Saturday, October 26, 2013

How to Turn a Simple Paper into a Scientific Breakthrough: Mention Junk DNA

Attanasio et al. (2013) published a paper in Science where they identified several thousand possible enhancers that were active in the facial area of developing mouse embryos. About 200 of them appear to be controlling genes that determine the size and shape of the face. (Recall that there are about 20,000 protein-encoding genes in mammals.)

Lynn Yarris of Lawrence Berkeley National Laboratory in California (USA) wrote up the press release [What is it About Your Face?]. It's a really good press release that fairly represents the published work and explains some of the significance. There's no mention of junk DNA in the press release or the published paper.

This is what it looks like when science correspondent Alok Jha published it in The Guardian.
Faces are sculpted by 'junk DNA'

Though everybody's face is unique, the actual differences are relatively subtle. What distinguishes us is the exact size and position of things like the nose, forehead or lips. Scientists know that our DNA contains instructions on how to build our faces, but until now they have not known exactly how it accomplishes this.

Visel's team was particularly interested in the portion of the genome that does not encode for proteins – until recently nicknamed "junk" DNA – but which comprises around 98% of our genomes. In experiments using embryonic tissue from mice, where the structures that make up the face are in active development, Visel's team identified more than 4,300 regions of the genome that regulate the behaviour of the specific genes that code for facial features.
It's pretty clear that science correspondent Alok Jha doesn't understand what he's writing and it's about time we started publicizing the names of those science writers who mislead the public about science. The consensus among knowledgeable scientists is that at least 80-90% of our genome is junk. It's time for science writers to admit that the science favors junk.

Scientists have known for decades that a lot of noncoding DNA is functional. The idea that all noncoding DNA (98%) is junk is false. No knowledgeable scientist ever made such a claim. It is a myth perpetuated, in part, by ignorant science writers; albeit, aided and abetted by ignorant scientists. Scientists have known for fifty (50!!) years that gene expression is controlled by regulatory sequences in noncoding DNA. Scientists have known for at least that length of time that during embryogenesis different genes are turned on and off and that this is due, in part, to binding of transcription factors to those regulatory sequences (enhancers). Scientists have known for one hundred years that the morphological features of mammals, including humans, are controlled by genes.

Move along folks. There's nothing to see here.


Attanasio, C. et al. (2013) Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers. Science 342: Oct. 25, 2013 [doi: 10.1126/science.1241006]

93 comments :

  1. Amazing. I had seen (somewhere) a quote from the Guardian report, and I was cursing the self-publicizing scientists who misused the concept of Junk DNA. But I never went to read the paper or the original LBL press release.

    I take back my curses laid upon the innocent authors and redirect them to the Guardian science writer. Unlike the ENCODE fiasco, this one cannot be laid at the feet of opportunistic scientists.

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  2. It is also worth mentioning that this paper is really just another in a series of papers using exactly the same approach from the same group of people:

    http://www.ncbi.nlm.nih.gov/pubmed/23375746
    http://www.ncbi.nlm.nih.gov/pubmed/22138689
    http://www.ncbi.nlm.nih.gov/pubmed/20729851
    http://www.ncbi.nlm.nih.gov/pubmed/19212405

    Which illustrates another curious aspect of the whole "Junk DNA is dead" problem - exactly the same thing has been said for at this point perhaps hundreds of papers, and for close to a decade. Doesn't it occur to anyone that you cannot be saying "Scientists thought for a long time non-coding DNA is junk, now they found out it isn't" so many times and for so long for the simple reason that once you proclaim it loudly in publica dozen of times or so it is just not true anymore? I am starting to think I will be reading exactly the same press releases in 2023 (that is, if there are any science-related press releases in that year, which might well not be the case given the direction things are taking).

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  3. Larry Moran: The consensus among knowledgeable scientists is that at least 80-90% of our genome is junk.

    The other consensus among *knowledgeable scientists* is that calling 80-90% of our genome junk is ‘narrow-minded’ and ‘inappropriate’:

    Calling something junk just because we don't understand what it does strikes me as narrow-minded. I suggest replacing this designation with 'funk' - functionally unknown DNA.
    [Gregory A Petsko. Funky, not junky. Genome Biol. 2003; 4(2): 104, (2003) (http://www.ncbi.nlm.nih.gov/pubmed/12620109)]

    “Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general because of the minority status of pseudogenes within genome sequences, but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction.”
    [Ryan T. Gregory, The Evolution of the Genome, Elsevier/Academic Press, 2005 ( http://www.genomesize.com/rgregory/book/)]

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    1. I've told you this before. You are misrepresenting Ryan Gregory's view on junk DNA. If you don't stop I will have to delete all posts where you lie about him.

