We’re beginning to see a recurring theme among the defensive responses to our scientific criticisms (here and here) of Siddhartha Mukherjee’s misleading piece on epigenetics in the New Yorker. So far, the responses of journalists (see here as well as below), of Mukherjee himself, and even of the New Yorker, are along these lines:
There are differing opinions on this issue. Since space is limited for hard-working journalists and word-limited magazines, we simply have to jettison alternative explanations in favor of stories that appeal to our readers.
The problem with Mukherjee’s piece, of course, is that he presented a story—that epigenetic markers and histone-protein modifications are THE mediators of differential gene expression in differentiated cells, working as a kind of “epigenetic code”—for which there is virtually no evidence. This was the cute and intriguing tale that he told readers of the New Yorker, who, of course, loved the good writing and assumed what Mukherjee said was accurate.
But what he left out—to the readers’ detriment—was the true story of gene regulation as we know it: a story identifying protein “transcription factors” and short bits of RNA as the factors that regulate gene expression. As Mark Ptashne and John Greally noted, neither Drosophila nor Caenorhabditis worms have DNA “markers,” yet both organisms—paradigms for the study of genetics and development—develop just fine, thank you. That alone should give pause to people like Mukherjee or the Epigenesis Mavens, and it comes on top of the lack of evidence for epigenetic or histone-regulated control of genes.
And yet the defenders continue to claim that it’s really okay to omit what we really know about gene regulation in favor of a well-written but completely speculative explanation for the same phenomenon.
That’s the problem with a piece on MukherjeeGate by Brian Resnick in Vox, “Why scientists are infuriated with a New Yorker article on epigenetics.” In fact, according to the Vox piece, that’s how the New Yorker itself continues to defend their indefensible piece:
And for it’s [sic] part, the New Yorker is standing by the story, too.
“None of it [the Mukherjee feature] negates the fundamental importance of transcription factors, and the foundational work on gene regulation done by a previous generation of scientists (or by scientists working on gene regulation today),” a New Yorker spokesperson told me in an email.
It is as if someone wrote an article on homeopathic medicine, adducing dubious evidence that it works, giving the opinions of homeopaths, leaving out the counterevidence that “scientific” medicine is the thing that really works, omitting the absence of evidence for the efficacy of homeopathic nostrums, and so on—and then defending such a piece by saying, “Well, none of our article negates the fundamental importance of scientific medicine, and the foundational work on those medicines done by a previous generation of physician-scientists.”
The New Yorker‘s defense is not only disappointing, but infuriating. It is just weasel words. It is unworthy of a magazine supposedly dedicated to factual reporting. It is the kind of answer you expect from politicians, not journalists.
The truth is that Mukherjee didn’t even mention transcription factors (or micro-RNAs that turn gene regulation down or off). It was completely ignored! It is to the New Yorker‘s disgrace that they justify an incorrect presentation of science in such a way.
In fact, according to Vox, even Mukherjee himself finally admits that maybe he didn’t do such a good job:
“In re-reading the piece in the light of the critics, I realize that I did not emphasize the role of transcriptional factors and regulation adequately,” Mukherjee writes in the email. “This was an error. I thought, sincerely, that I had talked about gene regulation, but an increased emphasis would have helped the piece, and not caused the polarizing response.” (He also mentioned that the New Yorker article is an excerpt from an upcoming book, which will cover these topics more thoroughly.)
Well, he didn’t emphasize the role of transcription factors in regulation AT ALL! But I laud him for the admission above, and perhaps the real story will be told in his upcoming book. Even so, a fuller presentation in a book cannot justify a misleading presentation in an excerpted piece.
Finally, Vox itself promulgates the “we didn’t have room to tell the truth!” trope. It does so by presenting Mukherjee’s epigenetic scenario as one “story”, and the protein-and-RNA-regulation scenario (which happens to be the truth) as a different “story”. Here’s a sidebar from the Vox piece:
And it’s echoed in Resnick’s text (my emphasis):
I can’t fully analyze all the critics’ concerns in this post. But this seems clear: If Murherkjee is guilty of something, it’s omission. He didn’t make it clear that other, prominent, scientists would choose to tell this story in a different way.
There are a lot of challenges in science writing, but one of the main ones is this: Research more often yields streams of caveats, not elegant conclusions. This fact makes trouble for another truth: As a writer, it’s your job to take a reader from the beginning to the end of a piece as elegantly as possible. [JAC: Isn’t it the first job to convey truth, and then comes the elegance?]
