Thursday, May 14, 2015

Another view of junk DNA from an Intelligent Design Creationist

Here's an excerpt from the latest post about junk DNA on Uncommon Descent [Tossing Out the Junk]. The author is Eric Anderson1.
It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins. Even with the proliferation of functions for non-coding DNA, we still hear regular pronouncements from the purveyors of the materialist creation myth that “yes, there may be some function for non-coding DNA, but most of it is still junk.”

The whole idea of pervasive junk in our DNA is so naive and absurd as to boggle the mind. Thankfully, the trajectory of the evidence is clearly trending toward a more rational and complete assessment of DNA. Yes, hindsight is 20/20, and soon enough every biologist worth her salt will claim that she “always knew” that most DNA had function. But let us not forget that there were a few lone voices, including prominent ID proponents, long arguing for pervasive function — in the face of ridicule and the stifling, science-limiting attitude of the Darwin establishment about their beloved icon of “junk” DNA.
We need to preserve these comments for posterity just in case our genome actually turns out to be full of junk as most knowledgeable scientists believe. At that point, probably within a few years, the world will see that an important prediction of "prominent ID proponents" was falsified.

Meanwhile, let's hope they keep digging.


1. Nobody seems to know much about him. I'm guessing that he's an engineer.

125 comments :

  1. It would be good as well to collect comments by IDiots who say that ID doesn't imply a lack of junk DNA, for comparison. There's plenty of each, because of course ID implies nothing other than that some unknown entity did something or other in some unknown way at unknown times, and we can learn nothing about that entity by examining the data. Or so many IDiots say.

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  2. It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.

    Quite so. The Nobel Prize for Monod, Jacob, and Lwoff for their work on operons is just an illusion crafted after the fact to make IDiots look like they don't know anything about biology.

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    1. And Mung verges perilously close to the insightful:

      "But surely there’s no selective advantage to all that junk. Can’t we prove that it’s junk by showing that it’s not under selection?"

      Gee, I wonder if we could.

      If he keeps on thinking that way, he might also realize that if there's no selective benefit to the junk, then it follows that natural selection does not fix and maintain the junk, and therefore the presence of junk DNA isn't a "Darwinist" proposition.

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    2. Oh my goodness, mung. And to think that biologists never thought of something so simple.

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  3. Note Eric Anderson's "editorial remark" (in boldface, which is the equivalent of shouting from a loudspeaker in the ceiling) added to one of the posters' comments. To those unfamiliar with UD -- defacing other people's posts in this way is their standard practice.

    Are you claiming that the fact that large swaths of DNA do not code for proteins has not been used by evolutionary proponents to bolster the claim that such DNA is “junk”? This has been an extremely common and pervasive tactic of Darwinist proponents for decades. Embarrassingly, some are still using this tactic today in the face of contrary evidence.

    And now that even many Darwinists are reluctantly admitting that “some” non-coding DNA might have function, whence the continuing and repeated claims that most DNA is still junk? Why on earth would any rational person make such a claim? It is a classic argument from ignorance: “We don’t know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true.” Evolution-of-the-gaps thinking.


    They have the amazing ability to pack so much nonsense into a few sentences that you would have to write an essay to expose and correct it all. Jesus F. Christ! The difference between non-coding DNA and junk DNA, and the actual arguments for the existence and estimated size of the "junk" part of eukaryotic DNA have been presented by better-informed commenters at UD itself scores of times (possibly hudreds of times, but I don't want to exaggerate). If Eric F. Anderson can't be bothered to read biology handbooks and journal articles, he might at least pay some attention to comments on the blog he helps to run. If he were only ignorant because the stuff is completely new to him, that would be something that could be fixed. But he comes across as wilfully ignorant and unable to assimilate information spoon-fed to him by well-meaning people whose only fault is that they suffer from the SIWOTI syndrome and can't resist the urge to try and educate the likes of Eric.

    {head-desk, head-desk, head-desk}

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    1. But Piotr, tell us how you really feel.

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    2. Not so bad, actually. As Larry says, they keep digging.

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    3. Like! I was going to post, again, "hey so what about onions", but...what's the point?

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  4. We need to preserve these comments for posterity just in case our genome actually turns out to be full of junk as most knowledgeable scientists believe. At that point, probably within a few years, the world will see that an important prediction of "prominent ID proponents" was falsified.

    For the benefit of those less informed on this issue (e.g. myself): What further evidence is likely to arise in the near future that will demonstrate beyond reasonable doubt that most of the genome is junk? From my inexpert perspective, the case already looks pretty airtight.

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    1. Eventually technology will advance to the point where large genomes are as cheap to sequence as small genomes. Right now there is a big bias towards sequencing small-genome species, and then we sequence humans cause we're humans. Some researchers, and others, have only heard about the sequenced genomes, and don't realize that genome size has been measured in thousands of species using old-fashioned cell biology techniques. So they draw conclusions from "yeast small, Drosophila bigger, humans biggest" and don't realize "onions even bigger, other onions even more bigger, some salamanders and ferns way bigger still". That's really what 90% of this debate comes down to, people who are aware of the huge variability in genome sizes, vs. people who aren't.

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    2. What really cooks the goose of the junk deniers, no REALLY, is that sequencing individual human genomes is getting cheaper and cheaper, so in the future, for medical reasons, we'll have *many millions* of individual human genomes, mostly for medical reasons (cancer treatment), so we can compute the full variability and tolerance to mutations *just within living humans* (which creationists admit are all of common descent) and we won't need to compare to apes. We can make a library of all non-lethal mutations everywhere in the human genome.

      Doing the math: let's say each human baby has ~100 novel mutations not in its parents (I'm ignoring standing variation inherited from previous generations, which is large.) The haploid human genome has 3 x 10^9 base pairs, so we need 3 x 10^9 / 10^2 = 30 million sequenced human genomes, then we'll have a record of all nonlethal mutations.