      Nobody, including Ryan Gregory, ever said that all noncoding DNA is junk. All knowledgeable scientists agree that this is inappropriate. There may have been a time when Ryan wanted to keep to a strict definition of junk DNA that only included pseudogenes but that time has long past [A word about "junk DNA"]. Today he is quite happy to use "junk DNA" to mean DNA with no known function and he is quite happy to advertise his belief that most of our genome is junk.

      I strongly suspect that Greg Petsko's view has also changed since 2003.

      Before posting again, you should learn the meaning of the word "consensus."

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    2. I wouldn't use "junk" to refer to DNA with no known function; it might have an unknown function. I would prefer to use the term for DNA that we have good reason to believe has no function, i.e. around 90% of the human genome.

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    3. John Harshman,

      How do you interpret no know function? Do you side with Larry on the issue or with Frankenstein?

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    4. I don't know if I can speak for "Frankenstein", but my view is close to Larry's. I'd say that junk DNA is DNA in which variation in the sequence does not cause fitness differences big enough to affect the fate of the variations. Of course for particular regions of sequence we don't precisely know that -- though we can see whether their sequence is evolutionarily conserved. There is ample reason to believe that most (not all, most) of our noncoding DNA is junk DNA.

      Claudiu Bandea has argued for a protective function of this DNA, but has never made the case that selection coefficients arising from this function would be big enough to cause it to maintain or increase the amount of this DNA. Others posting here who base their opposition to the widespread existence of junk DNA on theology are just being silly. "Evidence" that just consists of people finding some conservation, or some function, somewhere in the noncoding DNA is particularly unconvincing as a reason to think is not a large amount of junk DNA in most species.

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    5. Quest: That's FrAHnkenstEEn. I don't know how to interpret "no know function". I'm pretty sure that Larry, Joe, and I all agree on the issue of whether there is junk DNA and around how much there is. I was taking issue with the diagnostic criterion, which Larry knows well enough.

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    6. John -- I get the reference.

      Typo in my comment above. Last sentence should read "... as a reason to think that there is not a large amount of junk DNA in most species."

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    7. This comment has been removed by the author.

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    8. @Larry,

      I think you are way off and inappropriate in your comment above. In my previous comments, I tried to persuade you and other readers of this blog to read and study the published work of the scholars in the field of genome size evolution including Michael Bennett, Thomas Cavalier-Smith, Ryan Gregory and Ford Doolittle. These scientists have dedicated most of their career to these issues, so they are in position to offer some relevant insights into these highly important issues, and it makes little sense to ignore their scientific publications. I understand that their views might go against your beliefs about the roles of so called junk DNA (jDNA), but you cannot pretend that their published scientific ideas and models on the putative roles of jDNA, such as the ‘nucleoskeletal and nucleotypic fuctions’, do not exist.

      Consider, for example, Ford Doolittle’s statements in his recent PNAS paper (Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE”; Proc Natl Acad Sci U S A. 110:5294-300) ( http://www.ncbi.nlm.nih.gov/pubmed/23479647)

      “Cavalier-Smith (13, 20) called DNA’s structural and cell biological roles “nucleoskeletal,” considering C-value to be optimized by organism-level natural selection (13, 20). Gregory, now the principal C-value theorist, embraces a more “pluralistic, hierarchical approach” to what he calls “nucleotypic” function (11, 12, 17)”.

      "I submit that, up until now, junk has been used to denote DNA whose presence cannot reasonably be explained by natural selection at the level of the organism for encoded informational roles. There remain good reasons to believe that much of the DNA of many species fits this definition. Nevertheless, while still insisting on SE functionality, we might want to come up with new definitions of function and junk by (i) abandoning the distinction between informational and nucleoskeletal or nucleotypic roles for DNA, (ii) admitting that there may be strong selection for C-value as a determinant of many cell biological features, (iii) fully embracing hierarchical selection theory and acknowledging that different genomic features may have legitimate functions defined and in play at different levels, and (iv) expanding the SE definition of function to include traits that arise neutrally but are preserved by purifying selection (12). Much that we now call junk could then become functional.”


      Do you agree with these statements or not, and why?

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    9. Joe,

      I think that you know better than anyone that modeling selection is a *relative* process, as it depends on assumptions. I would also think that you agree that mathematical modeling in biology is such a powerful approach that with the *right assumptions* you can prove almost anything you want.

