The good thing about the internet is that you can debate scientific or other intellectual issues in almost real time, though the downside is that you don’t have reams of time to ponder and refine your answers.

Two days ago I criticized an article by writer Kas Thomas at Big Think: “The trouble with Darwin.” Thomas made many errors in his claims about the problems with modern evolutionary theory, and I tried to answer them. So did many commenters, both on this site and at Big Think.

Thomas replied by first calling his critics “haters,” and then by flaunting his biology degrees, tw**ting, “You need to get a couple of degrees in bio sciences from a real university (like UC Irvine or UC Davis) as I did, then come back and we’ll talk.” And he said that despite noting on another site that he “never used those degrees.”

Of course none of this constituted response to my original scientific criticisms, or those raised by the many commenters on Thomas’s original post.

For example, he claimed that we had no idea how speciation worked (cue the Juggalos here: “f*cking speciation—how does that work?). He claimed that we had no clues about how natural selection created new features (although we could understand how it eliminated features). He claimed that we didn’t understand how the bacterial flagellum evolved, or how the Cambrian Explosion proceeded, and so on.

Many of these criticisms—and note that Thomas’s title clearly implied that modern evolutionary theory was in trouble because of these problems—were taken from the creationist playbook. It’s no coincidence that Thomas used the flagellum, the Cambrian Explosion, and the inability of evolutionary theory to explain “gain of function” as his Big Problems with Darwinism. Those are, of course, common tropes of Intelligent Design flunkies.  Clearly, Thomas had simply digested the ID literature and regurgitated it at Big Think. I patiently tried to explain in my critique how many of these criticisms were misguided, and that our lack of understanding of how some things evolved does not constitute a fatal flaw in modern evolutionary theory.

Now, at his oddly named website assertTrur(), Thomas attempts a more substantive reply in an equally oddly named post, “Scientists should be humble, not arrogant.” You’ll recognize that title, too, as a common STFU tactic of theologians and faitheists towards scientists. But arrogance is writing provocatively titled articles without the knowledge to back them up—and that Thomas does that in spades.  In calling for “humility,” Thomas aligns himself closer with theologians and other critics of science. It’s the last resort of the desperate.

Thomas’s hurt feelings are paraded at the beginning of his new piece which, as a whole, is not a response to the scientific errors noted in his original post. (His words are indented.)

It’s shocking how much venom and bile you can stir up by criticizing Darwin in public. I more or less expected, when I wrote a post critical of evolutionary theory at BigThink.com, there’d be a few heated comments. I didn’t expect so many of the 350+ comments to be so heated. Quite a few of the comments were and are just plain ugly. And the most vitriolic attacks are coming not from the religious right, but from supporters of Darwin!

Looks like I struck a nerve.

Shades of Chris Mooney! For the “struck a nerve” trope is one often used by Mooney when making silly arguments that his critics jumped all over. It is a non-answer meant to imply that you’ve said something telling and thereby angered your misguided opponents. But the “nerve” that Thomas struck was not our knowledge that evolutionary theory is deeply problematic, but our resistance to the deep-seated ignorance shown by Thomas’s piece, and the fact that it was published at a once-reputable site.

Thomas goes on to aver that he is not a creationist, and that he doesn’t believe in “magical thinking.” Why, then, did he just regurgitate arguments taken from creationists? Did he not think before he wrote?

He then flaunts his degrees again—you know, the ones he didn’t use:

More than one commenter suggested I get some biology training before writing about evolution. (One person touted his bio degree from the University of California at Irvine, unaware that I also have a degree in biology from UCI.) I guess I should have made clear, up front, that I have two degrees in biology: a B.S. from UCI and a master’s in microbiology (summa cum laude) from UC Davis, where I was a Regents’ Fellow. I took (and passed) qualifying exams for a Ph.D. One of the specialty areas I was examined in was molecular genetics.

