Wednesday, September 26, 2012

Ewan Birney: Genomics' Big Talker

My copy of Science arrived in the mail last week and I wasn't surprised to see the article by Elizabeth Pennisi on ENCODE Project Writes Eulogy for Junk DNA. Pennisi has long been skeptical about junk DNA. She advocates the position that what makes us human is hidden in the "dark matter" of the genome. She has never lost an opportunity to promote those scientists who claim to have discovered function in junk DNA so it was natural for her to fall hook-line-and-sinker for the recent ENCODE publicity campaign [see Science Writes Eulogy for Junk DNA].

What did surprise me was a three-page spread on Ewan Birney: Genomics' Big Talker, written by Elizabeth Pennisi. This is extraordinary. I don't know of another example where a leading science journal has promoted a young scientist in this manner. Of course, it's doubly extraordinary because, in this case, Science is promoting a scientist who just made some serious mistakes interpreting his own data! The man who is so prominently featured in the Sept. 7, 2012 issue of Science magazine is coming under serious criticism for letting publicity rule his science. He has almost single-handedly1 damaged the reputation of 400 scientists in the ENCODE Consortium and he did it, in part, because he was not knowledgeable about his own field of expertise! [see ENCODE Leader Says that 80% of Our Genome Is Functional and The ENCODE Data Dump and the Responsibility of Scientists]

UPDATE:A reader has reminded me that Science published two pages (online) on Felicia Wolfe-Simon at the time of the arsenic affair. Hmmmm ... is this the beginning of a pattern?

Where is Ewan Birney? He must be aware of the controversy surrounding his paper and the criticism of his carefully managed publicity campaign (and self-promotion). He was active on tweeter for a bit but all this did was make it clear that he wasn't backing down.

Birney has a blog [Response on ENCODE reaction] but he has not responded to questions. Check out Ryan Gregory's post to see what Birney is avoiding: Comments on Birney’s blog. Pay particular attention to the questions asked by Diogenes. Let's hope that the reason for Birney's silence is because he's preparing a lengthy and scientifically accurate response!

I wonder if Science is going to publish anything else on this fiasco? Most of the other journals have at least acknowledged that there's a problem with the ENCODE publicity campaign. Some have even defended junk DNA and emphasized the misleading statements published by Birney et al. So far, there's nothing on the Science website in spite of the fact that Science published one of the worst interpretations of the ENCODE results.... Or maybe it's BECAUSE it published such a biased account that we're not seeing any follow-up.


1. A number of group leaders seem to share Birney's myopic view of genome research so it's not all Birney's fault.

78 comments:

  1. Larry: Science published one of the worst interpretations of the ENCODE results...

    If I’m not mistaken, Bruce Alberts, who is the Editor-in-Chief of Science magazine and ultimately responsible for its content, has been your mentor. Maybe you should tell him to clean up his shop!

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  2. Sorry Larry, Science (and Pennisi) did the same thing with Felicia Wolfe-Simon and the arsenic bacteria story, although it was only a 2 page spread/interview.

    (Newsmaker interview: Felisa Wolfe-Simon. Discoverer asks for time, patience over arsenic bacteria controversy. Interview by Elizabeth Pennisi.
    Wolfe-Simon F. Science. 2010 Dec 24;330(6012):1734-5. No abstract available.)

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  3. Science and Nature have become sensation-seeking tabloids. It's becoming increasingly clear that they can be ignored without missing out on much.

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  4. In my opinion, John Stamatoyonnopoulis' comments have been even more inaccurate and inconsistent than Birney's. Sometimes John Stam says most of the genome is involved in regulating genes, other times he says 40%.

    At least with Birney, he admitted he invented a new definition of the word "function" in order to get publicity. That, I understand.

    But John Stam, I have NO CLUE what he is talking about.

    Where is Georgi Marinov when you need him?

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  5. "Stamatoyannopoulos" comes from the same language as "Diogenes". Since you're a stickler for accuracy, spell it correctly and don't engage in the repugnant habit of shortening it to Saxon monosullables.

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    1. That's just like a Greek, to insist that everything has to be done just the way the ancients did it.

      This from NPR:

      "Most of the human genome is out there mainly to control the genes," said John Stamatoyannopoulis, a geneticist at the University of Washington School of Medicine, who also participated in the project." [NPR]

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    2. In fact, I am in the same department as John. I even ran into him at the elevator of the parking building two days ago, and declared I was now hypnotising him into believing in junk DNA (it did not work).

      John is the son of George Stamatoyannopoulos, who is former head of the Medical Genetics Division of the Department of Medicine. George was born in Greece, and he and John are quite proud of their Greek roots. But they both allow people to shorten their last name to "Stam".

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  6. @Joe,

    When you see J. Stam again you might want to recommend he joins the discussion at Sandwalk for nonsense-talk therapy!

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  7. Larry: I wonder if Science is going to publish anything else on this fiasco? Most of the other journals have at least acknowledged that there's a problem with the ENCODE publicity campaign

    My guess they will do it, eventually. Anyway, I just submitted a second comment trying to clarifying some of the issues and confusion about the potential functions of the ‘junk DNA.’ Because the comments in Science are behind a pay-wall, I posted the first one here at Sandwalk (http://sandwalk.blogspot.com/2012/09/science-writes-eulogy-for-junk-dna.html#comment-form), and here is the second one:

    *Evolutionary questions about junk DNA*

    As declared many decades ago by Dobzhansky: “Nothing in biology makes sense except in the light of evolution”. Accordingly, the ultimate arguments and data for, or against a functional role of ‘junk DNA’ (jDNA), might rely on evolutionary principles.

    One of the startling conclusion of the ENCODE project was that 80% of the human genome is functional. In a previous comment (*Multiple eulogies for junk DNA?*), I brought forward an old hypothesis proposing that jDNA functions as a sink for the integration of proviruses, transposons and other inserting elements, thereby protecting the genes and their regulatory elements from inactivation or alteration of their function.

    The rationale behind this hypothesis on the evolution of genome size and the protective function of jDNA was based on evolutionary data and principles. In order to explore this or any other theory on the potential functions of genomic DNA, it is critical to point out that functional DNA (fDNA) can fulfill two categories of functions: (i) informational functions, which are based primarily on the specific sequence, and (ii) ‘structural’ functions, which are more or less independent of the sequence.

    The informational DNA (iDNA) includes sequences that code for proteins, functional RNAs and regulatory elements, such as promoters, enhancers, and origins of replication. The ‘structural’ DNA (sDNA) can have organizational, ‘mechanical,’ or ‘spacing’ functions (e.g. DNA in centromeres and in regions located between iDNA sequences), or protective functions against insertional mutagenesis (presumably, all “junk DNA”).

    In exploring hypotheses on the potential functions jDNA, it is essential to consider its evolutionary origin. Approximately 50% of the human genome is composed of transposable elements (TEs), including thousands of human endogenous retroviruses; it is very likely, also, that much of the rest of jDNA are remnants of TEs that have lost their TE-sequence signatures.

