Wednesday, September 05, 2012

ENCODE Leader Says that 80% of Our Genome Is Functional

Ed Yong is a science journalist and usually he's a very good one. This time, however, he should have gotten the other side of the story.

Ed interviewed Ewan Birney for a story on the function of sequences in the human genome [ENCODE: the rough guide to the human genome].
According to ENCODE’s analysis, 80 percent of the genome has a “biochemical function”. More on exactly what this means later, but the key point is: It’s not “junk”. Scientists have long recognised that some non-coding DNA probably has a function, and many solid examples have recently come to light. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more,” says Tom Gingeras, one of the study’s many senior scientists.

And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”
The creationists are going to love this.

You blew it Ed Yong. Why didn't you ask him about the 50% of our genome containing DEFECTIVE transposons and the 2% that's pseudogenes, just for starters? Then you could ask him why he believes that all intron sequences (about 20% of our genome) are functional [What's in Your Genome?].

"Almost every nucleotide ..."? Gimme a break. Don't these guys read the scientific literature?

This is going to make my life very complicated.


132 comments:

  1. Yet another scientist speaking more words than what his data warrants. WTF? Isn't this guy a real biologist?

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    1. Ewan Birney is a real biologist.
      http://en.wikipedia.org/wiki/Ewan_Birney

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    2. Ewan Birney is a real biologist.

      I've taken to matching the CVs of scientists with their critics and the heroes of the atheist blogs. It can be rather revealing of who has the more credible credentials. I'd compare Birney's with PZ Myers'. But I've been doing a lot of writing about him this week.

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    3. What about Myers? He is a professor. Next step is nobel prize and there is none in biology. Birney deals with Bioinformatics, which acually doesn't mean any great competence in the field of genetics.....

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  2. There are already two new threads on talk.origins, begun by a creationist crowing about this publication. No mention of onions (or fugu), I see.

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  3. Larry, I'm more than happy to update the post with counterpoints. Sent you an email on this. Lemme know.

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  4. Prof. Moran, I applaud you for posting this idiocy. Not because it's amusing to see silliness, but because it's refreshing to see someone not hiding but rather publicising contrary opinions.

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  5. It's not idiocy, it's useful research. Of course the creationists will pounce on it and gloat but it doesn't help their cause and it's certainly no reason not to publish it. The creationists still have to explain why a single-cell organism Amoeba dubia, the flower Paris japonica, the marbled lungfish and even the humble onion have far bigger genomes than ours. Maybe we aren't so special after all or maybe the Creator likes onions on His butgers.

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    1. Ian, that in itself is an anthropocentric view. Assuming that there is a 'creator', and this creator has managed to do things that are, obviously, well beyond our own human understanding and abilities, why would we assume that 'his' creations would be engineered similarly to how WE would do it (if we could)? So I don't see how a creationist should be the least bit interested in the fact that amoebas have far bigger genomes than ours.

      The Sydney Opera House took much, much longer to build than the Empire State Building, although the latter is much larger. Both are architectural triumphs. Unless one is an architect capable of building one or both of them, I don't think it holds much weight to make value judgments about how much time it should take to build one or the other.

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    2. Good points, Andy.

      All any point of view human can take is an anthropocentric view because WE ARE PEOPLE. This whole "you're anthropocentric I'm not thing is a hoot. There is nothing, absolutely nothing more anthropocentric than the idea that the human invention of science can give an absolute and objective view of the universe. It is profoundly subjective to assert that a human invention made to assist HUMAN understanding can provide a non-human view of something.

      From what I recall reading, one of the reasons the Sidney Opera House took so long to build is that the architect didn't have any idea how those "sails" he wanted on it were supposed to be built. And, instead of making them merely decorative and non-functional, it was insisted that the form had to follow the function. So they had to invent both a function and a way to make it take that form. But that's what I read. I'm no architect anymore than most of the people getting into a swivet about this are geneticists.

      My union carpenter brother hates it when architects get creative like that, he's one of the people who have to try to figure out how to build something that the jackass with the big salary can only draw on paper.

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    3. Ian, that in itself is an anthropocentric view. Assuming that there is a 'creator', and this creator has managed to do things that are, obviously, well beyond our own human understanding and abilities, why would we assume that 'his' creations would be engineered similarly to how WE would do it (if we could)? So I don't see how a creationist should be the least bit interested in the fact that amoebas have far bigger genomes than ours.

      There's a huge body of biochemical and genetic literature dealing with transposable elements, and there is also another huge body of literature dealing with neutral and nearly neutral changes in the genome and how they affect the evolution of populations. Then there is also a very sizable body of literature showing quite conclusively that the abundance of junk DNA in some genomes (and their absence in others) is explained very well by our current understanding of molecular evolution and population genetics.

      Creationists have an awful lot of work to do in order to convince us their explanation is better.

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    4. All any point of view human can take is an anthropocentric view because WE ARE PEOPLE. This whole "you're anthropocentric I'm not thing is a hoot. There is nothing, absolutely nothing more anthropocentric than the idea that the human invention of science can give an absolute and objective view of the universe. It is profoundly subjective to assert that a human invention made to assist HUMAN understanding can provide a non-human view of something.

      Should we take this to mean that if science is not going to provide answers, then something else will.

      And what would that something else be?

      The anthropomorphic God that a group of ignorant illiterate goat herder from the Bronze age made up?

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    5. It means that science is an anthropocentric point of view, anything people come up with is an anthropocentric point of view, including any proposed religious scriptures which are written by people. The universe science finds is no less "made up" by people than the God which is described in scriptures. They are both the product of an entirely human point of view. To pretend they aren't is superstitious on both sides. I can well imagine 6,000 years from now people might look back and chuckle over the stupidity of "Plutonium Age extinction jockeys." That is if the combination of greed, science, technology and PR haven't managed to kill us off as well.

      Where do you think science came from? Prometheus?

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    6. Bullshit epistemic relativism.

      The universe science finds is no less "made up" by people than the God which is described in scriptures.

      Bullshit. We can replace Yahweh with Allah or 1,000 other gods and the predictive ability of the hypothesis does not increase nor decrease.

      But we CANNOT replace the equations of quantum mechanics or relativity with ANY other non-equivalent equations without affecting the predictive ability of the hypotheses.

      If you have a better, or equivalent, mathematical formulation of scientific theories like QM or relativity, cough it up or shut up. You don't have any alternative.

      But as for religion, there are perhaps 2,000 religions no better nor worse than yours.

      They are both the product of an entirely human point of view.

      Flattening argument. Science is constrained by having to make predictions about observable quantities.

      Your religion is not constrained by anything, except perhaps the fear of being burned as a heretic if you get some obscure detail wrong.