      30 million. That's less than the population of California. Standing variation will push the number down; errors in sequencing techniques will push the number up.

      The "death of Junk DNA" crew are screwed.

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    3. Lutesuite: One of us needs to learn to recognize irony. Either you need to recognize Larry's, or I need to recognize yours.

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    4. It seems the problem is mine. (blush)

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  5. Heck with junk DNA, Larry. Your position cannot account for DNA. There is a reason why evolutionism has to start with populations biological reproducing organisms that already have and use DNA. And even given starting populations of prokaryotes you don't have a mechanism of getting beyond populations of prokaryotes.

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    1. There are two logical answers to the question of how life began.

      1. We know exactly how it happened and here's the explanation ....

      2. We don't know exactly how it happened but there's no evidence to suggest that the process violated any of the known laws of physics and chemistry.

      I pick #2. Which one do you choose?

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    2. There is no evidence to suggest that life can be reduced or explained by physics and chemistry. My car's existence doesn't violate any known laws yet no one is stupid enough to posit that known laws can explain cars.

      So while 2 is the better of your 2 choices, it is too vague to be of any use.
      Coca Cola doesn't violate any known laws of physics and chemistry yet we know it was the result of intelligent design. Plastics don't violate any known laws of physics and chemistry yet again it is the result of intelligent design.

      You really didn't think that one through, Larry.

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    3. Joe G you IDiot, Larry did not say, life does not violate the laws of physics, therefore it is not intelligently designed. He said "the process" of OOL did not violate the laws of physics. So your "coke bottle" analogy is BS.

      Intelligent Design *does* claim that OOL violates their *alleged* laws of nature, their fictional "Law of Conservation of Information" and "Law of Biogenesis".


      We don't know exactly how it [OOL] happened but there's no evidence to suggest that the process [OOL] violated any of the known laws of physics and chemistry.

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    4. Joe G, by what criteria do you determine if a thing has been intelligently designed? For example, consider:

      Eubalaena australis
      prions
      smallpox virus
      a quartz crystal
      Congo floor maggot
      Hapuna Beach, Hawaii

      Which are intelligently designed, and why?

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    5. Diogenes, you ignorant slut. I never said Larry said life does not violate the laws of physics therefore it is intelligently designed. Larry has no idea if the OoL violated any known laws.

      And Intelligent design does NOT claim the OoL violates any known laws. Intelligent Design doesn't violate any known laws. Imbecile

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    6. Chris B, we use tried and true design detection techniques to determine if something is designed or not. Archaeologists and forensic scientists don't flip coins nor roll chicken bones.

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    7. Do archaeologists determine that chicken bones found at their sites were designed? If not, there must be something different between bones and coins that lets archaeologists distinguish them. And if so, archaeologists must not be using the techniques you think they are.

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    8. Well John, your position can't account for chickens, so that would be a problem, for you.

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    9. "Chris B, we use tried and true design detection techniques to determine if something is designed or not. Archaeologists and forensic scientists don't flip coins nor roll chicken bones."

      You didn't answer my question.

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    10. I answered your first question which empowered you to try to answer your other questions.

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    11. You didn't answer my question, just deflected.

      But yes, I can account for chickens pretty well. They're a domesticated form of red jungle fowl, which is related to other jungle fowl, other pheasants, other birds, and other dinosaurs. We can at least provide the main outlines of what's been happening to the chicken's ancestors for the past few hundred million years. It doesn't seem to have been designed, unless you're saying that the designer reached into the genomes of the chicken's ancestors and made little tweaks. Is that your claim?

      You may also want to seriously consider my original question this time. Clearly, archaeologists distinguish between chicken bones (not designed, as far as they're concerned) and coins (designed). So how did their design-detection methods fail, if they're the ones you claim?

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    12. Intelligent Design doesn't violate any known laws.

      Really? If as you yourself say, physics and chemistry can't even make a bacterium, what's your mechanism, in concert with these same "known laws," for coming up with a being so powerful and sophisticated that it can *intelligently design* a bacterium?

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    13. LoL! Just cuz you can spew some hypothetical history doesn't mean evolutionism can account for chickens.

      You may also want to seriously consider my original question this time.

      All it does is expose your agenda of obfuscation.

      Archaeologists determine if something is an artifact or not the same way the ID determines if something is designed or not. Namely eliminate mother nature and find a pattern that matches what known designers produce.

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    14. If as you yourself say, physics and chemistry can't even make a bacterium, what's your mechanism, in concert with these same "known laws," for coming up with a being so powerful and sophisticated that it can *intelligently design* a bacterium?

      Non-sequitur.

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    15. Either you don't know what "non-sequitur" means, or you're using it to avoid the issue. I'll pose the question again: What "known laws" allow a being sophisticated and intelligent enough to design a bacterium to arise in our universe?

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    16. Oh, bullshit Joe.

      "Archaeologists determine if something is an artifact or not the same way the ID determines if something is designed or not."

      No archaeologist ever computes specified complexity with Demski's method, because it would return "designed" when applied to the products of natural processes!

      Joe, I demand you cite one, just one peer-reviewed article in any archaeology journal that uses Dembski's bullshit "specified complexity" citing Dembski's work. Just one. You can't even cite one, you fraud.

      Dembski's method always involves computing the tornado probability of a structure, that is, the probability that a tornado assembled it by randomly scrambling all parts. If that tornado probability is small, and if the structure "matches an independently given pattern", then IDers say it's "designed."

      No archaeologist would ever use that method, because it returns false positives, for example, Landscape Arch, which could never be assembled by a tornado, or the numerous natural bridges with roads on them, which function the same as man-made bridges and match the same "independently given pattern" as man-made bridges.

      No, no archaeologist uses the methods of Intelligent Design because they return false positives: archaeologists are scientists, and you're witch doctors who think naturally produced stuff must be designed.