      Obviously, modeling the protective function of the so called junk DNA (jDNA) against insertion mutagenesis of germ-line or somatic cells, which can lead to neoplastic transformations, might reveal some very interesting insights. However, the protective function of jDNA is as evident as the protective function of the CRISPR/Cas immune system of bacteria and archaea (1), in which the amount of viral DNA sequences co-opted as an antiviral defense mechanism depends on the viral activity.

      1. Horvath P, Barrangou R (January 2010). "CRISPR/Cas, the immune system of bacteria and archaea". Science 327 (5962): 167–70.

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    10. John,

      I agree with you that Larry’s assertion that (in his opinion) Ryan Gregory uses "junk DNA" to mean *DNA with no known function* is poorly formulated. However, if we need to use this deceiving term, which some people consider ‘narrow-minded’ and ‘inappropriate’, I would prefer to use it for the genomic DNA that we have overwhelming evidence that it doesn’t perform informational roles, which in humans might represent more than 95%.

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    11. Are we now arguing over 90% vs. 95%, then? Are you excluding centromeric and telomeric DNA in order to make the distinction? I would prefer, if we have to, to talk about DNA with no sequence-related function. That would leave open the technical possibility of a bulk function, which is your big thrill.

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    12. What we know for sure is that genomic DNA can have: (i) informational (iDNA) roles, such as the DNA coding for proteins and functional RNAs or for other genomic functions such as gene regulation, genome replication, etc., and (ii) non-informational roles (niDNA), such as spacing, centromeric, and telomeric functions.

      As you know, there are also some putative ‘bulk functions’ attributed to genomic niDNA, such as the ‘nucleoskeletal and nucleotypic fuctions’ which have been discussed in dozens of scientific articles and books during the last few decades, and were recently emphasized by Ford Doolittle in his recent PNAS paper about the ENCODE project. Unfortunately, Doolittle did not specifically address how the ‘nucleoskeletal and nucleotypic fuctions’ explain the c-value enigma, or if they pass the pass the formidable ‘onion test.’ What do you think, do these theories pass the onion test?

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    13. Once again, you have to show us that the population genetics works in favor of your hypothesis for us to take it seriously.

      You have not even tried to do this

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    14. Please see my comment above addressed to Joe Felsenstein.

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    15. That post not an answer to the objection.

      Also, I don't see why you think it's necessary to bring up CRISPRs into the discussion of junk DNA as evidence for the idea that there is no such thing. To begin with, they are limited to the organisms that have almost no junk DNA and those repeats are not something anyone would call "junk".

      Does having a lot of extra DNA protect against TE insertion - sure it does. But then why wasn't it selected for by evolution in all lineages and instead we have a striking anti-correlation between N_e and selection efficiency on one hand and genome size on the other? The best thing for an organism is to have neither extra DNA (which creates a very long list of problems for the cell) nor TEs. Prokaryotes and many unicellular eukaryotes seem to have achieved that quite successfully

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    16. Claudiu Bandea's reply is not a reply. It does not show that an extra piece of junk DNA would have a selection coefficient large enough (greater than 1/N, where N is the population size). And no you cannot prove anything using models. You can prove anything using bullshit.

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    17. Claudiu BandeaSunday, October 27, 2013 6:10:00 PM
      Please see my comment above addressed to Joe Felsenstein


      I didn't see any population genetics arguments there.

      I will make a quick attempt at doing that exercise for you. If the positive contribution of an extra piece of DNA is based on its protective buffering role against TE insertions, then the benefit from genomic expansion would be roughly proportional to how much it lowers the probability of a TE inserting into exons and regulatory elements (the absolute value of the selection coefficient need not be the same but it would likely be significantly lower, otherwise organisms with active TEs and compressed genomes might not be able to exist; you need the actual frequency of TE insertions in each generation, the probability of inserting into important sequences, which is not exactly the same as the fraction of the genome occupied by such sequences, the negative effect on fitness of those insertions, and other parameters to actually estimate it and that quickly becomes complicated). A typical LINE element is 6.5kb or so, the human genome is 3GB and some 90% seems to be junk. If we assume $s$ approaching 1 for the protective role of all junk DNA (which, again, is likely a serious overestimate), an extra intergenic LINE insertion would have an $s$ on the order of $10^{-6}$. The long-term $1/N_e$ of the human lineage is two orders of magnitude lower than that, and note that I have greatly inflated the selection coefficient and I have ignored the negative effects of the insertion (which are actually greater). You would need megabase-sized insertions and duplications to make that theory work, which is not what we see in the human genome - half of it is defective transposon copies which are much smaller. Of course, you can argue that when the genome was smaller, the selection coefficients were higher. But you will have to also explain how lungfish got from 3GB to 30GB and then to 133GB, which was accompanied by a drop of the selection coefficients by another two orders of magnitude. In short, the numbers don't work.

