Let’s mercifully draw the curtain on L’Affaire Mukherjee, which started when a number of eminent scientists criticized Siddhartha Mukherjee’s May 2 New Yorker piece because it gave a completely distorted view of how genes are turned on and off to make bodies (see critiques here and here). I’ve been awaiting the New Yorker‘s and Mukherjee’s response to the criticism.
Well, the New Yorker has finally published 1 (one) letter criticizing the piece; it’s by Florian Maderspacher, a senior editor of Current Biology, and is a much-edited version of a letter that originally appeared on this website. Here’s his published letter and Mukherjee’s response:
THE REGULATORS
Siddhartha Mukherjee’s article about twins and epigenetics misrepresents the processes by which genes are regulated and how the environment influences the genome (“Same but Different,” May 2nd). Mukherjee centers his article on the work of David Allis and Danny Reinberg, who think that “epigenetic” mechanisms play a causative, instructive role in gene regulation. But many researchers consider these mechanisms to be downstream processes, secondary to the work of proteins called transcription factors, which turn genes on or off. Ignoring the vast body of work on gene regulation from the past half century, Mukherjee gives the lay reader the impression that “epigenetics” is providing new answers to an unsolved problem in biology, when scientists already have a very good understanding of how the environment influences the genome. (And, rather than referring to a process that functions “above genetics,” the term “epigenetic” was introduced in the nineteen-thirties as the adjective form of “epigenesis,” the process by which structures form de novo in the developing embryo.) Instead of explaining gene regulation to readers, Mukherjee introduces confusion into one of science’s most important domains, one that touches deeply on who we are as biological beings.
Florian Maderspacher
Senior Editor, Current Biology
Salt Lake City, Utah
Siddhartha Mukherjee replies:
I agree that the broader context of gene regulation is critical, and “Same but Different,” with its focus on recent research into histone modification and DNA methylation, left out foundational work by other scientists on transcriptional activators, repressors, and regulators, a class I refer to as gene “regulators” or “master regulators” in my new book, “The Gene: An Intimate History.” These regulatory factors (and regulatory RNA) are indeed the primary mediators of the biological response to the environment. My book, from which the article drew, details these fundamentals of gene regulation—such as Jacques Monod and François Jacob’s research on gene regulation in bacteria; Shinya Yamanaka’s ongoing work on regulatory genes in stem cells; and studies of transcriptional master regulators, such as SRY, which lie atop gene-regulatory hierarchies. Such material would have given readers a fuller, and sounder, view of gene regulation in response to various stimuli.
As one reader commented, “That’s about as close as you can get to an apology without saying he’s sorry.” It’s a good letter by Florian, and although Mukherjee was given a sound drubbing, he basically claims that the “foundational work” he neglected in the New Yorker article is all to be found in his new book—and I’ve heard it is. But that seems more like an advertisement for his book than an admission that he told an incorrect story in the article, which was NOT, as Mukherjee implies, an excerpt from his book.
Amy Winehouse might have sung, “What kind of Mukherjee is this?” But I’ll take the “correction,” such as it is, and hope that people learn two lessons from this fracas.
First, when you’re writing popular science, make sure you get the facts right, and don’t use word limits as an excuse to tell an appealing story that’s wrong or unsupported.
Second, all of us should have learned that the trendiness of “epigenetics”, at least as a primary method of gene regulation—as well as a supposed novel and Lamarckian process of evolution—is unwarranted. Epigenetic modifications of DNA produced by the environment and not coded in the DNA itself (as are “imprinting” phenomena) are most likely the results rather than the causes of differential gene action. And environmental modifications of the DNA are almost invariably wiped out after a single generation of reproduction, making them unable to be the basis of evolutionary adaptations.
The problem is that what Mukherjee espoused in the New Yorker article is beginning to seep into the culture. He was on Fresh Air with Terry Gross last week.
http://www.npr.org/sections/health-shots/2016/05/16/478204708/the-power-of-genes-and-the-line-between-biology-and-destiny
While on ‘Fresh Air’ did he continue to misrepresent epigenetics, do you know? Or did he begin to correct what his article has misrepresented?
As far as I know, his presentation on “Fresh Air” was MUCH better than on the New Yorker podcast or his response at the Scripps site. I haven’t heard the Terry Gross interview yet, but the genetics experts tell me that Mukherjee did a much better job on NPR. The response in The New Yorker is thus doubly disappointing.
No he did not continue to misrepresent epigenetics. When asked about it, he only mentioned transcription factors.
