Science and Culture Today | Page 1250 | Discovering Design in Nature

After having the premier of Darwin’s Dilemma canceled by the California Science Center, Avi Davis’s American Freedom Alliance really pulled things together in heroic fashion in Los Angeles. The AFA found a new venue, hardly inferior, where academic freedom may be less endangered: the University of Southern California. The sizable crowd on Sunday night of about 230 people was appreciative and intelligent. There were university students representing both sides of the Darwin debate, high school students from a church school in Santa Monica on a field trip, and a mix of other folks from the community.

The film is a powerful document. The word that came to my mind watching it was “spooky.” Besides very lucidly and compellingly laying out its scientific case that the Cambrian explosion can’t be remotely explained in Darwinian terms, and that the event 530 million years ago virtually compels a conclusion that purposive design was involved, I was struck by the atmosphere of mystery that director Lad Allen evokes. What does explain the sudden appearance of most animal body plans in a space of maybe 5 to 10 million years? The film quotes Richard Dawkins unarguable statement that, “Without gradualness in these cases, we are back to a miracle, which is simply a synonym for the total absence of explanation.”

Allen, David Berlinski, and Jonathan Wells all spoke afterwards on a discussion panel. The inimitable Berlinski, the William F. Buckley of Darwin doubters, was in fine form, at one point amusingly decapitating a rambling student challenge from the audience with the concise answer, “No.” I also loved his insight that the ugliness of the results of the Darwinian idea, its effects on our culture, are far from irrelevant in judging the idea’s truth. This is another one of Darwin’s dilemmas. Berlinski cited Keats, “‘Truth is truth, beauty truth,’ — that is all/ Ye know on earth, and all ye need to know.” No, he pointed out, you can’t separate the consequences of Darwinian theory from its truth. Beauty may well be an aspect of truth.

Heady stuff, but Berlinski brought it down to earth the next morning in the studio of Dennis Miller in Culver City here, discussing the new paperback edition of The Devil’s Delusion: Atheism and Its Scientific Pretentions. The last segment included David’s very funny riff on how a cow-like creature could take to the seas as a proto-whale, per the Darwinian just-so story, including the challenge of developing nipples that work underwater. Miller took up the nipple image and developed it in a manner that I’m not sure belongs on a blog intended for all the family, but was very entertaining nevertheless.

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the third of several posts addressing it. References will appear in the last post.

Now back to Thornton’s first point, the role of neutral mutations (which he sometimes labels “permissive” mutations). At several places in his post Thornton implies I’m unaware of the possibilities opened up by genetic drift:

Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution…. Behe’s first error is to ignore the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates…. As Fig. 4 in our paper shows, there are several pathways back to the ancestral sequence that pass only through steps that are neutral or beneficial with respect to the protein’s functions.

My interest in evolution by neutral mutation, however, is a matter of public record. It is an old idea that if a gene for a protein duplicates (3), then multiple mutations can accumulate in a neutral fashion in the “spare” gene copy, even if those mutations would be severely deleterious if they occurred in a single-copy gene. Four years ago David Snoke and I wrote a paper entitled “Simulating evolution by gene duplication of protein features that require multiple amino acid residues” (4) where we investigated aspects of that scenario. The bottom line is that, although by assumption of the model anything is possible, when evolution must pass through multiple neutral steps the wind goes out of Darwinian sails, and a drifting voyage can take a very, very long time indeed. But don’t just take my word for it — listen to Professor Thornton (1):

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the second of several posts addressing it. References will appear in the last post.

Now to Professor Thornton’s reply. He writes at length but makes just two substantive points: 1) that neutral mutations occur and can serendipitously help a protein evolve some function (“[Behe] ignores the key role of genetic drift in evolution”); and 2) that just because a protein may not be able to evolve a particular function one way does not mean that it, or some other kind of protein, can’t evolve the function another way (“nothing in our results implies that, if selection were to favor the ancestral function again, the protein could not adapt by evolving a different, convergent, underlying basis for the function”).

I’ll start with the second point since I can just quote myself to answer it. I wrote in one of my previous posts on Thornton’s work:

According to an international poll released by the British Council, the majority of Americans — 60% — support teaching alternatives to evolution in the science classroom. The percentage is the same for Britons, despite the fact that both countries have been inundated with pro-Darwin media coverage in this super-mega Darwin Year.

Of course, the British media reporting this are chagrined. Britain is the birthplace of Charles Darwin and his theory of evolution, and the official-sounding British Council, the UK group behind the “Darwin Now” campaign that commissioned the Ipsos MORI poll, have spent precious resources educating the world about Darwin. Now some believe the poll shows that efforts by Darwinist organizations aren’t working.

