Response on ENCODE reaction

The publication of ENCODE data raised substantial discussions. Clear, open, rational debate with access to data is the cornerstone of science. For the scientific details the ENCODE papers are totally open, and we have aimed for a high level of transparency e.g. a virtual machine to provide complete access to data and code.
There is an important discussion – which no doubt will continue throughout this decade – about the correspondence between reproducible biochemical events on the genomes, their downstream cellular and organismal functions, their selection patterns in evolution and their roles in disease. ENCODE provides a substantial new dataset for this discussion, not some definitive answer, and is part of a longer arc of science in this general area. I touch on this on my blog 
There are also “meta” questions concerning the balance of “big” and “small” science, and how “big” science projects should be conducted. The Nature commentary I wrote focuses on this.
ENCODE also had the chance of making our results comprehensible to the general public: those who fund the work (the taxpayers) and those who may benefit from these discoveries in the future. To do this we needed to reach out to journalists and help them create engaging stories for theirreaders and viewers, not for the readers of Natureor Science. For me, the driving concern was to avoid over-hyping the medical applications, and to emphasize that ENCODE is providing a foundational resource akin to the human genome.
With hindsight, we could have used different terminology to convey the concepts, consequence and massive extent of genomic events we observed. (Note to self: one can be precise about definitions in paper or a scientific talk to scientists, but it’s far harder via the medium of everyday press, even to the same audience). I do think we got our point to the general public: that there is a staggering amount of activity in the genome, and that this opens up a lot of sophisticated and highly relevant scientific questions. There was a considerable amount of positive mainstream press, sometimes quite nuanced. Hindsight is a cruel and wonderful thing, and probably we could have achieved the same thing without generating this unneeded, confusing discussion on what we meant and how we said it.
I am tremendously proud of the way that the consortium worked together and created the resources that it did. The real measure of a foundational resource such as ENCODE is not the press reaction, nor the papers, but the use of its data by many scientists in the future. 

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61 thoughts on “Response on ENCODE reaction

  1. @TheMayan:

    “There are many scientist today who have said and are still saying that much of what we have discovered was once thought to be useless junk DNA”

    No, not many; a few scientists, but many journalists.

    And, as Gregory would tell you, neither the journalists nor the scientists who say “Long dismissed as junk…” ever have citations to old-times scientists saying (for example) that regulatory elements were all junk, or that all non-coding DNA were junk, etc.

    As Gregory has said: beware unsourced citations. Beware phrases like “Long dismissed as junk…”

    In the phrase “Long dismissed as junk…” the verb is in passive tense. Passive tense verbs allow the speaker to NOT identify who, precisely, did the dismissing. Who dismissed all non-coding DNA as junk? Who dismissed regulatory elements as junk, or RNA genes as junk?

    If you say “Long dismissed as junk…” the passive tense verb absolves you of the responsibility to cite a source that did the dismissing.

    If you used an active tense verb, you would have to name names and give citations. “Prof. Smith dismissed non-coding DNA as junk…” No, if you said that, Prof. Smith would object.

    Beware unsourced citations and passive tense verbs.

  2. @ Dio;

    What is your take on Creation activists? As for me posting your real name, why bother, because of course you will deny it, but we both know who you are on CP, you are the one whom calls people *liars* on a regular basis. Hey, perhaps if you post as Igor or L Moreau no one will notice..

  3. Misc thinks I comment at Christian Post, posing there as a theist, but he will not reveal to me my “real name.”

    Misc: “As for me posting your real name, why bother, because of course you will deny it, but we both know who you are on CP, you are the one whom calls people *liars* on a regular basis”

    So, you will not reveal to me my real name. Oh, drat. So what bad things do you think I would do with that information, if you revealed to me my real name?

    And you think I am that person, because… he calls you a liar. And I too call you a liar.

    Just wondering… Do you get that a lot?

    Also. Do many people call you insane? If so, is everyone who calls you that also me?

    Do you see me everywhere now? Out your basement window?

    When your neighbor's dog tells you to do bad, bad things, do you think that's me too?

  4. Hey Igor, I mean L Moreau, I mean, Diogenes,

    Why didn't you answer my question on what your take is on 'Creation Activists'?

    And yeah, I'm not revealing your real name because of course you will lie and say it isn't you, just like Igor and L Moreau are not you. You're a joke and fortunately a no body in the world of Science, except a Larry Moran groupie kicking and screaming on a sinking ship.

    BTW, you never called me a liar on CP, but you do on a regular basis with many other people there, not to mention here, reddit, Larry's blog (there you did call me a liar), HP blogs and the list goes on and on.

    Hey, why don't go back to UD and finish what you started, oh yeah,, you ran off with your tail between your legs after you made a complete ass of yourself.

