Category: epigenetics

Another journalist falls for the modern-evolutionary-theory-is-woefully-incomplete scam: says human agriculture is an epigenetic “adaptation”

November 30, 2016 • 11:45 am

Yet another journalist seems to have fallen for the epigenetics mavens: those revisionists who think that a form of Lamarckian inheritance can be important in evolution. These people claim that the environment itself directly changes the DNA, not by altering the sequences of bases, but by somehow placing methyl groups on some of the DNA bases (“methylation”). Such changes can be passed on to the next generation, and so the revisionists (aka “careerists”) argue that the inherited epigenetic changes could be subject to natural selection, leading to a form of evolutionary change that is, roughly, the inheritance of acquired characters.

In a new piece on Big Think,”How about a new theory of evolution with less natural selection?“, journalist Robby Berman pushes this idea, noting that it was a big part of the recent Royal Society conference on “New Trends in Evolutionary Biology: Biological, Philosophical, and Social Science Perspectives.” (I discussed the problems with this conference’s proposals here.)

Among the problems with seeing environmentally acquired epigenetic changes as an important cause of adaptation—problems that I’ve discussed ad nauseam—are the following:

  • Virtually all epigenetic markers are wiped clean as the DNA goes through gamete formation, and wiped clean within a few generations after they arise. Such changes cannot serve as a basis for permanent adaptation, which is what the epigenetics mavens claim.
  • There is little evidence for environmentally induced epigenetic changes in vertebrates, an observation relevant to the article under discussion.
  • When geneticists are able to map adaptive changes in the genome using crosses and DNA sequencing, they invariably show changes in the base sequence of DNA, not to methylation of those bases.
  • If some DNA base sequences are more liable to environmentally-induced methylation themselves, and those methylated changes are adaptive, then the susceptible DNA base sequences will increase in frequency. But this is straight natural selection on the DNA, not a drastic revision of how natural selection works.
  • Some methylation changes are coded by the DNA: DNA bases that say to the genome “put methyl groups on bases X, Y, and Z”, and that form of methylation can be adaptive, for example in mediating parent-offspring conflict. But this form of evolution is not not induced by the environment; rather, it’s coded in the genome itself, and evolves via conventional natural selection (i.e., mutations that change the DNA sequence in an adaptive way become more frequent.)

We still have not a single instance of adaptive evolutionary change arising via environmental, epigenetic modification of the DNA, and yet people are still talking as if it’s a serious difficulty for modern evolutionary theory. Well, when you show me a dozen cases of it, then we’ll talk. In the meantime, the rest is simply unfounded speculations issued by ambitious evolutionists.

And such speculation is rife in Berman’s Big Think piece. (I’m starting to think that not a lot of thought goes into some of the Big Thinks.) First of all, though admitting there are detractors, Berman accepts epigenetics as a major challenge to evolutionary theory. It isn’t—at least until we get some data. Second, he raises the idea that human agriculture, of all things, is a genetic adaptation that arose through environmental modification of the DNA. Get a load of this:

Still, epigeneticists hope the field can help explain evolutionary changes that don’t seem to be accounted for by modern evolutionary synthesis.

For example, speaking at the Royal Society was Melinda Zeder, who talked about the way in which modern synthesis fails to provide a reason for mankind’s turning to agriculture 10,00 years ago and its ensuing evolutionary impact. Growing crops may have taken years, so there could not have been a short-term evolutionary benefit to it. As Zeder told Quanta, “You don’t get the immediate gratification of grabbing some food and putting it in your mouth.” It’s also been theorized that a climate shift caused agriculture to bloom, but there’s no evidence of such a shift.

Zeder suggests we take a different view of humans at the time as creative individuals who deliberately decided to change their environment by farming, pushing human evolution in that new direction. This process is called “niche construction,” and it’s more than just a human behavior; think beavers and their dams.

First of all, Berman doesn’t seem to realize that “niche construction”—the idea that organisms, by their behavior, can change their environment in a way that affects their future evolution—is not the same thing as epigenetics. Niche construction involves perfectly normal adaptive changes in the DNA that are not induced by the environment, but simply adapt the organism to a novel environment it encounters due to a change in behavior or physiology (and those changes themselves, like leaving the water for the land, could have resulted from conventional natural selection).

Berman has no idea what he’s talking about here.

