I’ve already commented on the paper by Eugene Koonin and the Darwinists’ concern that it might show that there is a serious controversy over the ability of random mutation and natural selection to account for the complexity of life at all, let alone in a gradual step-by-step process over eons of time.
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Koonin challenges the standard Darwinian view of the tree of life. His research shows that it lacks the ability to explain life’s complexity, but he hasn’t been fired from the National Center for Biotechnology or lost his funding from the National Institute’s of Health (yet).

Like Koonin, Michael Behe in his latest book The Edge of Evolution shows what evolution can do and what it can’t. Professor Robert Marks at Baylor uses the Evolutionary Bioinformatics Lab to showcase some of the limits of Darwinian evolution. Both have suffered serious repercussions. But not Koonin (yet).

How is it that his showcasing the limits of Darwinian evolution don’t result in his being vilified? Of course, we have seen a first glimpse of that. The Darwinist thought-policeman, Nick Matzke, has reminded comrade Koonin that he should show more caution when publicly challenging the reigning Darwinist orthodoxy.

Perhaps Koonin avoids further persecution by paying lip service to Darwin and denouncing intelligent design:

Comment by one of the paper’s peer-reivewers: “In each major class of biological objects, the principal types emerge “ready-made”, and intermediate grades cannot be identified.” Ouch, that will be up on ID websites faster than one can bat an eye.

Author’s response: Here I do not really understand the concern. I changed “ready-made” to “abruptly”, to avoid any ID allusions and added clarifications but, beyond that, there is little I can do because this is an important sentence that accurately and clearly portrays a crucial and, to the very best of my understanding, real feature of evolutionary transitions. Will this be used by the ID camp? Perhaps — if they read that far into the paper. However, I am afraid that, if our goal as evolutionary biologists is to avoid providing any grist for the ID mill, we should simply claim that Darwin, “in principle”, solved all the problems of the origin of biological complexity in his eye story, and only minor details remain to be filled in. Actually, I think the position of some ultra-darwinists is pretty close to that. However, I believe that this is totally counter-productive and such a notion is outright false. And, the ID folks are clever in their own perverse way, they see through such false simplicity and seize on it. I think we (students of evolution) should openly admit that emergence of new levels of complexity is a complex problem and should try to work out solutions some of which could be distinctly non-orthodox; ID, however, does not happen to be a viable solution to any problem. I think this is my approach here and elsewhere. (emphasis mine)

Thanks to the samizdat, the evidence speaks for itself.

Koonin does not accept ID. He doesn’t need to. What he is doing is challenging Darwinism and one is not allowed to do that, not even a little. If Koonin’s paper continues to reverberate, he will have to be brought into line. The question of federal research grants, for example, will have to be brought up.