I thought this article in the current New Yorker might generate some interesting discussion here.
http://www.newyorker.com/magazine/2016/05/02/breakthroughs-in-epigenetics
I thought this article in the current New Yorker might generate some interesting discussion here.
http://www.newyorker.com/magazine/2016/05/02/breakthroughs-in-epigenetics
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stcordova,
What does this have to do with the price of fish? Differential regulation is indeed a thing. That’s why you’re not a blob of cells.
Regarding Shelley Berger’s work on ants reported in the New Yorker:
http://genome.cshlp.org/content/23/3/486.long
In what way does that support Creationism?
I think this is just a sandbox.
Sal:
Therefore YEC and Jesus.
It is cold comfort that there are New Yorker quality writers out there doing the same shit.
Here’s a clue, Sal: Vernalization died with Lysenko. It is amusing in a sick sort of way that IDists are trying to reanimate Stalin’s geneticist.
I don’t have a problem with these guys disagreeing with the article, because they are qualified, which is more than I can say for Coyne.
As far as those who would be favorable to the New Yorker article, this lays out the battle lines:
My professors work in Felsenfeld’s NIH lab, so you know which side I’m going to be on.
As to this comment about Allis and Reinberg being controversial:
Note the authors on this textbook on epigenetics! Does a certain crowd of guys not like the direction of textbook biology being driven by Allis and Reinberg and the ENCODE consortium?
One of the anti-New Yorker Nobelists:
Well if he looked at Wikipedia, he might give a more charitable rendering:
Sal, evo/devo is not exactly new.
The wormhole to evolution is simply bullshit.
Walto,
My opinion and speculation only. I think there is an issue of reputation, prestige and grant money in play. Allis and friends have the ear of those holding the dollars especially for medical research. The Epigenetic Therapeutic market is estimated to be growing. The NIH has already cast big money in epigenetics.
One side (as represented in Coyne’s post) is not looking like they will be on the receiving end of future prestige and money:
There are no more “battle lines”! You lost the battle long ago! You forgot to attend your own funeral!
Great! Then do what you promised long ago and invite your professors to adjudicate. Ask them if you are on the correct side of any imaginary battle lines?
Until that happens – your failure constitutes a public and tacit admission of defeat!
The is money and prestige in epigenetics:
http://www.nature.com/nrd/journal/v5/n1/full/nrd1930.html
This shows Allis’ views are commanding respect:
http://epigenie.com/epigenetic-drugs-more-than-hype-in-the-pipeline/
Of course you are incorrect… yet again, and you demonstrate as much by failing to invite your own professors to adjudicate as promised.
Is Allis a creationist too then?
Sal, quit shitting your pants and tell us what this has to do with evolution. Particularly, how does the environment affect future generations?
I never made such a promise. If I said something that made you think that, that was not what I intended to say. Show TSZ where a promise was explicitly made, provide a quote, or otherwise retract your false claim.
I have no idea whether you made an explicit promise, but you have implied that your professors agree with you.
So put up or shut up.
The OP had nothing much to do with evolution did it? The OP does suggest how immensely complex biological systems are (an epigenetic code for each cell type — WOW!), which sort of flies in the face of the junk-proponents like Graur and Moran.
Many environmentally induced epigenetic marks are not inherited, but reset. A few persist, but the issue of epigenetics is the layers of complexity that it adds to biology. ENCODE has helped uncover this layer and explicitly used at least one of Allis’ experimental techniques (ChIA-PET), and it doesn’t sit well with Graur:
and
ENCODE (with Roadmap and E4) ~ $793 million. More likely to follow.
Looks like the prestige and money are going to ENCODE not so much to Dan Graur. Imho, just an opinion, Graur sounds kindda whiney that he isn’t getting a piece of the prestige and money pie.
Sal,
If evolution is wrong does that mean creationism is therefore true?
How does it support you in any way if evolution X is replaced with evolution Y, where neither X nor Y offer any support to any telic intervention nor creationism?
You might as well just pick a contentious topic in biology where many experts disagree and use the mere fact of that disagreement as some sort of evidence for your own veiled agenda.
Oh, wait now…
No, it doesn’t.
Everything is implied with Sal.
Here’s another quote from Dan for you Sal:
Dan Graur
The problem is when you glue your worldview from lots of little pieces of other peoples that you think support you then you are unable to produce anything new as you don’t have a coherent workspace.
So, If ENCODE is right and evolution is wrong then intelligent design continues to be wrong. And that’s according to Dan Graur. But don’t let that stop you slyly misrepresenting him and using slices of his world to compose your own. It’ll fall apart in the end.
Ah, he did say “sort of” which is more than enough wriggle room.
C’mon Sal, explain yourself.
Systems that have junk can’t be complex – discuss!
Here is a free PDF of the opening pages of Allis’ textbook. Chapter’s were reading materials for my chromatin class.
http://cshlpress.com/pdf/sample/2014/epigenetics2/EPIFM.pdf
The preface shows some of the things I’ve posted about at TSZ in the face of the usual litany of “Sal is clueless, confused,” blah blah blah.
