As Wikipedia notes, Project Syndicate “is an international not-for-profit newspaper syndicate and association of newspapers. It distributes commentaries and analysis (‘opinion pieces’) by experts, activists, Nobel laureates, statesmen, economists, political thinkers, business leaders and academics to its member publications, and encourages networking among its members.”

I can’t remember how I came across an article featured on Project’s Syndicate‘s latest webpage, “Evolutionary theory’s welcome crisis,” but a hat-tip to the reader who gave me the link. When I saw that title, and learned that the author, John Dupré, is a professor of philosophy of science at the University of Exeter and also director of Egeneis, a genomics institute at the university, I got worried.  We often see molecular biologists (e.g., James Shapiro) and philosophers (e.g., Thomas Nagel and Jerry Fodor) proclaiming the imminent death of modern evolutionary theory, so someone who wears both hats could be especially muddled—and dangerously misleading.  And my suspicions were correct. Dupré indeed proclaims a severe crises in evolutionary biology, but he’s absolutely wrong. The theory is not in crisis, but, as usual, the author simply describes new that supplements the theory but doesn’t lead to its drastic revision.

While decrying Biblical creationism as a threat to science, Dupré nevertheless sees that the modern, or “neo-Dawinian” theory of evolution is outmoded, and is about to experience a big sea change.

The creationists are right about one thing: contrary to the impression given by much popular writing on the subject, the theory of evolution is in crisis. But this is a positive development, because it reflects the non-linear progress of scientific knowledge, characterized by what Thomas Kuhn described in his influential book The Structure of Scientific Revolutions as “paradigm shifts.”

So what’s the big crisis? The way Dupré describes it at first, things don’t look so dire:

For the last 70 years, the dominant paradigm in evolutionary science has been the so-called “new synthesis.” Widely publicized in recent years by Oxford evolutionary biologist Richard Dawkins, the new synthesis unites Darwin’s theory of natural selection with Mendelian genetics, which explains heredity.

The current crisis in evolutionary science does not imply complete rejection of this paradigm. Rather, it entails a major, progressive reorganization of existing knowledge, without undermining the fundamental tenets of evolutionary theory: organisms alive today developed from significantly different organisms in the distant past; dissimilar organisms may share common ancestors; and natural selection has played a crucial role in this process.

Other assumptions, however, are under threat.

Well, since the factors outlined in the first and second paragraph are the major parts of modern evolutionary theory, and are still valid, what assumptions are now so threatened that they’ve engendered a crisis? Dupré sees four:

• Horizontal gene exchange.  As Dupré notes:

Other assumptions, however, are under threat. For example, in the traditional “tree of life” representation of evolution, the branches always move apart, never merging, implying that species’ ancestry follows a linear path, and that all evolutionary changes along this path occur within the lineage being traced. But examination of genomes – particularly microbes – has shown that genes moving between distantly related organisms are an important catalyst of evolutionary change.

Well, yes, we’ve known for a while that microbes can have “wide gene exchange”—movement of chunks of DNA between distantly related species of bacteria. That also can happen in eukaryotes: rotifers, for example, have genes from bacteria and plants in their own DNA, pea aphids have genes from fungi, and, more closely-related species, like butterflies, can exchange genes by hybridization that can be advantageous and used by natural selection to produce changes in pattern.  But this doesn’t constitute a crisis—it’s imply a very interesting finding that shows that variation in a genome can arise by processes other than mutation of an organism’s own DNA. The disposition of that variation still must occur via either natural selection (it can be good or bad) or genetic drift (no effect on fitness).  This hasn’t really changed the theory of evolution one iota, though it’s changed our view of where organisms can acquire new genes.

• Evolution based on “macromutations.”  One of the assumptions of modern evolutionary theory is that complex adaptations are usually built from several to many genes of small effect.  That doesn’t mean that genes that have large effects don’t ever occur, but they’re posited on theoretical grounds to be rare.  Dupré claims that we now know that much of evolution indeed rests on macromutations:

Moreover, the new synthesis assumes that the main drivers of evolution are small mutations generated by chance within a species. But recent evidence suggests that large changes, caused by the absorption of a chunk of alien genetic material, may be just as significant. Indeed, the absorption of entire organisms – such as the two bacteria that formed the first eukaryotic cell (the more complex cell type found in multicellular animals) – can generate large and crucial evolutionary change.