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    18. I said "And no you cannot prove anything using models". Which was an infelicitous wording. I did not mean that no, it's true that you cannot use models to make any proof. I should have written: "And no, it is not true that you can prove anything you want using models".

      Duh ,,,

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    19. Before evaluating any hypothesis it would make sense to fully understand it. That’s true about my hypothesis, as well as the nucleoskeletal and nucleotypic hypotheses on the putative functions of the so called “junk DNA” (jDNA).

      I assume that you read Ford Doolittle’s recent PNAS paper ( http://www.ncbi.nlm.nih.gov/pubmed/23479647) in which he specifically refers to the nucleoskeletal and nucleotypic functions of jDNA (see the passage from his paper I posted above).

      I already asked Larry Moran and John Harshman what do they think about these hypotheses and about Doolittle’s statements on jDNA, but apparently they prefer to be mute on this sensitive subject.

      What do you think about the nucleoskeletal and nucleotypic functions? Do they pass the ‘onion test’?

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    20. Again, how were those ''functions'' selected for?

      You need to explain that, and you refuse to do that

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    21. What do you think about the nucleoskeletal and nucleotypic functions? Do they pass the ‘onion test’?

      It would seem to me that they don't. Do different species of onions differ in their need for nucleoskeletal and nucleotypic functions? I can't think of a reason that they would. Can you?

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    22. The nucleoskeletal and nucleotypic hypotheses have been developed in dozens of scientific articles and books over the last few decades, and there is a very interesting data and elaborate theoretical work supporting them. As emphasized by Doolittle, this work represents “the state of the art” in the field of genome size evolution. I fully agree with him, and I highly recommend this work to anyone interested in the subject (including Larry!).

      However, when it comes to the ‘onion test’ I could not figure out how these highly popular hypotheses among the experts in the field (see Doolitle’s paper) pass the ‘onion test’. I have brought forward this issue numerous times during the last year (to the extent that Larry almost had a breakdown), but got no clear answer, except an attempt by Gregory (http://sandwalk.blogspot.com/2013/10/non-darwinian-evolution-in-1969-case.html#comment-form) which, I think, brought more questions than answers.

      So, John, I don’t have an answer either. Maybe the scholars promoting the ‘nucleoskeletal and nucleotypic functions’ can enlighten us with an answer.

      On more specific issue, what do you think about Doolitle’s statements I posted above?

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    23. Please give us some examples of the papers that contain the "elaborate theoretical work" that supports those model and that accounts for all the data (especially the distribution of genome sizes and genome content across various groups).

      Specifically, you need to show that the benefit of each individual insertion the sum of which drives genome expansion is sufficiently beneficial to be selected for by evolution. That means showing that:

      1) Such insertions are beneficial
      2) They are so beneficial that they are visible for selection (i.e. $s > 1/N_E$.
      3) There are vast differences in the selection coefficients in different species, and why they exist

      Only then will you have refuted the current theory, which is that individual insertions usually have a slightly negative effect on fitness and genome size is determined by the balance between insertions and deletions and the efficiency of selection (i.e. effective population size)

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    24. You want to start with the publications referred by Doolittle in his PNAS article:

      “Cavalier-Smith (13, 20) called DNA’s structural and cell biological roles “nucleoskeletal,” considering C-value to be optimized by organism-level natural selection (13, 20). Gregory, now the principal C-value theorist, embraces a more “pluralistic, hierarchical approach” to what he calls “nucleotypic” function (11, 12, 17)”

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    25. 1. If you think this is an endorsement, then you are quote mining; the overall message of the article is quite different

      2. The papers cited almost do not contain the population genetics work I asked you to provide

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  4. Dawkins agrees with you all... lol

    Richard Dawkins ENCODE 2013 "Junk DNA"

    http://www.youtube.com/watch?feature=player_detailpage&v=_bjKH43pRB0#t=94s

    Have a good laugh ;)

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    1. The main laughs are at the expense of the video maker for his feeble attempts to quote mine, and you for posting it. "Widespread function is just what a 'darwinist' would expect" and "hierarchical trees of common descent are just what evolution would predict" are not in any way incompatible viewpoints.

