I thought The Big Think site was devoted to innovative, cutting-edge ideas. But when I went over there, I was surprised by today’s Big Thought:

What? It’s good at explaining losses (degeneration of useless structures via random mutation or selective elimination, etc.), but not gains of function? That’s an old creationist trope. What gives?

So I read the article, “The trouble with Darwin,” by Kas Thomas. It was dreadful—truly dreadful, carrying the implication that there’s something pretty wrong with modern evolutionary theory.

But modern evolutionary theory is not by any means “Darwin,” although he conflates that theory with what Darwin said in 1859. That’s not kosher because Darwin, while being right in the main, was wrong on several counts (genetics for one). And while there were problems with the theory Darwin adumbrated in 1859, advances in the last 155 years have resolved many of them. Yes, of course there are still things that evolutionary biologists don’t understand, but that doesn’t mean that there’s something wrong with its basic framework.

But first, who is Kas Thomas? I hadn’t heard of him, so I looked at his bio at Big Think. This is it:

Kas Thomas is a longtime cognitive dissident and menace to sacred-cow-kind. A graduate of the University of California at Irvine and Davis (with degrees in biology and microbiology) and a former University of California Regents Fellow, Thomas has taught biology, bacteriology, and laboratory physics at the college level. He was on the Inventions Committee at Novell, Inc. and is the holder of seven U.S. software patents. He has a long and varied background in technical writing (most recently serving as a Technology Evangelist for Adobe Systems) and is in love with the word heterodoxy.

Thomas almost certainly wrote that himself, and seems proud to be a contrarian. The problem is that when he applies his heterodoxy to evolution, he produces not a Big Think but a Big Fail.

What, exactly, are those shortcomings of evolution? It turns out that none of them are shortcomings. Some are areas where we already understand stuff (and where Thomas doesn’t seem to know the literature), and others are areas of active research. Further, the implication that evolution is impotent to explain gain of function, as noted in the “Big Idea of the Day,” is not even wrong.

Here’s what, according to Thomas, is supposed to elude evolutionary biology (Thomas’s words are indented.)

1. An understanding of speciation (and the origin of life):

Darwin’s landmark work was called The Origin of Species, yet it doesn’t actually explain in detail how speciation happens (and in fact, no one has seen it happen in the laboratory, unless you want to count plant hybridization or certain breeding anomalies in fruit flies).

Wrong. We we’ve actually seen speciation happen in nature over human lifetimes, via that same mechanism used in the lab (polyploid speciation). And we’ve seen incipient speciation among populations within a species (try the three-spined stickleback fish.)

Yes, Darwin failed to explain the origin of species because he didn’t conceive of species properly—as reproductively isolated entities—and so couldn’t address the problem. Nor did he know about genetics, which is essential to understanding speciation. But we now have a good handle on how speciation works: we know the reproductive barriers that arise in lineages to divide populations into new species, and we know something about the evolutionary forces and the genetic changes that go into making those species. I should know, for I wrote an entire book on the process (Speciation, co-authored with Allen Orr). Thomas is way, way out of his depth here. He also says this:

[Evolutionary theory] is also terrible at explaining the speed at which speciation occurs. (Of course, The Origin of Species is entirely silent on the subject of how life arose from abiotic conditions in the first place.)

Well, since speciation is often promoted by the origin of geographic barriers or climatic changes, or rare migration events, it’s not easy to predict the rate. But in many cases were are perfectly cognizant of why speciation is faster or slower. Invasion of islands, for instance, speeds it up, as does the origin of geographic barriers like the rise of mountains. The rise of the Isthmus of Panama promoted speciation in several marine species in the last 3 million years. Sexual dimorphism seems to speed up speciation in birds because it allows for stronger sexual selection, which can create mating isolation. Chapter 12 of my book is, in fact, devoted largely to investigating which factors speed up or slow down speciation.

As for the origin of life, that is of course a tough problem, for it’s hard to investigate what happened in a primordial broth even where not even cells were present. Nothing is preserved for us to see except extant descendants of the Ur-organism. But that’s hardly a criticism of evolutionary theory. We do in fact have theories to explain how life began; we just don’t yet know how to distinguish among them. But we do know some things, and one of them is this: life on earth today descended from a single primordial species. (You can Google the evidence, which involves the use of similar genetic codes in all organisms to make amino acids, the ubiquitous use of L-amino acids, phylogenetic trees, and so on.)

2. How natural selection creates new features.

Almost everything in evolutionary theory is based on “survival of the fittest,” a tautology that explains nothing. (“Fittest” means most able to survive. Survival of the fittest means survival of those who survive.) The means by which new survival skills emerge is, at best, murky. Of course, we can’t expect Darwin himself to have proposed detailed genetic or epigenetic causes for speciation, given that he was unaware of the work of Mendel, but the fact is, even today we have a hard time figuring out how things like a bacterial flagellum first appeared.

When I saw this, and the reference to both the “tautology” argument (a creationist notion long since discredited) and the bacterial flagellum (a trope of the Intelligent Design [ID] movement), I realized that Thomas is simply regurgitating ID and creationist “problems” with evolution. That’s a pretty dire thing to publish on the Big Think.