There could be a lot of reasons why Mukherjee decided to focus on histones rather than transcription factors. They perhaps make for a more visual, compelling illustration of the inner workings of a cell. Maybe Allis was just a great interview, and a more compelling character upon which to carry the story’s narrative. [JAC: This is journalism?]
These choices are compounded by this: “The original piece was almost twice its current length, with a lengthy historical section mentioning gene regulation,” Mukherjee writes me. The print New Yorker only has so much space.
These choices aren’t always easy, but in journalism, they’re necessary. We can only tell one story at a time.
[Note the misplaced “only,” which should be between “tell” and “one.”]
Well pardon my French, but screw that! If journalists can present only one story at a time, how come good journalists are always careful to present opposing points of view? In fact, as I said yesterday, Mukherjee could have presented the best story—the one supported by evidence—in the generous space given him by the New Yorker. He chose not to do so, for presenting a decades-old and widely accepted story of gene regulation doesn’t have the panache of a shiny new hypothesis, even if that hypothesis has no evidence behind it. Why tell the truth when you can tell a shaky but provocative story, covering its flaws with blankets of fine prose?
What is going on here? My guess is that this “all stories are equal” view is the odious legacy of postmodernism, which sees no “truth” as privileged over another one. If that view, derived from the humanities, bleeds into science journalism, you get Resnick’s view that “we have to make choices, as we can’t tell every story.” That doesn’t wash. If you want to choose a single story, choose the one best supported by the data. Vox has failed in its mission to provide good, unbiased science reporting.
There will be more stories about this in the press, I suspect. I hope, but am not confident, that they won’t take the “space limitation precludes us from telling the truth” attitude.
________
UPDATE: Wally Gilbert, Nobel Laureate, molecular biologist and retired Harvard professor, has this to say about the Vox piece (quoted with permission):
Yes that piece is bad–but the real problem with it is its statement of the problem: “In the story, what links these mysteries is the science of epigenetics, which, basically, explores how the environment can leave a lasting mark on how our genes work.”
This is fiction. Not fact. “What is being described as the “science of epigenetics” at best may explore how the environment leaves marks on our cells–the twins in his piece with their scars and their different behavior. But not on their germ line. The genes they pass on to their offspring are the same (if the aunt had children.)
Every statement of this form–lasting mark–suggests to the lay audience that Lamarckisnism is true–since lasting coupled with the word gene implies inheritance for the organism. (While to the expert one is discussing the division of cancer cells).
Prominent blogs related to Vox consistently get science wrong.
See: http://www.theverge.com/2016/5/4/11581994/fmt-fecal-matter-transplant-josiah-zayner-microbiome-ibs-c-diff
But this is not surprising. It just reflects how much post-modernism has infiltrated communication departments. The mentality is that if the truth doesn’t sell, you can opt for better interpretations since truth is subjective. It is also consistent with news organizations as profit centers first, news organizations second.
Another consequence is reporting all opinions as equally valid. Obama had a great line at the WHCD. He said “reporting the truth does not mean you are compromising your objectivity”. This was said as something profound and not obvious.
What did this story get wrong? I heard this story 2 days ago on NPR- Ira Flatow’s ‘Science Friday’
The guy took antibiotics for two days and scraped his skin with tetracycline powder to replace his flora with fecal pills.
Anyone with any medical training know this is ridiculous. In fact the reporter was told as much by experts. She continued reporting on as a medical breakthrough.
Strange, because to me it seemed that she gave a lot of emphasis to the professional inputs she herself solicited, and that the story was full of caveats.
You worried me and I checked SciFri. They reported on legitimate fecal transplant research and not the Verge’s quack.
I heard Arielle Ross interviewed about the story. It mentioned that the whole thing was a bad idea and dangerous, but not that it wouldn’t actually work…and I’m pretty sure it was Flatow that interviewed her
Is this what you heard. This was Verge ESP, not SciFri.
https://m.soundcloud.com/vergeesp/microbiomes-biggest-losers-and-other-gut-related-tragedies#c=0&t=0:01
I saw that story going past several times a few days ago and thought “what an idiot” and never went further than that.