    Therefore, from an evolutionary perspective, the central issue is whether jDNA has accumulated simply because its rate of deletion has been lower that of its amplification (in this case, jDNA might be thought of being parasitic in nature), or because the host organisms possessing jDNA have a selective advantage (in this case, jDNA is symbiotic)? In other words, is the evolution of genome size and jDNA under host selective constrains, or not?

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  8. Gotta love the line, "some have even defended junk DNA".
    I'm sure that junk DNA appreciates its champions. :)

    Perhaps the Sanskrit greeting, 'Namaste' can be reinterpreted to say, 'The junk DNA in me honors the junk DNA in you'.

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  9. CB: the central issue is whether jDNA has accumulated simply because its rate of deletion has been lower that of its amplification

    How could it have accumulated if the rate of deletion were higher than the rate of amplification?

    Your question is more properly phrased as whether selective pressure acts solely at the level of the parasitic sequences themselves, or whether there is additional selective pressure at the organismal level.

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    1. Anonymous: How could it have accumulated if the rate of deletion were higher than the rate of amplification?

      My comment doesn’t say that “the rate of deletion was higher than the rate of amplification"; on the contrary, it says that: the rate of deletion was lower than the rate of amplification. Probably, you misread it by accident.

      Anonymous: Your question is more properly phrased as whether selective pressure acts solely at the level of the parasitic sequences themselves, or whether there is additional selective pressure at the organismal level.

      Here is a follow-up comment in Science, in which I explain this issue in more detail:

      *Evolutionary constrains on genome size evolution: the Hummingbird Case*

      In a previous comment, *Evolutionary questions about junk DNA*, I asked: is the evolution of genome size and junk DNA (jDNA) under host selective constrains?

      One of the main lines of evidence supporting the hypothesis that jDNA serves as a defense mechanism against insertional mutagenesis was the evolution of alternative protective mechanisms such as specific integration sites in organisms that have little jDNA (e.g. Bacteria).

      Indeed, the evolution of specific integration sites is strong evidence for the high selective pressure imposed by insertional elements on their hosts; it should be pointed out, however, that from an evolutionary perspective, the evolution of specific integration sites was a co-evolutionary event, as both the hosts and the inserting elements benefited from this mechanism.

      Unlike Bacteria, which have been under strong selective pressure to maintain a small genome, other organisms, which for various reasons could relax this constrain, used a different strategy for preventing insertion mutagenesis: accumulation of an increasing number of transposable elements including endogenous viruses in their genome in order to serve as a defensive mechanism against insertional mutagenesis. Likely, during its evolution, this novel protective mechanism was enhanced by the presence of additional protective features, such as (sequence-directed) preferable DNA islands for the integration of inserting elements, which relied on the activity of recombination machineries, including homologous recombination.

      Although the process of generating protective DNA was based on the amplifying activity of inserting elements, the sites or regions of the host’s genome in which this DNA accumulated (i.e. was evolutionary ‘fixed’), and its overall quantity, were under evolutionary constraints by the host.

      Whereas the constraints regarding the sites for the accumulation of protective DNA were relatively strict, those on the size of the genome and the amount of jDNA were more relaxed, but at work. Probably, the best example of these host evolutionary constrains at work, even in complex organisms such as vertebrates, is the Hummingbird Case: the hummingbirds have the smallest genome size, not only among birds but all tetrapods, apparently because of the selective force imposed by their high metabolic demands associated with powered flight.

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    2. the rate of deletion was lower than the rate of amplification. Probably, you misread it by accident

      The question was rhetorical. It is a tautology that if a sequence exists, the rate of its creation was necessarily higher than the rate of its deletion, at least at one time. If the total number of sequences is currently stable, then the creation rate equals the deletion rate.

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    3. Anonymous: The question was rhetorical. It is a tautology that if a sequence…

      I understand, but what about the theory that the so called ‘junk DNA’ (jDNA) serves as a defense mechanism against insertional mutagenesis. Do you agree with this theory and with the associated paradigm that all genomic DNA is functional?

      For a scientific definition of ‘functional DNA’ (fDNA), in context of evolutionary and biological principles, see the comments above and those posted here: http://sandwalk.blogspot.com/2012/09/athena-andreadis-writes-for-sceintific.html, and here: http://sandwalk.blogspot.com/2012/09/read-what-mike-white-has-to-say-about.html

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    4. No, I don't believe that junk DNA provides a defense mechanism against insertional mutagenesis, at least not to a sufficient degree to have selective advantage and thereby evolutionary relevance. I think the resulting loss of fitness from alleles inactivated by insertional mutagenesis provides all the selective pressure needed to maintain these alleles in the insertion-free state.

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    5. Anonymous: No, I don't believe that junk DNA provides a defense mechanism against insertional mutagenesis…

      The defense function of the called junk DNA (jDNA), which in humans apparently represents most of the genome, is a fact; it’s not about ‘believing’, at least not from a scientific perspective.

      Anonymous: …at least not to a sufficient degree to have selective advantage and thereby evolutionary relevance

      First of all, the jDNA is there, so it is easier to argue, from a parsimonious perspective, that it provides a selective advantage for the host, than to argue that it doesn’t. However, to shed some scientific light on this, consider the organisms that have little if any jDNA, such as Bacteria, which are a much larger pool of organisms (by a huge margin) than the organisms that have high quantities of jDNA. Why do these organisms have alternative defense mechanisms in form of specific site for integration against insertional mutagenesis?

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    6. what about the theory that the so called ‘junk DNA’ (jDNA) serves as a defense mechanism against insertional mutagenesis.

      It does not seem like a very good one. In essence, a region of such 'blotting DNA' will become, in pretty short order, clogged up with more and more of the stuff, since insertion there does least damage. Which is all very nice I'm sure - we get more and more of this 'functional' fluff, until 95% of our genome is composed of sacrificial DNA ... When selective pressure against bloating diminishes, genomes are likely to expand, and most rapidly in mutation-resilient regions ... but I think it stretches the definition of 'functional' to view this propensity as adaptive.

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    7. Allan Miller: It does not seem like a very good one

      It might not seem so, but the more you think about it, and look at it from different perspectives, the more it makes sense, both common sense and evolutionary sense; that’s the beauty of it!

      Allan Miller: In essence, a region of such 'blotting DNA' will become, in pretty short order, clogged up with more and more of the stuff, since insertion there does least damage. Which is all very nice I'm sure - we get more and more of this 'functional' fluff, until 95% of our genome is composed of sacrificial DNA ...

      Yes, that’s a good graphic representation of how it works. However, I’ll rather call it ‘protective DNA’ rather than ‘sacrificial DNA’; similar to the ‘burden’ of maintaining any other components, including the immune system, maintaining the jDNA as a protective mechanism at the genome level does require some ‘sacrifice,’ but it is for a good cause: evolutionary survival.

      Allan Miller: ... but I think it stretches the definition of 'functional' to view this propensity as adaptive

      In my previous comment, above, I pointed out the evolution of protective mechanisms against insertional mutagenesis in Bacteria, in form of specific integrations sites, which testifies for the selective pressure imposed by inserting elements on their hosts.

