Available here. Axe’s analysis was motivated in part by the recent flurry of papers dealing with the problem of the waiting time for multiple independent mutations. Here is Doug’s abstract: To explain life’s current level of complexity, we must first explain genetic innovation. Recognition of this fact has generated interest in the evolutionary feasibility of complex adaptations–adaptations requiring multiple mutations, with all intermediates being non-adaptive. Intuitively, one expects the waiting time for arrival and fixation of these adaptations to have exponential dependence on d, the number of specific base changes they require. Counter to this expectation, Lynch and Abegg have recently concluded that in the case of selectively neutral intermediates, the waiting time becomes independent of d as d becomes Read More ›

ID critics often complain that ID advocates go ON AND ON (and ON) worrying about Weasel-type models of evolution, as illustrations of how undirected variation and selection can rapidly converge to apparently designed outcomes. No one takes such models seriously as biology, the critics say. Weasels are toys with a strictly limited teaching purpose. Over to the latest issue of the Proceedings of the National Academy of Sciences (PNAS). Looks like a weasel in the tall grass: Suppose that we are trying to find a specific unknown word of L letters, each of the letters having been chosen from an alphabet of K letters. We want to find the word by means of a sequence of rounds of guessing letters. Read More ›

Some scientists grow more conservative with age; others, more radical. Carl Woese (age 82) represents a vivid example of the latter group. His latest paper, “Life is physics: evolution as a collective phenomenon far from equilibrium,” co-authored with fellow U of Illinois scientist and frequent collaborator Nigel Goldenfeld, includes more heterodox ideas per page than just about anything I’ve read recently. (The paper is forthcoming in the Annual Reviews series.) For instance (p. 12): IS EVOLUTION RANDOM? We would be remiss in ending this article if we did not briefly mention the fascinating question: is evolution random? More precisely, does variation precede but not cause adaptation—the central tenet of the modern synthesis—or do environmental changes alter the stochastic nature of Read More ›

Michael Shermer and I are taking our ID versus Darwinian Evolution show back on the road, this time at Northern Arizona University in Flagstaff. The date is Tuesday, November 16, and the venue is Prochnow Auditorium; here are some details: Debate on Evolution vs. Intelligent Design with Michael Shermer and Paul Nelson. This event is only open to NAU students, faculty and staff and is free with a ticket and ID. Tickets can be picked up at the NAU Central Ticket Office starting October 26. A limited number of tickets will be available at the door. Please… bring NAU ID with you to the event. This event is part of SUN Entertainment’s Lecture and Debate Series. Here’s the Facebook entry Read More ›

…the “machines” of the cell will still be what they are: complex, sophisticated molecular systems, essential for the living state. Like the proteasome on the right, a sub-cellular machine that degrades proteins, among its other functions.

Oops, there I went and did it — used the “machinery” language that Massimo Pigliucci (CUNY) and Maarten Boudry (Univ. of Ghent) argue not only plays into the hands of ID advocates, but also misleads scientists themselves:

…if we want to keep Intelligent Design out of the classroom, not only do we have to exclude the ‘theory’ from the biology curriculum, but we also have to be weary [sic] of using scientific metaphors that bolster design-like misconceptions about living systems. We argue that the machine-information metaphor in biology not only misleads students and the public at large, but cannot but direct even the thinking of the scientists involved, and therefore the sort of questions they decide to pursue and how they approach them.

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Leigh Van Valen — an evolutionary biologist for whom the word “polymath” is entirely appropriate — died this past weekend, after a long illness. Leigh was a student of both Theodosius Dobzhansky and G.G. Simpson at Columbia University, and spent most of the rest of his career at the University of Chicago, where he served on the faculties of the Department of Ecology and Evolution, and the Committees on Genetics, Evolutionary Biology, and the Conceptual Foundations of Science. Like I said: a true polymath. As any of his students or colleagues will tell you, one’s first meeting with Leigh was unforgettable. Slight of stature and soft-spoken, with a long white beard and hair, Leigh had an incomparable knowledge of the Read More ›

Do you still think God is good?

— George Williams, 1987 (p. 157)

In the commentary following the death on September 8 of leading neo-Darwinian theorist George C. Williams — go here for a representative selection — I’ve seen no mention of the considerable role of theology in Williams’s thought. I’d speculate that this silence follows naturally from the wide, albeit tacit, acceptance by Williams’s closest colleagues of the theological assumptions he made. As Ludwik Fleck (1979, 41) understood, a premise on which a group of scientists agree (if they are conscious of holding the premise at all) is not likely to elicit comment.

But no one can open The Pony Fish’s Glow (Basic, 1987) or Natural Selection: Domains, Levels, Challenges (Oxford, 1992) and miss the theology.
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Details here.

