Mukherjee’s controversial piece on epigenetics #Drama

The scientific community is in uproar over Siddhartha Mukherjee’s latest piece for the New Yorker titled: Same but Different (you may know him from his novel Emperor of all maladies: a biography of cancer). His article highlights the study of epigenetics, and how recent findings may blur the line between nature and nurture. So why is the scientific community outraged? Vox explains:

 

Here’s the beef scientists have with Mukherjee and the New Yorker

The article is the type of piece the New Yorker usually is very good at: diving deep into a crevice of science and connecting it to veins of either history, politics, or the poetry of everyday life.

Mukherjee starts off with a personal tale. His mother and aunt are identical twins, and he muses on how their life experiences made them different people later on. He then connects this personal mystery with other mysteries in nature: Why are two ants genetically near identical but one is a worker and one is a boss?

In the story, what links these mysteries is the science of epigenetics, which, basically, explores how the environment can leave a lasting mark1 on how our genes work.

DNA is the instruction manual for life. So epigenetics may determine how likely those instructions are to be read. Understanding epigenetics is important because it could help us understand how we become more susceptible to disease (or not) over our lifetimes. And there’s some not-yet-conclusive evidence that epigenetic information is inheritable. As Vox’s Susannah Locke has explained, epigenetics means a person may pass on genes as well as experiences to a child.

But the article seems to have hit a nerve with some researchers who feel “epigenetics” has become a buzzword that’s distorting the science.

What Mukherjee (mainly) gets wrong, according to the scientists, is his explanation of how this process is thought to work. Mukherjee’s explanation is anchored in a discussion of histones, which are tiny proteins that act as a kind of a scaffolding for DNA. He leans heavily on the work of David Allis, a researcher at Rockefeller University, who has foundthese histones open and close specific sections of DNA, which he says changes the output of the genes.

“The coils of DNA seemed to open and close in response to histone modifications — inhaling, exhaling, inhaling, like life,” Mukherjee writes.

Next, Mukherjee notes (more vaguely) that scientists have found “other systems, too, that could scratch different kinds of code on the genome.”

There are two main points the scientists are clamoring over.

One is that they say Allis’s theory that histones actually change the output of genes is far from proven. In a second post on Coyne’s blog, Greally and Mark Ptashne, a biologist at Sloan Kettering, write, “there is no evidence that coiling and uncoiling of DNA has a causal effect on gene activity.”

The second is the critics say those glossed-over “other systems” are actually the prevailing theory on how it all works, and should be at least discussed at greater length.

The big, overarching, concept Mukherjee missed is “transcription factors,” which are proteins that can turn specific genes on and off. It’s these factors that scientists say should be the main focus of the explanation of how our genes are differentiated. And despite decades of research on them, transcription factors are hardly mentioned at all in the piece.

Steve Henikoff, a molecular biologist, writes on Coyne’s blog:

Mukherjee seemed not to realize that transcription factors occupy the top of the hierarchy of epigenetic information, that this has been widely accepted in the broader chromatin [i.e. DNA] field, and that histone modifications at most act as cogs in the machinery that enforces the often complex programs specified by the binding of transcription factors.

(To note: The scientists have other concerns with the piece. You can read more about those here.)

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John Oliver discusses Scientific Studies

If you didn’t catch the latest episode of Last Week Tonight with John Oliver, be sure to do so. Summary here:

On Sunday’s Last Week Tonight, John Oliver debunked scientific studies that make outrageous claims. Oliver pointed to an example of an all too familiar subject of studies: Coffee. “In just the last few months, we’ve seen studies about coffee that claim it may reverse the effects of liver damage, help prevent colon cancer, decrease the risk of endometrial cancer, and increase the risk of miscarriage. Coffee today is like god in the old testament: It will either save you or kill you, depending on how much you believe in its magic powers.”

These studies can have serious consequences. Oliver explained that they are rarely replicated or fact checked, but that hasn’t stopped news organizations from actively reporting on the studies as truth. The contradictory nature of the these salacious studies can lead people to dismissing actual science that has been peer reviewed… like climate change.

There are always scientific experiments that haven’t yet been replicated or that are just waiting to be disproven. That is because science is a work in progress… we are always improving techniques, and learning more about subjects. I think the real problem lies with the media taking scientific evidence and portraying it as “fact” in order to boost viewership of the story. While scientists can always work harder to improve communication skills, this is a two-way street, and the media simply needs to do a better job of reporting on science.

Anti-science quotable: Jodi Ernst #Ebola #wrong

Several days ago in an interview with Esquire’s Charlie Pierce, Iowa senator-elect Jodi Ernst defied all odds when it came to Ebola.

Ernst has been bashing Obama about how he is dealing with the Ebola crisis.  In the interview, Pierce asked, “What should [Obama] have done about Ebola? One person in America has Ebola.”  And the anti-quotable response from Ernst,

“OK, you’re the press and you’re giving me your opinion”

JUST TO CLARIFY, the number of people that have ebola is not up for debate, and it is not an opinion.  You either have it, or don’t.  No opinions there.

How many grants and jobs does your state get from NIH funding? Check out this awesome interactive map from @UMR4NIH

ufmr

Check out this awesome interactive state-by-state map of NIH funding and its impact from United for Medical Research. When you click on each state you will get the amount of NIH funding and the number of jobs this funding supports. It also includes a list of the top NIH funded institutions and the leading causes of death by disease! The announcing press release states that the interactive map will be a resource for the public, lawmakers, and media… but I’m a scientist and I think it is super useful!

United For Medical Research, a coalition of leading research institutions, patient and health advocates, and private industry, today launched a user-friendly map spotlighting the state-level impact of federal research funds provided by the National Institutes of Health (NIH). NIH awards support more than 400,000 jobs nationwide, funding the nation’s leading research institutions and spurring investments and research by the biopharmaceutical industry.