Monday, July 15, 2013

How the IDiots View Genome Research

It's safe to say that a majority of knowledgeable scientists now agree that the most of our genome is junk. This is bad news for Intelligent Design Creationism because they have staked their credibility on the idea that if the DNA is present is must be the product of god(s) the intelligent designer and it must be there for a reason.

One of the latest posts on Evolution News & Views (sic) emphasizes this point [More Clues that Intergenic DNA Is Functional]. Its author doesn't identify herself/himself. The point of the post is to cherry-pick a couple of papers from the scientific literature, including the horrible paper by Hangauer et al. (2013) [see How to Make a Scientific Argument ].

Here's what the IDiot concludes ...
It’s clear that the search for function is driving this cutting-edge research. Search for function is exactly what intelligent-design science would recommend. Darwinians describe natural selection as a tinkerer, generating useless parts as well as structures cobbled together that might do something by chance, since there is no supervising designer to guide the process in a particular way. By contrast, intelligent design expects that what exists, as the product of mind, is there for a reason.

Remember how Darwinists call ID a “science stopper,” since it supposedly counsels just giving up and saying, “God did it”? The real science stopper is Darwinism. It focused only on protein-coding genes and dismissed everything else as “transcriptional noise” or “junk DNA” left behind by the blind tinkerer. Why waste time studying junk? Were it not for that attitude, our understanding of intergenic DNA function might have been much farther along by now.
I wonder what they'll say when this debate is over and junk DNA wins? Maybe they'll abandon Intelligent Design Creationism?

Note that in spite of years of effort by real scientists, the IDiots refuse to admit that there's plenty of solid evidence for junk DNA. We've told them time and time again that there's plenty of functional DNA that isn't in protein-encoding genes and we've told them time and time again that hundreds of labs have studied genome and concluded that we have evidence of junk. The IDiots have never admitted that they understand pseudogenes, broken bits and pieces of transposons, genetic load, introns, lack of sequence conservation, megabasepair deletions, repetitive DNA, DNA-binding proteins, and genome size variation.

Why is that? Is it because they're IDiots?


25 comments :

  1. Anonymous liar at Evolution News and Views writes: "The real science stopper is Darwinism. It focused only on protein-coding genes and dismissed everything else as “transcriptional noise” or “junk DNA”"

    This is a lie. No molecular biologists nor geneticist ever equated Junk = non-coding DNA, and no IDiot has ever produced a quote from a molecular biologist or geneticist stating that he personally believed Junk = non-coding DNA; that is a scurrilous lie promoted by ID creationists and muggle newspapers desperate for sensational stories.

    Do we need to remind you of the basic history of 20th century science? Yes we do. How many times do I have to copy this list?

    Nobel Prize for Jacques Monod and co-workers, 1965, for finding functions in non-coding DNA (regulatory elements).

    Nobel Prize for Barbara McClintock in 1983 for her discovery of new functions in non-coding RNA (mobile genetic elements.)

    Nobel Prize for Tom Cech and Sidney Altman in 1989, for discovery of catalytic functions resulting from non-coding DNA (catalytic RNA= ribozymes).

    Nobel Prize for Jack Szostak and co-workers in 2009, for research in 1980’s on function in non-coding DNA (telomeres).

    Nobel Prize for Richard Roberts and Phillip Sharp in 1993 for discovering introns (in non-coding DNA).

    The structure of tRNA was known by 1964, crystal structure solved in 1974. tRNA is made from non-coding RNA.

    The ribosome was known to be largely nucleic acid in the 1950's, general molecular structure known since the early 1970s, by the 1980's it was known the ribosome was a ribozyme-- based on functions residing in non-coding DNA.

    Explain to me how scientists did not pay enough attention to function in non-coding DNA?

    T. Ryan Gregory Further Summarizes Functions Found in Non-Coding DNA:

    "Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966)."

    [A word about "junk DNA". T. Ryan Gregory, on April 11th, 2007. ]

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    1. Diogenes,

      You forgot to mention Ryan Gregory’s nucleotypic hypothesis explaining the c-value enigma and the evolution of genome size. According to Ryan:

      Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA "free-for-all" there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates (emphasis added) (Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9:317-24).

      “These are the “nucleoskeletal” and “nucleotypic” theories which, though differing substantially in their specifics, both describe genome size variation as the outcome of selection via the intermediate of cell size” (2). (emphasis added) (Gregory TR. 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324:15-34).

      I have previously posted these straightforward quotes from Ryans collection of papers discussing the nucleotypic hypothesis, but for whatever reason Ryan’s hypothesis is treated like the plague. I wonder why!

