
Growing Pains for Field of Epigenetics - tosseraccount
http://www.nytimes.com/2016/07/02/science/epigenetic-marks-dna-genes.html?rref=collection%2Fsectioncollection%2Fscience&action=click&contentCollection=science&region=rank&module=package&version=highlights&contentPlacement=9&pgtype=sectionfront&_r=0
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medymed
Demethylating agents, HDAC inhibitors, and their like can induce powerful
effects on malignancies via (purportedly) primarily epigenetic mechanisms.
I've seen patients with astronomically high leukemic counts return to normal
blood counts on a few weeks of romidepsin, for instance.

But when groups use epigenetics to study poverty related stress, risk of
depression, etc, there is a very different political structure than when
comparing drugs to see what kills cancer cells in a dish. The trend seems to
be to publish borderline findings with a nature vs nurture argument to explain
differences as environmental, not genetic, and call for action as well as
_more funding_ to expand the research and find ways to environmentally or
behaviorally prevent the problem. Optimistically, it's trying to solve
problems. The issue is that important findings will be mixed in with a lot of
questionable results that sound appealing to liberal academic journal editors
and get a free pass at publication in top journals, a process which feeds back
into the SJW gravy train of getting more academic grants to do more of the
same. And with sciency techniques and big data approaches, what could be more
fashionable? It really does a disservice to the subset of epigenetic research
which is well conducted and reproducible. If the epigenetics bubble pops a
bit, good. Other fields could use the attention.

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Intermernet
Your argument was cogent and reasonable until you used the term "SJW". It's a
useless term, meaning different things to different people.

The point you seem to be arguing could also be applied to the funding of
string theory, and is one that I agree with. You won't find people like Lee
Smolin saying that the disparity in research funding in these areas is due to
"SJWs", rather they would point to the short term vision of those who provide
the funding (amongst other factors).

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medymed
I agree, SJW is a pretty useless term. You're right. And I don't know much
about string theory funding. I can only postulate. Regarding short term
vision, medical research funding has consequences on huge outlays of public
resources outside of the short-term vision of research funding you mentioned.
Maybe string theory has very close parallels, but for example when it was
recommended everyone get interval colonoscopies at certain ages, hundred of
millions of dollars of government money suddenly shifted to this purpose
yearly for just one procedure (in this case a heavily vetted evidence backed
decision). When, in contrast, attention is cast on politically popular issues
with questionable research methods and publish-bait articles, it siphons
funding away from less hot-topic issues that stagnate or die (for example, the
defunding of even the best state psychiatric programs, which are popularly are
associated with horror movies and don't get much too love by activists). The
impact is immediate and severe outside of the world of researchers, and
enormously politicized throughout the nation/media. I'd love to hear the
string theory side of this though!

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Intermernet
This has a lot to do with PR and how it relates to research and development
funding. The root problem is that, with regards to funding (as far as I can
tell), a headline in a popular newspaper or popular-science magazine is worth
orders of magnitude more than a peer-reviewed paper in a journal. This will be
a problem for all of the sciences in the near future, as long as there are
differing tracks of research being explored.

The scientific method dictates that something should be ideally explored until
it's dis-proven. Unfortunately, the realities of limited R&D funding dictate
that only the most popular, or public, research tracks tend to attract the
funding. This has a carry-on effect in that new students in these fields are
_forced_ to go into the most popular fields of study, lest they not get
funding.

WRT string theory, have a look at
[https://en.wikipedia.org/wiki/The_Trouble_with_Physics](https://en.wikipedia.org/wiki/The_Trouble_with_Physics)
. I'm not sure I 100% agree with Lee Smolin on this (he has a definite axe to
grind), but the points he raises are equally applicable to any field of
contentious, or cutting edge research.

Solving this is difficult. Obviously education of the general populous will
help, but in lieu of this, perhaps we need mandated percentages of funding to
each viable research track (a solution rife with problems of it's own).

In any case, this is a hard problem to solve, and will certainly cause
problems in many areas of fundamental research in the future.

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patall
As I see it pretty much from inside, this is not a general problem but just
the evolution of science, as we are able to determine more and more things
which lead to better and better conclusions. The problem in what is cause and
effect comes from the sheer amount of data you create (for a current study we
have whole genome methlaytion data for 19 cell populations in mice, all in
triplicates and at medium coverage), which is obviously prone to many false
positives. And as we are now approaching single cell level (which will
dramatically improve results), this number is only going up. And of course it
is hard to check all these positives extensively. But yeah, this is sciece and
we are only getting better, so no pain but just an opportunity. A problem is
rather the amount of data we create (we are speaking about Petabytes) that
have to be stored and made accessible for decades so we can later recheck our
conclusions. Nobody wants to pay for that

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delinquentme
Im interested in chatting on versioning in this data ( and possibly by
extension, compression ) . Happen to have a method to contact you ?

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patall
Not in this case as the data I described is on embargo. The problem is more
general for all genomic data that has already been made public but were
funding runs out after 5 years or so. I happend to chat to a postdoc the other
day who is involved in the ICGC cancer consortium and had already some
thoughts about the problem. If you want I can ask him whether he wants to
contact you.

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delinquentme
Would love to chat with him!

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daemonk
I am working with some epigenetics data right now (chip-seq on histone
modifications). The main problem I see is that there doesn't seem to be any
mature framework for analyzing the data. There are a bunch of disparate
methods for different aspect of the data analysis that all seem to give
different results.

From the data generation perspective, there are so many possible sources of
biases from preparing the biological sample to sequencing of the sample, it
can be difficult to control for all these variables in the down-stream
analysis.