I noted that the oft-repeated photo attached to the article showed the idiot with a prominent cross tattooed across chest and left shoulder (he may have tried to have it centred over his heart, and missed ; that would be about the right level). So, not thinking through on some pretty basic biology, doing something self-harming, being an attention-seeker, AND being a god-squaddie. All together marks a pretty consistent syndrome of new-age hard-of-thinking buffoon.
“We can only tell one story at a time.”
If someone’s values are very flexible, they will always find it necessary to flex them. For those who hold certain values sacrosanct, they will always find ways to live up to them.
I like this series of tweets:
https://twitter.com/upulie/status/729276896857366528
Divisekera posted a sequence of six tweets. Those are the last two. Take a look at all of them.
I retw**ted them all, despite my reluctance to use Twi**er.
And I have begun to respond to these tweets, as well.
A shameful failure on the part of the New Yorker and Mukherjee is that the woo-inspiring presentation will be read and translated by experts in public health (my field)–who will get it wrong and propagate Chopra-esk ideas along the lines of thinking your way to a healthier epigenome. It’s insufferably irresponsible to not correct the error in mass communication.
I’m getting my PhD in public health genetics and know at least a dozen Lamarckians who will run with the New Yorker piece to suit their own agendas. It’s sickening at best, but I will go further and say that Mukherjee is violating the medical principle of “first do no harm” by not using this opportunity to make it right.
If fear my comments about “first do no harm” will be experienced as over-the-top. The reason I chose them is that, a physician using the New Yorker is not a naive choice. There is a political statement being made with the knowledge that many non-expert intellectuals read it and will trust what they see in the New Yorker from a well-regarded doctor and author.
Mukherjee is not blameless in this and should recognize how his words will get associated and lumped with those like Chopra. But maybe he knows that and is choosing this? That is the impression that is being sent by not taking a stronger stand to rectify the cognitive (epi)-meme.
I do not think you are over the top, and I agree that Mukherjee did harm.
Ah, I’d noticed your account occasionally doing things other than the automatic posts. Wasn’t sure if you had been hacked or not. So it is you.
On has to assume that the New Yorker is neutral or conservative on CO2 and climate change.
Jerry – Is it OK to post tweets in the comments for the Twi**er impaired?
These from Cynthia Wolberger at Johns Hopkins:
https://twitter.com/CWolberger/status/729334720589398017
https://twitter.com/CWolberger/status/729335531205758976
https://twitter.com/CWolberger/status/729338063881699330
Yeah, sure–at least on this issue. I’m developing retw**ting skills. 🙂
Much appreciated, George. Saves time and, yes, dealing with my “impairment.” 😉
So Mukherjee adjusted the science to fit his larger goal of telling a story with transcendent themes: fate, destiny and what makes us what we are.
There’s a term for this. Its the exact definition of science fiction.
+1!
Maybe he’s on to something…SF writers are only getting a harder time to convince the general public what is possible…if you make stuff up, like ‘thermal oscillator’ in order to contain the power of a star, you better make sure it has some kind of possible explanation behind it threaded to reality.
Note that some explanations are near full proof, circular. When Roddenberry was asked how do Heisenberg Compensators work? He quipped, “They work very well.” 😊
Why are so many people eager to defend Lamarckism? Is it just because it’s different (from the truth) and sells newspapers? Or is it because that leaves some space for … you know who?
Why do people like Lamarckism? Interesting question.
Perhaps people think like that because culture and technological progress is Lamarckian.
Also, if people work hard, build up a farm or business, and leave it to their kids, then their kids benefit, which again is a Lamarckian process.
My poorly informed take on it is that for some stupid reason people think that genetics equates with genetic determinism. And worse, we have been locked into our deterministic genes by naughty Crick and Watson who said environment can’t alter genes. And worse still, naughty Richard Dawkins tells us our genes are selfish, and still worse, Darwin says its all an aggressive struggle for survival of the fittest… It’s highly popular to do battle against all those straw men.
(I don’t mean to imply that Mukherjee is doing this, but rather, that’s the popular view I pick up from spiritual folk and some sociologists etc.)
Sure beats getting into a proper fight.
I think, because it is easier than genetics. For too many, even Weismann’s experiments with the cut mouse tails is rocket science.
“Isn’t it the first job to convey truth, and then comes the elegance?”
YES!!!!!!!!!!!!!
Those who choose not to read Prevention or the National Enquirer expect their reading material to be vetted properly. The editor should have asked some hard questions before letting this go to print, and the writer should have been honest.