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    17. "And even given starting populations of prokaryotes you don't have a mechanism of getting beyond populations of prokaryotes."

      The ID darling Lynn Margulis actually had a pretty good explanation.

      "Archaeologists and forensic scientists don't flip coins nor roll chicken bones."


      Why would they? They are looking specifically for the artifacts of human activity - a known entity. Like I said before - analogies are not evidence, yet analogies to human activity are all the IDC camp seems able to offer.

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    18. Ever notice how Joe never answers a direct question?

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    19. Yes, Security Clearance never, ever answers a question directly. Joe always responds by stating a falsehood about another topic, so we'll go chasing that.

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    20. No, Joe G, you didn't answer my question. From the brief list I presented above, which of those are intelligently designed, and how do you know?

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  6. Joe,

    "And even given starting populations of prokaryotes you don't have a mechanism of getting beyond populations of prokaryotes."

    What are you talking about? You have never heard of endosymbiosis theory of eukaryotes with "... many eukaryotic genes turn out to be unlike those of any known archaea or bacteria; they seem to have come from nowhere..."

    Page 95

    http://labs.icb.ufmg.br/lbem/aulas/grad/evol/treeoflife-complexcells.pdf

    Darwinists neither have the mechanism nor the genes to move beyond the prokaryotes but people who point that out to them are idiots and liars...

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    1. Yes, I have heard of endosymbiosis. It = "it looks like those organelles coulda been bacteria". But hey, when their PoV requires that bacteria give rise to eukaryotes, they have to pull out all of the stops. That includes calling us idiots and liars...

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    2. IDiots and liars saying "Darwinists have neither the mechanism nor the genes to move beyond prokaryotes" have not heard of the recent lokiarchaeota results (or that endosymbiosis is observed).

      Note that Intelligent Design by contrast has no mechanism, no starting materials, no pathway, no testable predictions, no research strategy and no experimental successes.

      Just "We're losing! Change the subject, fast" over and over.

      "God did it by magic" is not an explanation, does not account for anything, does not explain anything, makes no testable predictions, cannot be tested and does not follow as a deduction. So it's not science. You never had an "explanation", you had an allegation about a supernatural cause. Not the same thing.

      You lost on junk DNA, so you tried to switch the subject to OOL. But lokiarcharota mean you got nothing there too, nor here nor anywhere.

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    3. http://en.wikipedia.org/wiki/Lokiarchaeota

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    4. Lokiarchaeota, Tiktaalik.

      The lesson is that gaps arguments evaporate over time.

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    5. What about Lokiarchaeota? Just another candidate for the engulfing organism. And the Lokiarchaeum are just as evolved as any other organism alive today. That doesn't help any scenario which occurred some hundreds of millions of years ago.

      Thanks to the tetrapod tracks in Poland, Tiktaalik now gives us the fossil succession of fish-> tettrapods-> fishapods

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    6. Diogenes- ID has mechanisms. just that we don't have to know what those are before we can determine if design is present. ID did NOT lose on junk DNA as the jury is still out. OTOH you lost on DNA so shut up.

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    7. Interesting. When I taught genetics last year, we went over an entire chapter on the generation of new genes.

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    8. "OTOH you lost on DNA so shut up."

      How was that again?

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    9. Joe "Security Clearance" Gallien says: "Diogenes, you ignorant slut... Intelligent design does NOT claim the OoL violates any known laws. Intelligent Design doesn't violate any known laws. Imbecile"

      Gee, it's so hard to prove Joe Security Clearance wrong! it took me almost 15 seconds of googling.

      Larry Arnhart writes: "After Michael Behe's lecture, some of us pressed him to explain exactly how the intelligent designer created the various "irreducibly complex" mechanisms that cannot--according to Behe--be explained as products of evolution by natural selection. He repeatedly refused to answer.

      But after a long night of drinking, he finally answered: "A puff of smoke!" A physicist in the group asked, Do you mean a suspension of the laws of physics? Yes, Behe answered."


      Jibbers Crabst, Joe, are you that dumb? Or do you just think "I'll just disagree with anything they write" is a good debating strategy?

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    10. "Thanks to the tetrapod tracks in Poland, Tiktaalik now gives us the fossil succession of fish-> tettrapods-> fishapods"

      This is just hilarious. These people cannot get out of their "great chain of being" middle-ages mindset and keep projecting it onto evolution...

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    11. Source of the Michael Behe "puff of smoke" quote, above.

      Joe "Security Clearance" Gallien says: "Diogenes, you ignorant slut... Intelligent design does NOT claim the OoL violates any known laws. Intelligent Design doesn't violate any known laws. Imbecile"

      To this day, "magic puff of smoke" remains the most detailed model presented by Intelligent Design theorists.

      Here's Proof of the Poof:

      William Dembski's model for Intelligent Design: "I’m certainly not an advocate of universal common ancestry. I just don’t think the fossil record bears it out. I think the Cambrian explosion is a perfect example, where you have just utter, you have these forms which are just there, Poof! And there are no precursors. [Hitchens-Dembski Debate, Nov 2010]

      David Berlinski's ID model: "That densely reticulated tree, [Diogenes notes: if it's retiuclated, it's not a tree, and if it's a tree, it's not reticulated] with its lavish foliage, is an intellectual construct, one expressing the hypothesis of descent with modification. Evolution is a process, one stretching over four billion years. It has not been observed. [Diogenes notes: Macroevolution and microevolution have both been observed]

      … Before the Cambrian era, a brief 600 million years ago, very little is inscribed in the fossil record; but then, signaled by what I imagine as a spectral puff of smoke and a deafening ta-da!, an astonishing number of novel biological structures come into creation..." -- [David Berlinski, The Deniable Darwin (June 1996), Commentary magazine.]