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    2. You've got to love the way he tries to reconcile reality with his definition of "function" in the video description, though. He disappears up his own ass, emerges out the other end then disappears again with that one.

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    3. Those of us who are alumni of talk.origins are familiar with the lies and distortions of creationists. We've been telling them for two decades that true Darwinists like Richard Dawkins are uncomfortable with large amounts of junk DNA in our genome. That is not what "Darwinism" would predict.

      We've also been telling the IDiots that every scientist knows and understands that pseudogenes exist. Furthermore, every knowledgeable scientist knows that the existence of common pseudogenes in related species (e.g. chimps and humans) is powerful evidence of common ancestry—especially when somewhat distantly related species have active genes at that site.

      The video shows Dawkins expressing both of these entirely consistent points of view. The fact that the IDiots still don't get it after all these years is solid proof that they are, indeed, idiots.

      "Quest" and "lutesuite" are perfect examples of the stupidity that rational people are up against in the evolution-creation wars. Not only are they ignorant of biology, they seem to be very proud of showing off their ignorance.

      I encourage them to keep posting comments. It's very educational for the students in my class because a major topic in class is, "How can average people believe things that are completely wrong?"

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    4. To be clear, my comment above was referring to the creationist who posted the video, and his written comment that accompanies it. I was not referring to Dawkins.

      I would have hoped that my posting history here would have made it quite apparent that I do not agree with Quest on pretty much anything.

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    6. This comment has been removed by the author.

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    7. Larry, do you have lutesuite mixed up with LouiseG?

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    8. Yes, I apologize to lutesuite. I was thinking of LouiseG.

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    9. The video-maker Richard Raspberry is apparently one 'Josh Shelley'. He has written a book. And got it published. He presumably wrote this Amazon blurb:

      If you're an Atheist or a Christian, Wasp on the Moon is a book which shines a light on Creationism proven as fact with easy to follow information and contains collections of Evolutional refuted arguments. This book makes mockery of up to date evolutionary arguments including Richard Dawkins and natural selection arguments. God is evident in microbiology as described in this book. Including (cell formation. the fused chromosome argument, bacterial mutation) all refuted in up to date scientific evidence.

      I kid you not.

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    10. It's being a bit generous to say he "got it published." "Paid someone to print and bind a buch of copies of a document he typed up" is more accurate. The "publisher" is listed as www.lulu.com.

      Several of the Amazon reviews mention that Shelley cites his own hard drive as a source of references. LOL! I think I'll suggest him for The Sensuous Curmudgeon's "Self-published Geniuses" series:

      http://sensuouscurmudgeon.wordpress.com/partial-table-of-contents/self-published-geniuses/

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    11. You can "look inside" the book. It's an edifying experience: it shows that even a semi(il)literate imbecile can publish a book. Praise the Lord, there's hope for everybody!

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    12. @Larry, I have not commented on this issue at all as far as I can remember. Are you trying to get back at me and Quest for demolishing your blog on the origins of life theme? There is no other reason I can think of why you would include me in your comment here. Can you?
      Also, I'm not sure if I fully understand your comment. You call Dawkins a "true Darwinists" who is "uncomfortable with large amounts of junk DNA in our genome. That is not what "Darwinism" would predict". I thought that evolution is a fact and there is no uncomfortable issues here? Is it, if everyone here has not clue about? Are you a Darwinist?

      Junk DNA is not my favorite subject, because even creationists are lost in it. Don't know about Quest, but I hope he does the same as he did with me on the origins-kick your ass :)

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    13. LouiseG sez:

      I'm not sure if I fully understand your comment.

      You're telling us. And here's a prediction: Even after Larry's forthcoming patient and clear explanation, you still won't understand.

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    14. Lutesuite,

      What else can you say? You got slapped around a bit on the origins, so now all you have left is pretend that it never happened?

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    15. LouiseG, it's obvious that Larry's remark about your and Quest's stupidity is not based solely on comments in this thread. The two of you have provided numerous examples of your stupidity in previous threads.

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    16. Louise,

      Are you trying to get back at me and Quest for demolishing your blog on the origins of life theme?

      If something as idiotic as Quest presenting a paragraph that he/she misinterpreted out of reading comprehension disabilities passes to you as "demolishing" an origins theme, then I should not be surprised that you think that you demolished something either. Incredible. I hadn't guessed that you were this much stupid Louise, all this time I thought that you were just ignorant. And there I was still giving you some explanations. Of course you will never understand any of it. Quest would only look convincing to someone who is mentally ill and unaware of it.