This whole thing smells like the kind of pseudoscience that vilifies GMOS as “additives” (as if they’re all the same). How many of New Yorker’s readers were primed to make the leap to “aspartame will bring down humanity”?
correction: GMOs *and* additives
In the modern publishing industry – are you insane? Editors cost money, and do nothing but make it slower to get advertorial from the journalist and PR flacks to the reader.
Most editors (and the sub-editors that used to fill the role you’re referring to) were sacked or retired years ago.
Hmmm, should have put a smiley on that. Obviously you’re not insane, since you post here.
‘My guess is that this “all stories are equal” view is the odious legacy of postmodernism, which sees no “truth” as privileged over another one.’
I disagree. What you are seeing is not a side effect of an esthetic movement. It arose to the status of a standard approach to discourse because it was a carefully-crafted and oft-used tactic of those who wish to be able to pitch a false view to those who don’t-quite-but-almost know better. The people using it were originally religious fundamentalists arguing against evolution, and other anti-scientists. What you are seeing is either the linguistic overflow from that propaganda movement, or actual evidence of it. As I said, in this particular case I’m not sure which it is — I’d say that’s your call.
But postmodernism and other forms of antirealism *are* used to “insulate” religious beliefs, and always have been, from Bellarmine to Duhem to …
In fact, B. Latour had his epiphany about his long time critics when he heard, as he put it, the Bush administration talking like him! (Haven’t seen too much from him lately, and good riddance!)
The NYT review of Mukherjee’s book The Gene is out –
http://www.nytimes.com/2016/05/09/books/review-siddhartha-mukherjees-the-gene-a-molecular-pursuit-of-the-self.html
Perhaps Mukherjee’s New Yorker piece was simply a ploy to get people fired up to buy a book that per this review is way more dense with science than enthralling personal stories. He should pay the New Yorker for his seductive ad! 🙂
Mukherjee will be at the NY Public Library with the New Yorker’s editor David Remnick on May 17. You can see them for $40.
http://www.nypl.org/events/programs/2016/05/17/siddhartha-mukherjee-david-remnick
I refer the honourable gentlebeing to my comment of a few moments ago concerning the vital role of editors in NOT getting between advertorial-spewers and advertorial-readers.
(And I should have put a smiley in after the “are you insane?” – hope it wasn’t taken the wrong way.)
If Dr. Mukherjee is aligning himself with purveyors of woo, I abhor it. If Dr. Mukherjee
has misrepresented epigenetics due to ignorance, he should have read more of the science by experts before venturing into print. Since Dr. Mukherjee is such an
exceptionally talented writer, I hate to see him use this talent to provide biased, unclear or erroneous information. It is my hope that he continues to write and that he uses this New Yorker snafu as a learning experience.
Another set of tweets:
https://twitter.com/rtraborn/status/729417969336344576
https://twitter.com/rtraborn/status/729418401639104512
A whole string of tweets – read them on Raborn’s feed
https://twitter.com/rtraborn/status/729435327895474176
Ugh. This is just like when physicists write about consciousness and the brain.
I think the days of real physicists writing about consciousness is over, thankfully. Those ships (WuLi Taoist Mongers) have sailed.
Are you really saying that histone modifications and DNA methylation do nothing or that there really is no evidence of their role in gene expression.
You are right, the article excluded the roles of TFs and small RNAs. They misused the term “epigenetics” and may also be guilty of promoting Lamarckism, but I feel as if the argument is going way to far in the other direction.
DNA methylation and histone modifications are involved in regulating gene expression to various extents. Drosophila and C. elegans may not have DNA methylation, but they do have histone modifications. And so what? What is dispensable for some organisms is not for others. Animal life isn’t the only form of life either and its helpful to sometimes look at what is known from other species.
From plant biology, we know not only of many examples of these factors regulating gene expression, we have very clear examples of transgenerational epigenetics…where transmission of DNA methylation across generations results in variation in not only gene expression, but also physical phenotype:
Peloric mutants in Linaria vulgaris
QQS gene in Arabidopsis
FOLT1 in Arabidopsis
PAI genes in Arabidopsis
CmWIP gene in Melon
Colorless non-ripening in Tomato
Karma in palm oil
FWA in Arabidopsis and others
Never mind that loss of DNA methylation and H3K9 dimethylaiton also results in reactivation of many transposons….which clearly indicates a role in silencing expression.