      However, this selection pressure takes a new dimension in organisms, such as humans, in which the insertional mutagenesis can lead to cancer. Indeed, considering the number of somatic cells and their rapid turnover, the selective forces against insertional mutagenesis in these organisms is extraordinary. And, I can’t find a more profound way of emphasizing this, but to quote one of our fellow bloggers, Abbie Smith, at ERV ( http://scienceblogs.com/erv/2012/09/18/ervs-and-multiple-sclerosis-5/):
      …insertional mutagenesis, it’s just a fancy way of saying CANCER.

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    8. The reason I don't see it as adaptive is because there is no evidence (I am aware of) that the fraction of the population with more of it is fitter than that with less. It could conceivably have a protective side-effect (unproven) but adaptive explanations do require some kind of mechanistic reason why the beneficial consequences promote a change that would not happen otherwise.

      I also think that mutational 'protection' by increasing DNA volume, even accepting the possibility, would only work against mutagens that have a per-genome probability, rather than a per-base one.

      insertional mutagenesis, it’s just a fancy way of saying CANCER.

      That may be a factor - somatic mutation in multicellular organisms - but does not contribute to an explanation of junk in single-celled eukaryotes.

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    9. …insertional mutagenesis, it’s just a fancy way of saying CANCER.

      You might think that, but actually, it is almost never observed. Mostly we see are straight up point mutation inactivation of tumor suppressor genes (P53) and activating mutations in oncogenes (KRAS), with a significant amount of whole chromosome gain/loss.

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    10. Cancer is actually rather a weak evolutionary force - which is why it's such a prevalent bastard. The longer we live the likelier it is that probability will bite us in the backside and we suffer the fateful mutation. But we've generally done our breeding by then. So I'm not convinced that somatic arguments on junk have much evolutionary force.

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    11. @Allan Miller re: cancer is a weak evolutionary force
      I have to disagree. I would argue that cancer is such a strong evolutionary force that organisms have of necessity evolved to limit the damage to post-reproductive age. You can see this at work for example with P53. The knockout mice are viable, but die early of cancer. Human heterozygotes are also viable, but die early of cancer. That a lot of "decoy" DNA isn't relevant to cancer doesn't mean cancer predisposition isn't a potent evolutionary force.

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    12. Hmmm ... perhaps not too well expressed. Maybe wrong, even! I was thinking more "weak evolutionary force wrt junk".

      Cancer is (IMO) our unicellular heritage rearing its head. It's what our cells do 'naturally' if they get the chance. So, simply defined as runaway mitosis, its suppression has clearly been a strong evolutionary force in multicellular lines. Cells eventually find a way through that suppression, like bacteria through an antibiotic barrier.

      But huge variations in junk occur in organisms that have already tuned their multicellular lives, such that cancer is deferred. In that respect, it is a weak force for further tuning. That's kind of what I meant, anyway!

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    13. @Allan Miller

      In my previous comments, I pointed out the evolution of protective mechanisms against insertional mutagenesis in Bacteria, in form of specific integrations sites. Here are 3 questions:

      (i) How do you explain this protective feature?

      (ii) Is it adaptive?

      (iii) And, doesn’t it testify for the strong selective pressure imposed by inserting elements on their hosts?

      Allan: I also think that mutational 'protection' by increasing DNA volume, even accepting the possibility, would only work against mutagens that have a per-genome probability, rather than a per-base one

      That’s a good point. Indeed, junk DNA (jDNA) doesn’t offer protection against many chemical or physical mutagens, except in rare case when jDNA might be able to ‘titer out’ the mutagen. For that reason my hypothesis is primarily about the protective function of jDNA against insertional mutagenesis.

      Let’s focus on facts, for a moment. I think that, except a few researchers such as some the spokesmen for the ENCODE project, most scientists and scholars, particularly the contributors here at Sandwalk, consider that approximately 90% of the human genome is jDNA. Leaving the issue of how this jDNA originated and whether it has been ‘adaptive’ or not aside, my questions are:

      (i) is this jDNA protective against insertional mutagenesis?

      (ii) if it is not, why?;

      (iii) if it is, by how much does it reduce the chance of insertional mutagenesis?

      Allan: That may be a factor - somatic mutation in multicellular organisms - but does not contribute to an explanation of junk in single-celled eukaryotes

      Again, a good point. Indeed, some of unicellular eukaryotes, such as some amoeba and some dinoflagelates, do have very large quantities of presumed jDNA, much larger than humans (parenthetically, maybe we should replace the Onion Test metaphor with a stronger and more sophisticated one, such as the Dinoflagellate Test!).

      I refrain from addressing Allan’s question and the Dinoflagellate Test here, as it would ruin my own challenge to readers (see the ‘the fifth reason’) I posted in my scientific parody entitled: Five reasons why my theory on the function of ‘junk DNA’ is better than theirs; see it at: http://sandwalk.blogspot.com/2012/09/read-what-mike-white-has-to-say-about.html

      However, I’ll give a clue, a big clue: inserting elements!

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    14. Anonymous referring to …insertional mutagenesis, it’s just a fancy way of saying CANCER says: You might think that, but actually, it is almost never observed

      I think, it is observed quite often, and it is not observed more because of the protective function of jDNA against insertion mutagenesis which is …just a fancy way of saying CANCER

      Anonymous referring to Allan Miller’s “cancer is a weak evolutionary force” says: ”I have to disagree. I would argue that cancer is such a strong evolutionary force that organisms have of necessity evolved to limit the damage to post-reproductive age”

      I fully agree “cancer is such a strong evolutionary force that organisms have of necessity evolved to limit the damage to post-reproductive age”; and, the organisms have done that by using jDNA as protective mechanism against insertion mutagenesis, which is …just a fancy way of saying CANCER

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    15. That's why onions don't get cancer? Great hypothesis. Lets see some supporting data.

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    16. Here is another recent comment I posted in Science on the connection between junk DNA and cancer (http://comments.sciencemag.org/content/10.1126/science.337.6099.1159):

      *Junk DNA and cancer: an extended and unexpected association*

      The role of endogenous or exogenous inserting elements, such as retroviruses, in causing cancer in humans and many other species is well established. What is not established, however, is that ‘junk DNA’ (jDNA), which contains many cancer-inducing inserting elements, might also protect against cancer; it might be a case of ‘fighting fire with fire’!

      One of the main lines of evidence supporting the hypothesis that jDNA serves as a defense mechanism against insertional mutagenesis was the evolution of alternative protective mechanisms, such as specific integration sites, in organisms that have little jDNA (e.g. Bacteria)(1). Indeed, the evolution of these alternative protective mechanisms is strong evidence for the high selective pressure imposed by insertional elements on their hosts.

      However, this selection pressure takes a new dimension in organisms in which insertional mutagenesis can lead to cancer. In humans, for example, given the enormous number of somatic cells and their high turnover rate during the reproductive span, the number of insertion events that would potentially lead to cancer in the absence of protective mechanisms would be evolutionarily drowning (1).