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    7. Diogenes, you have no idea what "my religion" might be so you have no idea how it is or is not constrained. For all you know I could be a Reformed Muggletonian. Though not without resorting to Wikipedia.

      So, the answer would be that, yes, Diogenes believes that science is a gift of Prometheus?

      Where the hell does an atheist imagine where science came from if not human beings?

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    8. This straw man argument:

      Diogenes believes that science is a gift of Prometheus?

      Does not support this conclusion of bullshit epistemic relativism:

      The universe science finds is no less "made up" by people than the God which is described in scriptures. They are both the product of an entirely human point of view.


      Bullshit. "Point of view" is like whether creamy peanut butter is better than chunky peanut butter. Quantum mechanics and relativity are not "points of view." If you think the equations of gravity are a matter of opinion, please jump out a window and test the importance of an optimistic point of view.

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    9. Diogenes, you think a person can see anything except from their point of view? How? By some out of body experience? Well, unless they can simultaneously see something from every possible point of view, they will still be seeing something from their point of view.

      Do you people ever, ever think about things like that?

      Quantum mechanics and relativity are not "points of view."

      Oh, good Lord. If you'd even watched NOVA you'd know what was wrong with that sentence. You clearly know nothing. Here's a hint, what do you think is relative about RELATIVity?

      So, where do the equations of gravity exist, disembodied in the universe, floating there like some celestial teapot? Where to they exist unexamined by human consideration? How can you tell me that except from a human point of view? How do you know that some other species existing in this universe doesn't have an entirely different conception of it? Lewontin once said that bacteria in a liquid medium don't experience gravity because Brownian motion was so much more relevant to their size and experience. Which is a fascinating idea to consider, only, how does Richard Lewontin know that? Only, I'd listen to what he said about it before I'd listen to what you said about it so don't bother answering that question. Not that there is much of a danger of that happening.

      Or are you announcing you're not a member of the human species?

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    10. Oh, I forgot

      "Diogenes believes that science is a gift of Prometheus?"

      Does not support this conclusion of bullshit epistemic relativism:


      I'd ask if you understood that a question is not a conclusion but it would be pointless. You are nuts.

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    11. Oh, good Lord. If you'd even watched NOVA you'd know what was wrong with that sentence. You clearly know nothing.

      In every thread, when TTC is proven to be wrong, he always falls back on, "My evidence is my intellectual superiority." If you were intellectually superior, you would have used your superior intellect to present evidence. You never presented relevant evidence, thus disproving your hypothesis of intellectual superiority.

      Why do you never use your allegedly vast intellect to present relevant evidence to back up your outlandish, yet ego-flattering, claims?

      Under normal circumstances I would not make an issue of the uneducated and stupid nature of an opponent if that opponent were humble, but TTC always falls back on, "My evidence is my intellectual superiority," which makes it relevant to point out that TTC is dumb as a box of rocks-- perhaps the least educated, least experienced commenter on this blog.

      You are a stupid asshole who apparently learned his quantum mechanics from NOVA, of all places. Physicists do not need to watch NOVA nor to read Hawking's pop books to learn physics. I sure as fuck did not learn quantum field theory from Hawking's stupid books or NOVA.

      There are many people who are quite smart in other fields, but never learned real QM or quantum field theory. Some of these people can be extremely smart in other fields; but when it comes to QM or relativity, they are humble enough to admit their limitations. I would never call them stupid, because they admit when they are not experts.

      But TTC is not humble-- so we must say that TTC is not just stupid, but a narcissistic egomaniac.

      By constantly falling back on the fallacy, "My evidence is my intellectual superiority", TTC has made his ignorance and stupidity directly relevant.

      The fact that you are a stupid POS who learned his quantum mechanics from NOVA is not the reason why you are wrong.
      Your egomania and boasting is not evidence of intellectual superiority, and intellectual superiority, if you had it (obviously you don't) is not evidence that quantum mechanics is a mere matter of opinion, as you claim.

      TTC has done this in one thread after another-- for example, asserting that none of us have read Darwin, or that none of us can read German-- this based on no evidence except TTC's egomania and fantasies! Now we get the accusation that I don't know quantum field theory. Another accusation based on no evidence except TTC's egomania and fantasies!

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    12. But TTC is not humble

      And answering your nonsense is doing nothing to make me so.

      You obviously hadn't read Darwin or you wouldn't have taken the same old "quote mined" passages that people have been using to lie about what he said for the past half a century. You wouldn't name a single book of his that you'd read, I assume because you're afraid I might have read them and could have called you on misrepresenting it. I'll tell you what I've read, Voyage of the Beagle, On the Origin of Species, The Descent of Man, his collected letters edited by his son Francis Darwin and various shorter things, letters, etc published online. I'll put that against your dribblings from the Darwin Industry any day.

      So, what works of Schallmeyer did you read in the original German? I believe I provided a Googlebooks link to Vererbung und Auslese, in which you could have seen that Leonard Darwin was correct, Schallmeyer attributed his founding German eugenics directly from reading On the Origin of Species.

      You are a drooling nut job.

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    13. Judging from Mr. McCarthy's moronic comments on relativity and quantum mechanics, he is at least as ignorant on those topics as he is on statistical inference. I must say that never have I heard anyone write so knowledgeably from such a vast fund of ignorance as Mr. McCarthy.

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    14. Every argument with TTC boils down to his claim: "My evidence is that I'm intellectually superior."

      TTC: You obviously hadn't read Darwin

      You just got done accusing me of not knowing quantum mechanics. Now we're back to accusing me of not having read Darwin. Next up will be accusing me of not knowing German.

      This just shows TTC is an idiot who cannot understand how to draw inferences from evidence.

      With this kind of logic, I could prove TTC is the one who never read Darwin, because TTC repeatedly used the same quote mine of Darwin (from DoM) that was used by Ben Stein in "Expelled" and by many other creationists.

      TTC asserts that his "proof" that I never read Darwin is that I use the same quotes (from his letters) that other anti-creationists use. But TTC himself uses the same quotes that creationists like Ben Stein use, so that illogic would likewise would "prove" TTC never read Darwin.

      Is there anyone, anyone anywhere on the internet, who does not immediately see the illogic of TTC's argument? TTC is incapable of even the most basic logic.

      So, what works of Schallmeyer did you read in the original German?

      None. Why the fuck is it relevant? Reading Schallmeyer in German is only relevant if you can demonstrate that the English translation is relevant yet incorrect, or tricky, or context-dependent.

      I never put down anti-Darwinists by saying to them, "You don't read German so I'm smarter than you." It's not even relevant unless there's some passage in "Mein Kampf" or the Table Talk where the translation is relevant yet incorrect, or tricky, or context-dependent.

      If the standard English translation is accurate enough, there's no reason for accusing anti-Darwinists of being dumb because they (supposedly) don't read German.