      I think you have always been up-front with your thoughts and opinions. So what do you think about the nucleotypic hypothesis and how do you interpret the two quotes above? BTW, the first quote is from the abstract of the article, so it represents its essence.

      Delete
    2. Claudia, simply citing pieces of a paper detailing a hypothesis does not establish that hypothesis as fact. No matter how many times you do it. It's not that it's "treated as the plague", it's that at this stage, it is and remains nothing more than an idea.

      Delete
    3. Here's a wonderful opportunity for the IDiots to do real science, by going out and spending time and resources testing Ryan's hypothesis for example.

      I predict that they won't. Ever.

      Delete
  2. In order to see how IDiots at "Evolution News and Views" lie about science, consider how they quote from the Hangauer et al. 2013 paper. Here I will preserve the bold-facing as used by the IDiots at "Evolution News and Views":

    [Hangauer et al. 2013 as quoted by ENV IDiots]: "The remaining 97% [of the genome] is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about... whether these intergenic RNAs are functional. ...we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell..." [Hangauer et al. 2013 as quoted by ENV IDiots, emphasis as at ENV]

    Now let's read that again, with emphasis on the bits that the IDiots don't boldface:

    "The remaining 97% [of the genome] is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about... whether these intergenic RNAs are functional. ...we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell..."

    One copy per cell! Wow! So if a protein-coding gene has 10,000 transcripts, and one copy of a lincRNA binds to a transcript, that will reduce the coding transcripts to 9,999. The IDiots call that efficient regulation and proof positive of functionality designed by an omniscient creator.

    And lincRNAs can be 200 nucleotides in length, as defined in the paper (the ENV IDiots quote that bit, but again, do not boldface the length.) If they have 20,000 lincRNAs and each is 200 nucleotides, that's 4 million nucleotides out of 3.2 billion.

    That's 0.125% of the genome, by an envelope calculation. According to Larry, a more accurate figure is 2%.

    Evolution News and Views can't do long division.

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  3. "Darwinians describe natural selection as a tinkerer, generating useless parts"
    Already here the IDiot author is flailing around, like an idiot. Actually, most "Darwinians" (people who put a lot of emphasis on Natural Selection/adaptationism), are kind of like the IDiots on this one, since they often reason that Natural Selection would get RID of junk.
    The idiot here is constructing a particularly specious piece of propaganda. First by throwing all of evolutionary biology under the term "Darwinians", then by falsely stating misrepresenting what "Darwinians" say by conflating it with an idiotic version of what Neutral theory states.

    Natural Selection doesn't "generate junk", it can't. Replicating a lot of junk costs energy, so there must be some other mechanism at work that generates junk faster than selection can weed it out, for there to be junk. In this way, Natural selection (and therefore the "Darwinians") actually predict the directly diametrically opposite of what the IDiot here declares.

    A typical particularly gruesome and idiotic error. One that has been corrected so many times before, on this blog in particuler, which we KNOW the idiots read because they often respond both here and on UD, the fact that this error persists can ONLY be explained by malice.

    As in DELIBERATELY PRESENTING FALSE INFORMATION. LYING.

    What all IDiots should ask themselves is therefore: If your fundamentalist religious doctrine of ID is really true, why do you have to LIE to support it?

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  4. "Its safe to say that a majority of knowledgeable scientists now agree that most of our genome is junk"

    Is this based on an informal poll or just talking to people at meetings? And more to the point; have any of the ENCODE people come clean about hyping up their results with a bit of hyperbole?
    I havent seen anything on it ( not that I scour the literature looking for it) but there are still papers making claims of function for most junk - which the DI always finds.
    It seems to me there are reasonable scientists making no-junk claims...so how do they explain the positive evidence for junk?

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    1. have any of the ENCODE people come clean about hyping up their results with a bit of hyperbole?
      I havent seen anything on it


      Yes. I have compiled a list of quotes from ENCODE people "coming clean". I'll write it up on my blog.

      Delete
  5. "Its safe to say that a majority of knowledgeable scientists now agree that most of our genome is junk"

    Is this based on an informal poll or just talking to people at meetings? And more to the point; have any of the ENCODE people come clean about hyping up their results with a bit of hyperbole?
    I havent seen anything on it ( not that I scour the literature looking for it) but there are still papers making claims of function for most junk - which the DI always finds.
    It seems to me there are reasonable scientists making no-junk claims...so how do they explain the positive evidence for junk?

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    1. How do they explain the positive evidence for junk?

      Long story short: They don't. Many of them aren't even aware of it, and they are totally clueless about the history of the discovery and debate surrounding junk-DNA. How the term originated, why it eventually won over. They simply don't know about it.