In fact, we do have a good idea how the bacterial flagellum first appeared: it is related to a secretory system that was already present in bacteria. If you want to see a likely explanation, read Pallen and Matzke’s paper in Nature Reviews Microbiology (vol 4:784-790; 2006).

I’m not sure what Thomas means by the murkiness of how new survival skill arise, but we now have several hundred examples of natural selection in action, which is of course is how those skill arise. We have seen the origin of antibiotic resistance in bacteria, insecticide resistance in insects, changes in the size of finch beaks, the darkening of moth colors due to selection in a new, polluted environment, and many other cases (Wikipedia gives some as well, and for many other examples you can read John Endler’s book Natural Selection in the Wild.) These are all, of course, “survival skills”, or rather “reproduction skills”, since the currency of natural selection is offspring number.

3. “Gain of function.”

When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Most mutations lead to loss of function, not gain of function. Evolutionary theory, it turns out, is great at explaining things like the loss of eyesight, over time, by cave-dwelling creatures. It’s terrible at explaining gain of function.

This again is a creationist trope, which makes me even more certain that Thomas has simply absorbed and regurgitated things from the ID literature (see below as well). Yes, of course most mutations are deleterious, but new ones arise that are advantageous, and those can lead not to loss of function (which we understand about as well as we understand gain of function) but to new functions.

Gene duplication, whereby a single gene simply duplicates, resulting in two or more copies on a chromosome, is a great way to gain functions, as it has in human hemoglobin (the various forms of human hemoglobins, which have different functions, arose from duplication of one ancestral locus). My colleague Manyuan Long in Chicago has shown the origin of new genes in fruit flies—genes with novel functions—by splicing together drastically different genes.

Further, Rich Lenski and other microbiologists have shown the origin of new functions in bacteria in both the lab (ability to digest citrate) or the wild (bacteria that evolved the ability to digest nylon).

We can see new functions originating in the fossil record, too. They come from coopting of old functions, which is how natural selection almost always works. The legs of land animals evolved from the bony fins of ancestral fishes. Feathers started out as small filaments on dinosaurs, useless for flying but perhaps good for thermoregulation. The swim bladders of fish evolved from lungs (people usually get this backwards), and swim bladders surely represent new functions. I could go on and on, but this is enough to show that Thomas is again out of his depth, spewing ID claims without knowing that they’ve already been refuted.

4. The Cambrian Explosion, human intelligence, and other stuff.

[Evolutionary theory] doesn’t explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids, or the rapid recovery (and net expansion) of the biosphere in the wake of at least five super-massive extinction events in the most recent 15% of Earth’s existence.

The mention of the Cambrian explosion, of course, comes straight from Stephen Meyer’s new Intelligent Design book saying that because we don’t understand how many major body plans originated so rapidly (by “rapidly,” we’re talking 20 million years), Jesus must have done it. But our lack of understanding is due not to a paucity of theories, but to a surfeit of theories (oxygen, predators, gene regulation, and so on), and our present inability to distinguish among them.

And yes, we don’t understand how human intelligence arose: again, we have a surfeit of theories but a paucity of evidence. Some scientists, like Dick Wrangham, think that our big brains were the result of the taming of fire, others by sexual selection, tool use, bipedality, or other features. Perhaps some day, when we can unravel the genetic basis of differences in intelligence between humans and other primates, we’ll understand more.

But these are simply the problems inherent in any historical discipline, like science and cosmology. A science that has solved all its problems is a dead science. Here are a few more unsolved problems of evolutionary biology: how did sexual reproduction originate? What is the evolutionary significance in the difference of human morphology among ethnic groups? How does sexual selection operate to create differences between males and females? How important is “neutral” genetic variation in the evolution of trait differences (not DNA sequences) between species and populations?

At the end, Thomas offers a lame disclaimer:

Of course, the fact that classical evolutionary theory doesn’t explain these sorts of things doesn’t mean we should abandon the entire theory. There’s a difference between a theory being wrong and being incomplete. In science, we cling to incomplete theories all the time. Especially when the alternative is complete ignorance.

Note that “Darwin” has now been replaced by “classical evolutionary theory,” which I take to mean “modern evolutionary theory,” or neo-Darwinism. That, after all, is the current state of the art. So why did Thomas drag Darwin into his title? Because he wanted attention.

And yes, Thomas says that, just maybe, evolution theory might not have to be abandoned. But the damage has already been done. In his piece, Thomas raised a number of non-problems with evolutionary theory that will mislead the general reader, and most of those problems are lifted from the Intelligent Design/creationist playbook. That kind of article does not belong on The Big Think. It’s a lame, error-ridden piece designed to bolster Thomas’s self-described penchant for heterodoxy and sacred-cow goring.

“The trouble with Darwin” is a mischaracterization of evolutionary theory, laden with distortions. It’s damaging to the public understanding of science, for the average reader won’t know the relevant science, and it’s contemptible. Shame on The Big Think. And, especially, shame on Thomas.

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UPDATE: Reader “profon” posted Thomas’s Twitter response to the comments, and many of those responses cited scientific arguments against Thomas’s position. I want to put profon’s capture above the fold, for it shows how clueless Thomas really is about his opposition:

When someone calls their intellectual and scientific opponents “haters,” then you know they’ve lost all credibility. Thomas won’t respond except to ad-hom his “haters”. That’s truly lame.

h/t: Ant