      One of the major objectives of the ENCODE project was to help ‘connect’ the human genome with health and disease. Considering that jDNA might be one of the main protective mechanism against insertional mutagenesis leading to cancer, this hypothetical model on the protective function of jDNA aligns with the ENCODES’s objective and with those of the next wave of genomic projects addressing human diseases.

      Notably, this hypothetical model can be fully addressed, both analytically and experimentally; for example, transgenic mice carrying DNA sequences homologous to infectious retroviruses such as murine leukemia viruses (MuLV) might be more resistant to cancer induced by experimental MuLV infections as compared to controls.

      1. Bandea CI. A protective function for noncoding, or secondary DNA. Med. Hypoth., 31:33-4. 1990.

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  10. Larry,

    you should re-check the Reddit thread. ENCODE grad student Rule_30 ("good riddance to Junk DNA") responded to you, and stated directly that ENCODE did not and could not disprove Junk DNA.

    He/she also wrote a long, thoughtful response to my (rather obnoxious) flame-post, all well done and well thought out, for which I thanked him.

    Ironically, the creationists I'm arguing with on Mike White's HuffPost blog pointed this out to me-- the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side-- they hadn't noticed that Rule_30 checked back in with new comments.

    I have to thank the creationists for pointing out to me some quotes that help demolish them.

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  11. "the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side"

    FALSE.. IS lying a hobby of yours or does it come naturally. The argument WAS (on my part), it shouldn't be called "Junk" in the fist place as stated by the researchers themselves you twit, which they more or less further supported in their recent responses. Tell me how much of your DNA are you be willing to give up so it may be examined to support your beloved 'Junk' Idea. You never did answer that question.

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    1. Who the hell are you, Anonymous? I'm arguing with several different creationists at the same time on various blogs. If you are going to accuse me of misrepresenting your hysterical blurts, you could at least identify yourself, so I know which hysterical shrieks I'm supposed to massage into coherence before I demolish them once and for all time.

      Anonymouse: "The argument WAS (on my part), it shouldn't be called "Junk" in the fist place as stated by the researchers themselves you twit"

      Oh, now you don't like the name? I'm sorry I called your precious acidic biopolymers "Junk" thus hurting your fragile prissy feelings. You may unclutch your pearls, prissy lady. From now on I'll call it Bob. Your genome is 80% Bob.

      Your allegations above are not what any of the ENCODE researchers said, except Rule_30, who stated directly that ENCODE had not disproven the Junk-- pardon me, the Bob DNA hypothesis.

      Rule_30: "Also, no, our data can’t disprove the junk DNA hypothesis, we are still in agreement on that."

      Except he/she should have called it something else, not "Junk".

      Larry Moran: "We have plenty of evidence that much of our genome is junk. The evidence comes from ... 1. genetic load arguments 2. comparative genomics 3. direct evidence that the sequence of junk DNA is not constrained by natural selection 4. direct evidence that junk DNA is composed of broken transposons 5. direct evidence that different individuals in the human populations can tolerate different amounts of DNA in various parts of our genome 6. direct evidence that a megabase of mouse DNA can be deleted with no effect"

      Rule_30 replies to Larry: "I agree with all of this, though I object to the terminology "junk" because I think it seems too black-and-white."

      So, Rule_30 is the only researcher at Reddit who objected to calling it "Junk" but nevertheless stated directly that ENCODE could not and did not disprove the...Bob... DNA hypothesis.

      Anonymouse: "Tell me how much of your DNA are you be willing to give up so it may be examined to support your beloved 'Junk' Idea. You never did answer that question."

      As Ewan Birney himself pointed out, the genome of the pufferfish is 1/8 that of a human's, so we could start at 1/8 non-Bob and assume you need a few more genes (not much, less than Daphnia) and some more tiny, tiny regulatory elements at 6-8 bp a pop. If we need three times more regulatory elements than a pufferfish, we've still got 4/5 Bob.

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    2. Diogenes: From now on I'll call it Bob. Your genome is 80% Bob

      What about calling it jDNA (as in Juice DNA); I think is gender-neutral and it might reflect its fluidity!

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  12. "I'm arguing with several different creationists at the same time on various blogs"

    Golly Gee, but in your initial comment you specifically stated "the creationists I'm arguing with on Mike White's HuffPost blog DUH!

    And since you can quote mine what you want to hear in their response, I can do the same; "Here is what I SHOULD have said: "over time, “junk DNA” is disappearing. Good riddance: this is just a term for DNA where we don’t have any guesses about its origin, function, or lack of function. The more we learn about the genome, the more information we uncover, thus fewer unknowns and a more seemingly “useful” genome. Or at least one we understand more thoroughly and are less inclined to write off as "useless junk"."


    Also, AS I stated over at Whites blog, perhaps the Junk DNA groupies should consider preparing themselves for the demise of their beloved Science stopping "Junk DNA" paradigm, as it's not looking too promising. Let's watch now, as DIO has another meltdown..

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    1. Who are you prissy lady (as I asked already)? Are you TheMayan or rjop? Or perhaps Shapiro himself?

      All the scientists at REDDIT admitted that they did not disprove that most of your genome is Bob. You claimed ENCODE disproved Bob DNA, so you were lying or stupid.

      Larry Moran: "(Regarding "good riddance to junk DNA") Statements like that strongly imply that you have discovered functions for most of our genome and that you are ready to dismiss the existence of junk DNA ("good riddance")."

      Rule_30: "No. That is absolutely not what I meant to imply, and it actually took me aback when I read this interpretation, until I realized that, darn it all, I abused the word "function" as well. Many apologies."

      Larry Moran: "We have plenty of evidence that much of our genome is junk..."

      Rule_30: "I agree with all of this, though I object to the terminology "junk" because I think it seems too black-and-white."

      As I told you before prissy lady, we'll call it "Bob" if I've hurt your delicate feelings.

      Rule_30: "Since ENCODE ended up not publishing any functional studies, ENCODE should not have said anything that remotely hinted that we knew the function of the elements in question"

      Larry Moran: "There's no question that the press has announced the death of junk DNA. Do you agree that you have demonstrated function for most of our genome?"

      Rule_30: "ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome. In fact, ENCODE has not demonstrated function for ANYTHING because we published no functional studies." [caps in original]

      Much more like this, more later.

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    2. You claimed ENCODE disproved Bob DNA

      Where? Also, if you don't know who I am, how do you know what I "claimed"

      Who are you

      Who are you? Why don't you tell us all your real name?

      as I asked already

      As I asked already why you desire DNA to be junk so badly with no answer.

      ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome. In fact, ENCODE has not demonstrated function for ANYTHING because we published no functional studies."

      Another quote mine to support a position they themselves do not think you should hold. OH GOODY.

      As I told you before prissy lady, we'll call it "Bob" if I've hurt your delicate feelings

      And as I you, it's not looking too hopeful for your beloved Junk DNA which inhibits Scientific progression.

      Waaaaaah, Dio has been stomping his feet, berating others like a spoiled child for days, because his Junk DNA security blanket appears to be loosing ground. Shall I get you a tissue?





