A senior research scientist at the National Center for Biotechnology Information has published a paper that claims: “The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution.”

The author is Eugene Koonin of the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health, and the paper is entitled: “The Biological Big Bang model for the major transitions in evolution.”

It’s now available on-line.

Koonin is widely regarded and is certainly at the center of the scientific establishment. So it is no surprise that the orthodox Darwinian priesthood were careful in denouncing his heresy.

Witness geographer Nick Matzke, a former staffer at the Darwin-only lobby group National Center for Science Education:

I will say at the outset that I have immense respect for Eugene Koonin and his contributions to numerous fields, and criticize his work with some trepidation. However, I think with this paper he has unfortunately tumbled into a series of mistakes that have repeatedly afflicted those trying to understand macroevolution without taking sufficient care in examining the concepts they are relying upon.

This is the same Nick Matzke who told University of Idaho flagellum researcher Scott Minnich that he did not “have a friggin’ clue what [he is] blathering about when it comes to flagellum evolution.” So it seems that Nick has a long history of knowing more than specialists in their fields and putting established scientists in their place by showing them their ignorance. Regardless, what exactly is it that Matzke proceeds to criticize with very little trepidation at all?

He thinks that Koonin (and incidentally Stephen J. Gould) has mistakenly assumed certain things, like “that the series of characters that are associated with a particular ‘phylum’ always occur together and ’emerged suddenly’ with no evidence of transitions.”

Matzke clears that up for us by explaining (I assume with a straight face):

Paleontologists can and have put the Cambrian animals, e.g. arthropods and close fossil relatives, into cladograms, and the order of step-by-step acquisition of characters — i.e., a gradual transition (‘gradual’ = ‘graduated’, =step-by-step, not ‘smooth constant-rate-ism’) has been reconstructed. These prove that the origin of characteristics that we now associated with the arthropod ‘phylum’ did not all originate at once, instead they were assembled piecemeal. The transitional grades do exist in this case, it’s just that Koonin is unaware of them. The appearance of suddenness is based on staring at the living groups (or equivalently, staring at their molecular trees), treating them typologically, and then mistakenly assuming that the lack of living transitional forms means that there never were any. When you have a decent fossil record, this provides the stem groups below the crown, and inevitably (cambrian phyla, birds, whales, mammals, etc.) this shows that apparently puzzling ‘big bang’ transitions occurred in a long series of stages.

But the reality is we don’t have a “decent fossil record,” if by “decent” you mean one that has actual evidence of this “‘gradual’ = ‘graduated’, =step-by-step, not ‘smooth constant-rate-ism'”. The lack of evidence means that you cannot just assume that your theory that “apparently puzzling ‘big bang’ transitions occurred in a long series of stages” is inevitable.

Matzke continues on highlighting Koonin’s mistakes, still without trepidation.

It is simply an unavoidable, automatic, intrinsic feature of phylogenies based on crown groups that you will have less and less information about events as you trace them back. And it is inevitable, automatic, and intrinsic that the crown groups will seem more and more distinct — the modern organisms, which is what we have to look at, are actually less related, so they are more distinct! Assuming common ancestry of life on an arbitrary life-supporting planet, this would happen *no matter what* actually survived to be discovered by observers 4 billion years later. No matter what, eventually the phylogeny would trace back to a few fundamental groups, and these groups would appear to be the most distinct, the least information would be available about their origins, and they would provide the most fodder for speculation that something ‘unusual’ must have gone on.

“No matter what,” then, we know the evidence must point to Darwin, and the utter lack of evidence causes plenty of materialist speculation. Matzke himself makes an innocent assumption about common ancestry. And it leads him and other Darwinian biologists to speculate about how that might have happened. But as of this writing, it is nearly all speculation.

At last, Matzke expresses some trepidation on behalf of Koonin’s judgment in publishing this paper. Here’s how he spins it himself.

In summary, I think Koonin should give a little credit where credit is due to gradual, stepwise evolution, and not try to argue that Darwin’s eye discussion is all that orthodoxy has going for it. *Being revolutionary and unorthodox is much more fun, of course, but sometimes you’ve got to wonder how many hangovers (i.e., creationist quote-mining and general confusion over the status of evolution outside of the specialist community, and needless wrangling within the specialist community) could be avoided if scientists would exercise just a little caution during the party* (i.e., spending a little time soberly comparing their revolutionary ideas with more prosaic explanations).

The words “if scientists would exercise just a little caution” must be understood in context: They mean: if scientists would only shut up when it comes to criticizing Darwin.

And finally, we see that the devil is in the details.

Until this week I worked at the National Center for Science Education, where we oppose the ID/creationists and develop a finely-tuned sense of the sorts of things they will pluck from the literature and desperately portray as evidence that they aren’t completely nuts. However, I am well aware that telling scientists to censor themselves to avoid giving creationists talking points is a non-starter, so hopefully my comments came out as being substantive rather than just the boring voice of orthodoxy.

Or the boring voice of the political officer, tasked with making sure that all comrades toe the party line.

It isn’t often that the wise and all powerful Oz pulls back his own curtain, steps down among the mortals and confesses that the smoke and mirrors are well, just smoke and mirrors. And, he shouldn’t have to say it, but, shhhh! Don’t tell anyone.