      For all I know, they might read German. If I presume they don't, and they really do, I might make a TTC-style ass of myself.

      I could say, "What works of Hitler did you read in the original German, asshole?" but it's not always relevant to the topic. Sometimes it's relevant, sometimes it isn't.

      Every argument with TTC turns into his claim, "My evidence is that I'm intellectually superior." That's a logical fallacy and I'm rejecting it. Unlike TTC, I'm not going to boast of what I read, because my evidence is the evidence itself, and will have to stand or fall on that basis.

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    15. Intellectual superiority? In my day it was called backing up what you say with evidence and citations. Back then no one would mistake doing the minimum to support what you say a display of arrogance. Backing up what you said was the MINIMUM required to maintain basic credibility.

      I said why I wouldn't translate Schallmeyer, it would just give your side a chance to quibble over every word and suffix. I wasn't the one who made Schallmeyer relevant, that would be Leonard Darwin, old Chuck's boy, who said Schallmeyer was inspired to found German eugenics by reading On the Origin of Species. Oh, and Schallmeyer did too, but, unfortunately, no one from Charles Darwin's inner circle or Joseph McCabe, the Christopher Hitchens of Brit atheists at that time translated Schallmeyer into English, as they did Haecel. It was the only place in my argument I relied on a credible, secondary source instead of primary source material.

      As to my citing Charles Darwin's Descent of Man, noting what he said and who he cited in the book, anyone who wasn't a drooling idiot would know that what he said in that book constituted the primary source document IN AN ARGUMENT ABOUT WHAT HE SAID ON THE SUBJECT! You are a total idiot if you don't understand that in order to present what Darwin said, you have to use what Darwin said. I don't make it up like you do.

      Jeesh! How stupid can you be and still be considered credible among atheists?

      I made no arguments about Hitler that would require citing him. I only dealt with people who Charles Darwin knew and cited in my argument. Hitler was born seven years, almost to the day, after Charles Darwin died. AS I NOTED.

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    16. Judging from Mr. McCarthy's moronic comments on relativity and quantum mechanics, SLC

      I don't recall making a single statement about quantum mechanics. I don't discuss the topic. The only thing I recall saying about relativity was that point of view was rather relevant to it. You want to quote what I said, in my words, SLC? And link to where I said it?

      You are typical of the Kurtz school of atheist polemics, SLC, fundamentally dishonest.

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    17. Oh shit, there goes another irony-meter ...

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    18. NE, no one's interested in your sex life.

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    19. TTC,
      This would be an excellent joke except that we know it was accidental, and that your comment is yet another incoherence due to your reading comprehension disabilities.

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    20. TTC: I don't recall making a single statement about quantum mechanics.

      TTC said this about ALL SCIENCES, and that includes QM and relativity:

      TTC: It means that science is an anthropocentric point of view, anything people come up with is an anthropocentric point of view... The universe science finds is no less "made up" by people than the God which is described in scriptures. They are both the product of an entirely human point of view.

      People "made up" all sciences, including quantum mechanics and relativity. So logically, that mean TTC believes QM and relativity are just "points of view", no different from, say, I like creamy peanut butter, you like chunky peanut butter.

      I think the Earth is round, you think the Earth is flat. It's all just different "points of view", right TTC?

      Diogenes: Quantum mechanics and relativity are not "points of view."

      TTC: Oh, good Lord. If you'd even watched NOVA you'd know what was wrong with that sentence. You clearly know nothing. Here's a hint, what do you think is relative about RELATIVity?

      Asshole accuses me of not knowing quantum mechanics and relativity.

      Asshole also accuses everyone on this site of not having read Darwin and not being able to read German.

      I will answer this stupid question about relativity. If two events, E1 and E2, occur at time-space points (x1,t1) and (x2,t2), is the quantity [(x1-x2)^2 - c^2(t1-t2)^2] invariant for all observers, or is its value merely a "point of view"?

      Asshole will not answer. Asshole will change subject.

      In a previous thread, asshole asserted that positivism had been disproven in the 1930's by means of "physics". Remember that? I repeatedly asked asshole which laws of physics, specifically, in the 1930's were used to disprove positivism.

      Asshole did not answer. Asshole changed subject.

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    21. TTC: I don't recall making a single statement about quantum mechanics.

      TTC said this about ALL SCIENCES, and that includes QM and relativity:


      Diogenes, it's a temptation to wonder whether you are really stupid or just totally nuts. But it's a false alternative as you prove you can be both.

      YOU! are the one who talked about quantum mechanics.

      My point that people could only address anything from their point of view covers everything they think about or say. It was not any more a point about quantum mechanics than it is about whether you like chocolate or vanilla. If you could read what I said, the only part of physics I mentioned was RELATIVITY, which takes POINT OF VIEW into account in a rather basic way, thus the name. And that's the only thing I said about it.

      You wouldn't name any of Darwin's books you'd read. You chopped off paragraphs and Darwin's letter to Gaskell, distorting the meanings of both of them in exactly the same way that the Darwin Industry always does, I WAS THE ONE WHO GAVE THE ENTIRE THINGS IN CONTEXT.

      The new atheism is the product of basic intellectual incompetence and ignorance, a symptom of a defective school system too fixated on superficial scientific knowledge. Maybe if they taught more people the kind of basic PHILOSOPHICAL methods that used to be taught in Freshman Rhetoric you'd know what a total moon calf you are being.

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    22. This would be an excellent joke except that we know it was accidental, Negative Entrophy

      I have no more interest in whether what you did when you broke your irony meter was an accident anymore than I want to know where you stuck it.

      Delete
  6. From the abstract:

    The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

    The paper:

    An integrated encyclopedia of DNA elements in the human genome

    To Ian- why do old computers, which are less powerful and much slower, contain more parts than their modern counterparts?

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    1. That depends on what you mean by a "part".

      The processor chip on a modern computer contains far more nand gates than older CPUs.

      The Intel 4004 manufactured in 1971 contained 2,300 transistors while the 2011 10-Core Xeon Westmere-EX contains 2,600,000,000 transistors.

      Ditto for hard disk drives and memory with respect to bytes of data.


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    2. But you already know that the genome/computer analogy is not a very good one.

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    3. Joe G enters, hilarity ensues.

      This is what always gets me: Talk to Joe G about junk DNA, and he'll INSIST that until you have tried removing all of it, you can't say it's junk.
      Now, if he was intellectually honest and fair, he'd insist to see data to show that these transcribed regions were in fact functional, not just transcribed. But no, this specific paper, in fact, THE ABSTRACT he just swallows uncritically. No questions asked. It says functional in the abstract so it must be right.

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    4. Discrete components = parts and the analogy works for this scenario.

