When is PuffHo going to realize that they’re publishing criticisms of evolutionary biology that are deeply misguided? Do they have no worries about misleading the public with bad science?
I refer to the recurring posts of my Chicago colleague James Shapiro, who is making a PuffHo blogging career out of attacking “neoDarwinism,” the modern theory of evolution. Not that we haven’t a lot to learn yet about evolution, but Shapiro has repeatedly been going after the importance of natural selection (see screenshot below) without offering a viable alternative. That is, Shapiro sees organisms as “self organizing” units controlled by “natural genetic engineering”, which of course doesn’t explain in the slightest why those organisms are adapted to their environments.
I almost don’t have the heart to criticize his latest piece, “Why the ‘gene’ concept holds back evolutionary thinking“, except that there may be some people out there (including the science editor of PuffHo) who think that Shapiro’s lucubrations are scientifically supported. They aren’t: they’re the misguided ideas of a contrarian who thinks that he alone has the key to overturning the modern theory of evolution.
Now we do know a lot more about the genome than we did when Beadle and Tatum proposed their “one gene/one enzyme hypothesis.” We know now that there are more than just protein-producing units in the DNA: there are parts of those units that regulate their expression (though this was posited by Jacob and Monod in the early Sixties), there are non-coding regions within genes (“introns’) that get snipped out, there are “transcription factors” (protein-producing genes) that regulate the expression of many other genes (e.g., Hox genes), and now we know that there are “microRNAs”, small molecules that serve to shut off genes.
In other words, we’re starting to learn how genes (originally defined as “stretches of DNA that make proteins”) are regulated, and the definition of a “gene” has become somewhat blurry. But I still don’t see the harm in using its original definition so long as we realize that the genome comprises much more than just protein-coding units. (The ENCODE project, however, has drastically oversold the notion that what we thought of as “useless” DNA is really functional. There’s still a lot of junk in our genome that doesn’t seem to do anything.)
Anyway, Shapiro’s point is that our modern understanding of how genomes are constructed and regulated when building organisms has completely overturned the modern theory of evolution—including the importance of natural selection—by making the notion of a “gene” fuzzier.
He’s wrong, and he’s wrong because he doesn’t seem to understand how evolution works.
The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term “gene.” In March 2009, I attended a workshop at the Santa Fe Institute entitled “Complexity of the Gene Concept.” Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term.
The modern concept of the genome has no basic units. It has literally become “systems all the way down.” There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other “DNA elements” (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.
. . .A particularly important novelty highlighted by the Genome Biology paper is the unexpected and burgeoning role of so-called “non-coding” RNAs (ncRNAs) in all aspects of genome function. Cells transcribe many functional ncRNAs from so-called “intergenic” regions that had no functional importance according to the genocentric theory.
From an EVO-DEVO point of view, it is important to note that many morphogenetic changes in evolution occur at regulatory sites rather than coding sequences. Moreover, we continue to discover how many of these changes occur “intergenically” and involve supposedly “selfish” mobile elements. . .
. . . Conventional thinkers may claim that molecular data only add details to a well-established evolutionary paradigm. But the diehard defenders of orthodoxy in evolutionary biology are grievously mistaken in their stubbornness. DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function.
I’m baffled. Yes, these new discoveries are exciting, but they have absolutely no bearing on two issues: 1) whether natural selection acts on these new bits of the genome, and 2) whether natural selection is the primary process that produces “adaptations” in organisms. After all, all these units of the genome are still bits of DNA residing within the genome (usually on chromosomes), and therefore must obey the laws of population genetics. And those laws say that if a bit of DNA helps the organisms’s reproduction, it proliferates. If it hurts the organisms’s reproduction, it gets expunged from the population. That’s natural selection. Ergo, all of those genomic things that regulate other genes are subject to natural selection (and, of course, genetic drift).
In fact, there’s little doubt (except in the mind of contrarians like Shapiro) that the mechanisms of gene regulation themselves evolved by natural selection.
Shapiro still hasn’t provided a credible alternative theory of how adaptive features of an organism arise. “Natural genetic engineering” certainly can’t. And until he provides a credible theory, he will be a voice crying out in the wilderness, thinking himself a paradigm-changer but sounding more like a crank. For it is sentences like these—the last in Shapiro’s piece—that verge on the crankish:
Shortly before he passed away, Kurt Vonnegut told a radio interviewer that the public senses something amiss with what they have been told about evolution. Maybe the new, high-tech understanding of genomes will help reverse the disastrously low level in the U.S. of public understanding of evolutionary biology.
That is real hubris—to think that if evolutionists would only agree with your bogus biological notions, creationism would decline! Nope, it’s not misunderstanding of modern genetics that buttresses creationism—it’s religion. Only someone completely blinkered could think otherwise.
It isn’t the “gene concept” that holds back evolutionary thinking; it’s not only creationist opposition, but also people like Shapiro who, without any scientific support, mislead readers by arguing that the modern theory of evolution is fatally flawed.
Finally, from the comments, here’s Shapiro’s explanation about why I criticize him:
Sorry, Dr. Shaprio, but I’ve built my career on understanding the genetic basis of how species arise, not on “accepting the central role of natural selection as a creative force in evolution.” I do think natural selection is the only viable explanation for the adaptations of organisms, and we have plenty of evidence for that contention, but it’s hardly the cornerstone of my career.
And, thank Ceiling Cat, I haven’t aspired in my middle age to overturn well-established paradigms. The reason I defend natural selection is not because I’m somehow wedded to that idea to buttress my career, but because it is still the best explanation that we have for adaptations.