Well, none of that training is in evolutionary biology per se, but let’s put that aside. The fact is that had Thomas done even the minimal amount of research, or consulted a real evolutionary biologist, he would have known that his criticisms of evolutionary theory were tripe. He would have known, for instance, that we know a good deal more about speciation than we did in the 1930’s, and a huge amount more than Darwin did. (Despite the title of Darwin’s book, he had very little to say about how one lineage divides into two or more.) And we know in many cases precisely how “gain of new functions” arises. Gene duplication, which I mentioned in my original critique, is one; and the cooption of old features to new (e.g., lactate dehydrogenase enzymes recycled to make lens proteins in animal eyes) is another.

In response, he either stands his ground or makes even more mistakes. Here’s an example of the latter:

What did I say in my BigThink blog that was so shocking? First let’s get clear what I did not say. One of the commenters claimed I said changes in DNA were not responsible for evolution. I never said that. What I said was that point mutations (of the kind the give rise to single-nucleotide polymorphisms) are almost certainly not a major driver of evolution. We know this because it’s been demonstrated many times that the majority of non-neutral point mutations are deleterious, leading to loss of function, not gain of function. Spend some time reading about “Muller’s ratchet” if you don’t believe me.

The fact is that in many, many cases, we know that point mutations are drivers of evolution; in fact, I’d say we have enough evidence to say that they are major drivers of evolution. Even in gene duplication, where the new functions arise after genes duplicate and then diverge (e.g., alpha versus beta hemoglobins), you have to have those post-duplication point mutations to get adaptive evolution. Or, when adaptation arises via changes in “regulatory regions” (or transcription factors: those proteins that regulate the expression of other genes), that, too, occurs via point mutations.  And even in “neutral evolution” (changes in DNA that aren’t “adaptive,” but either neutral or slightly deleterious), we see divergence via the accumulation point mutations as well.

I am in fact hard pressed to think of much evolution, adaptive or not, that doesn’t involve point mutations. Simple gene duplication without divergence, so that you duplicate genes to make a lot more of an identical protein, is one example. (I believe that’s how cold-water fish make antifreeeze proteins.) But Thomas is simply wrong in his logic that because most mutations are deleterious, point mutations cannot be a major driver of evolution.  Mutations are numerous and recurrent, and some of them will be beneficial. They just have to be sufficiently frequent to be the substrate of adaptation. And we know that populations have reservoirs of low-frequency mutations that are deleterious but can become adaptive when the environment changes. Her are two examples: white coat-color genes in mice that are maladaptive in their normal habitats but are useful when those mice invade white beaches. Or, the low frequency of insecticide resistance genes in mosquitoes that can become adaptive once humans apply insecticide. The success of artificial selection in almost every case testifies to the reservoir of deleterious forms of genes (kept in the population by recurrent mutation) that can suddenly become useful.

But Thomas’s real failure to educate himself is shown in what he says about speciation, a topic with which I’m well acquainted, having written an entire 500-page book on it with Allen Orr.

How, then, does speciation occur? We don’t know. No one has seen it occur in the lab. Nature no doubt relies on a variety of tactics, some of which we know a good deal about, many of which we barely understand, no doubt others of which we haven’t yet discovered. We know that sexuality (which is probably around a billion years old) has led to an explosion of diversity (and has kept Muller’s ratchet from sending countless species into extinction). On a molecular level, there are still many things we don’t understand about how chromatin is managed, how micro-RNA is regulated, when and why DNA methylases come into play, the relative importance (or unimportance) of translocases, and much, much more. To assert that we understand how speciation occurs is to assert a half-truth. It’s like saying we understand the weather because we can measure atmospheric pressure.

Of course we don’t know everything about how speciation worked, but we now understand the process a lot more than we did in, say, 1930.

We know that it involves the evolution of barriers to reproduction, so that to achieve speciation, two populations must become mutually intersterile (i.e., unable to produce fertile hybrids). We know that in many cases that intersterility is promoted by natural selection, and occurs most readily when the populations are geographically isolated. We know in some cases the precise genes involved in reproductive isolation, and how they interact with other genes. We know that speciation is unlikely to occur without the involvement of natural selection, and is promoted by things like sexual dimorphism. We know that a substantial amount of plant speciation occurs via chromosome duplication (polyploidy), and we know exactly how this happens. We also know that some species of plants and animals have evolved reproductive barriers after hybridizing with other species (“hybrid speciation”), and, as with polyploidy, we can replicate that process, at least with plants, in the lab.