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  7. I just skimmed what was written over at the Science website. One thing that jumped out at me was that 76% of the genome is transcribed. But how much of this RNA actually has some downstream function? How are they defining "biochemical function"? If being transcribed is considered function, but the RNA has no function, then who cares?

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  8. To be fair, if one read's Ewan's own account of this, on his own blog, he can find a much more balanced treatment of the subject:

    http://genomeinformatician.blogspot.com/2012/09/encode-my-own-thoughts.html

    Q. Hmmm. Let’s move onto the science. I don’t buy that 80% of the genome is functional.
    A. It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e., if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons.

    Q. So remind me which one do you think is “functional”?
    A. Back to that word “functional”: There is no easy answer to this. In ENCODE we present this hierarchy of assays with cumulative coverage percentages, ending up with 80%. As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising.

    However, on the other end of the scale – using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNA:protein contact, such as a transcription factor binding site to the actual bases – we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons, this is surprisingly high for many people – certainly it was to me!

    In addition, in this phase of ENCODE we did sample broadly but nowhere near completely in terms of cell types or transcription factors. We estimated how well we have sampled, and our most generous view of our sampling is that we’ve seen around 50% of the elements. There are lots of reasons to think we have sampled less than this (e.g., the inability to sample developmental cell types; classes of transcription factors which we have not seen). A conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20%

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    1. If you'll follow the link to the rest of the piece that Larry has not quoted, I discuss exactly this later on. Under the section "So… how much is “functional” again?". My name should link to it.

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    2. I know. And you link to it too.

      The problem is I saw several mainstream publications reporting on the papers that focused on the "functional" portion of the genome without establishing the context and explaining the details at all. Because face it, while a lot of people read your blog, this:

      http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all

      will be much more influential in shaping people's perceptions on ENCODE (which they don't even bother to spell correctly), and you see on what level it is written.

      This is obviously very bad.

      Given what happened with the first phase of ENCODE, I have been expecting this issue to stir a storm when the second phase of ENCODE publishes its integration paper for a very long time, including the creationist posts which are yet to come but surely will and Larry's post, which we're commenting on right now. It was an easy prediction to make and it turned out to be correct

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    3. So we're up to 20% of the sites whose nucleotides affect fitness? Or is it 80%?

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    4. We're literally up to 9%. The author is counting chickens on the other half he has not yet sampled to get to 18-20%. 80% holds only if transcription = function (we ignore spurious transcription).

      -Anaxyrus

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    5. @Georgi Marinov

      I'm not sure you can really fault the NY Times, et al. After all, the abstract claims quite baldly:

      These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.

      Nothing in that abstract gives sufficient context for me to realize that "biochemical function" can include merely being transcribed. If the authors can't make it clear enough in the abstract for someone like me (I have a PhD in mol bio & 20 yrs experience) is it any wonder that even a seasoned science journalist might be misled?

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    6. Fair point - keep in mind though that I am not someone who's approaching this from the outside and for the first time and I have very hard time actually reading it from the perspective of the unfamiliar reader

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    7. We're literally up to 9%.

      So this doesn't contradict anything Larry wrote-- right? Larry has estimated for some time that the genome was 8 or 9% functional. (I mean real functional here, not transcribed = "functional.") The ENCODE project had previously stated that most of the genome was transcribed (though often at extremely low levels.)

      So what's new about this scientifically? Not much. What's new politically? The creationists can now use equivocation, switching between one definition of "functional" and another definition of "functional."

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    8. Joe Felsenstein asks,

      So we're up to 20% of the sites whose nucleotides affect fitness? Or is it 80%?

      Well you know that it can't be 80% because you're a population geneticist. You know that our species would be extinct if the sequence of 80% of our DNA was important.

      You also know that a huge percentage of our genome is full of variants that seem to be accumulating at the mutation rate. That means they are neutral and they are segregating by random genetic drift.

      The actual number of sites where the nucleotide matters for fitness looks like it's about 10% of the genome. The ENCODE project hasn't changed that number as far as I'm concerned.

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    9. Larry, the argument from mutation and substitution rates does not rule out these segments having fitness-affecting functions. It could be that some of these segments are just acting as spacers needed for some protein-building or folding activity. Their actual base sequences would not matter, only their length and location, so the sequences could well drift freely even though the segment has a function.

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    10. Larry, the argument from mutation and substitution rates does not rule out these segments having fitness-affecting functions.

      Which is why he gave the qualification "where the nucleotide matters".

      It's no small distinction--if the nucleotides matter in a sequence of N bases then the sequence could constitute something on the order of 2 x N bits of hereditary information, but if only the length matters then it could only constitute log_2 N bits.

      E.g. consider a sequence 32768 bases long.

      2 x 32768 = 65536 bits

      log_2 32768 = 15 bits

      So even a vast pile of sequences each of whose length was biologically relevant would still only represent a tiny amount of hereditary information compared to even a few sequences where the nucleotides matter.

      Delete
  9. I heard about this on NPR and thought is was going to spawn blowback. Basically his trigger for 'functionality' being 'specific biochemical activity' sets a pretty low bar. It's about the lowest set-point I think you can have short of 'having a sequence that can be digested with a DNAse'.

    An unfortunate choice of words, unfortunately.

    ReplyDelete
  10. So, by their definition, if I synthesize a random string of DNA, put it downstream of the CMV promoter in some retroviral vector, and transduce it into a cell, that's a functional sequence, right? It's transcribed, so it has a biochemical activity. So what that it's a completely random, made-up sequence, right?

    It's nice that Birney acknowledges the ambiguities, but let's be serious. If random DNA can be made to fit their definition of 'functional' in such a trivial way, then their definition is massively flawed.

    ReplyDelete
  11. Can someone explain what "specific biochemical activity" means, if anything?

    ReplyDelete
    Replies
    1. It shows up as a reproducible ChIP-seq peak, DNAse hypersensitive or a transcribed region.

      Delete
    2. a reproducible ChIP-seq peak, DNAse hypersensitive or a transcribed region.

      Forgive my ignorance, can you explain what that means? The transcribed part I get. But why is DNase hypersensitivity an indicator of function? What is a ChIP-seq peak?

      Delete
    3. Enhancers and promoters are as a rule DNAse hypersensitive and DNAse hypersensitivity in general indicates disruption of regular nucleosome packaging of DNA by some other protein.

      ChIP-seq peaks = transcription factor binding sites.

      The "reproducible" part is key, BTW, an enormous amount of effort went into devising statistical methods for properly assessing reproducibility:

      Li Q, Brown JB, Huang H, Bickel PJ. 2011. Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5(3):1752-1779.



      Delete
    4. Thanks, but...

      Enhancers and promoters are as a rule DNAse hypersensitive and DNAse hypersensitivity in general indicates disruption of regular nucleosome packaging of DNA by some other protein.