Head of the British Council’s Darwin Now program Fern Elsdon-Baker said, “Overall these results may reflect the need for a more sophisticated approach to teaching and communicating how science works as a process.”
While Darwin’s apologists might try to explain the poll numbers as an example of ignorance influencing people’s beliefs, the numbers themselves suggest a different picture.

Across the board, most respondents from the ten countries polled thought that “other perspectives on the origins of species” “such as intelligent design and creationism” should be taught in science class*. When the poll is weighted to include only those respondents who have heard of Charles Darwin and know something about his theory of evolution, the percentage supporting alternate theories increases, from 60% to 66% in Britain and 60% to 64% in the U.S.

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the first of several posts addressing it. References will appear in the last post.

I must say, it never ceases to amaze me how otherwise-very-smart folks like Zimmer and Thornton fail to grasp pretty simple points when it comes to problems for Darwinian mechanisms. Let me start slowly with a petty complaint in Carl Zimmer’s intro to the post. Zimmer is annoyed that I think Thornton’s latest work is “great,” yet I thought his previous work published a few years ago was “piddling.” “Why the change of heart?” wonders Zimmer.

A few days ago we saw Ida fall from her overhyped status as an ancestor of humans. Now some scientists are claiming that Archaeopteryx should lose its status as an ancestor of modern birds. Calling Archaeopteryx an “icon of evolution,” the Wall Street Journal (WSJ) borrows a term from Jonathan Wells while reporting that “[t]he feathered creature called archaeopteryx, easily the world’s most famous fossil remains, had been considered the first bird since Charles Darwin’s day. When researchers put its celebrity bones under the microscope recently, though, they discovered that this icon of evolution might not have been a bird at all.” According to the new research, inferences about growth rates made from studies of Archaeopteryx‘s ancient fossilized bones show Read More ›

A few months ago, “Ida” was sitting on top of the world. She’d been lauded as the “eighth wonder of the world” whose “impact on the world of palaeontology” would be like “an asteroid falling down to Earth.” Falling, indeed. On October 21, Nature published an article announcing that “[a] 37-million-year-old fossil primate from Egypt, described today in Nature, moves a controversial German fossil known as Ida out of the human lineage.” Wired also published a story, noting that, “[f]ar from spawning the ancestors of humans, the 47 million-year-old Darwinius seems merely to have gone extinct, leaving no descendants,” further quoting a paleontologist calling Ida “a third cousin twice removed … only very distantly related to living and fossil anthropoids.” Read More ›

Originally, proponents of neo-Darwinian evolution lauded “junk” DNA as functionless genetic garbage that showed life is the result of blind and random mutational events. Then “junk” DNA was disproved by the discovery that the vast majority of DNA is being transcribed into RNA. Did the failure of this Darwinian assumption cause evolutionists to terminate their love affair with biological “junk”? Of course not. They just shifted their argument back, claiming that the cell is full of “junk RNA”–DNA that is being transcribed into RNA but still does nothing in the cell. Earlier this year we reported on a Nature paper suggesting function for “junk” RNA. Now a Science Daily NewsArticle is confirming that finding. Aptly titled “No Such Thing As Read More ›

What do Discover magazine, The London Gazette, The Wichita Eagle, Commentary, Forbes, The Weekly Standard and UC Berkeley’s student paper, The Daily Californian, all have in common? They are just some of the publications that have published an essay or opinion piece by David Berlinski in the past 15 years. And those pieces are among 32 of Berlinski’s finest finally collected together in one volume: The Deniable Darwin. Berlinski, there is little argument, is a skeptic’s skeptic — the last of a dying breed. Lately it seems that everywhere one looks there is someone with the answer to everything. There are precious few true skeptics left, and Berlinski is certainly in the top rank in regards to the sciences. When Read More ›

A new paper from Richard Lenski’s group has appeared in Nature and has garnered a fair amount of press attention. Some people asked me for my thoughts about it.

The new paper continues the grand experiment that Lenski has been publishing about lo these many years — allowing a culture of the bacterium E. coli to continuously grow and evolve under his close observation. The only really new thing reported is a technical improvement — these days one can have the entire genome of E. coli “re-sequenced” (that is, determine the sequence of the entire DNA of the particular E. coli you’re working with) done for an affordable cost. (There are companies which will do it for a fee.) So Lenski and collaborators had the whole genomes — each and every nucleotide — sequenced of the E. coli that they have been growing for the past twenty years. Since they froze away portions of their bacterial culture at different times along the way, they now have the exact sequences of the evolving culture at many time points, from inception to 2000 generations to 10,000 to 40,000. Thus they can know exactly which mutations appeared when — an almost-complete paper trail. Very very cool!