This pisses me off. This is NOT what I expected from a writer with the stature of somebody like Mukherjee. And the error is so fundamental as to almost look egregious. I wouldn’t expect a writer who is a practising oncologist and a Pulitzer-winner for a book on cancer to have f***ed up basics of gene regulation and shroud them in BS.
What irks me is both Mukherjee’s adamant stand (he could just have said sorry, seriously), and the fact that the post-article debates are much, much harder to access. Think about how many people are likely to read the article and walk with wrong and woo-ish ideas about epigenetics, versus people who will read about this rebuttal letter published in New Yorker and this blog.
But I am optimistic because people like Jerry, Mike Eisen @ UC Berkeley, Florian Maderspacher and Mark Ptashne quickly came to the fore to stop the spread of misleading notions about biology. Thanks for guarding the fort of sense AND science!
Yes, Chopra and Tanzi will be quoting this article.
Yeah, Chopra & Tanzi will play this up big time (if their past misleading behavior continues.) Chopra is disgustingly adept at attaching to anything that can benefit his woo (and most of his admirers have little ability, nor care, to distinguish nonsense from reality.) That, unfortunately, is the real transformative aspect of Chopra: applied delusions.
Now we know what kind of person he really is. He cares much more about his sales than the facts. This in my opinion is one of the biggest problems with “science writers”. They write stuff to get attention/hits/PR etc., and sometimes ignore the scientific facts. And they are all so well connected with each other and promote each other that other “science writers” simply won’t correct them. Quid pro quo. I bet the majority of people have never read Prof. Coyne’s and others’ critics about that New Yorker piece.
I think that he made a legitimate mistake in the NYT article. The problem is, that he got defensive and doubled down instead of just accepting the criticism and stating “Yes, I was wrong and stand corrected”. From what I know of Dr. Mukherjee, I don’t think that he would be intentionally writing falsehoods in order to create controversy and boost sales. Instead, he may have lost some sales among the people who have read the criticism.
But its the wooishness that that is so irresistibly attractive. This will be one of the ZOMBIES. Jerry et. al. will have their work cut out for them.
Hear, hear!
Just 2 days ago a brazilian journalist made a small piece about the book The Deeper Genome by John Parrington. According to the journalist, the book says epigenetic is the Lamarck’s revenge against Darwin.
Since Darwin was (sort of) Lamarckian for a while, the reported view is wrong on so many levels.
I know it is.
It’s also timely that happens close to the Mukherjee’s piece on epigenetics , since who is really interested could be informed about how some researchers have unfairly reported epigenetics.
I remember that a friend of mine, a biologist undergraduate student, talk to me years ago that “Lamarck was being discussed back again”, failure to realize that this was in fact a misrepresented view of the evidence.
“And environmental modifications of the DNA are almost invariably wiped out after a single generation of reproduction, making them unable to be the basis of evolutionary adaptations.”
I may be wrong, but haven’t some publications provided evidence that epigenetic markers can be “inherited” (up to three generations)? (http://www.scientificamerican.com/article/descendants-of-holocaust-survivors-have-altered-stress-hormones/)
(**This, of course, would not provide evidence to support the claim that they are the basis of evolutionary adaptations.**)
Also, what about gene editing or “genetic engineering” of the organism, such as that exemplified by protists (http://www.cell.com/cell/abstract/S0092-8674(14)00984-2) or retrotransposons as regulators of gene expression (http://science.sciencemag.org/content/351/6274/aac7247.full). Is it too lofty to presume that retrotransposons can restructure germline DNA?
I am not an advocate of Lamarckianism, nor the superior power of epigenetics, but can we keep an air of skepticism? Or is my ignorance preventing me from understanding more?
I wondered the same thing and, then, thought that I’d probably gotten most of my “facts” from science magazines, apparently not a reliable source. I have also read some books on epigenetics (until I got beyond my depth).
Can a few of you savvy epigeneticists provide
a short list of top-flight books to read on epigenetics?
I continue to be disappointed in Dr. Mukherjee.
As a member of the confused lay public, none of this discussion is helping me make sense of what I read previously: that descendants’ development had been affected by starvation experienced by their grandparents. Is that true, and if so is the mechanism understood? Is there any reading anyone can recommend to me?
My advice: forget it. It is unlikely to be true, but even if it is, it will be a small fact insignificant in the whole picture. Like the existence of RNA viruses does not shake the paradigm that DNA is the carrier of heredity.
It would be nice to draw a curtain, but a whole new round of creationist apologetics has arisen, and one of its cornerstones is the legitimacy drawn from the New Yorker article.