      There's a few of them who's aware of it and understand it, but they just have some kind of intellectual or philosophical difficulty with accepting the concept.

      Most of these people are some kind of "Adaptationist". They put a massive emphasis on the role of natural selection in evolutionary biology, so they reason that if "it's there, it must be doing something". These people don't so much "deal with" the evidence FOR junk, as they ignore it and instead simply ad-hoc rationalize what "yet to be discovered functional DNA might be doing".

      This is also what makes the IDiot assertion above so particularly gruesome and ironic. They think (or actually, they PRETEND) evolutionary biology predicted junk and then a priori dismissed most nc-DNA as junk on that basis alone, and then nothing was done for a lot of years. This is a specific fantasy they have erected for propaganda purposes and couldn't be further from the truth.

      As I wrote earlier, the IDiots actually read this blog and have been doing that for a long time, so they can't be unaware of the real history of the junk debates. This makes their assertions above nothing short of deliberate misinformation. Lying. Breaching the 9th commandment of the very deity they purport to be trying to gather converts to by finding "evidence of design". The sheer irony of it...

      Delete
  6. "The real science stopper is Darwinism. It focused only on protein-coding genes and dismissed everything else as “transcriptional noise” or “junk DNA” left behind by the blind tinkerer".

    Again, this is a deliberate misrepresentation of the history. It needs to be hammered out again and again: Junk DNA was discovered to be junk much to everyone's surprise. It was never fucking assumed and then just dismissed.

    Exactly for the reasons stated above. The "Darwinians", the people who put a lot of emphasis on Natural Selection, actually expected the entire genome to be functional (and many of them still do), so they searched and searched and searched, and no matter what they came up with, the evidence simply wasn't there.

    Grudgingly they simply had to accept that something else was going on. That various biochemical processes was and is accumulating defective DNA faster than Natural Selection can get rid of it. They didn't expect this, but they had to bow before the evidence.

    The rate of deletion of DNA due to mutations is lower than the rate at which transposons mutate, get copied and become selfish parasites that insert themselves in many places in the genome.

    That the rate of retroviral insertions over evolutionary time is also greater than the rate of deletion.

    That there are degrading pseudogenes we no longer need because their original function has become redundant (like GULOP).

    And so on and so forth, all this has been covered before on this blog and elsewhere.
    So we now understand not only why there is junk, but also why there's so much of it.

    Of course it doesn't even stop there. Occasionally someone who doesn't know the history of the junk debate will come up with the "some kind of biochemical activity"-like argument that's supposed to tell us that "it's not junk, it might do something". But even THEN, this has already been discussed before. We understand why there would be "activity" (however it is extremely low, which is evidence in favor of junk), and yes, one such activity is actually transcriptional noise. We understand why there would be this. It's an intrinsic property of atomic scale interactions, they simply sometimes stick together briefly and weakly, and this can be enough to be identified as a transcriptional product in an assay. The mistake here is to think this means it was "on purpose" and therefore has some kind of important biochemical function.

    And then there's the whole c-value paradox. Another line of evidence for junk, which also functions as a counter-argument to the "there's activity"-rationalization that IDiots and "Darwinists" come up with. They can't explain these huge variations in genome sizes between even closely relates species that have very similar lifestyles. Famous case in point: Onions.

    We now understand WHY this junk is there, having spend so much time trying to figure it out. By doing actual research, in laboratories, with real work. In contrast to the IDiots who just sit on the sidelines and shout, yeah, "goddidit".

    All they can offer here endless ad-hoc rationalizations. But they have to keep doing it on this case-by-case basis. While each of these points can be rationalized, there's no overarching, single-fits-all hypothesis that can successfully deal with all the evidence for junk in all these different species and circumstances.

    If the IDiots really think all this DNA is functional, why don't they do some of this research themselves? Hmmmm...

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    1. "Why waste time studying junk? Were it not for that attitude, our understanding of intergenic DNA function might have been much farther along by now."
      This accusation is particularly ironic coming from (the supporters of) an institution that does no genomic research at all, and simply has a priori declared that all DNA is functional because that's what their designer wanted(one wonders who they can know this, some designers ARE wasteful).

      HEY, IDIOTS, when are you going to get off your supremely lazy asses and do the work?

      Delete
  7. The ID post reads like it comes from Cornelius Hunter. He tends to use the word "Darwinists" pejoratively and the wording sounds like his. I see that they have disabled comments again. Probably a good thing in this case.

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  8. I have also never seen any evidence that they understand the significance of shared ERV fragments.