      By adding the word "Ta-da!", Berlinski has produced the most detailed version of the Intelligent Design hypothesis so far. In a few more years, IDers may finish work on their super-sophisticated "Abra Cadabra" model. Perhaps in half a century, Poof! theorists can tell us if their magic poof-ball was sparkly, or what shade of purple, and how much pixie dust it contained.

      David Klinghoffer's ID model (not a puff of smoke): "The rest of evolutionary history, of course, similarly weaves together etiological and teleological development, where long periods of mellow stasis are suddenly interrupted by the crash of lightning, precipitating bursts of what appears to be intelligent design. The story of man reveals this pattern of stasis and explosion in a particular dramatic way, laden with emotion and significance that... ” [Diogenes notes: Urk, take a creative writing class Dave.] -- [David Klinghoffer. Casey Luskin Reveals the "Big Bang" of Human Evolution. ENV (blog), June 28, 2012.]

      Barb's ID model, at Uncommon Descent: "Because you [evolutionists] cannot imagine why God allowed such a long span of time (4 billion years, give or take) before organisms appeared, then God obviously doesn’t exist.
      Your entire argument boils down to “I can’t imagine why he’d [God would] do it this way, so he obviously didn’t do it!” How utterly ignorant.
      A magical designer can do whatever he wants given the fact that he is all powerful and all knowing. Unlike you."
      -- [Comment #29 by Barb, Uncommon Descent, June 22, 2013 at 9:16 am]

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    12. I'm not done with Security Clearance yet.

      Joe "Security Clearance" Gallien says: "Diogenes, you ignorant slut... Intelligent design does NOT claim the OoL violates any known laws. Intelligent Design doesn't violate any known laws. Imbecile"

      This is seriously just Security Clearance trolling us by disagreeing with whatever we write.

      Joe, is biogenesis a law, according to anti-evolutionists? If non-living matter became a living cell, would that violate the law of biogenesis? Or is the "law" just a fiction that anti-evolutionists lied about?

      Joe, if non-living matter became a living cell, would that, or would that not, violate Dembski's Law of Conservation of Information?

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    13. Joe Security Clearance writes: What about Lokiarchaeota? Just another candidate for the engulfing organism. And the Lokiarchaeum are just as evolved as any other organism alive today. That doesn't help any scenario which occurred some hundreds of millions of years ago.

      Bullshit, it directly refutes what "Inquirer" wrote above.

      Inquirer stated: "Darwinists neither have the mechanism nor the genes to move beyond the prokaryotes"

      Wrong. Those genes are in lokiarchaeota, which directly refutes Inquirer.

      ID creationists said the genes didn't exist anywhere, that proved God made them by magic. Intelligent Design was a science stopper. No ID proponent would do the research that led to the discovery of lokiarchaeota, so no IDer did that research.

      Some evolutionist did, and disproved a central claim of Intelligent Design, so Security Clearance stupidly tries to dupe his readers into thinking it's no big deal-- "What about Lokiarchaeota? Just another candidate for the engulfing organism"-- Nothing to see here, move along!

      Those genes were pretty darn important, crucial, critical when you IDiots said they didn't exist and were impossible to find. Now we found them, you say not important, trivial, insignificant! With creationists, "the impossible" turns into "the boring" as soon at is discovered, without ever going through an intermediate state of "interesting." Move along people, nothing to see here! Why trivial now, Joe?

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    14. Diogenes the cry-baby loser- your ignorant spewage, while entertaining, just proves that you are an ignoramus.

      lokiarchaeota is a hypothesized phylum. The bacteria they found is of TODAY. That does not help endosymbiosis, moron.

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    15. Joe G:
      "lokiarchaeota is a hypothesized phylum. The bacteria they found is of TODAY. "

      It is my understanding that you have been arguing against evolution for many years. Yet you write things that indicate that you have either never once actually done any non-creationist reading on the subject or that you have an exceptionally poor memory or ability to understand the things you rant against.

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  7. Earth to the scientifically illiterate:

    The design inference is a top-down approach. That means first you determine if intelligent design is present and THEN, and only then, do you ask about the who, how, why, where and when. You don't even ask those questions until you have determined intelligent design is present.

    And, as science haz it, the only possible way to scientifically address those questions is by studying the design and all relevant evidence.

    ID does not prevent anyone from asking or trying to answer those questions. They are just separate from ID and offer ID research programs.

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    1. That means first you determine if intelligent design is present and THEN, and only then, do you ask about the who, how, why, where and when.

      OK, so it has been established, to the IDiots' satisfaction, that life is intelligently designed. Fine. Now you can tell us the who, how, why, where and when.

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    2. OK, so it has been established, to the IDiots' satisfaction

      Great, then you are satisfied.

      Now you can tell us the who, how, why, where and when.

      No. But once ID is the accepted paradigm I am sure people will get right on it.

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    3. Oh. The ACCEPTED PARADIGM.

      It works the other way round, Joe. Research can't wait till you erect a new paradigm; it has be done first, or there will be no new paradigm. The whole ID project is a bunch of amateurs whining on the Internet, plus a few fringe scientists publishing dubious stuff in Potemkin "journals". There's little chance it can ever get off the ground.

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    4. "That means first you determine if intelligent design is present and THEN, and only then, do you ask about the who, how, why, where and when. "

      Actually, all you can actually do is determine if you think human design is present.

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    5. Piotr, You are confused. The research confirms the design inference/ You are a cowardly amateur, piotr. You don't have a viable alternative to ID.

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    6. Joe Security Clearance's standard chatbot reply:

      1. Disagree with whatever you just wrote (even if it means Joe must contradict what he just wrote)

      2. Present no details as to why you're wrong

      3. Present no evidence why you're wrong

      4. Insult, name-calling

      5. He's done

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    7. Joe G sez:
      "The research confirms the design inference/"

      What research? Since you refused to answer my question above about your "scientific" theory, let's try a different approach. The viable alternative to ID/creationism is evolutionary theory, which has decades of peer-reviewed research to support it, while ID has zero. So pick a paper, any paper, out of the journal Evolution, or Journal of Evolutionary Biology, and make your case. Explain how evolutionary theory is wrong, and how the 'design inference/' explains the empirical data in the paper better.