      That's the "rule"? Shouldn't the rule be re-evaluated now that we know that a large part of the genome is DNAse hypersensitive?

      So the nucleosome packaging at that point is disrupted, presumably by a protein, thus exposing some DNA to get chewed up by DNAse. All this shows is that that DNA binds some kind of protein-- right?

      Shouldn't the "rule" that a protein bound to DNA indicates "function" therefore be questioned, too?

      I mean where's the negative control for that? It's like if you have a geiger counter that clicks at everything. It could be that everything is radioactive... or it means your geiger counter is broken.

      Widespread DNAse hypersensitivity calls into question whether these people have a negative control for their claims.

      Suppose you generated large amounts of random DNA sequence. Then threw it into the nucleus, with its vast diversity of proteins. What percentage of random DNA would bind AT LEAST one protein enough to disrupt nucleosome packaging?

      Delete
    5. Shouldn't the "rule" that a protein bound to DNA indicates "function" therefore be questioned, too?

      Nobody is claiming such a rule, all that is claimed is that statistically significant enrichment has been detected for the assay in question.

      In fact, one of the most depressing (even if not heavily advertised) results of the last 5 years of doing ChIP-seq is that there is no relation between transcription factor binding and expression of nearby genes. One obvious explanation for which is that a lot of that binding is non-functional.

      Delete
    6. Marvelous and thanks for the help, but...

      one of the most depressing (even if not heavily advertised) results of the last 5 years of doing ChIP-seq is that there is no relation between transcription factor binding and expression of nearby genes. One obvious explanation for which is that a lot of that binding is non-functional.

      Do you happen to have a reference for that at hand?

      Delete
    7. The one paper where this is most obviously stated is this one:

      http://www.ncbi.nlm.nih.gov/pubmed/20412780

      Other than that it's an internal observation that pretty much everyone who is working with that kind of data has made for themselves

      Delete
  12. It's about the lowest set-point I think you can have short of 'having a sequence that can be digested with a DNAse'.

    heh heh, nice one. Or a how about: a sequence subject to replication.

    ReplyDelete
  13. Sorry if this is an overly simple question from a biologist who is not a molecular biologist: does this mean that all transposons and retrotransposons are by this definition "functional"?

    ReplyDelete
    Replies
    1. all transposons and retrotransposons are by this definition "functional"

      Holy Shmoly. The authors got some splainin to do.

      Delete
  14. Come on now. Ewan, and the rest of the ENCODE team, have thought about this for a while. BUT, forget about the exact numbers. They have defined a ridiculous number of functional elements, far more and far more exquisitely interacting, let alone the amazing complexity of the transcriptome. So why quibble about the exact precise % that should be reported (is 80% excluding transposons? are transposons not a functional part of the genome? what if a transposon is co-transcribed), and just marvel at the data and its analysis.

    ReplyDelete
    Replies
    1. Ewan, and the rest of the ENCODE team, have thought about this for a while

      No they haven't. They may say they have thought about it but the evidence suggests otherwise.

      They have defined a ridiculous number of functional elements...

      No they haven't. They have identified sites where proteins bind. We don't know is those sites are functional but our understanding of basic biochemistry suggests that most of them aren't.

      You seem to be confused about what the data actually says and what the authors conclude from the data.

      Delete
  15. Anyways, there is concrete evidence that expressed pseudogenes are important for regulating gene expression. So why toss them out?

    ReplyDelete
    Replies
    1. I think you mean 'transcribed pseudogenes'. And even some untranscribed pseudogenes affect gene expression but again, it's a stretch to say that the vast majority of pseudogenes, transcribed or otherwise, are functional in a physiologically meaningful sense. Their experiments simply don't capture the information required.

      Delete
    2. Pseudogenes make up 1% of the genome. And as Argon puts it:

      it's a stretch to say that the vast majority of pseudogenes, transcribed or otherwise, are functional in a physiologically meaningful sense.

      This bears repeating.

      Delete
  16. Wow. Stop the hate. Seriously. Stop blaming science journalists, science writers, and others who write about this stuff. Who cares what creationists think? When you fight their fight, well, you fight their fight (and essentially validate their nonsensical misuse of science). I agree with Bruneau. Marvel at the data and its analysis. Marvel at how far scientists have come since the brilliant Barbara McClintock make her bold predictions so many decades ago.

    ReplyDelete
  17. I have to admit I find it a bit sad, this trashing of a massive data-intensive study and the people who conducted it, simply because a bit of hyperbole in the abstract of one paper will make your arguments with creationists "very complicated".

    ReplyDelete
    Replies
    1. None of us are even going to attempt to read all the papers. Most of them are very boring and most of them are far too complicated for a mere biochemist/molecular biologist.

      We want to know the bottom line. What's the take-home message? That's the important part of the project, not the data dump.

      The spokespeople for the ENCODE project are misrepresenting the bottom line. That's a serious issue and it reflects poorly on every member of the consortium.

      I really don't care about the creationists. If it turns out the the conclusions are correct then I'll just have to live with their gloating. What I care about is good and accurate science. That's what I meant when I said that this is going to make my life complicated.

      Delete
    2. Ian- it's not hyperbole, it's equivocation, declaring victory by equivocation in an ongoing scientific controversy is cunning and deliberate.

      Delete
  18. If I understand it correctly being transcribed makes DNA functional for ENCODE researchers. Just wondering if if they provide any information on copy numbers/per cell for individual non-coding transcripts and if they give a cut-off which would separate noise from signal.

    ReplyDelete
  19. Once ENCODE defines being replicated as functional the proportion of junk DNA will approach 0% and we will have another 30 papers in Nature et al.

    ReplyDelete
  20. Wow. The ability of some people to digest 30 papers in a few hours and then have an informed position on why they are wrong is astounding. I am clearly doing something wrong.

    I agree with Ian Holmes. Screw the Creationist jack-asses. If we change how we do/report science just to pander to their pathetic distortions of reality, they win. The big point that Ewan Birney and Ed Yong are making is that the genome is a lot more active (and complex) than is generally thought. If you can't be bothered to read their definitions of "functional" - and the explanation/difficulty of even coming up with a definition of "functional" - that's your problem, not theirs. Stop being lazy and read the content, rather than making erroneous value judgements based on the language.

    It's going to be years before we know what all this stuff means and how much of it is important. Years of wonderful, real science - not speculation and soundbites. I thought this was a science blog. Apparently not.

    ReplyDelete
    Replies
    1. None of this appears to be new. We've discussed it all before in 2007. It looks like the ENCODE consortium learned nothing from that discussion and the subsequent papers published in the scientific literature.

      Delete
    2. I think ENCODE's attitude is one of pride and power. They know they can publish no matter what, and they will not show "weakness" by admitting prior mistakes. Mere power showing-off.