    Later looser..

  5. Misc: Later looser..

    Misc, if you do not start spelling your ad hominems correctly, you will loose this debate as you always loose.

    Misc asserts that I comment at Christian Post under my “real name” which he will not reveal to me, because if I knew my real name, I might, I don't know, get superpowers or something. He's vague on why he won't tell me my “real name.” At Christian Post, of all places.

    Misc: Hey Igor, I mean L Moreau, I mean, Diogenes…

    And yeah, I'm not revealing your real name because of course you will lie and say it isn't you, just like Igor and L Moreau are not you.

    What other names do you call me by? Genghis Khan? Cthulhu? Pazuzu? Voldemort?

    When you hear a voice at night telling you you're worthless, do you think that's me too?

    Wikipedia: The Fregoli delusion, or the delusion of doubles, is a rare disorder in which a person holds a delusional belief that different people are in fact a single person who changes appearance or is in disguise. The syndrome may be related to a brain lesion and is often of a paranoid nature with the delusional person believing themselves persecuted by the person they believe is in disguise.

    Does it comfort you to believe that when you are made to look foolish everywhere on the internet, there's only one person behind that?

    I suppose it is comforting believing that only one person is vastly smarter than you. Alas, the truth is that there are many.

  6. @ Diogenes

    I posted two replies addressing your BS on Moran's blog, but it appears he is now moderating and not sure if it will get through. If it doesn't, not wasting anymore time on a Psycho such as yourself.

    “What other names do you call me by? Genghis Khan? Cthulhu? Pazuzu? Voldemort”

    Nope, just Igor and L Morea as you were too chicken to face Shapiro on his confrontation about you, and you kept whining all over the place he banned you, which he did not. BTW, he just did a similar assessment on your ideology zealot friend Kwok, wonder why he wasn't 'banned'

    To put my suspicions to rest about CP, why don't you tell me your first name? This person's communication style is strikingly similar to yours, such as calling people liars left and right, using the phrase 'Waaaaahhhh' and an over the top hate for ID, to name a few.

    So go ahead, set the record straight and can check around to see if your telling the truth…

  7. Misc:
    you were too chicken to face Shapiro on his confrontation about you

    Shut your lie-hole, psychopath. I wrote a bunch of comments at Shapiro's blog and they were all deleted.

    I must conclude Shapiro is terrified of me, because it would explain why he deletes ALL my comments.

    Why doesn't Shapiro go over to my blog and comment? What's he afraid of? Go tell your cowardly wuss Shapiro to attack me at my blog, or any blog where I can't be banned.

    Why doesn't he show up again at Mike White's blog? Because at Mike Whit'e blog, I kicked his tail cherry red and he ran away. Gutless Shapiro will never return.

    I wouldn't delete his comments, but he deletes mine. That's because I'm not afraid of him; he's terrified of me.

    Shapiro wrote an entire blog post that consisted of no scientific evidence, no data, nada, just ad hominem attacks on me. He's got nothing.

    and you kept whining all over the place he banned you, which he did not

    How do you know? Present the evidence he did not ban me, or shut your lie-hole.

    Igor and L Morea

    You think I am them and many other people because so many people on the Internet are vastly smarter than you and defeat you in debates.

    You don't know any science, and at no point have you posted any comment with any scientific evidence. All you do are ad hominem attacks, like your cowardly Ken doll, that ignorant gutless Shapiro.

    It makes you feel better to imagine everyone smarter than you is the same person, but they're not. There are many, many, many people smarter than you who defeat you in debates.

  8. “I must conclude Shapiro is terrified of me, because it would explain why he deletes ALL my comments”

    Riiight, here is a direct quote by him:

    03:50 PM on 09/21/2012
    “Diogenes is upset that I quoted his words that were posted on my blog. He claims that he has been blocked from posting further comments here. I have not seen any of them”

    > http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html

    (Isn't it ironic that both L Morea and Igor's only 'fan' is you, and when I (rjop) called L Morea out, he never showed up again but immediately after we see Igor show up, funny that)

    We then have Shapiro's statement to your friend Kwok:

    01:48 PM on 09/30/2012
    John,

    “Don't worry about having your posts rejected as abusive. Since I singled out your comments for the blog, you are entitled to have your say”

    http://www.huffingtonpost.com/james-a-shapiro/could-bill-nye-have-done-_b_1919558.html

    Sorry, I will take his word over yours any day.

    “I must conclude Shapiro is terrified of me”

    So says the person who appears to suffer from delusions of grandeur. Next I suppose you will say Ewan is 'terrified' of you.

    Also, you didn't answer my question on what your first name is, why do you think this is so?

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