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    8. Just for the record, Joe G, I don't think you will even attempt it. You will obfuscate, change the subject, fling insults, claim victory, anything but address the challenge in an intellectually honest way. You have nothing.

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    9. All research, Chris. The research into ATP synthase is a good example.

      And there isn't any "evolutionary theory". Pick a paper and show us how it supports unguided evolution. Or shut up.

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    10. Thanks for proving my point, Joe G. You still have nothing.

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    11. Joe "I can't tell you what I do for a living unless you get a security clearance" Gallien was asked:

      "The research confirms the design inference" What research?

      And Security Clearance answered

      All research

      I am reminded of the time creationist dumbshit former Governor Sarah Palin was asked "What newspapers do you read?" and she answered

      "All of them"

      Translation: none of them. When Joe is asked "What research supports ID?" And he answers "All research," it means "no research."

      He continues:

      The research into ATP synthase is a good example

      Oh. ATP synthase, the rotary structure of which was figured out by Nobel Prize-winning atheist Paul Boyer. Great guy, I used to say hi to him in the elevator.

      But tell us, Joe "I lost my job because I made threats from my work computer" Gallien, how does the structure of ATP synthase support Intelligent Design?

      How? Does ID theory predict that ATP synthase must have a rotary structure? How does ID predict that? If ATP synthase had a non-rotary structure, would that falsify Intelligent Design?

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  8. The design inference is a top-down approach.

    Yes, that's managed to take astronomy back 500 years to before Newton with its "inference" that gravity can't be enough, it's gotta be Gawd the Creator.

    I prefer my science post-Renaissance, thanks.

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    1. You don't know what science is. What does materialism have, exactly?

      All you have are you bullshit accusations.

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    2. All you have are you bullshit accusations.

      Why no, what I have are the references you yourself cite, such as "Privileged Planet." Speaking of bullshit:

      - "Privileged Planet" says the orbit of Earth is "unusually circular" as part of its argument that the Solar System was intelligently designed perfectly to ensure life and of course people would arise. Actually, the orbit of Earth isn't even the closest to circular in the Solar System. Venus's is.

      - That "circular orbit" thing is actually the weaker form of a prior argument that said if Earth's orbit was even 2% closer to the Sun or further away, life as we know it would not be possible. That one was laughed out of town when it was pointed out Earth's own orbit varies in distance from the Sun during the course of a year by *more than* 2%. So the weaker form of the argument was substituted, but unfortunately that one, as I noted above, is factually incorrect as well.

      - "Privileged Planet," in trying to claim the formation of the Moon is unique, says it was virtually unknown during the early formation of the Solar System, for large planetoids to smash into each other. HAHAHAHAHA!! Go to your local planetarium and check out their animation of the early Solar System. This is so wrong it almost seems like a deliberate lie - oh, wait....

      So yeah, speaking of bullshit....

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    4. Judmarc says: "Privileged Planet," in trying to claim the formation of the Moon is unique, says it was virtually unknown during the early formation of the Solar System, for large planetoids to smash into each other.

      Judmarc, you're so ignorant. It says so right in the Bible: "For God so loved the world that he crashed a Mars-sized planet into it."

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    5. Judmarc: "That "circular orbit" thing is actually the weaker form of a prior argument that said if Earth's orbit was even 2% closer to the Sun or further away, life as we know it would not be possible."

      Do you have a source for that? I know presidential candidate Ben Carson said 1 million miles different and we'd all freeze.

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    6. Jud, Thank you for proving my point.

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    7. Jud, Thank you for proving my point.

      If your point was that Privileged Planet is complete nonsense, you're darn right.

      Delete
  9. The ID creatinists can maintain their whole "ID predicted this..." lie as long as they continue to refuse to do simple literature reviews. Predicting something a decade or more after the subject matter had been discussed openly in the literature is not an actual prediction, but it is what charlatans and liars engage in, knowing that their sycophants will not bother to call them on it, even if they did somehow realize that they were being lied to.

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    1. What does unguided evolution predict?

      Delete
    2. What does IDcreationism predict? Surely not anything to do with junk DNA - their claimed predictions on that issue are a total, documentable lie.

      Delete
  10. Piotr - "fringe scientists publishing dubious stuff"
    Not that dubious. Pretty certain it's bullshit.

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    Replies
    1. I only mean that a few IDiots are real biologists or biochemists with some real research papers to their credit (usually published years ago, before they became professional liars for doctrine). Of course anything published in their "peer-revieved" cargo-cult journals like BIO-Complexity is dubious at the very, very best, and obvious bullshit most of the time.

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    2. Where is the research for unguided evolution? Where is unguided evolution's peer-reviewed support?

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    3. Where is the research for unguided evolution? Where is unguided evolution's peer-reviewed support?

      Right near those big signs at the local college that spell "L-I-B-R-A-R-Y".

      Delete
    4. "Where is the research for unguided evolution? Where is unguided evolution's peer-reviewed support?"

      Wow... So I guess you DO know something that Todd Wood missed.
      But wait a sec -

      https://scholar.google.com/scholar?q=evolutionary+biology&btnG=&hl=en&as_sdt=0%2C5&as_vis=1

      2.2 million returns. Have at it, Security Clearance.

      Where is the peer reviewed support for IDC? The mere handful of circle-jerked 'reviewed' papers available at Bio-Complexity? What a joke.

      Delete
  11. Joe: "The design inference is a top-down approach. That means first you determine if intelligent design is present and THEN, and only then, do you ask about the who, how, why, where and when. You don't even ask those questions until you have determined intelligent design is present."

