University of Pittsburgh physicist David Snoke has posted a favorable review of Stephen Meyer’s new book, Darwin’s Doubt, on the website of the Christian Scientific Society. Someone writing under the name gandaulf thinks it was too favorable, judging by the series of critical comments he posted in response.

Although most anonymous comments don’t merit a reply, I knew from multiple credible sources that this gandaulf is a serious scientist: molecular cell biologist Martin Poenie from University of Texas at Austin. I identify him here with his permission. Since some of Poenie’s criticisms touch on my work, I’ll offer my perspective in a few posts, each focusing on one of Poenie’s posted comments.

Poenie’s first critical comment questions Meyer’s basis for thinking that the Cambrian explosion must have involved the origin of many new protein folds. According to Poenie (gandaulf), “the argument that many new folds are needed at the Cambrian explosion is without foundation.”

I suppose we could approach this topic by putting on either of two hats: the hat of an engineer (someone who designs things) or the hat of a reverse engineer (someone who dissects things to gain some understanding of how they were designed). But considering how far human technology is from designing anything like life, it would be presumptuous for any of us to wear the engineer’s hat here. The role of the reverse engineer is much humbler, and much more appropriate.

Poenie may be thinking that Meyer made the mistake of putting the engineer’s hat on, speaking about what is needed to build an animal as if he knows how to build one. But any reasonably charitable reading of Meyer would suggest that in raising the question about the requirements for building complex animals, he was approaching the question retrospectively in the manner of someone attempting to reverse engineer these systems. So let’s assume that he wrote from the perspective of a reverse engineer, not claiming to have mastered the art of making new animals, but rather recounting some of the things science has established after considerable experience in the study of cells and the dissection of animals, both genetically and anatomically, about what the evolutionary process would have needed to generate in order to build a novel form of animal life.

One well established fact is that individual species carry lots of genes that, so far as we can tell, are unique to their kind. If you search Google Scholar for the term orphan genes, you’ll get over a hundred thousand results. According to a recent paper, “Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred.” The term is also sometimes applied to genes that are restricted to groups at a higher level than species, the key point being that many, many genes are specific to particular taxonomic types. In fact, a whopping majority of the full catalog of gene types identified by genome sequencing projects appears to be restricted in this way. As this recent paper put it, “only a small set of genes seems to be universal across kingdoms, whereas the phylogenetic distribution of all other genes is restricted at different levels.”

Now, since each gene carries the sequence instructions for making a protein, it seems likely that orphan genes tend to encode orphan proteins — proteins that are substantially distinct from any found in other kinds of organisms. And if so, it also seems likely that many of these orphan proteins have distinct structures, or folds, as they are known.

Again, we could criticize this claim on the grounds that no one presently knows how to design new protein folds with any proficiency, but this is pointless because reverse engineering has shown that the inference is correct. Proteins with no detectable similarity to any protein of known structure have been found to have unique fold structures in about half of the cases examined. Considering that orphan genes typically account for 10% to 30% of the genes in each sequenced genome, and that multicellular animals have about ten thousand or more genes, this means we can expect to find many dedicated protein folds in each specific kind of animal, right down to the level of species.

So while the passage of half a billion years prevents us from actually examining the proteins that were used within the cells that made up the animals that appeared in the Cambrian explosion, the diversity and number of these animal forms leads us to believe that there must have been a corresponding explosion of protein forms. This certainly follows from the facts as we now see them, so Poenie’s assertion is misinformed.

To me his assertion also seems a bit disingenuous, in that Poenie appears to be trying to dismiss a critical problem without answering it. Protein folds are a biological reality, presently catalogued by the thousands with more being added all the time. So any theory of biological origins that can’t explain the origin of protein folds is in trouble. Period.

Drawing on a wide body of evidence, I’ve argued in detail that Darwinian evolution is in trouble for precisely this reason. Failure to explain protein folds certainly isn’t the only trouble plaguing Darwinism, but it is major trouble of a particularly stark kind that only gets worse as the science progresses. Poenie ought to grapple with this instead of trying to sweep it under the rug.