      Delete
    3. I think that's true.

      There are two meanings of functional here:

      1. Interacts with any molecule
      2. Contributes to fitness via some biochemical pathway essential to metabolism, reproduction etc.

      The ENCODE project had evidence for (1) for 80% of the genome. However, in their ABSTRACT they make it appear-- and they essentially state that-- they have evidence for (2).

      What is the evidence that (1) proves (2)? They had no evidence, but via equivocation, they made it appear there was evidence. That is irresponsible to the max. Unforgivable. There's got to be a rule against equivocation of this sort.

      Delete
    4. @Diogenes:

      Doesn't (1) imply 100% is not "junk"? After all, you can't duplicate something without interacting with it.

      Delete
    5. True. But Birney considers his criteria restrictive because he excluded phosphodiester bonds! Real restrictive there.

      Delete
  21. The research is valuable and pathbreaking work (some of the groups involved are people I know from my own department, and they do fine work). The complaint here is about the publicity and the way it was described. not the actual research.

    ReplyDelete
    Replies
    1. There is more to good research than just generating data. You also have to be able to interpret your data correctly.

      Delete
    2. I do not think that it is pathbreaking. It is "stamp collecting." It might be important, foundational, stamp collecting, but stamp collecting nonetheless. This might be another reason why they overstate their findings. To claim some new biological insight after so much expense and effort.

      Delete
  22. cabbagesofdoom,

    It's not just creationist jack-asses. Already we can see the general public (and many biologists!!) are getting the totally wrong message from this.

    ReplyDelete
    Replies
    1. I agree - I could care less about how the creationists will spin this - what I'm trying to process is how to explain to my intro bio students who pay attention to science news what everyone is really talking about when they use the word "functional" - they're just at the beginning of their biological education and when they hear "functional" they automatically assume translated or directly regulatory.

      Delete
  23. Here we go:

    http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html

    Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome"

    ReplyDelete
  24. Thanks God for freeing us from the nonsense junk DNA!

    ReplyDelete
  25. God, don't people realise the future of Darwinism is at stake? That if we are forced to conclude by data that X% of sequence has a phenotype beyond just existing and being replicated, the entire edifice of evolutionary theory will collapse in a mangled heap? Focus, people: the existence of junk qua junk is the bottom Jenga-piece of the evolutionary synthesis ... according, that is, to ENV, UD &c.

    /Poe

    ReplyDelete
    Replies
    1. No, Darwinism is going to dissolve as more about evolution is discovered and people lose their emotional attachment to old Chuck. Maybe the BBC will produce just one costume drama about him too many and he'll become unfashionable, so will Jane Austin. Evolution will have other explanations as more is known about it. Creationism will still be wrong and intelligent design will still be an idea that science can't address but evolution will still be a fact. We can only wait to see if that prediction is right.

      Delete
    2. The DNA has many other characteristics which are not at all mentioned in this discussion.

      Delete
    3. No, Darwinism is going to dissolve as more about evolution is discovered and people lose their emotional attachment to old Chuck.

      Apparently you have failed to notice one very clear trend in the development of biology in the 150 years since Darwin - things have been getting progressively worse and worse for creationists. What makes you think that trend is going to reverse?

      Delete
    4. Georgi writes that TTC has failed to notice that "things have been getting progressively worse and worse for creationists" and asks what TTC thinks will reverse this trend.
      Meanwhile, TTC wrote, "Creationism will still be wrong..."

      I think perhaps it is Georgi who failed to notice something.

      Delete
    5. andyboergerThursday, September 06, 2012 10:22:00 AM
      Georgi writes that TTC has failed to notice that "things have been getting progressively worse and worse for creationists" and asks what TTC thinks will reverse this trend.
      Meanwhile, TTC wrote, "Creationism will still be wrong..."

      I think perhaps it is Georgi who failed to notice something.


      1. The term "Darwinism" is almost exclusively used by creationists who think it equates modern evolutionary biology

      2. I explicitly replied to a statement that "No, Darwinism is going to dissolve as more about evolution is discovered". Either this or the "Creationism will still be wrong and intelligent design will still be an idea that science can't address but evolution will still be a fact." sentence must have been ironic. Given the other posts in the thread, the logical inference wast that it was the latter

      3. I prefer to apply the label "Creationism" not just to the YEC form, but to pretty much everything that is based on denying the proper current scientific understanding of the subject - at its core, it all has a religious root.

      4. I just realize who the person behind TTC is. Which means I made a huge mistake by replying and feeding the troll.

      Delete
    6. I think I'm still unclear as to what TTC is talking about. Are you (TTC) saying that natural selection is an insufficient explanation and/or comprises a smaller part of evolution than Darwin initially proposed? That's nothing new, and I don't think that most biologists ascribe to the idea that natural selection on expressed traits explains the complexity of the genome in its entirety- genetic drift, neutral changes in the DNA, gene duplication providing raw material, etc . My "issue" with this whole bit of science reporting is simply that "functional" can be interpreted in many different ways - and that it risks being read as "directly affecting fitness / form at this particular moment in time" when that is not necessarily warranted from the data. Do transposons have the potential to affect fitness? Sure, but any one particular transposon at any one particular site that is not altering an exon, regulatory region, histone modification site, etc. might just be a bit of genetic baggage that makes very little difference to the overall fitness of the organism. Might that transposon affect fitness in the future / did it affect fitness in the past? Maybe. I'm not casting aspersions at the science itself - this cataloging effort is tremendous and important but language matters in communication efforts and my concern is ultimately less about creationists/ID people but the educated public and my biology students.

      Delete
    7. The term "Darwinism" is almost exclusively used by creationists who think it equates modern evolutionary biology

      As it happens, I wrote a short essay on that bit of ScienceBlog (thanks Orac) folk etymology, a couple of weeks back, and the fact that if those who repeat it had ever read any of the literature of Darwinism from Thomas Huxley to Richard Dawkins they would find the word used, by them, continually for the past hundred-fifty years. Darwin's greatest fans have never read the literature of Darwinism.

      http://zthoughtcriminal.blogspot.com/2012/08/a-note-about-word-darwinism.html

      As Andy pointed out, you seem to miss things that are right there in plain sight.

      Delete
    8. coco,

      TTC can't read. He only takes a few words here and there, especially if he can conclude something "evil" against his perceived antagonists. Besides taking a few words, he can only remember a few of such words at a time, but, again, as long as he thinks that those words confirm his preconceived conclusion. Nothing else matters. By now you will have no problem noticing that TTC does not make any sense and is incapable of following a conversation. He jumps all over the place, will blame you for someone else not giving him an answer to some unrelated matter, and so on. TTC is just too stupid.

      Delete
    9. I think I'm still unclear as to what TTC is talking about. Are you (TTC) saying that natural selection is an insufficient explanation and/or comprises a smaller part of evolution than Darwin initially proposed? That's nothing new....