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    17. Larry,

      I hope your students read this blog... I hope they have some brains left after your brainwashing ... I hope they can see the reality of shit here... I hope they acknowledge you have not made even one comment to defend my challenge on the origins of life issue... I hope at least one has the guts to challenge you on that one day....If not, too bad....I will not teach anybody how to think...rationally... Hell with those!!!

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    18. I hope they can see the reality of shit here

      Yes, the quality of your contributions is obvious to all visitors.

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    19. I can probably reply for Richard Dawkins that, contrary to Larry's statement, he doesn't find that large quantities of junk DNA in genomes are contrary to a strongly Darwinian point of view...

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  5. Claudiu Bandea,

    Wait! The onion test or C-value enigma is being rolled out... lol Let's see if NickM and T Ryan Gregory will join you in the discussion. I have one question to ask them ;)

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    1. You have answers to the onion test and the C-value paradox, Quest? Please, don't be coy. Let's hear them!

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  6. I wonder if Visel agreed to the 80% figure in the main ENCODE paper when he accepted co-authorship.

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    1. It should also be added that we have a quantitative idea (even if quite imperfect) of what the negative effects of extra DNA are, which means that he has to demonstrate a positive contribution to fitness greater than 1/N plus the absolute value of that. In addition to that he will have to explain why if additional DNA is so beneficial, lineages in which selection is more efficient have more streamlined genomes, and why the anti-correlation between N_e and genome size, intron size and number, and a whole bunch of other things fits so well our current models. My bet is on that being a highly convoluted and completely artificial model, if he ever comes up with one.

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  8. Larry,

    Did you see this video from Discovery News on the same paper?
    Your Face Is Made Of Junk DNA!

    This is truly awful, on so many levels. I'm beginning to suspect that science journalists' salaries depend somehow on the number of times they screw up the concept of junk DNA a year. The guy seems to be citing a different, yet equally clueless, article by Bahar Gholipour over at Science Live:

    Face-Shape Secrets May Lie in 'Junk' DNA

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  9. Should knowledgeable scientist say that part of the DNA with no known function is junk, just because he or she has no idea what that function might be YET? The mouse controversy is a perfect example. Many so called knowledgeable scientists had been saying that 98% of mice DNA is junk, because they didn't know what function it had.

    Look at them now! Some of that junk DNA turned out to be functional, so what makes you feel so confident that the rest of non-coding DNA will not turn out to have other functions? It’s just pure arrogance to me typical for the other so-called knowledgeable scientists.

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    1. That's your pure arrogance talking. You know nothing about the subject yet feel willing to tell those who do that they're arrogant? Your main premise is wrong: the reason we think most of the human genome is junk is that that it has no known function. It's that it displays evidence of non-function. Are you capable of seeing the difference?

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    2. First of all, I'm using an example of mouse junk DNA here, not human, which you don't know anything about, but arrogantly pretend that you do.
      If I were talking about human junk DNA, I would mention it don't you think? Anyways, if you are so confident that human DNA,or mouse for that matter, is mainly junk, why don't you put you career on the line like Dan Graur did by saying that if human DNA turns out to be largely functional, evolution is wrong.

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    3. It's a misunderstanding of the theory of evolution to think that if it turns out there is no junk DNA then evolution is wrong.

      Common descent rests on a lot more than junk DNA, in fact there was no junk DNA concept for the first 100 years since Darwin, for the simple reason that it was only in the 1940s that DNA was firmly established as the carrier of inheritance.

      If it turns out that there is no junk DNA, that would mean that our understanding of the population genetics environment of multicellular organisms is completely wrong, not the theory of evolution is worng. That's highly unlikely, but more importantly, note that I have actually quite carefully worded this - it would change our understanding of the population genetics environment, and that's all - population genetics would still be the basis for evolutionary theory because that's really at its core simply basic probability theory applied to Mendelian mechanisms of inheritance, and unless our understanding of inheritance changes dramatically (what are the odds of that?), it's going to remain that way.

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    4. Here is Dan Graur presentation:

      http://twileshare.com/askq

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    5. OK, I suppose it's time for you to cite some of the "many so-called knowledgeable scientists" who claimed that 98% of the mouse genome was junk. Even one would do.

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    6. I don't know about you but chimp genome being 12% larger than ours stinks just as much as the junk DNA shit....Knockout mice is another stinky shit Larry likes....but I DON'T. Larry and Grower should go back to school to learn the fundamental shit instead of being coy....lol

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    7. I was unaware that facts of nature are something we should express likes or dislikes of.