Believe me, I could not have written that long book with Allen just to say, “Well, folks, we still don’t know anything about speciation.” The book, which Thomas clearly hasn’t read, is a compendium of what we do know about speciation.

As for methylases, translocases, the management of chromosomes and the regulation of RNA, Thomas is just throwing sand in our faces. We have no idea whether any of those things are involved in speciation (except for changes in chromosome number and structure, which we do understand). Thomas is just spewing molecular-biology jargon to sound knowledgeable.

Finally, Thomas emits some god-of-the-gaps arguments. That is, he doesn’t invoke God, but argues that something is wrong with evolutionary theory because we can’t yet explain everything. To wit:

One of the major embarrassments of modern biology is that more than a decade after having sequenced the human genome, we still don’t know what most of our DNA does: We can account for 30,000 human genes (which is not even ten times the number of genes in E. coli). Meanwhile our DNA has enough base-pairs to encode 3 million genes. But we’re pretty sure the “true number” of human genes is under 50,000. What does all that DNA do? We have some hints at answers, but no more than that. (Note: When the surplus of DNA in the human genome was first discovered, scientists called it “junk DNA.” It took years for that unfortunate terminology to disappear.) The honest answer is, we’re still not even close to understanding what all our DNA is doing.

So frickin’ what? First of all, that’s not evolutionary theory, but molecular genetics. It has nothing to do with “Darwinism”, as Thomas mistakenly calls modern evolutionary theory. And, yes, we don’t understand the function of all “junk DNA,” but we do understand some of it: inactive ancient viruses that have inserted themselves into our genome. We also know that we have inactive remnants of ancient DNA in our genome that were once active in our ancestors. One example: our many inactive olfactory receptor genes that we no longer need because we’re auditory and visual rather than olfactory beasts.

Of one thing I’m sure: eventually we will resolve the question of what all that extra DNA is doing. But in the meantime, in what sense is this an “embarrassment” to modern biology? Only Thomas, with his drive to discredit evolutionary biology, could see unsolved problems as “embarrassments.” They are challenges, and without them all science would grind to a halt. Is “dark matter” an embarrassment to physics? I don’t think physicists would agree. They are excited by this new possibility.

Finally, after playing the “butthurt” card and the “I haz credentials” card, Thomas plays the “humility card,” one that theologians often have up their sleeve when they’re losing at science poker:

It’s been my experience that the best scientists are humble, rather than proud. They’re willing to concede the immensity of what they don’t know. Arrogance and over-confidence are hallmarks of immaturity, in science as well as in life.

So we’re immature? Give me a break! All of us scientists concede what we don’t know, and where the unsolved puzzles lie. I mentioned several of them in my previous post.

And talk about overconfidence: what about a man who makes specious arguments about problems with speciation and inability to explain evolutionary novelty—all without having read the relevant literature? Sorry, but I won’t be lectured at by Thomas. I know where the unsolved puzzles are in my field, but I also know what we do know. So I don’t need Thomas to tell us this:

The list of things we don’t understand is far longer than the list of things we do understand. If we don’t understand that, all is lost.

That’s just a platitude. The person who is lost here is Kas Thomas, who badly needs to brush up on his evolutionary biology.

One thing is sure, though: the man is sufficiently arrogant that we’ll never hear him back down from his claims about speciation, evolutionary novelty, or point mutations. He’s not humble enough to admit that he was mistaken. And he’s not humble enough to stop flaunting the biology degrees that he admits he never used.

I have put a link to this post as a comment on Thomas’s website. But now I’m wondering why I just wasted an hour of my time—an hour when I could have been doing useful things like reading about the latest doings of the Kardashians—responding to someone who seems impervious to reason.