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    3. This is actually a classic example of the creationist mind.

      The first rule of creationism:

      Never answer a direct question relevant to the issue you yourself raised, and claimed was critically important. When confronted by a direct question relevant to the issue you yourself raised, change the subject.

      Thus, Anonymous accuses me of misrepresenting something he shrieked at Mike White's blog-- a blog where none of the creationists call themselves Anonymous.

      Anonymous: FALSE.. IS lying a hobby of yours or does it come naturally. The argument WAS (on my part), it shouldn't be called "Junk"... you twit

      Me: Who the hell are you, Anonymous? ...If you are going to accuse me of misrepresenting your hysterical blurts, you could at least identify yourself, so I know which hysterical shrieks I'm supposed to massage into coherence

      Anonymous: Who are you? Why don't you tell us all your real name?

      OK, I'm a bad person for not accurately transcribing your incoherent glossolalia. But you won't say who you are, or quote what you actually shrieked in the first place, for comparison.

      And you won't tell me your name. OK, we'll call you, uh, fuckhole.

      No... that would be disrespectful. OK-- Mr. Fuckhole.

      Mr. Fuckhole, if you accuse me of misrepresenting your glossolalia, which you wrote under another name, and under the influence of the Holy Spirit, somewhere out there on the interwebs, then OK-- prove it. That was the crux of your argument: you accused me of misrepresenting your blurts.

      So prove it, Mr. Fuckhole. Copy and paste whatever you were blurting from there, over to here, and compare it to my words, thus proving I misrepresented your blurts.

      Delete
    4. Oh, and above you accused me of "quote mining" the line where Rule_30 says "ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome" (caps in original).

      Please back up your accusation that I quote mined, by pasting a great deal of text before, and after, my quote of Rule_30, then we'll let the audience decide if I quoted out of context, or if you're full of it.

      Delete
  13. Creationists always get angry when they get cornered. Nothing new to see here, move along.

    ReplyDelete
  14. "then we'll let the audience decide if I quoted out of context"

    Umm I never said you quoted out of Context, I said you quote what you *want* to hear and stated you use another quote mine to support a position they themselves do not think you should hold, in which the additional quote below supports my assertion;

    "I guess I'm getting too much into semantics here and really don't like the terminology "junk." To me it seemed (and still seems) like "junk DNA" is really about being unimaginative and failing to care about parts of the genome that are outside of our individual worldviews (i.e. cis-reg for me and ENCODE, transposons for you and yours). If, for example, I were studying a part of the genome and found transposons, tested them, and was really convinced that they had absolutely no effect on gene regulation or chromatin structure, I would NOT call this region "junk" (I'd just call it a region of transposons that don't appear to have an effect on chromatin structure or gene regulation and then I'd focus on how in the world the genome could "know" not to let these regions affect structure or gene function). I think perhaps you would call these regions "junk DNA", so to me this is more an issue of semantics than anything else. Please pardon me if "junk DNA" has a specific definition in your field; from where I sit, it seems like more of an informal term. (No, it is a dogmatic ideologue term by the junkies of Junk DNA, which of course this researcher is unaware of) *Emphasis mine

    They also stated, which you left out: "Yes, the sound bite the public got is incorrect (well, we don’t know if it’s correct or not yet"

    Now, you can quote mine back what you desire to hear yet again and we can go on Ad nauseam playing the endless quote game.

    We then have.....

    "Who are you prissy lady"

    You then state:

    "You claimed ENCODE disproved Bob DNA"

    So which is it? You first say you don't know who I am, then assert "You claimed ENCODE disproved Junk DNA. Again, I will ask, IF you don't know who I am, how can you make the assertion "You claimed ENCODE disproved Junk DNA" This is a very simple and logical question. I was actually going to state who I was, but then saw this and decided to make you think a bit, as I am the only one at White's blog whom linked to the entry; "good riddance to Junk DNA"

    However, I was not focusing on this one statement in which you did quote out of context while leaving out 99% of the remaining researcher statments to bolster your claim "the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side" Which again is FALSE. This assertion is only from your paranoid delusional mind, which you are acquiring quite a reputation for having, as I will "quote" Shapiro stating today;

    "When history is one your side, you can put up with delusional people like Diogenes. The number of scientists who are beginning to have a more enlightened view of genomes and their capacity for re-organization is growing exponentially. I don't think we will have to wait more than another decade or two for denial-laden ideas about genomes like junk DNA to disappear completely.

    It is just plain amusing to observe people like you, who exhibit such a defensive posture of outraged orthodoxy, which in your case, you have taken to new heights. Keep up the good work, your doing wonders for your cause, which really has nothing to do with Scientific progression.



    ReplyDelete
    Replies
    1. Anonymous: I was not focusing on this one statement in which you did quote out of context

      Oh did I? What statement was that? What statement did I quote out of context? What statement? Copy and paste the statement which you allege I quoted out of context. Then put the context around it. Let the audience decide whether I quoted out of context, or whether you're just the nine millionth lying creationist.

      Don't accuse, Mr. Fuckhole-- present evidence.

      In my previous post I gave you a direct order.

      I wrote: Oh, and above you accused me of "quote mining" the line where Rule_30 says "ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome" (caps in original).

      Please back up your accusation that I quote mined, by pasting a great deal of text before, and after, my quote of Rule_30, then we'll let the audience decide if I quoted out of context, or if you're full of it."


      This was a direct order. You accused me of quote-mining the line "ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome".

      I demanded evidence. You repeated your accusation, with no such evidence.

      Another ID creationist pathological liar! Not one of you creationists gives a shit about data or evidence. You all pretend to care about data and evidence, but you don't know and you don't even care. You're lying when you even pretend to care about evidence.

      As for Shapiro, your quote from him shows that all your side has are ad hominem attacks and emotional blurts. If Shapiro had evidence, he would have presented it.

      All Shapiro has is his hysterical rage and ad hominem attacks, which shows he has no evidence that most of the genome is not junk.

      Rule_30 wrote to me: "Also, no, our data can’t disprove the junk DNA hypothesis, we are still in agreement on that."

      We are in agreement on that. If you are not in agreement with me, then you are not in agreement with ENCODE scientists, so stop thinking you can create that illusion with quote mining and outright lying.

      Delete
    2. Talking of various types of "mining", there's also research mining:

      Anonymous: Keep up the good work, your doing wonders for your cause, which really has nothing to do with Scientific progression.

      What's ID creationism got to do with science that it should be so concerned about its progress, anyway? It has no research program of its own, no published studies, no consistent theoretical model. Instead, it goes cherry-picking among genuine scientific data for whatever might, with a little twisting, confirm ID wishful thinking (the rest can be ignored, of course). Once hijacked, such findings are instantly canonised as the capital-letter Truth, and who wouldn't gladly, uh, lie for the Truth? Hence, anyone who criticises those findings differently is (by decree) the enemy of the Scientific Truth. Bloody hell, what arrogance and dishonesty!