And would be the worst, whether one is an ID proponent or not. Many UD readers know the Australian molecular biologist John Mattick as a leader in thinking about functional roles for so-called ‘junk DNA.’ Mattick has earned the implacable ire of ID critics such as Larry Moran and T. Ryan Gregory, although not because Mattick is an ID proponent. He’s not — see the opening sections of this interview, which is also available as a video. (Scroll to the Supplementary Material at the end; SIZE WARNING: 46M.] It’s a fascinating exchange, although I think Mattick greatly underestimates the significance of clade- or taxon-specific novel proteins in eukaryotes. If nothing else, however, empirical discovery itself stands entirely on Mattick’s side. Read More ›

The enormously influential mathematics and science writer, skeptic, and encourager of many, Martin Gardner, has died at the age of 95. I came to know Gardner through a mutual friend, the late science writer and skeptic Bob Schadewald (1943-2000), who occasionally visited Gardner at the latter’s home in North Carolina. [Here’s a tiny but relevant fact that shows the surprising reticulations of the science-and-theology debate in America. During one such visit, Gardner gave Schadewald much of the contents of his library, which he found had grown unwieldy. Then, years later, following the devastating fire that destroyed nearly all of YEC paleontologist Kurt Wise’s library, Schadewald packed much of his personal library into boxes to send to Kurt. Schadewald died a few days later, at nearly the same time his books arrived at Kurt’s home in Tennessee. Kurt unpacked the books, carefully wrapped in tissue, in tears, knowing that the person who sent them had just died. So, chances are, at least some of Martin Gardner’s personal library now resides with Kurt Wise. Go figure.] Schadewald told Gardner about this crazy YEC philosophy of science graduate student he knew, at the University of Chicago, and in response, Gardner sent back a letter to me. Read More ›

Specifically, Bacon’s essay on atheism: God never wrought miracle to convince atheism, because his ordinary works convince it. This is an obsolete, but still relevant, sense of “convince.” It means “to overcome or vanquish.” “‘Convince me!’ said the atheist.” In the original sense, this would mean, “Come on — defeat me.” Anyway, their video is here. WARNING: NSFW language.

Not that Massimo — this one. And “it,” of course, is neo-Darwinism, or the Modern Synthesis: textbook evolutionary theory. There’s nothing especially novel in saying that evolutionary theory can function as a secular religion, which is Piattelli-Palmarini’s main point in his new article. Michael Ruse has said as much for years. What has changed within the past couple of years, however, is the rapid growth in the overtly religious (anti-religious, but that anti doesn’t really matter) content of the writings of prominent neo-Darwinian biologists, such as Jerry Coyne and Richard Dawkins. The Accomodationist Wars, which show no signs of slacking, illustrate that for many, the whole point of evolutionary theory is Getting Rid of God. A biologist who nonetheless professes Read More ›

Yours? His? Theirs? Anyone’s?

I’ve known Todd since we were graduate students in the 1990s, and have a hardbound copy of his UVA dissertation (Theory and Application of Protein Homology, 1999) sitting on my office shelves. Todd knows more evolutionary biology than many evolutionary biologists. Yet, perversely, or inexplicably, in the eyes of his critics and growing number of blog readers, Todd is also a young-earth creationist (YEC). What’s up with that?

But he’s not much of an admirer of ID. Think about it this way.

Suppose you visit Stonehenge with a group of “Stonehenge is naturally caused” theorists, who vigorously dispute that ancient humans built the monument. No intelligence was involved, they say; some yet-to-be-discovered evolutionary scenario did the building. Stonehenge-is-natural research (or science) thus consists of looking for the unknown natural mechanisms or processes, which shaped the monoliths, caused them to aggregate into a circle, and so on. No “intelligence of the gaps” need apply.
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The article is open access, so you can choose to download it. Or choose not to download it. Or choose to click over to YouTube, or the Huffington Post, to see what’s doing there.

Whatever happens, “you” — meaning the person reading this right now — won’t be making a decision. Physics and chemistry will. These forces will inform you of their “decision,” so to speak, by the perceptual illusion, constructed in the infinite wisdom of natural selection, which gives you the misleading sense of having made a choice. Otherwise known as free will, which doesn’t exist.
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Stephen Barr misunderstands the place of natural laws and regularities in design inferences. Barr writes:

…whereas the advance of science continually strengthens the broader and more traditional version of the design argument, the ID movement’s version is hostage to every advance in biological science. Science must fail for ID to succeed. In the famous “explanatory filter” of William A. Dembski, one finds “design” by eliminating “law” and “chance” as explanations. This, in effect, makes it a zero-sum game between God and nature. What nature does and science can explain is crossed off the list, and what remains is the evidence for God.

Frank Beckwith (in the comments following Barr’s post) echoes the misunderstanding:

As I have already noted, the ID advocate tries to detect instances of design in nature by eliminating chance and necessity (or scientific law). This implies that one has no warrant to say that the latter two are the result of an intelligence that brought into being a whole universe whose parts, including its laws and those events that are apparently random, seem to work in concert to achieve a variety of ends.

Hm. To quote Hamlet (Act 2, scene 2): “Nay, that follows not.” Here’s a vignette to make the point.
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