This is true, but what Dupré doesn’t mention—and I hope he knows better, because he should if he’s learned anything about evolution—is that these big events of symbiosis that produced mitochondria, chloroplasts, and perhaps flagella, are extremely rare, and we’ve known that for a few decades.  This is not new information, and it hasn’t caused a “crisis,” for most adaptive change within species is, contra Lynn Margulis, not caused by symbioses or even horizontal gene exchange. When we examine the genetic basis of adaptations, we find that it is almost invariably due to mutations within an organisms’s DNA, not ingestion of another species.  Moreover, for complex adaptations, several to many genes are involved, although for simple traits, like a color change in moths (e.g., speckled to black in Biston betularia, the “peppered moths”) single mutations can be important.

• Evolution based on epigenetic change (i.e., environmentally induced changes in DNA that aren’t coded in the genome). As Dupré notes,

Recent developments in molecular biology have put the final nail in the coffin of traditional genetic determinism. For example, epigenetics – the study of heritable modifications of the genome that do not involve alterations to the genetic code – is on the rise.

Yes, we now know that DNA can be modified in regular ways: “imprinted” in different ways by male vs. female parents, and that imprinting can have crucial evolutionary significance, for example in producing conflicts between paternal and maternal genes in fetuses.  But what Dupré doesn’t recognize is that this methylation is actually coded in the DNA itself (which tells a genome how to get modified when it finds itself in one sex or another), so yes, it does involve alterations of the genetic code. Other kinds of epigenetic change that are produced solely by the environment and not by the genome itself, such as changes in weight or flower color, are not stable because the DNA reverts to earlier forms. Hence such changes do not last more than a few generations, and so cannot be the basis of permanent evolutionary change.

• Evolution based on miRNA (“microRNAs”).  We have learned in the last few years that tiny molecules of “microRNA” can play a crucial role in regulating gene expression since they can bind to the “messenger RNA” that produces proteins, preventing protein production.  As Dupré notes:

And the many kinds of small RNA molecules are increasingly recognized as forming a regulatory layer above the genome.

Well, no, not really, because microRNAs are made by the DNA: their production is coded in the genome!  Thus they are in no sense a “regulatory layer above the genome,” any more than regulatory proteins are “above the genome.” The evolutionary dynamics of microRNAs can be completely analyzed and understood in a normal evolutionary framework: whether or not changes in their code are adaptive will determine if they increase or decrease in frequency, or float around if they have no effect on fitness.

So what Dupré has done here is combine several interesting findings about evolution—findings that are easily incorporated into our existing framework—and cast them as somehow causing a “crisis” for modern evolutionary theory. While these findings are interesting (evolution would be boring if we didn’t find new phenomena to study), they’re not paradigm changing, as Dupré insists, nor do they undermine the gene-centered framework of modern evolutionary biology:

Beyond undermining the gene-centered theories of evolution that have dominated public consciousness for several decades, these developments call for new philosophical frameworks. Traditional reductionist views of science, with their focus on “bottom-up” mechanisms, do not suffice in the quest to understand top-down and circular causality and a world of nested processes.

Almost every word in these two sentences is either wrong or obscure.  Gene-centered theories are not undermined. We do not need a new philosophical framework for evolution, much as Dupré wants one. Traditional reductionist views are still valid and yielding valid insights (what is microRNA other than a “bottom-up” phenomenon that regulates genes?).  And what in the world is “top-down and circular causality”? I don’t think he means the environment, which is a big factor in natural selection. Absent the environment, there are no “top down” processes in evolution: everything is bottom up.  “Top down” in fact, is a phrase used by theologians to add God to the workings of science, which has always been best understood by reductionist thinking (granted, there are also epiphenomena like the wetness of water, but those must always be consistent with lower-level phenomena). Now Dupré doesn’t seem to be a goddie, but he still seems susceptible to the nebulous woo of “top down causation.”

What bothers me about Dupré is not so much his bringing to public attention new insights into how organisms work, for that’s a good thing. What bothers me is that, like so many others, he casts these new discoveries as things that throw the theory of evolution in crisis. And that plays into the hands of creationists, no matter how strongly Dupré decries creationism. As an evolutionary biologist—which Dupré is not—I think I’d know if my field was in crisis.  Yet I haven’t heard any recent lamentations from my colleagues.

And there are findings that could put modern evolutionary theory in crisis. If we found, for example, that in most species mutations weren’t random, that is, if they didn’t occur irrespective of the adaptive “needs” of the organism, that would be a major revision of evolutionary theory.  But it hasn’t happened.

As usual, rumors of the death of evolutionary biology are greatly exaggerated.