      Delete
    3. Diogenes,

      I don't think that creationists know the difference between quote-mining and quoting. They tend to be so stupid (or dishonest, and I do consider that with no remorse), that they can only hold a couple of words in mind. Thus, when they quote, for example, a little piece by Darwin that, out of context, makes it appear as if Darwin himself considers that evolution is a ridiculous proposition, they do so convinced that such was the actual meaning of the whole. This because by the time they read the rest, they have forgotten the previous sentence. Thus, if you quote anything, they think that saying "quote-mining" will stop you in your tracks because to them quote-mining means the same as quoting, and they think that "atheists" and "evolutionists" (which they also think of one and the same, and both as a single kind of ideology) just consider quoting to be wrong.

      See ya man.

      Delete
    4. @ NE;

      Yes, you are correct, in most instances I should have not used 'quote mine', my bad. However, my point still stands, one can 'quote' what they desire to hear, while ignoring the full content of what is said as I demonstrated above.

      The rest of your response is nothing but projected nonsense, which I virtually said nothing about what you state above.

      Delete
    5. @NE,

      "I don't think that creationists know the difference between quote-mining and quoting. ...they can only hold a couple of words in mind. Thus, when they quote, for example, a little piece by Darwin that, out of context, makes it appear as if Darwin himself considers that evolution is a ridiculous proposition, they do so convinced that such was the actual meaning of the whole. This because by the time they read the rest, they have forgotten the previous sentence. ...to them quote-mining means the same as quoting

      Yes, I've often thought this. I've often thought that their super-power, in extracting quote mines, is that they have near zero reading comprehension. When they "read" things, they skim vast numbers of sentences, and each sentence is like an atom to them, disconnected from the sentences before it or after it.

      They can't understand the context of text, which gives them the super-power of instantly grasping how a sentence sounds when taken out of context. For us, we read things slowly and understand them in context, so it's harder for us to quote mine their stuff, if we wanted to, because we have to think to imagine "How would this sound of context?" and for us that takes time.

      Delete
    6. Diogenes,
      As you can see below, this "anonymous" person can't read. Notice what this person thought that you said. Obviously anything you have written has gone way over this person's head. You would have to use puppets or something like that.

      Delete
  15. @ Dio,

    Since you are such a cry baby and can't bother to take another look at White's blog, which you whined about above, I will spoon feed it to you; http://www.huffingtonpost.com/social/rjop/media-genome-science_b_1881788_188974418.html

    1. No where do I make the assertion "good riddance to Junk DNA" as evidence for "my side" I never even brought up the selected quote, you chose to use above.

    2. I am the only one who posted this link, therefore, when you state; "the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side" I naturally assume this is me, since I am the only one that used the reddit link which contains your selected quote mine, oops I mean quote above.

    3. No where on White's blog does ANYONE use your selected quote "good riddance to Junk DNA" as evidence for their side.

    4. Therefore, one can logically conclude you're FoS!!

    You clowns give Science a bad name, like I said keep up the good work.

    ReplyDelete
  16. @ Dio,

    Since you are such a cry baby and can't bother to take another look at White's blog, which you whined about above, I will spoon feed it to you; http://www.huffingtonpost.com/social/rjop/media-genome-science_b_1881788_188974418.html

    1. No where do I make the assertion "good riddance to Junk DNA" as evidence for "my side" I never even brought up the selected quote, you chose to use above.

    2. I am the only one who posted this link, therefore, when you state; "the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side" I naturally assume this is me, since I am the only one that used the reddit link which contains your selected quote mine, oops I mean quote above.

    3. No where on White's blog does ANYONE use your selected quote "good riddance to Junk DNA" as evidence for their side.

    4. Therefore, one can logically conclude you're FoS!!

    You clowns give Science a bad name, like I said keep up the good work.

    ReplyDelete
    Replies
    1. I suggest you take a very good reading comprehension lesson. You stated yourself that Diogenes said:

      "the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side"

      Clearly, Diogenes is giving the comment a name. He is not saying that you mentioned those words, but that you used a comment by this "Rule_30" person as evidence for your position. Which, clearly, you were. He goes on to say that, actually,the comment does not favour your position.

      Give it another look. Maybe you will notice that Diogenes does not even suggest that you said "good riddance to Junk DNA." That was just the name that Diogenes decided to use for that comment.

      Got it? I know. I wrote too many sentences. If you got that mistaken by just one phrase, I guess my explanation will leave you perplexed. Yet, I tried. Sorry if you just feel flabbergasted.

      Delete
    2. @ NE,

      Your rambling makes no sense and if you yourself can read, my response above begins with @ Dio. What's the matter, little Dio can't speak for himself, he has to have mommmy, who was not part of the discussion, run in and protect him. Kindly butt out, I was not corresponding with you on Huffpost nor was my response addressed to you above. Sorry if you just feel flabbergasted by this simple concept.

      Delete
    3. I just guess that Diogenes does not have the patience to teach reading comprehension. I am a teacher on the other hand. But maybe I should quit it. You don't seem too receptive to any lessons. (Or maybe you just lack the mental capacity for them.)

      Delete
  17. "Clearly, Diogenes is giving the comment a name"

    Yep

    "He is not saying that you mentioned those words"

    Wrong... what part of "the creationist were citing Rule_30's COMMENT "good riddance to Junk DNA" as evidence for their side" do you not understand? Sorry you are having such a hard time accepting this simple point, perhaps you should go crawl back under your rock.


    ReplyDelete
    Replies
    1. Anonymous,

      Sorry, but you are the one who's wrong. It is obviously saying that you cited that comment, not that you quoted the words "good riddance to Junk DNA." Again, that is the name Diogenes gave to the comment. Why is this so hard for you to understand? Let's look at it once again:

      the creationist were citing Rule_30's COMMENT "good riddance to Junk DNA" as evidence for their side

      See? It does not say:

      the creationists were quoting "good riddance to Junk DNA" from Rule_30's COMMENT as evidence for their side.

      There is a difference between citing a comment, and quoting from a comment. (I shouldn't be too surprised, after all you have difficulty understanding the word "quote" all by itself.) I know this is too much for you to absorb. So I leave it there now not to keep you too flabbergasted.

      Try and keep just one idea in your mind for now: reading comprehension.

      Now back under my rock. I'm a bit sleepy.

      Delete
    2. @ NE;

      cit·ed, cit·ing, cites

      1. To *quote* as an authority or example.
      2. To mention or bring forward as support, illustration, or proof: cited several instances of insubordinate behavior.
      3.
      a. To commend officially for meritorious action in military service.
      b. To honor formally.
      4. To summon before a court of law.

      Dio claimed above, the creationists cited THE COMMENT, this is again FALSE. I cited the link, not the comment, and again was not even focused on this particular comment, it was part of the researcher's response in which DIO decided to pull out and lie about it here. Sorry you can't seem to get this through your dense head.