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    8. LouiseG,

      Graur's position is no different than Georgi's. That's exactly what Larry explained right after the SMBE conference, and Graur agreed that this is indeed what he was saying. You're misrepresenting him and his position here.

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    9. I should also point out that the argument for junk DNA itself does not depend on the assumption of common descent.

      Of course, in order for it to turn out to be wrong, so many fundamental pillars of our understanding of biology would have to be wrong, that indeed evolution as we know it would most likely turn out to be wrong too. But it does not mean there is an absolute mathematical equivalence between those things.

      The argument for junk DNA is based on mutation rates, selection coefficients and effective population sizes.

      With or without common descent, genome evolution would still be governed by those thins because, again, that's just what some quite basic math applied to the basic principles of Mendelian inheritance mandates.

      Pretty much the only situation in which the above is irrelevant is a very recent special creation.

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  10. John Harshman,

    In this case you may be right and Louise wrong..... as I have never seen any reputable papers making such a claim...

    I think Louise got it mixed up with human genome not that old claims...though I would not be surprised if we see otherwise.

    Even if 20% of mouse genome is functional, you, Larry, Joe, or PZ Mayers can't prove beyond any doubt that the majority of mouse genome is junk. No way.

    BTW: Too bad you were so quiet on the origins of life...I was hoping that you, NickM and possible Dan Growler would pop in... I used to hope I would challenge Jerry Coyne on the issue but he is out of this planet right now with the "our will being controlled by the laws of physics". Well, I guess you can't control what you are going answer to this comment? Let the laws of physics do their job!

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    1. I have seen many claims that mice junk dna =98%. Don't remember where. Maybe on Coyne's blog.

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    2. You saw MANY claims to that effect and don't remember a single source? Too bad, but let me lend you a hand, Louise. You (or whoever you borrowed the number from) possibly have a hazy memory of the first sentence of Nóbrega et al.'s abstract:

      http://escholarship.org/uc/item/4fd0v6b0

      The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined.

      If you (or your fellow creotards) had no reading comprehension issues, you would understand, even from this single out-of-context sentence, that the authors don't claim that 98% of the mouse genome is junk. They only say that we don't know the functional importance of MUCH (not ALL) non-coding DNA. Their study suggests that some of it is junk:

      The deletions carried out in this study represent the largest reported viable homozygous deletions in mice and supports the existence of potentially “disposable DNA” in mammalian genomes.

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    3. I have seen many claims that mice junk dna =98%. Don't remember where. Maybe on Coyne's blog.

      Or maybe in the very article that this post is about? Junk DNA/=noncoding DNA. Noncoding DNA = 98%. Junk DNA MUST be less - regulatory elements and functional RNA transcripts are neither junk nor coding. If you've seen the claim, you've seen someone make exactly the same mistake as Jha. You will now be in a position to correct their misunderstanding, armed with this info.

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    4. Since LouiseG is a Sandwalk regular, he (?) must have seen this claim debunked several times. If he repeats it notwithstanding, then either he did not grasp the correction the first (or second, or third) time it was offered, or he couldn't remember anything more complex than a single piece of information at a time ("98%", plus the vague recollection that it had something to do with junk DNA). The figure will forever rattle about in the cavity where his brain ought to be, so I predict that he will make the same mistake in the future -- not once, but again and again and again, and again and again and again.

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  11. Do you know the arguments advanced in favor of most of the human (or mouse) genome being junk? Can you state them briefly? And if so, can you refute any of them? You must understand that science does not "prove beyond any doubt"; we provisionally accept hypotheses that fit the data better than others. The junk DNA hypothesis fits the data much better than the no junk hypothesis. Much, much better. But if you can present evidence to the contrary, I'm willing to change my mind.

    As for the origin of life, that's definitely not my field.

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    1. I can....Night vision...

      What are you going to do now John? Ask more questions? Or pretend you didn't understand? The latter may be better...but not for you....

      The origins is not your field and now genetics failed you.... What are you going to do now John? Intimidate me by calling me names; that I'm stupid, mentally ill and uneducated like your buddies had done so for who call themselves scientists? Go ahead!

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    2. Quest, I'm confused about your last comment reg. night vision. What do you mean by that?

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    3. Quest,

      I pick your second option: pretend I didn't understand. It's easy, because I have absolutely no idea what you're talking about. I'm somewhat comforted by the suspicion that you don't know either.

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    4. John,

      Are you trying to tell me you didn't know that mouse almost entire nuclear genome is transformed into some sort of an optical device-night vision?

      http://www.cell.com/abstract/S0092-8674(09)00137-8

      If that is the case how could the majority of mouse genome be junk?