Brilliant work in Arabidopsis has produced epigenetic recombinant inbred lines (epiRILs) that are largely isogenic, varying primarily in epigenetic states that are stably transmitted over generations. These show a wide range of phenotypes, which have been mapped to epigenetic QTL and which show no evidence of genetic variation in those regions.
If you really want to get weird, read up on paramutation in Maize.
Do I think any of these exclude the primacy of TFs or small RNAs? Absolutely not. Do I think any of these support Lamarckism? Absolutely not.
There is a very fine line in the proper understanding of epigenetics here, and implying that there is no evidence that DNA methylation or histone mods play any role in gene expression is contrary to the evidence.
Agreed, Chad. It would appear that fifty years of epigenetic research in plants isn’t relevant. It is absurd to assume that since Larmarkism isn’t true, epigenetic isn’t a real phenomenon. I’ve studied both heritable transposon silencing and paramutation in plants, and the idea that changes in DNA methylation and histone modification can mediate transgenerational silencing is entirely uncontroversial. At least in plants…
Chad, absolutely. I don’t think any of the critics would argue that the histone modification or DNA methylation machineries don’t play a role in gene expression. In fact many of these folks have dedicated their whole lives to figuring out their contributions. And of course, why would mistress evolution maintain such baroquely complex systems if they wouldn’t serve an important function? But as you say the question is which subsystem has the primacy, where is the specificity coming from? It seems clear that histone modifications and DNA methylation aren’t able to provide it. And yet, the article made it sound as though they are the be all and end all of how the environment controls genes.
And the same is true for permutation and the many transgenerational effects in plants (and the few in animals, such as transgenerational virus resistance in C. elegans). No one doubts that these phenomena are real and meaningful, but most people familiar with them would not say they underlie long-term evolutionary change…
My problem is with statements in this article that would imply, especially to those unfamiliar with the nuances that they do nothing. In particular this statement:
“and it comes on top of the lack of evidence for epigenetic or histone-regulated control of genes.”
I have reread this article many times and there really is no nuance in that assertion. If we are going to attack Mukherjee for overblowing the importance of epigenetics, then I think it is equally important not to underplay it either with such statements.
Okay, here’s a statement that I made earlier in the article, which you either didn’t read or ignored. Let this stand for my assertion.
This statement, which is about the specificity of gene action, and where it comes from (the topic of Mukherjee’s piece) is similar to what FloM notes above. Enough nuance in that?
End of discussion for me.
Chad: I THINK your note goes to the heart of the matter by (apparently) interchanging gene EXPRESSION with gene REGULATION…many enzymes etc are involved in the complex events that comprise transcribing a eukaryotic gene. No one is arguing that, for example, some histone modifier cannot be involved in transcription per se. The question is what role such non-specific enzymes play in REGULATING that process – ie
determining at which gene the process is triggered. For that you need a specificity factor – usually protein, sometimes RNA.
“We can only tell one story at a time.”
You say: ‘[Note the misplaced “only,” which should be between “tell” and “one.”]’
No, that “only” is in its normal English position. Even H.W. Fowler deplored the mechanical peevers who insisted on “precise” placement. Don’t encourage them, please.
It means something different in the “wrong” position. And don’t tell me what to say, please, or imply that I’m a “mechanical peever.” I suggest you go police the language on other websites, after having read the Roolz.
Will Jan be back? Time will only tell!
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I can recommend a course on Epigenetics I just completed on Coursera taught by Dr. Marnie Blewitt from University of Melbourne, a 7 week very detailed course getting into the biochemical mechanisms of action of methyl groups, acetylation, histone modifications, non coding RNAs and small RNAs and other mechanisms. And the course made no sweeping generalizations, did address trans generational modifications but cited the examples of such more as the exceptions than the rule and overall, presented a window into this clearly emerging field of study. In a way, I could see renaming ‘epigenetics’ ‘gene modifications’ which I think conveys the idea better without the extra baggage that the term ‘epigenetics’ now seems to have in the popular media. I think a new course is beginning in the next month or so. By the way, I found the weekly quizzes to be quite challenging.
R. Taylor Raborn is a postdoc in computational genomics at Indiana. Yesterday, he posted numerous tweets about the article. He has now consolidated them into a short article which you can read here:
https://storify.com/rtraborn/getting-started?utm_content=storify-pingback&utm_source=t.co&awesm=sfy.co_i1O9z&utm_campaign=&utm_medium=sfy.co-twitter