      Delete
    3. *http://www.thefreedictionary.com/citing

      Delete
    4. Anonymous,

      I see that you are trying to show that you can use a dictionary. However, reading comprehension is not the same as dictionary quotation. For one, you need to read the words in their context and thus decide which kind of meaning might be intended. For another, seems like you forgot to check the meaning of "quote," which coincides with "cite" a little bit, but note the first and third definitions:

      -------
      v. quot·ed, quot·ing, quotes
      v.tr.
      1. To repeat or copy the words of (another), usually with acknowledgment of the source.
      2. To cite or refer to for illustration or proof.
      3. To repeat a brief passage or excerpt from: The saxophonist quoted a Duke Ellington melody in his solo.
      4. To state (a price) for securities, goods, or services.
      -----

      Clearly, if Diogenes wanted to say that you copied from another source, the proper wording would have been "quoted such and such words from such and such source."

      Check yet again:
      the creationist weres citing Rule_30's comment "good riddance to Junk DNA" as evidence for their side

      Now if we changed citing to quoting in that sentence the meaning changes completely:
      the creationist weres quoting Rule_30's comment "good riddance to Junk DNA" as evidence for their side

      The latter would be confusing because it could mean that the creationists copied and pasted the whole comment, or that they just cited it. Since you did not quote those words (you did not copy and paste them), but you did mention the comment (as you admit), Diogenes words were not lies. You cited the comment.

      I can see how you could be mistaken. What I cannot understand is why when the most proper meaning matches the circumstances, you rather hold to a meaning that equivocates Diogenes words into something that does not correspond to reality. After all, anybody with a little reading comprehension would notice that no matter how you can make the mistake, it should be just as easy for you to understand the intended message. After these many rounds, and these many clarifications, I suspect that, while your lack of reading comprehension abilities started this mess, you are now veering into plain dishonesty (ironically to claim that somebody else is being dishonest).

      Need more help?
      http://en.wikipedia.org/wiki/Reading_comprehension

      (Check how the word "citations" is used at the top of that web page. It might help you improve your concept for "citing.")

      Delete
    5. @ NE,

      Sorry, no go.. You can keep trying to defend him all you want. But any objective observer (which I'm sure we won't find here) would see my point is valid. He took a quote of his preference and asserted this single comment was being used when it was not. Get over it..

      Delete
    6. Anonymous,

      Fine by me if you prefer to dishonestly hold to your misguided assessment. It just adds to the evidence that to be a creationist you have to be stupid and/or dishonest.

      Enjoy it.

      (Though I bet you just did not understand my explanations. Too much of an imbecile to understand any of it.)

      Delete
    7. "Fine by me if you prefer to dishonestly'

      Nope, not being dishonest.

      "It just adds to the evidence that to be a creationist you have to be stupid and/or dishonest"

      And it just adds to the evidence that to be an ideologue you have to be a jackass and most definitely dishonest.

      (BTW, I am not a creationist in the sense it should be considered science or be taught in schools. I believe in evolution, just not the current ToE and strongly believe there is a paradigm shift coming within the next decade or two, which hopefully will divorce Science from crackpots such as yourself and company.

      "(Though I bet you just did not understand my explanations. Too much of an imbecile to understand any of it)"

      And I bet you did understand my explanations, but willfully ignore it, because, again you're a jackass. Enjoy it.

      Delete
    8. Nice double projection there NE.

      Delete
    9. Anonymous: I am not a creationist in the sense it should be considered science or be taught in schools. I believe in evolution, just not the current ToE and strongly believe there is a paradigm shift coming within the next decade or two...

      Wow, how intriguing! I love new paradigms. What would that novel view of evolution be like, O prophet? Most people here would presumably agree that evolution means descent with modification (the latter basically fuelled by random mutations and fixed by adaptive selection and/or drift). What's wrong with this view and what makes you think that the ENCODE stuff is so incompatible with it that a paradigm shift is imminent?

      Delete
    10. @NE-

      thanks for your clarifications and defenses. I was a bit too busy over the weekend to parse through the comments on Mike White's blog and try to figure out who Anonymous is.

      Negative Entropy is right, when I called the comment "Good riddance to Junk DNA" I was giving the comment a name.

      There are way over 400 comments at Reddit, and I don't expect the people here to be familiar with all the Reddit threads, so I gave that comment a name.

      I gave that name to that comment because that line from Rule_30 was immediately challenged by Larry Moran, and cited approvingly by creationist UDite, BornAgain77. There was then considerable back and forth about the meaning of "junk DNA".


      Delete
    11. @Anonymous-

      You have repeatedly accused me of misrepresenting the words you wrote on another blog [Mike White's] under another identity, but you won't tell me what your identity was over there.

      Instead of just telling me your identity over there, you expect me to play Sherlock Fucking Holmes, and then figure out your identity. I was too busy last weekend to play Sherlock Fucking Holmes.

      At Mike White's blog specifically, I'll assume that you, Anonymous, are "rjop".

      Rule_30's comment at the Reddit thread, which I called "Good riddance to Junk DNA" because that is its topic, has been both cited and quoted by creationists on many blogs.

      Over At Mike White's blog, rjop, who I'm assuming is our "Anonymous", cited that comment from Rule_30 which I called "Good riddance to Junk DNA."

      I claimed that ENCODE researchers admitted that they didn't disprove Junk DNA.

      rjop then cited Rule_30's comment to rebut me.

      rjop at Mike White's blog: The researchers themselves refuted your assertions, but you refuse to see it. Example; http://www.reddit.com/r/askscience/comments/znlk6/askscience_special_ama_we_are_the_encyclopedia_of/c66dha3

      This logically means rjop (who is Anonymous, I believe) was claiming that ENCODE researchers said they HAD disproved Junk DNA in that comment.

      Moreover, both rjop and Misc (at Ewan Birney's blog) have been taunting me to reply to creationist TheMayan-- they treat TheMayan as an authority. Over there, TheMayan says:

      TheMayan: Again, I say in response to ENCODES eulogy, not just rest in peace, but good riddance to this outdated paradigme. When speaking of parts of the genome we dont yet fully understand, lets be wiser and learn our lesson from history and replace this term, and instead use the term 'no known function'

      rjop cites TheMayan as an authority that I'm supposed to rebut, which I did, and TheMayan uses the "good riddance" language explicitly.

      I have rebutted TheMayan, demolishing his factually incorrect statements at Ewan Birney's blog.

      Delete
    12. Ups, Anonymous is still in kinder garden! Sorry Anonymous, I didn't know. Otherwise I would not have hurt your feelings. Well, that also explains your problems with reading comprehension. Don't worry. With practice you'll get there!

      Delete
    13. This comment has been removed by the author.

      Delete
    14. "I was a bit too busy over the weekend to parse through the comments on Mike White's blog and try to figure out who Anonymous is"

      More complete BS, why would you have to parse through the comments on White's blog, over the weekend, when I gave you the link on Friday? Also, I will ask again, why did you state I claimed ENCODE disproved Bob DNA, when you did not know who I was? A recap of your comment below:

      Thursday, September 27, 2012 5:53:00 PM
      "Who are you prissy lady (as I asked already)? Are you TheMayan or rjop? Or perhaps Shapiro himself?"

