(Updated) Despite getting plenty of ink, the Darwinists don’t come off looking so well in Kenneth Chang’s story about intelligent design in the Science section of today’s New York Times.

Imagine intelligent design is an elephant in the next room. A cat lies crushed on the floor before us, with the clear mark of an elephant’s toe imprinted on his poor, flat, fuzzy body.

You say, “I hear and smell an elephant in the next room. I say the most likely culprit is the elephant.”

But then some guy who hates cats almost as much as he hates elephants–and therefore doesn’t want to give the elephant credit for killing the cat–insists there is no elephant. When it’s finally clear that the empirical evidence for the elephant can no longer be ignored or denied, the elephant denier disappears and comes back with a large stuffed elephant and begins literally beating the straw out of it. He’s trying to tell you the elephant isn’t worth bothering with, isn’t up to snuff.

If you desperately want to ignore the real elephant, then you’ll find this ridiculous display quite convincing. Everyone else will know immediately that the man hasn’t torn the real elephant to shreds but only a straw mock-up of the creature. This is what we find the Darwinists doing in the Kenneth Chang article. They set up strawmen of several intelligent design arguments, then dismember them most effectively.

I’ll offer just two of several instances here. A brief summary of Stephen Meyer’s argument for design as the best explanation for the Cambrian explosion of animal forms some 530 million years ago is rebutted by this passage:

But molecular biologists have found genes that control the function of other genes, switching them on and off. Small mutations in these controller genes could produce new species. In addition, new fossils are being found and scientists now know that many changes occurred in the era before the Cambrian – a period that may have lasted 100 million years – providing more time for change.

However, Meyer’s argument takes both these points into account, and his rebuttals are based on well-established evidence in the peer-reviewed literature. One of his articles on the subject was edited by a biologist with two Ph.D.s in evolutionary biology, and peer-reviewed by three scientists with relevant Ph.D.s from well-respected institutions here and in Europe. If Meyer had not addressed those points, they no doubt would have insisted that he do so.

Similarly, biologist Kenneth Miller knocks down a straw man of Doug Axe, a long-time Cambridge University researcher with a Ph.D. from Cal-Tech who is now doing cutting edge research in protein mutations. The passage begins:

Penicillinase is made up of a strand of chemicals called amino acids folded into a shape that binds to penicillin and thus disables it. Whether the protein folds up in the right way determines whether it works or not.

Dr. Axe calculated that of the plausible amino acid sequences, only one in 100,000 trillion trillion trillion trillion trillion trillion – a number written as 1 followed by 77 zeroes – would provide resistance to penicillin.

In other words, the probability was essentially zero.

Dr. Axe’s research appeared last year in The Journal of Molecular Biology, a peer-reviewed scientific publication.

Dr. Kenneth R. Miller, a professor of biology at Brown University and a frequent sparring partner of design proponents, said that in his study, Dr. Axe did not look at penicillinase “the way evolution looks at the protein.”

Natural selection, he said, is not random. A small number of mutations, sometimes just one, can change the function of a protein, allowing it to diverge along new evolutionary paths and eventually form a new shape or fold.

But Axe’s experiments take this into account, are set up to test the Darwinian model. Axe provided a rebuttal to Miller’s facile objection, but the New York Times didn’t include it. Chang, however, should be complimented for engaging the scientific arguments over intelligent design rather than merely chasing conspiracy theories and questioning people’s motives. This is clear progress.