      It sure is news to Darwin's fan boys. I believe there was a post a few months back in which Larry Moran cited the ignorance of the highly supported other explanations even by the those with advanced degrees at his own university. And I'd never mistake most of the Darwin fan club as being informed about the modern conception of evolution.

      Time will tell, won't it. Whether or not people stop calling the further syntheses of "natural selection" by that name or not. I strongly doubt that Darwin would recognize the idea as it stands today. I doubt that even he and Wallace really had the same idea in mind. Wallace hated it being called "natural selection", the told Darwin that in the 1860s.

      Delete
    10. Yes, given that my comment was a deliberate Poe, I did not put Darwinism in the quotes that might have been appropriate. TTC, of course ... well, y'see, he has a knee-jerk reaction whenever he sees the name "Darwin"...! Costume dramas, mascot, idol, fanboys, eugenics, Hitler, yadda yadda yadda. SSDD.

      Anyone who's interested can read TTC's blog, or look for any post here with more than about 100 comments.

      Delete
    11. Ah, Allan, as you admitted, yourself, you're the one who inserted Hitler into the mix. I'd only gone as far as Haeckel. Though, as you could see in my last post dealing with Haeckel, Leonard Darwin certainly did his part in muddying the waters the year Hitler invaded Poland by associating his father with Schallmeyer AND Ploetz.

      I had a lot of fun putting together my notes on that topic.

      http://zthoughtcriminal.blogspot.com/2012/09/updated-temporary-linked-index-of.html

      Delete
    12. QED.

      Push the button and out pop the links - associative and html! That Darwin, eh?

      Delete
    13. I'd really rather not go off topic, as you did when you said I was associating Darwin with Hitler. I just don't see any reason to repeat answers to you I've already given. At considerable length, with cited primary source documentation and links, when available.

      Delete
  26. You all do know that "the creationists will love this" isn't a scientific argument against something, don't you? Their loving it or hating it has nothing to do with the truth of an idea. Your hating it or loving it, either. This isn't supposed to be the equivalent of a sporting event. Is it?

    ReplyDelete
    Replies
    1. The statement "the creationists will love this" isn't presented as an argument for/against something so I don't really see your point here. Is a call for rigour in the use of scientific terminology and in science reporting, and a discussion that centers around this, especially because creationists will use this misunderstanding to convey false information to the uneducated and the credulous, really equivalent to a sporting event? I think not. Then again, what sporting events are we talking about here? Some might consider debate a sport.

      Delete
    2. TTC,
      Just because you can't read and understand the rest of the comment, for example the very paragraph that follows that sentence, does not mean that it is not there.

      Delete
    3. @ Negative Entropy

      Click on TTC's name and you will see who he is - a notorious anti-science troll and blog thread wrecker who you might have seen elsewhere. Do not feed him because this is shaping up to be a vintage performance from him and there is much more serious stuff to be discussed here than to answer him.

      Delete
    4. Georgi Marinov, what's wrong? Can't answer my points?

      I am 100% in favor of science that is supported by evidence and quite a conventional evolutionist, though not a Darwinist. I am not a supporter of pseudo-scientific assertions that are so popular with blog atheists (evo-psy,cog-sci, scientism) and the folk lore that flows in such abundance from the blog chatter on the atheist blogs and the "Science" Blogs.

      If you guys would stay out of the leftist politics that I'm really interested in, I'd never bother with you. But you guys do.

      As I keep pointing out my blog, where I am identified with my two formerly used pseudonyms, my name is no secret. I just happen to have used my Google identity when I first posted a comment here.

      You'll love my PZ Myers series. Though, as he's got not much of a career in science, there's not that much to write about.

      Delete
    5. You'll love my PZ Myers series. Though, as he's got not much of a career in science,

      Far more of a career than yours, Troll, and PZ gets his facts straight, at least.

      Delete
    6. I've looked at his publications record, Diogenes. As to him getting his "facts" straight, he couldn't even get his story straight in his great PR stunt:

      PZ's Great Desecration A Fake?

      http://zthoughtcriminal.blogspot.com/2012_09_01_archive.html

      Delete
    7. Thanks Georgi,

      I knew that TTC is a troll and proud of it. I just love pointing out to his reading comprehension disabilities. He seems rather bothered by it. Might be something his kindergarden teachers told him again and again and got him traumatized.

      Delete
    8. Negative Entropy, it's kind of funny for someone calling himself "Negative Entropy" to be snarking on someone posting here with the name of their blog. You sure you're not the same "wowbagger" who set off my skepticism of PZ Myers' Great PR Stunt. Though I've suspected that "wowbagger" might also be "gilt". I've got one more post almost ready in the PZ Series. Though there could always be more if I go through his archive.

      Delete
    9. See Georgi? TTC does not know who he is talking to. He answers me as if I were you, and such. His mental disabilities are fun to watch ... at times ...

      ------

      TTC, when have I been snarky about the name you use to post at all? Oh, sorry, your reading comprehension disability of course ...

      At PZ's I am "entropy." But have not visited for a very very very very very very long time.

      Delete
    10. No one knows who they're talking to online if they use a pseudonym.

      I think you're "entropy" under any name you use.

      Delete
    11. No one knows who they're talking to online if they use a pseudonym.

      Nice try at dodging. Yet. Since you do this all the time, the clear conclusion is that you can't keep up because of your mental disabilities. Plain and simple.

      I think you're "entropy" under any name you use.

      There might be god(s) after all. I agree.

      Delete
    12. Negative Entropy, so, how do you know who you're talking to if they use a pseudonym? Your Sci-ranger powers? SLC, get a load of NE and his super powers. Only you might want to wear waders if not a haz-mat suit. It's quite a load.

      Um, hum. Keep whistling in the dark, NE. You might convince yourself.

      Delete
    13. I should not be surprised that you think that we require superpowers to tell apart two pseudonyms, after all, the task looks impossible from your viewpoint. Given that, an explanation might help (if you can keep up with these many words, which I doubt). I might not know who is who, but, unlike you, I am quite able to keep up with the pseudonym used by whomever is talking to me. Joe D and you, for example, might be one and the same, but, since I do not know that, I will not tell you as TTC, something that corresponds to a chat with Joe D.

      In reading the above, please be calm. Try and take the meaning of one sentence at a time, try to keep it in mind while reading the next sentence, and you might get the idea. Poor TTC.

      Delete
    14. Oh, don't let the laughing fool you, I'm quite calm.