Despite this, there were the naysayers and critics of Allis mentioned on Coyne’s blog — reminds me of Graur calling the ENCODE scientists crooks and ignoramuses.
Watson? As in the famous Watson of Watson-Crick?
I don’t see the part where epigenetic changes are passed on to future generations.
Is it in another chapter?
Regarding Henikoff’s criticism of the New Yorker article:
Mincing words, Steve? Of course something has to modify the histones.
Btw, it’s not always a transcription factor that modifies the histones. A key feature of transcription factors is the recruitment of RNA polymerases, but many histone modifying complexes don’t immediately recruit RNA polymerases such as the Polycomb Repressive Complex PRC2 which methylates H3K27 (H3K27 mentioned in Shelley Berger’s paper — the H3K27 acetylation may block PRC2 methylation).
Steve’s claim of transcription factors being at the top of the epigenetic hierarchy is not a hard and fast rule. The hierarchy model is probably not the best way to describe things. Witness this study on how Royal Jelly makes a bee a Queen vs. a worker!
And to Henikoff’s other uncharitable claim:
Oh really?
Henikoff fails to mention only the 1% success rate of transcription factor induced pluripotency, thus failing to mention the 99% unknown as to why it fails. It shown that it is because there epigenome isn’t completely controlled by transcription factors!
There is a chapter from Allis textbook that is free online that is relevant. It’s not as simplistic as Henikoff insinuates. It seems to me, Henikoff is just trying to insult the author of the New Yorker article.
Sal,
When did regulation by transcription factors binding to promoters stop being within the definition of “epigenetic”? When was it ever a thing that insect castes were supposed to be due to genetic differences? Or is it perhaps important that the part you didn’t put in bold talks about “the epigenetic changes initiated by transcription factors”, which suggests you might be misunderstanding something?
Regarding the effect of Royal Jelly on creating Queen Bees — it refutes Henikoff and Ptachne’s assertions that transcription factors have primacy on the epigenome. This is like trying to argue whether the spark plugs or wheels have primacy in the functioning of a car.
There is more than one route to modifying the histones and DNA methylome, it’s not just transcription factors. In the case of the Queen Bee it appears 10HDA (which is not a transcription factor) affects histone modifications critical to making the Queen Bee. Ergo, Henikoff is avoiding experimental evidence.
Regarding pluripotency, it seems there are other influences to pluripotency than just the Yanakama factors. It seems micro RNAs are important, and if so this refutes Henikoff’s hierarchical model where transcription factors have primacy:
What do you mean? I have to agree with them, not the other way around.
I posted something like the following diagram straight from peer review and shown in class slides and totally relevant to this discussion. You have a problem with it? Instead I saw a never ending litany of “Sal doesn’t understand, this is irrelevant, you haven’t supported your claims….” blah blah blah.
I said epigenome is like RAM, hundreds of comments protesting my claim, but then I supported it with pages from the stem cell handbook. Has that caused retractions by my critics now that I supported my point with mainstream literature?
Well this stuff is quite relevant, especially to the OP. Why should this diagram be disagreeable? It came from here:
http://www.nature.com/ni/journal/v11/n7/full/ni0710-565.html?message-global=remove
FwIw, all I think the NYer article needed was an acknowledgment that there are some current controversies and that the author’s statements on those issues shouldn’t be taken as a recitation of a scientific consensus. I take it none of the top contending positions make iD more or less likely or plausible. If that’s so, as many here seem to believe, maybe Sal’s suspicion that money is playing a role here (rather than religious ideology) makes sense.
The author was out to unch in suggesting that any of this was new or that any of it had anything to do with evolution.
Yes it did! See:
NIH Roadmap Epigenomics (300 million dollar budget, with that amount of money they can set the standard for the definition)
What is “new” is the improved understanding of the mechanisms of non-DNA memory that enables Queen Bees that have the same DNA as worker bees to become queens. Allis and friends helped bring a little understanding into the mechanisms.
Regarding the Carpenter Ants in the New Yorker article, here is a 2015 press release from UPENN:
http://www.uphs.upenn.edu/news/News_Releases/2015/12/berger/
One can’t fault the author of the New Yorker for misunderstanding or misreporting, he stated was is accepted as science in some respectable quarters. Obviously some other scientists took exception to the claims. It doesn’t make the New Yorker article’s claims untrue.
I’ve stated my opinion, Henikoff is demonstrably wrong, and one Nobelist who said there is no epigenetic code is not even acknowledging the phrase “epigenetic code” is a hypothesis that is on the table.
There is something going on that doesn’t strike me as wholesome in the criticisms of the New Yorker article. Why go after the article when then go after the actual researchers like Shelly Berger?