But that aside, can epigenetics explain agriculture? Why do we assume, as both Zeder and Berman seem to have done, that growing crops is coded in the human genome? It seems much more likely that it’s a cultural adaptation: something useful figured out by our ancestors and then passed on by learning. If humans were raised in an environment without having any access to such learning, would their genes tell these naive people to put seeds into the ground? I doubt it! There’s no need to explain agriculture as a genetic change, much less a Lamarckian, epigenetic change.

Nor do we have to invoke a climate shift as the impetus for agriculture. All we need to happen is for someone to discard seeds and see that useful plants grew from them. Or to have someone pick some useful plants and realize that they could be propagated from shoots or seeds.

Finally, it often takes less than a year to grow a crop, so why does Berman repeat the idea that “growing crops may have taken years.” It may have taken years to refine agriculture, but not to get it started.

This is what we call abysmal scientific journalism.  But does Berman know any science? His Big Think bio describes him like this:

I’m a writer, musician, and father living in the very upper Midwest with my wife, two daughters, three cats, and countless questions. I’m especially interested in animal rights, creativity, politics, the nature of things and time, and in making a worthwhile contribution. You can follow me @everyrobby.

Well, good about the cats, but this doesn’t show much training in science. Now I don’t often go after people for lacking formal sceintific credentials, but when someone fails as spectacularly as Berman, one might pin the blame on his lack of scientific training. At any rate, the Big Think has created a Big Stink, making naive readers think that epigenetics is not only a novel and important source of evolutionary change, but one responsible for a cultural shift—agriculture—that might not even be a genetic adaptation.

Woe is me! Or, as the landsman says, “Oy vey!”

Mukherjee corrects his new book in light of epigenetics kerfuffle, still defends his mischaracterization of gene regulation

July 30, 2016 • 10:00 am

You may remember—but not want to remember—the Big Epigenetic Kerfuffle documented on this website (see list of pieces here). It involved Siddhartha Mukherjee, doctor and Pulitzer-Prize-winning author, who was taken to the woodshed by a passel of famous molecular biologists for distorting the state of epigenetics research in a popular article. Mukherjee’s piece, “Same but different,” was printed in the May 2 issue of The New Yorkern and was a summary of (not an extract from) his new book, The Gene: An Intimate History.

For an overview of the whole episode and the scientific issues at hand, see Chris Wollston’s piece in Nature, “Researcher under fire for New Yorker epigenetics article.” In short, many prominent workers in the field felt that Mukherjee’s piece completely ignored what we know about how genes are regulated—largely by small bits of RNA and “transcription factors”—proteins produced by the DNA—in favor of Mukherjee’s pet hypothesis, “epigenetic” regulation via bases of the DNA methylated by the environment or, alternatively, by the histone-protein scaffolding of the chromosomes. There is, in fact, virtually no evidence for Mukherjee’s thesis, nor for the proposition that inherited changes in DNA, and the traits they produce, can be produced by the environment. That “non-Darwinian” form of evolution is purely speculative, and Mukherjee did note that it was not supported by much evidence.

Initially, both The New Yorker and Mukherjee batted aside the criticisms, but when the issues became public in other magazines and journals, they finally backed down a bit—Mukherjee more so than the magazine, which published only one brief letter criticizing the article. The main defense was that there was not enough space in the magazine to cover the whole field (i.e., to tell the truth), and that a more correct description of gene regulation could be found in Mukherjee’s book.

But now there’s been a bit more defense of Mukherjee—reported on a website article in the Wall Street Journal (WSJ) by Jennifer Maloney. Maloney first reports that, the publisher of Mukherjee’s new book, Scribner, says it’s “tweaking” it to bring its discussion of epigenetics in line with reality:

“The original book did not need corrections,” [Mukherjee] said. “These were clarifications to reemphasize things that were already in the original book.” Dr. Mukherjee said he would share the changes with the New Yorker so the magazine could decide whether to publish a clarification.

Given the New Yorker’s reluctance to ever admit that Mukherjee’s article was seriously flawed, I doubt a “clarification” will be forthcoming. Still, Scribner’s willingness to correct the book is good news.

But wait! There’s bad news, too! The first bit is that Mukherjee is rationalizing the “tweaking” by implying that it reflects new developments in epigenetics:

“The field is going through a transition,” said Dr. Mukherjee, whose Pulitzer Prize-winning book on cancer, “The Emperor of All Maladies,” was published in 2010. “I’m trying to keep up with it. The science changes literally every day… Fields of science where there’s deep uncertainty still need to be written about. That’s what I do.”

That’s just wrong. Mukherjee’s error was this: not keeping up with the science that had already been done. Since his article and the book came out, there haven’t been any radically new developments changing our current view of gene regulation. In a field where honesty is highly prized, yet so rarely on offer when a researcher is wrong, Mukherjee is simply unwilling to admit that he screwed up.