      Look, another atheist who can't tell the difference between an evolutionist and a creationist. It's my experience that a majority of the time new atheism is a sign of a definite lack of intelligence mixed with arrogant certainty that their scienciness, as opposed to scientific knowledge, gives them a carte blanche to speak out of ignorance. My evidence? PZ, himself, says atheists don't know what they're talking about before they say it.

      http://zthoughtcriminal.blogspot.com/2012/09/atheists-granted-indulgences-by-pz-myers.html

      Delete
    15. Re Negative Entropy

      Mr. McCarthy (aka TCC)is just in a snit about PZ Myers because he was given the heave ho over there, just like he was given the heave ho over at Jason Rosenhouse's blog. He's challenging John Kwok as the heave ho champion of the internet.



      Delete
    16. OH, SLC, don't you know that PZ himself, has denied he has "given me the heave ho"? To which I said, "It's all the same to me"? Though you anticipate a PZ Post that isn't quite ready yet.

      I don't care who bans me and who doesn't. It's a big blogosphere. I've seldom looked at PZ's blog because it's hardly the ideal venue for reading about science and finding mature commentary. Too many of his regulars take his permission for atheists to talk about stuff they don't know about as a permit to make it up as they go.

      You did read my denial of his Great Hoax, which I posted yesterday, didn't you? PZ made his biggest claim to fame up.

      Delete
    17. Hey SLC,

      Well, as you can see TTC could not understand but one sentence from my comment: "please be clam." Notice, from his answer, that he could not even understand the context within which I used that sentence. Then notice that he starts talking about atheists mistaking evolutionists and creationists, about PZ, et cetera, all of which has nothing to do with what I said. His mind is addled. I doubt he is attempting to be banned from as many places as possible. He is just incompetent and mentally challenged. That's all there is to it. To hide his incompetence and stupidity he builds these stories about evil atheists and materialists, and logical positivists, and other big words that he has half learned after painful years. Years memorizing words too long for him to understand, just to give the appearance of an intelligence that escapes him to a point that he just does not understand that his attempts at appearing intelligent are doomed to fail miserably. Man, I can write all this sure that he will not understand but maybe half a sentence and then he might answer with some new incoherence.

      Poor TTC.

      Delete
    18. NE, your comments tend towards disorganization and that's at the start of them.

      SLC is a True Disbeliever such as the late Richard Kammann documented in his essay of that name. You aren't even that sophisticated.

      "Years memorizing words too long...."

      Oh, brother. What a moon calf.

      Delete
    19. Just as predicted TTC answered with some new incoherence. Good job TTC, good job. Now have a cookie.

      Delete
    20. Re Negative Entropy

      It should be noted that, on another thread, I challenged Mr. McCarthy to cite one paper in the peer reviewed literature that claims a 5 standard deviation effect for PK. He finally responded with a link to the blog of Dean Radin where the latter, in commenting on the Higgs experiment at CERN, claimed that the results of the various experiments for PK all add to to far more then 5 standard deviations. Apparently meathead McCarthy thinks that a blog is peer reviewed literature. It should also be noted that nutcase Radin also didn't cite any of the technical literature or provide an explanation as to how he conflated these experiments to arrive at such a conclusion. It would appear that Radin is as ignorant of statistical inference as McCarthy is. Two experiments, each reporting a 2 standard deviation effect doesn't add up to a 4 standard deviation effect.

      Delete
  27. 'Ian HolmesThursday, September 06, 2012 1:18:00 AM

    I have to admit I find it a bit sad, this trashing of a massive data-intensive study and the people who conducted it, simply because a bit of hyperbole in the abstract of one paper will make your arguments with creationists "very complicated".'

    Yeah, who cares about accuracy, anyhow!

    The fact is that even completely ignoring the creationists, there is a longstanding dispute within science over the "how much of the genome is functional" issue. The arguments against the majority of the human genome being functional are: (1) Ohno's argument, (2) lack of evidence for conservation, (3) a lot of it is clearly the product of parasitic elements, and, most importantly, (4) various animal and plant species can have 10 times smaller genomes than humans, or 10 times bigger genomes than humans, with the differences due mostly to the amount of parasitic elements, and yet the species don't really look different in any obvious way.

    This stuff has been known for decades, and these are powerful points, yet the ENCODE PR just came out and declared to the public that the question is answered and repeated the lame old "scientists thought everything was junk, now we know everything was functional" story -- when in fact actually it is the scientists who are best-informed about genome size variability and the like, who are the ones most skeptical of claims that most of the genome is functional.

    Also, I just gave the arguments against the "80% functional" claim above. Don't worry about the creationists, provide the counterarguments, or admit that we have a point.

    No one is saying that there isn't a lot of amazing science in the ENCODE project, we're just complaining that the media and the public are being mislead about what the central point of it all was. When you have a megaphone, pick a main point that isn't wrong, please.

    ReplyDelete
    Replies
    1. It is NOT just a bit of hyperbole in an abstract: Here is a nature video where he litterally repeats the claim that 80% of the human genome is functional.

      http://www.youtube.com/watch?v=Y3V2thsJ1Wc

      Delete
    2. I misread your post, I see now that you replied to someone making the statement I intended to correct. Nevermind then :)

      Delete
    3. (5) The genome can only absorb so many mutations in functional regions per generation before genetic meltdown occurs. This number is about 5, but the actual number of mutations per generation in humans is 50-150. So if 80% of the genome was important, we would be in serious trouble.

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    4. (6) trangenic experiments in many different organisms show that large pieces of the genome can be deleted (ex. http://www.ncbi.nlm.nih.gov/pubmed/15496924) or have other DNA randpmly inserted into it, without any affect on the viability of the organism (ex. http://www.ncbi.nlm.nih.gov/pubmed?term=3892534).

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  28. Junk is functional. I thought one of the biological definitions of junk was stuff that used to be active in some context but is now broken in some way.

    If you look in my garage you find it full of stuff that used to be in use, but is either in storage because something better is in use, or it is awaiting a decision to donate it or dispose of it. In either case it is tending to deteriorate.

    Analogies, I realize, can be misleading, but this one seems to have some utility.

    It seems to me the creationists can't gain anything from this. If it is actually "functional" in its current context and not being conserved. the definition of "islands of function" needs to include a lot more of sequence space. Essentially most of it.

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    1. Junk is functional. I thought one of the biological definitions of junk was stuff that used to be active in some context but is now broken in some way.

      A lot of that junk is junk that was functional but functional not for the organism in which genome it resides, but for the narrow purpose of its own propagation. Also, a lot of transposons were dead on arrival when they were inserted, so they were never functional even in that sense.

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  29. This is going to make my life very complicated.

    Heh, so let me say: I am not a regular reader of your blog, but I am familiar with it and your positions on, um, certain controversial issues in evolutionary biology. I was about a third of the way through reading Yong's article when I couldn't contain myself any longer: I said, "Oh, I have got to pop over to Sandwalk and see what Larry Moran makes of this..." ;p :D

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