    But how do you determine if intelligent design is present unless you know how the intelligent designer works? CSI is a non starter. Gordon (KairosFocus) Mullings FIASCO never even got close to the starting gate. What else do you have? Other than profanities?

    ReplyDelete
    Replies
    1. Question is 'Where did acartia tonsa come to the conclusion that organisms mutate without regard for a target when organism actually have a built in target.

      You know the one where when the environment changes, organisms change so that organisms can SURVIVE.

      I wonder how evolution explains organisms penchant for wanting to survive. They are NOT goal oriented. They have NO preference for life or death.

      Yet, there it is. No organism lays dead for the scythe.

      Evolution simply HAS to believe organisms SOMEHOW acquired an ID like design object of WANTING something, NEEDING something,

      Its curious that organism simply dont get slammed by the tidal wave, and wash up in pieces all over the place.

      Organism instead brush off the water, chuckle and say....hey that was FUN!! Lets do that again....while we CAN!!!!

      How is that Acartia???????????

      Delete
  12. "You know the one where when the environment changes, organisms change so that organisms can SURVIVE."
    False: Organisms don't change so the can survive. You cannot see the future and choose the mutations that will be handy for the next generation. That's plain silly! Change the environment and you get mass extinctions where only a few with the correct mutations survive.
    "Its curious that organism simply don’t get slammed by the tidal wave, and wash up in pieces all over the place."
    In a manner of speaking that's exactly what happened. 98% of species that existed on earth are now extinct. Change the environment and you get mass extinctions where only a few species survive.

    ReplyDelete
  13. I hesitate to argue with a real biochemist about his specialty, but I have to wonder: do "most knowledgeable scientists" really "believe" that "our genome" will "actually turn[...] out to be full of junk"?

    Perhaps it's a matter of what you mean by "junk"? Stuff that was once useful but now isn't? So perhaps all those long strings of random (if they are) DNA might have had a use during our species' evolution, but now that we're here, they aren't useful?

    I'm well aware that closely related species have been found where one had large amounts of "junk" DNA and the other didn't. But we're looking at a snapshot of evolution. How can you (or anyone) be sure that the one with all that extra DNA doesn't have much greater potential for evolution of some sort? Perhaps by offering a much greater target for acquisition by lateral gene transfer (without damage to existing useful structures)? Just to name one I can think of. And don't forget that that "junk" could easily have functions nobody's thought of.

    Evidently most of the genome is actually transcribed into RNA:

    http://www.nature.com/nrg/journal/v10/n3/full/nrg2521.html

    http://iris.nyit.edu/~apetro01/old-postings-Fall-2011/Week-11/W11-C1/non-coding-RNA.pdf

    http://genesdev.cshlp.org/content/23/13/1494.long

    There are many known functions performed by parts of this "junk", of which sequences almost certainly remain to be discovered:

    Transcription Factor (TF) binding sites,

    Ribozymes,

    snRNA,

    Attachment points for packaging proteins,

    Targets for DNA editing processes,

    And many others which you could probably name more easily than I.

    For me, an important hint from the fact that most of the sequence is transcribed involves the tertiary structure of the resulting transcript, and the potential editing processes it may participate in.

    Much of the "junk" could well make sense in terms of tertiary structure, including simply empty space: a stretch of so many bases, regardless of type, participates in creating a specific tertiary structure.

    The same goes for DNA: empty space between TF binding sites can be very important in controlling their activity, regardless of sequence. Or perhaps I should say almost regardless, since the presence certain sequences can have major influences. Even the length can potentially have only a small, fractional effect within certain limits.

    But that empty space, in addition to participating in the calculations that drive transcription initiation, can also store (or not) potential mutations: sequences that, while not active in themselves, can by a single point mutation become active, changing the behavior of the gene(s) controlled, with downstream changes to cell behavior, including development and neural behavior in post-infancy. And thus organism behavior.

    The last-mentioned might not matter to a species that evolves as a bunch of mostly separated individuals. But there's good evidence that human ancestry involves social mammals going back at least to the Cretaceous, and I see no reason to rule out effectively continuous sociality (in the evolutionary stem populations) all the way back to the origins of the chordates.

    And the presence of potential individuals with a certain mutation could easily provide an adaptive advantage for its local population, even if said mutation is lethal to the individual itself.

    All of the above, of course, is probably better known to you than to me. It does seem to add up to a lot of potential functions for all that "junk DNA", considering the present, the past, and the potential future development and evolution.

    In view of it, I'm surprised that you seem to be saying that "most knowledgeable scientists" "believe" that "our genome" will "actually turn[...] out to be full of junk".

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    Replies
    1. I hesitate to argue with a real biochemist about his specialty, but I have to wonder: do "most knowledgeable scientists" really "believe" that "our genome" will "actually turn[...] out to be full of junk"?

      Yes.

      Some of the potential functions you mention are not selectable ("future evolutionary promise"), some are just noise (transcription) while others involve only a teensy portion of the genome. Nothing says that most of the genome isn't junk.

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    2. "Future evolutionary promise" most certainly is selectable. Past lineages that lacked it didn't evolve. Or, potentially, not as well. Past lineages that had a particularly good version of it have a very good chance to be more highly represented in future successful lineages.

      I know, the whole issue of "evolvability" as as an adaptation is a matter of controversy. I'm not sure what logic opponents of the idea have in their defense, if any.

      And the dismissal of whole genome transcription as “just noise” strikes me as argument from incredulity. True, the fact that most of the sequence is transcribed hardly "proves" the transcription performs any useful function, in the sense of contributing to survival, reproducibility, or future evolutionary potential.

      But it does mean that if we ask how such supposed "junk DNA" might actually perform a useful function, we don't have to wonder how it gets transcribed. And once present as RNA, it will form the appropriate tertiary structure, given the environment, with who knows what results.

      Nothing says that most of the genome isn't junk.”