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  9. Thanks Diogenes, I'll check it out when I have more time!

    Rumkaret- so on what basis does Larry say the majority accept junk? I'm sure many believe the 80% function claim was careless but very few are concerned about the mileage IDers are getting from it so on one is in a hurry to correct it.

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    1. I asked for a show of hands at the SMBE2013 session on junk DNA and two-thirds of the people in the room thought that a majority of our genome was junk. I personally asked 31 people at the meeting and 21 of them said that most of our genome is junk. This included all twelve of the people who had posters on genome content.

      I conclude that among those people who are knowledgeable about the subject a majority believe that most of our genome is junk.

      I have yet to meet anyone who is knowledgeable about the subject but believes that most of our genome is functional. One way to assess knowledge is to ask them to explain genetic load and to explain the difference between noncoding DNA and junk.

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    2. Here is Larry again, restricting the biological functions of genomic sequences to informational roles.

      Delete
    3. Here is Claudia again, insinuating a hypothesis that still can't explain all the facts.

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    4. Onions and megabase deletions. Your "non-informational role" hypothesis can't explain it.

      Delete

    5. Ok,
      So two-thirds accept majority junk. But this was in a room of people very knowledgeable on the subject, so why so many holdouts? Could it be in how they interpret "majority"
      My impression is that a reasonable guess now would be 70% junk - allowing for alot more functional RNA...so maybe the holdouts think its 45%.
      When the ENCODE results first came out Larry said he'd be doing damage control for years...he was right

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    6. Heh, the crazy part is that, as Graur's slides from his talk show, even the ENCODE people themselves ended up backpeddling a lot and down-adjusting their initial 80% claim. Apparently it got as low as 9% at one point, after which they went up again to 20%.

      Pure, unadulterated hype and sensationalistic journalism. It really is quite despicable.

      Delete
    7. @Rumraket

      Because of the overwhelming evidence (such as lack of sequence conservation) that most of the genome in species with high c-value, such as humans and onions, does not have informational roles, most of the scholars in the field of genome evolution, including Michael Bennett, Thomas Cavalier-Smith, Dmitri Petrov and Ryan Gregory’s have abandoned this paradigm decades ago, and focused instead on potential non-informational roles.

      Therefore, in light of this evidence and scholarly work it makes little sense to have serious discussions about potential informational roles for the so called ‘junk DNA” (jDNA). To me it would make sense to first study the work of the scholars and then discuss the weaknesses or the strengths of their work. And even better, if there are new ideas that can explain the c-value enigma bring them forward. That’s what I think is a recipe for a constructive and progressive discussion.

      Delete
    8. Rumraket: “Onions and megabase deletions. Your "non-informational role" hypothesis can't explain it.”

      I don’t know what you know about my hypothesis, which BTW does explain the c-value paradox (and the “Onions and megabase deletions”). However, there are other hypotheses that apparently explain the evolution of the genome size.

      For example, Ryan Gregory’s, who according to Ford Doolittle is now “the principal C-value theorist” wrote that “there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates.

      Don’t you think that the host of this blog, Laurence A. Moran, who has discussed the evolution of genome size in dozens of posts, and apparently is Ryan’s friend, should bring forward the nucleotypic theory to which Ryan has dedicated much of his scientific career?

      The question is why doesn’t Larry want to bring forward Ryan’s scientific work. Maybe because it brings evidence that the so called “junk DNA” has a biological role and that goes against his scientific ideology?

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  10. ID proponents are such liars. Stephen Meyer asserted in 'Darwin's Doubt' that ENCODE showed that 'at least' 80% of the human genome is functional. Not between 20% and 80%. All to justify his assertion that he can take the genome size of modern species, such as Drosophila melanogaster (around 140 million base pairs) and an estimate of the minimum genome size of a complex unicellular organism (one million base pairs) to claim that the Cambrian 'radiation' involved the injection of a large amount of new genetic information.

    He thinks that the Cambrian phyla developed from single celled organisms in less that 6 million years. It's also the reason he denies that the Ediacaran phyla are animals. They are, although they're almost certainly not the ancestor of the Cambrian phyla.

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  11. To see some YEC scientific research on genetics, check out Jeff Tomkins' papers:

    http://www.icr.org/index.php?search=AdvancedSearch&f_keyword_all=&f_context_all=any&f_context_exact=any&f_context_any=any&f_context_without=any&f_search_type=articles&section=0&f_constraint=both&=Search&module=home&action=submitsearch&f_authorID=207

    He's not an IDiot as far as I can tell, just a plain old idiot. Sad, as he was until recently an actual researcher.

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