Btw, let’s follow the money trail as posted on that press release:
stcordova,
Ha bloody ha! Instant-expert-on-everything Sal Cordova won’t take Coyne’s criticisms because he’s not qualified! Chortle. Where’s me coffee.
stcordova,
G’grief, the very first sentence reads: “Conrad Waddington (1905-1975) is often credited with coining the term epigenetics in 1942 as “the branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being””
No mention of inheritance. So now people have chosen to ADD inheritance, and you have decided it “no longer necessarily implies it!”. Start at the beginning, and you may see why I said what I did. It never did necessarily imply inheritance, notwithstanding the emendment on a blogsite that (wrongly IMO) restricts the topic to heritable changes in expression ‘in the 21st Century’.
stcordova,
About junk DNA, not about the use or validity of ChIA-PET!
As with his choice of religion, it is Fortunate Indeed that Sal happened upon professors who are on the ‘right’ side of every debate!
Doesn’t a “serious” magazine like the New Yorker have to do more than simply say this article only presents one side of the story? For example, what if the article came out in favor of homeopathic medicine or said that cold fusion was about to become mainstream science? Would it be enough to say this article does not present the scientific consensus?
However, unlike those two examples, I understand that there is a real scientific controversy about the extent and reality of “epigenetic inheritance”. But, as far as I can tell, only a (small?) minority of informed scientists believe it has more than short term effects.
The article was flawed because it did not make that clear and because it did not provide the arguments of the scientific majority.
ETA: In case anyone missed it, the second post from Coyne is the unpublished New Yorker letter by Mark Ptashne and John Greally which provides a point-by-point refutation of the original New Yorker article.
Mukherjee has replied to it, I understand, but I have not seen his reply. I’d be interested to know if he attempts to address the science or simply stays with making excuses due to the limitations of publishing in the popular press.
Coyne is not alone, and while he published the point by point analysis, he didn’t write it.
The thing that ticks off biologists is the New Yorker article ignores 50 years of research and presents epigenetics as some wonderful new idea.
That, plus the suggestion, barely qualified, that it might provide a wormhole for Lysenko-ian inheritance. All in all, it’s barely above the coffee enemas cure cancer level of science reporting. Just dressed up in a New Yorker quality tuxedo.
Sal needs to take another look at bees and royal jelly.
Coyne didn’t write the bloody criticism. He published it.
petrushka,
True. Tremendous irony though.
The article was flawed because it was poor science journalism. I expect articles about scientific controversies to first be about an actual scientific controversy, and then to explain both sides of the controversy and to be clear on what the majority of informed scientists currently believe.
What do you think of the point-by-point refutation of the science in the article presented in the second Coyne post?. If you have time and are interested in doing so, I’d welcome an attempt to address its points, preferably in your own words (since I have little background in this area and often don’t understand the relevance of the large sections of text you sometimes quote).
stcordova,
An analogy is made no better (or worse) by being placed in the mainstream literature. Analogies serve a pedagological purpose; you are trying to spin it into something which in itself has major scientific import. It doesn’t. Science is not advanced one iota by saying ‘it’s like RAM/ROM’.
What’s important is (for example) methylation and demethylation – mechanisms and consequences. The fact that this might strike one as ‘a bit like’ flipping a bit on a silicon chip is completely unimportant. Pasting diagram after diagram, quote after quote that ‘agrees with you’ does nothing but service your own ego.
BruceS,
You’re not the only one, heh heh!
What interests me, in the quotes collected by Coyne, is the view of numerous experts that various small-molecule modifications do not support the view of these marks contributing to a system of epigenetic ‘memory’. Such marks are downstream of genetically specified transcription factors in all cases so far elucidated.
Whatever percentage of the total that might be, it requires at least one concrete counterexample before we can move on from ‘methylation is a-bit-like-like RAM’ to ‘methylation is-a-form-of RAM’.
As pointed out, analogies are teaching aids. One does not reason from analogy. Analogies have no entailments.
Map. Territory.
There are two Coyne articles; what do you think of the second one?
Asking for ‘entailments’ is asking for too much, I think. There’s a sense in which no empirical entailments are legitimate. If an analogy is good, it may be fruitfully illustrative. That’s all that can be expected of it, but it’s not nothing.
BruceS,
I don’t disagree with any of your post, but it’s kind of a matter of degree IMO. I too would like to see the response. And if it’s true that the NYer is refusing to print critical letters on the article, that strikes me as completely inappropriate (as well as couinter-productive from their own point of view, since it makes them look chicken).
The point is that you can not prove anything about reality by reasoning from the implied entailments of an analogy.
If something in biology resembles something in the realm of digital computers, very well. It may pry loose some brain cells and enable thinking about processes.
But drawing conclusions about chemistry or biology from such analogies is crankery.
I agree with that (and note that sausages flinch and squeal when tossed on a hot grill). My point was that ‘proofs’ are tough to come by using ANY means.
I’m not thinking about formal proofs. I’m thinking of heuristics.
Thinking about genomes as like computer programs leads one off the tracks.
Computer instructions are strict and formally defined. Chemistry is messy and fuzzy.
Genetic “instructions” are more like tendencies than they are like formal causes.