      Well, nothing says that it is. I'm sort of surprised that so many "scientists" would confuse absence of evidence (of useful function) with evidence of absence.

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    3. "And the dismissal of whole genome transcription as “just noise” strikes me as argument from incredulity. True, the fact that most of the sequence is transcribed hardly "proves" the transcription performs any useful function, in the sense of contributing to survival, reproducibility, or future evolutionary potential."

      It is not an argument from incredulity. It is backed up by what we know of the poor fidelity in RNA-Pol specificity for true initiation sites. Please read http://www.nature.com/nsmb/journal/v14/n2/full/nsmb0207-103.html

      Delete
    4. Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes by Alastair Crisp, Chiara Boschetti, Malcolm Perry, Alan Tunnacliffe, and Gos Micklem Genome Biology 2015, 16:50 13 March 2015 Open Access

      Background
      A fundamental concept in biology is that heritable material, DNA, is passed from parent to offspring, a process called vertical gene transfer. An alternative mechanism of gene acquisition is through horizontal gene transfer (HGT), which involves movement of genetic material between different species. HGT is well-known in single-celled organisms such as bacteria, but its existence in higher organisms, including animals, is less well established, and is controversial in humans.

      Results
      We have taken advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies and four nematodes) and a simplified analysis in a further 14 vertebrates. Genome-wide comparative and phylogenetic analyses show that HGT in animals typically gives rise to tens or hundreds of active ‘foreign’ genes, largely concerned with metabolism. Our analyses suggest that while fruit flies and nematodes have continued to acquire foreign genes throughout their evolution, humans and other primates have gained relatively few since their common ancestor. We also resolve the controversy surrounding previous evidence of HGT in humans and provide at least 33 new examples of horizontally acquired genes.

      Conclusions
      We argue that HGT has occurred, and continues to occur, on a previously unsuspected scale in metazoans and is likely to have contributed to biochemical diversification during animal evolution.

      Why is this important? Well, the argument that "junk DNA" protects the effective DNA by offering an alternative target for damage is absurd. But the same argument becomes effective when we're talking about something with the potential to be a highly adaptive (but very low probability) mutation.

      Inserting a gene through horizontal transfer such that it lands in the middle of an existing gene (or even in its cis-regulatory area) would have a high probability of being mal-adaptive. But the more "junk" there is, the higher the chance the horizontal transfer would land in a harmless position.

      The paper linked above suggests that early in chordate evolution a number of highly beneficial mutations of this sort occurred:

      In the human we find genes in five of the six categories: amino-acid metabolism (two genes), macromolecule modification (15 genes), lipid metabolism (13 genes), antioxidant activities (five genes) and innate immune response (seven genes).

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    5. It is not an argument from incredulity. It is backed up by what we know of the poor fidelity in RNA-Pol specificity for true initiation sites. Please read http://www.nature.com/nsmb/journal/v14/n2/full/nsmb0207-103.html

      Response 1: It doesn't matter how (functionally) it happens, only that it does, and since it does new adaptive functionality using it can arise through mutation.

      Response 2: See Long noncoding RNAs: functional surprises from the RNA world by Jeremy E. Wilusz, Hongjae Sunwoo and David L. Spector Genes & Dev. 2009. 23: 1494-1504 Open Access (AFAIK)

      Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional “noise” as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell.” [my bold]

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    6. AK: How can you (or anyone) be sure that the one with all that extra DNA doesn't have much greater potential for evolution of some sort?

      Please show how extra DNA correlates with "greater potential for evolution". Saurischian dinosaurs reduced their DNA content considerably in comparison with mammals. Their modern descendants (still with a small genome) are a few thousand highly diverse species of birds. True, an asteroid impact did for their bigger cousins, but you can hardly blame their DNA for that. Sauropods and theropods were rather successful in their time.

      Among mammals, the group with the smallest genomes are bats, the second largest mammalian order (with ca. 20% of all mammal species). Their evolution is a success story. The vertebrates with the largest genomes are lungfishes. Would you say that their evolutionary potential is proportional to the extra DNA they have?

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    7. Neither response is actually a response to my point. Transcription initiation is sloppy. So in any large piece of DNA there is a probability that all non-target DNA could be transcribed at any timepoint. These are just errors

      Your reply 1 would make some sense if you were discussing mutations leading to a higher probability of transcription. But a transient event in a cell will not be heritable, nor selectable, as it may not happen again.

      And reply 2 - even if all 10,000 of the human lnrRNAs observed have a function, you are still only accounting for a tiny piece of the non-mRNA/tRNA/rRNA transcripts being discussed. Not actually a point relevant to the topic at hand.

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    8. Piotr, interesting tidbits about mammal genomes!

      Delete
    9. @Piotr Gąsiorowski...

      Please show how extra DNA correlates with "greater potential for evolution".

      I thought I did, above. Adding "safe" targets for HGT adds potential for evolution through increased potential for low-probability, high-value mutations. Such as (especially) “lipid metabolism (13 genes), antioxidant activities (five genes) and innate immune response (seven genes).

      These genes were added (probably) early in the chordate lineage, and almost certainly contributed to that clade's success.

      Delete
    10. @TheOtherJim...

      Transcription initiation is sloppy.

      Actually, that's not what your reference says.

      In principle, evolutionary conservation is a useful criterion, as by definition, conservation is a measure of some kind of biological function. As a group, noncoding RNAs in mammalian cells are more conserved than expected by chance. However, this indicates only that some noncoding RNAs are biologically meaningful, and it leaves open the possibility that others (perhaps even the majority) of noncoding RNAs are transcriptional noise. Conversely, there might be little evolutionary conservation if the true biological function associated with an RNA is not the product itself but rather the act of transcription (and associated chromatin modifications), or if the RNA is the byproduct of a nearby enhancer that controls distal genes. Thus, the absence of evolutionary conservation is not a reliable indicator of transcriptional noise. Lastly, it would be useful to have an experimental measurement of transcriptional noise that is not confounded by the possibility that the observed RNAs are biologically significant. By definition, transcription (and protein binding) from evolutionarily unrelated DNA is noise, so analysis of cells containing large regions of evolutionarily unrelated DNA (for example, Escherichia coli DNA in human cells) will be of interest.