The other bad news is that one prominent researcher in the field, Danny Reinberg, has decided to characterize the criticism in an ad hominem way (my emphasis):

Danny Reinberg, a researcher in gene expression at Howard Hughes Medical Institute in Maryland and a professor at New York University School of Medicine, is mentioned in the article and helped fact-check it. He said the critics went too far.

“I think that it was a bunch of babies overreacting,” he said. “That piece was written for the public. We scientists… [need to] accept some flexibility.”

Reinberg isn’t just mentioned in Mukherjee’s New Yorker piece—his work, characterized as highly innovative, formed a major part of that article, including his idea that major evolutionary innovations, like the different “castes” of ant colonies, could be due to differential gene expression produced by methylation and histone/gene interactions.

There was strong criticism of Mukherjee’s article, and you can see some of it in the Nature and Wall Street Journal pieces, but all of it dealt not with Mukherjee’s character but with his mischaracterization of science. It’s therefore reprehensible for Reinberg to brush off the critics as “overreacting babies.”  That criticism could be turned on Reinberg himself for ignoring the science to defend a piece in which he’s glowingly portrayed as a scientific revolutionary.

But I’ll leave that be. What is just as odious is Reinberg’s claim, made earlier by others, that any scientific distortion was necessary, engendered by the fact that Mukerjee’s article was both short (it wasn’t) and written for the public. As I’ve said several times, the real situation isn’t so complicated that it couldn’t be described in a few paragraphs. It’s just that the real knowledge we have about gene regulation isn’t revolution—it’s been building since the 1950s.

Wally Gilbert, who won the Nobel Prize for figuring out how to sequence DNA, and who made major contributions to gene regulation, answered Reinberg:

Dr. Gilbert responded with a withering assessment of Dr. Reinberg’s website: “Too silly for words.” He added, “The deeper arguments are really about the nature of evolution and the mechanisms by which genes are controlled.”

Mukherjee had another defender, but one not as nasty as Reinberg:

Geneticist Eric Topol, who praised the book in a review for the scientific journal Cell, said in an interview that the criticism of the New Yorker article was unfair. The science, he said “isn’t settled… The controversy in epigenetics runs deep. It’s been a very confusing topic for a long time. This just brought it out. It was a foil for the ambiguity of the term and the science.”

At least he didn’t make fun of Mukherjee’s critics! (Those critics, by the way, included three Nobel Laureates and virtually every big name working on epigenetics.) But the criticism was not unfair. What was unfair was Mukherjee’s portrayal of the state of research on gene regulation. Yes, science can produce ambiguous results, and the current consensus could change, but it’s not kosher to completely mischaracterize the current consensus.

Finally, the WSJ reports a bit more about the nature of the changes, and, sadly, Mukherjee makes the argument that controversies about gene regulation should be hashed out in professional journals, not the press. And both Gilbert and Florian Maderspacher, an editor of Current Biology who wrote the one critical letter published by the New Yorker, say that even the new revisions aren’t good enough. (I haven’t seen them.)

Ms. Graham [Nan Graham, Scribner’s senior publisher] said the changes in the new edition address a range of issues, from typos and missing photo credits to scientific details.

Dr. Mukherjee “is a perfectionist, and I try to be,” she said. “These are standard corrections on a book of such ambition, with tight deadlines, about a field of science that advances every day.”

The author added more caveats about epigenetics and additional clarification on how genes are turned on and off. He also nodded to the recent maelstrom: “Whether these marks contribute to the activity of genes, how they do so—and what their functions might be—is still hotly, often viciously, debated among geneticists.”

Dr. Gilbert and Dr. Maderspacher said the changes to the book’s epigenetics section didn’t go far enough to satisfy their concerns.

“How much more explicit can one be?” Dr. Mukherjee said. “This is a crossfire of people who are debating fundamental terms… These disputes should be professionally handled in scientific journals.”

 As one of my friends commented after reading this defense by Mukherjee, “The hypocrisy of saying that these arguments should be settled in journals, while being happy to publish books and popular articles on the subject, is rather striking.”

Meanwhile, the dogs bark, but the caravan moves on. Or, to use an anglophone rather than an Arabic metaphor, Mukherjee is crying all the way to the bank. His new book has sold 150,000 copies and is in its fifth printing. Why would he want to scotch a moneymaking name by admitting that he screwed up?

h/t: Charleen