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    5. Louise,

      Please confirm that you are a woman....

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    6. No, I didn't know that. Very interesting. But of course most of the genome can still be junk, even if the genome itself has a bulk-dependent function. If the sequence doesn't matter and the quantity likewise doesn't matter, it's junk.

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    7. That paper doesn't say what you say it does, Quest.

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    1. I did. And? What do you want me to do?

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    2. Become subject to the experience of reasoned thought, just for change.

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    3. Doesn't it seem odd that "the designer" would fill the blueprints with self-inserting parasitic instructions?

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  13. Doesn't it bother you all that chimp genome is 12% larger than human? How do you explain it from evolutionary prospective to your students Larry? Soon you may have to...My son's one choice is U of T. Who knows...You may have to deal with even more difficult client than me....lol

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    1. I hope you never go away. Like with Robert Beyers, I would hope to see you as the front spokesperson of the ID-creationist position.

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    2. 1. Are you sure it really is 12% larger? I am not saying it isn't but it's not like it has been fully assembled - the PanTro3 version of the chimp genome has more than 300Mb is unassembled contigs and this is what makes those 12%. When the assembly is completely finished, some portion of those 300Mb may well disappear.

      2. And more important, how does that invalidate the theory of evolution? I just don't see the logic, so please enlighten us

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    3. If the chimp genome is larger, does that mean chimps are more complex than humans?

      Oooohhhh....

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    4. You may have to deal with even more difficult client than me.

      I assume you are referring to the chimp.

      Given, for the sake of argument, that it's genome is 12% larger than yours (I'm giving you the benefit of the doubt with regards to your status as human).

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    5. Curios that looking for a 12% difference between human and chimp genomes leads only to creationist web sites. I'm not about to start reading those. They give me headaches with the amount of stupidity they can concentrate in one paragraph.

      I went through the articles on the chimp genome. Nothing. Hum. We are left therefore knowing that Quest goes to some creationist web sites, copies some sentences from there and comes here to make "hard" questions.

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    6. Actually for once they are correct, at least technically:

      If you take these two files:

      http://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips/panTro4.fa.gz

      http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

      And count the total number of base pairs in them, you get the following:

      hg19 (excluding the haps): 3101804741
      human chrY (the chimp that was sequence was female so it is fair to exclude it): 59373566
      panTro4: 3309577922

      It's not 12%, but the chimp genome is indeed bigger.

      The problem is that, as I said above, the size of the unassigned contigs in the chimp genome is 300-400mb, so some of that may disappear when it eventually gets fully assembled.

      Of course, it is absurd to present this as evidence against evolution, it boggles the mind how someone could be so silly

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    7. Good job... Are you comfortable with the results? I'm just wondering... Coz you don't seem like guy who buys shit...

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    8. Even if the chimp had 2x, 20x, 100x the DNA, why would it matter? Why are you so hung up on size, Quest?

      Amoeba dubia 6.7x10^11 bp ("protist")
      Bufo bufo 6,9x10^9 bp (frog)
      chimp 3.3x10^-9 bp
      human 3.2x10^-9 bp.
      Rhinolophus sp. 1,9x10^9 bp (bat)

      Not that the single-celled Amoeba sp. has ~200x the DNA of us. This is the classic C-value "paradox". The paradox was solved when we a) stopped assuming humans were "more complex" than anything else, and b) figured out that number of bp is not relevant to any definition of complexity that you want to use.

      Why would you assume this bothers any scientist with knowledge of comparative genomics?

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    9. Quest very helpfully reminds us that creationists suffer not only from ignorance, but from rank stupidity as well. That is to say, it is not simply that they lack awareness of certain information and facts. Even if they are provided with the information and facts needed, they are not able to make use of them because creationists lack the basic ability to think correctly.

      I mean, how is it even conceivable for someone with a properly functioning mind to spend as much time reading this blog as Quest has and still think that someone who understands the concept of junk DNA should be troubled by the fact that the chimpanzee may have a larger genome than we do? That's the kind of finding that should be causing consternation to the creationists, instead.

      It seems that creationists are not just unable to understand evolution. They don't understand creationism. either.

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  14. Dan Graur asked Axel Visel about his views on junk DNA. Visel replied
    "…while I agree that equating every reproducible protein binding event with “function” is probably a too relaxed definition of the term “function” for most purposes, dismissing any sequence for which we cannot demonstrate evolutionary constraint at this point as “junk” doesn’t seem quite right either."

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