      We then have directly below it:

      "All the scientists at REDDIT admitted that they did not disprove that most of your genome is Bob. You claimed ENCODE disproved Bob DNA, so you were lying or stupid"

      Perhaps you are the one whom is both lying and stupid.

      "There are way over 400 comments at Reddit, and I don't expect the people here to be familiar with all the Reddit threads"

      More excuses, then why not simply link the link to the whole response, verses pulling a specific quote, and then charging the creationists were using it, which again is false.

      "Negative Entropy is right, when I called the comment

      Diogenes most likely says to himself, yeah, that's it, thanks NE, I would not have thought of that myself, thanks for bailing me out of my own shit hole.

      "I gave that name to that comment because that line from Rule_30 was immediately challenged by Larry Moran, and cited approvingly by creationist UDite, BornAgain77"

      First off, how many "that's" can you fit in to one sentence. Second, BA77 was not at Whites blog, which is what you whined about in your opening statement above. More diversion and BS from Diogenes.

      "Rule_30's comment at the Reddit thread, which I called "Good riddance to Junk DNA" because that is its topic"

      No it is not the topic, except in your diluted mind. There are many topics made in the researchers comments, yet you choose to pull this specific one out, because this is all your worried about. AGAIN I will ask, why do you desire DNA to be "Junk" so badly. Of course you will fail to answer this question yet again.

      Delete
    15. Cont;

      "I claimed that ENCODE researchers admitted that they didn't disprove Junk DNA. rjop then cited Rule_30's comment to rebut me"

      Nope, wrong, I did not cite the link to to rebut your claim, I cited it to show the researchers, including Birney BTW, does not think it should be called 'Junk' in the first place. You are so absorbed in protecting your 'Junk', you can not comprehend anything else.

      "Moreover, both rjop and Misc (at Ewan Birney's blog) have been taunting me to reply to creationist TheMayan-- they treat TheMayan as an authority"

      Nope, more diluted errors, my asking you this question had nothing to do with me supporting what he said, I was simply curious as to why you would respond to me only, and not him. You then explained your comment was not showing up, but of course in your diluted mind you think the myan is an 'authority', whatever that means.

      "rjop cites TheMayan as an authority that I'm supposed to rebut, which I did, and TheMayan uses the "good riddance" language explicitly"

      Can you copy and paste, link included, where TheMayan used the "good riddance language explicitly" I do not see it.


      "I have rebutted TheMayan, demolishing his factually incorrect statements at Ewan Birney's blog"

      Of course you think you have 'demolished him', just as you delusionally believe Shapiro is 'terrified and scared to death of you' because all you care about is your beloved "Junk" which is a dead end. But of course you won't admit that and can't see beyond your narrow ridged view and refuse to do so. Fortunately, true scientific progression will continue on, leaving you and your ilk in the rubble of true idealoges. Enjoy it.

      "Good riddance to Junk DNA" has been both cited and quoted by creationists on many blogs

      Evidence of these many blogs please. Also, if there were many blogs, why did you only complain about White's blog?

      You're so full of shit, you can't keep your own shit straight.

      Delete
  18. Anonymous, apparently you don't like the idea of 'junk DNA', and you also apparently think that the Encode project put an end to that idea. I'm curious, and would like to hear why it matters to you so much? Is it because you think that finding 'function' in most or all DNA would prove that evolution did not and cannot occur? Is it because you think that finding 'function' in DNA would prove the existence of a creator/designer/god or a particular creator/designer/god? And so that there's no confusion, will you please state your definition of 'function' in regard to DNA?

    ReplyDelete
    Replies
    1. Anonymous said:

      "(BTW, I am not a creationist in the sense it should be considered science or be taught in schools. I believe in evolution, just not the current ToE and strongly believe there is a paradigm shift coming within the next decade or two, which hopefully will divorce Science from crackpots such as yourself and company."

      So, you are a creationist but not one when it comes to a particular sense or two. And you "believe in" evolution. Interesting.

      For a comparison, I'm not a creationist in any sense and I also don't "believe in" evolution. I accept that natural evolution has occurred, does occur, and will continue to occur, unless and until positive evidence is shown to the contrary.

      I'm curious as to what you think the "paradigm shift" will be (From what to what?).

      Scientific theories, hypotheses, and inferences are all subject to change as more data is gathered and more understanding is gained. Even if there is a "paradigm shift" of some sort in evolutionary theory, so what? If there's evidence, and it's solid, and evolutionary theory changes, it will just be the way that science is supposed to work and does work (albeit seemingly slowly sometimes, humans are impatient creatures).

      Besides answering the other questions I asked you, will you state what it is that you think a "paradigm shift" will do, or will prove, or at least what you want it to do, or prove? Since you've admitted to being a creationist (except for the two alleged exempted senses) it appears that you'd like the "paradigm shift" to open the door to letting your particular god into the ToE. Is that what you want?



      Delete
    2. The whole truth: Scientific theories, hypotheses, and inferences are all subject to change as more data is gathered and more understanding is gained. Even if there is a "paradigm shift" of some sort in evolutionary theory, so what?

      Come to think of it, there have already been a few "paradigm shifts" in evolutionary biology and there's little doubt that will shall see more shifts in the future. What we can hardly expect, however, is a shift backwards to some sort of pre-Darwinian paradigm, as if the past one-and-a-half centuries had never happened.

      Delete
    3. Following up on Piotr Gasiorowski's comment, I always suggest people read Asimov's "Relativity of Wrong" in times like these.

      http://chem.tufts.edu/answersinscience/relativityofwrong.htm

      Delete
    4. @Anonymous: You are not talking to school kids and you really don't have to explain the obvious. We all understand no theory is ever final and no hypothesis should be left uncontested. But you have promised an impending paradigm shift that will make modern theories of evolution obsolete, and the question is: a shift from what to what? How is your concept of evolution different from that of mainstream biology?

      Delete
    5. Piotr,

      I strongly suspect that this was another anonymous.

      Delete
    6. NE: LOL, there's too much anonymity about. I assumed a creationist was trying to make a point by quoting Asimov, which was so strange that I wasn't sure what to think of it. My apologies for the confusion to the other/another Anonymous.

      Delete
    7. Oooops. That was me on Monday, October 01, 2012 3:53:00 PM. I was supporting your position with the Asimov essay. I just forgot to sign underneath.

      My old blogger account got hacked, so I had to kill it, and never bothered to make a new one. Apologies for the confusion.

      -The Other Jim

      Delete
  19. This whole thing seems to boil down to equivocation over the meaning of "function". Both rivers and canals are waterways. You could say for both their function is to channel water. That is what they do. The difference is that one came about through natural processes and one was designed by intelligent agents - human beings. The existence of function in this sense does not necessarily imply design.

    In the ENCODE brouhaha there seems to be an additional equivocation over "function". Does it just mean 'something happens' or does it mean 'something happens which contributes to the overall function of the organism'. In other words, does simply copying the broken gene for vitamin C count as function - because something is happening there when it is transcribed - even though the gene no longer enables us to produce our own vitamin C.

    ReplyDelete