hasn’t/can’t produced any novel adaptations, genes, or protein-protein binding sites during the evolution of HIV, the virus that causes AIDS, unless you are one of the several Discovery Institute fellows who denies this along with denying evolution.

Oh, and speaking of the Discovery Institute and Behe, Behe is apparently going to be on the Colbert Report tonight. Colbert has been setting an excellent example by making a point of it to bring scientists on his show – Kenneth Miller, Neil DeGrasse Tyson, Shubin I think. Hopefully Colbert knows that Behe isn’t quite like these other guys. I recall that Dembski claimed he was sick after he appeared on The Daily Show next to some weird new-ager in 2005.

Anyway, if Colbert doesn’t hit the appropriate snark mark tonight, you’ll get it from Abbie for sure. I thought I got Behe pretty good in Of Cilia and Silliness, but this really takes the cake.

—Nick Matzke


Michael Behe, please allow me to introduce myself…

I’m ERV. This is my dog, Arnold Schwarzenegger. And this is my friend, Vpu. I presume you and Vpu haven’t met, as you recently repeated in an interview with World magazine the same sentiment you gurgled ad nauseam in ‘Edge of Evolution’:

Gert Korthof reviews Behe’s latest book “The Edge of Evolution” and shows a level of internal contradiction one has grown accustomed to from ID proponents

Common Descent is based on genetic continuity in the history of life on earth. Design, according to Michael Behe, is based on genetic discontinuities in the Tree of Life. Therefore, Design and Common Descent are not compatible. Make your choice: it is either Design or Common Descent. Contrary to Behe, both cannot be true.

Korthof shows how Behe’s book does little to explain ‘Intelligent Design’, leaving it once again scientifically vacuous.

Reality 1, Behe 0

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Or …

T-urf13 redux

A few months ago I posted an essay about a remarkable example of the evolution of Irreducible Complexity from scratch, via natural, unguided mechanisms. While the reaction to this essay has been pretty muted (precious little to take note of, save for one well-hidden reference on Uncommon Descent to “No Free Lunch”, citing pages that make arguments clearly refuted in the PT essay), I had no idea that a much bigger response, or target, would emerge from the Halls of ID. This would, of course, be Mike Behe’s recently-released follow-up to “Darwin’s Black Box”, entitled “The Edge of Evolution”.

More follows beneath the fold, but here’s the short version for those of us with miniscule attention spans -the previous essay refutes (or, better said, refuted) the EoE in no uncertain terms, showing that the centerpiece of the EoE, the value Behe assigns to the “probability” of occurrence of a protein interaction or binding site, does not agree with what we can and do know about the history of a bonafide multiple simultaneous mutation.

2007-07_NG_cover.jpgGiven that malaria is more or less the preeminent case of intelligent design in Michael Behe’s The Edge of Evolution, I think everyone would find it interesting to read the July 2007 cover story of National Geographic, which is on malaria and the history of attempts, failures, and hopes of eradicating it. The story focuses on Zambia, where the infection rates are sometimes over 100% (i.e., people are infected more than once a year). I have a somewhat personal interest in this since when I was seven my family went to Zambia for a year, as my dad was on sabbatical. We all took chloroquine weekly – a nasty-tasting drug to a seven-year old, mind you. And despite religiously taking the nasty-tasting drug, I got malaria in the end anyway (the chloroquine-resistant kind, naturally), came down with it on the plane ride back to the states, and then, sick as a dog, I was paraded around undiagnosed before baffled American doctors who had never seen malaria, until someone had the bright idea that maybe I had picked up the most common disease in Africa. More nasty medicine cured it, but that was an early lesson in evolution for me, let me tell you.

A new ID book, a new selection of yummy delicious quote-mines to ponder. EoE offers up quite the little smorgasbord. Over at EvolutionBlog I analyze a tediously commonplace example of Behe not merely removing a quotation from its proper context, but actually deleting part of it to give a false impression of its meaning. Behe has done this before, as I also discuss. Comments can be left there.

Jason Rosenhouse has already noted that Tom Woodward opined that "in the next six to twelve months, Darwinism will go into a steep nose dive as the result of Behe’s new book." How is this "tremendously important" book going to change the landscape of ID? Early indications appear to say ... not at all.

Read more at Stranger Fruit where comments can be left.

Jerry Coyne educates Behe about a few common misconceptions about evolution and shows why Intelligent Design, especially ‘at the edge’ is fully scientifically vacuous.

Coyne reviews Behe’s latest book ‘the Edge of evolution’ and like many before him finds the book unconvincing and ‘rather pathetic’.

What has Behe now found to resurrect his campaign for ID? It’s rather pathetic, really. Basically, he now admits that almost the entire edifice of evolutionary theory is true: evolution, natural selection, common ancestry. His one novel claim is that the genetic variation that fuels natural selection–mutation–is produced not by random changes in DNA, as evolutionists maintain, but by an Intelligent Designer. That is, he sees God as the Great Mutator.

Well, my own personal copy of Michael Behe’s new book The Edge of Evolution arrived via amazon.com today, so I suppose it is fair game. I have linked to a few early blog comments (see more from ERV), and Michael Ruse has a short newspaper comment out today. And several other reviews are coming out in the near future in Science, Discover, etc. None of them positive at all, but it’s amazing how much attention someone can get by sacrificing scientific rigour and inserting divine intervention instead.

I don’t have a full review of the book and I won’t for a bit since I am working on other things. But I want to get dibs on one peripheral but particularly shocking and egregious error that Behe makes in The Edge of Evolution. The error is simple but it points to what I have become convinced is the true core of the mishmash known as “intelligent design”: sloppiness and wishful thinking.

Best Behe takedown *ever*

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So I guess DaveScot and Dembski didn’t like Mark Chu-Carroll’s critique (which I linked to) of Behe’s usage of fitness landscape concepts in The Edge of Evolution.

Well, if anyone is still having trouble getting it, check out Good Virus, Bad Creationist at the blog ERV. The reason I say it’s the best Behe critique ever is the style. L.O.L.

PS: And watch out for ERV. She’s clearly going to run the planet someday, or at least the NIH.

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