      Basically, he's speculating:

      I suggest that ~90% of Pol II initiation events in yeast represent transcriptional noise, and that the specificity of initiation is comparable to that of DNA-binding proteins and other biological processes.

      Speculating based on incredulity is hardly "proof". It's barely a theory.

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    11. @Piotr Gąsiorowski...

      The vertebrates with the largest genomes are lungfishes. Would you say that their evolutionary potential is proportional to the extra DNA they have?

      I'd guess that they've changed little in that regard since their common ancestor with land vertebrates. Which may well also have had such large genomes.

      And yes, I'd say they have a strong potential to acquire HGT mutations.

      But you can't assume that a mechanism that's adaptive towards evolvability will always work to benefit every possessor. Suppose the mechanism was there during the Cambrian, and effectively all metazoan lineages that prospered from there had it. Then some sort of genome-expanding process might kick off in an occasional lineage, and sometimes that lineage might acquire a highly adaptive mutation via HGT, and in turn kick off a major radiative event. It wouldn't matter if in 99% of the lineages whose genome expanded it was mildly non-adaptive (or even strongly so, since their unaffected cousins could carry on) as long as all the major clades a few hundred megayears on are descended from the successful 1%.

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    12. This comment has been removed by the author.

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    13. AK: But you can't assume that a mechanism that's adaptive towards evolvability will always work to benefit every possessor.

      That's why I ask you to show that there's a significant correlation between "extra DNA" content and (some measure of) evolvability. It doesn't have to work in every case, but at least it should work often enough to be demonstrable. To suggest a potential scenario is one thing; to show that such a scenario is realistic is another.

      Delete
    14. @Piotr Gąsiorowski...

      That's why I ask you to show that there's a significant correlation between "extra DNA" content and (some measure of) evolvability.

      The measure I'm using is the probability that a random HGT event (in the germ line,since otherwise it wouldn't matter) will have a chance to test its adaptive potential in its new home, because it hasn't "broken" something already valuable to the cell.

      The fact that such HGT events have occurred, presumably with some significant value to the new lineage, would seem to at least suggest that an improved chance of success would correlate to an improved evolutionary potential.

      It would seem intuitively obvious that the larger the fraction of DNA that could be targeted without significant loss of fitness, the greater the chance of a successful HGT event.

      I'm not trying to prove an adaptive value, just demonstrate that the assumption that there is none is unwarranted.

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    15. Such events are extremely rare in most animal lineages. For example, among the human genes attributable to HGT, the vast majority were acquired at some time between the common ancestor of Chordata and the common ancestor of Primates; only a few are more recent (some time in the last 60 million years). What force would maintain loads of junk DNA waiting for a "successful HGT event" -- something that seems to happen once per, say, 20 million years on the average (that is, per one or two million generations)?

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    16. What force would maintain loads of junk DNA waiting for a 'successful HGT event'

      That sounds like an argument from incredulity to me. The "force" need be nothing but a difficulty in getting rid of it while preserving all the useful stuff scattered through it. Do you have a study of average length and frequency of deletion mutations in "junk DNA" that can be compared to the distribution of distances between even known useful bits?

      And don't forget you can't include introns. If nothing else, they offer an increased number of sites for recombination among different versions of proteins, by functional sub-unit, without hybridizing the sub-units themselves.

      I can certainly think of ways that non-functional copies of genes can contribute to the general evolution in the population, even over short time-frames (via recombination). So it's possible (not proven of course) that the difficulty in removing "junk DNA" would be increased by the mal-adaptive effects of removing such copies.

      And I'd certainly speculate (but no more) that the innovative chromosome structure peculiar to birds (AFAIK) may have had something to do with their much more compact genome.

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    17. @AK

      Stick random DNA into a cell, and you will see transcription where you expect none.

      http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043283

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    18. @TheOtherJim...

      Well, in the case of natural HGT mutations, inappropriate transcription would be selected against. But the article you linked is talking about problems with repeatability in experiments sticking pre-packaged DNA in random locations. Among other things.

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    19. No - I'm pointing to their data showing that inserting random sequence into a genomes 1) leads to weird RNA 2) which are not catastrophic to the cell, as a hyper-selection model that you seem to be inferring would require.

      My first problem with your assertion - what sort of selection coefficients would rare, transient, spurious transcription place on an organism? To ensure all of the billions of bases fail to mimic 6-10bp recognition sites, you are going to come up with evidence for massive effects.

      A second problem - we work with mouse random-BAC transgenesis. Assuming this RNA machine is so finely tuned, how can we stick these enormous gene constructs (which would locally mess with transcription by virtue of their own promoters and enhancers) at random into the mouse genome, and get viable mice indistinguishable from wildtype? You would expect in a highly tuned transcriptional background there would be relatively few sites available for insertion, but they go all over the place. Why is it that when we study the expression from these constructs, they seem to just plug into the genome and behave precisely as predicted by boring, old pre-ENCODE understanding of transcription? And conversely how the the megabase deletion mouse survive the deletion of these sections? And why is all of this so much harder in a junk-light organism like Drosophila? If all the the extra DNA was functional and so finely tuned, should we not have similar difficulties in inserting DNA into a mouse?

      And third - pseudogenes of mitochondrial DNA are constantly dumping DNA fragments into the nuclear DNA (http://nar.oxfordjournals.org/content/early/2014/10/27/nar.gku1038.full.pdf). How are these fragments not messing with this supposed tightly regulated transcription machine? Again - if you are going to assume "must be selected against", I'm going to need some selection coefficients, or evidence of inter-individual effects to explain how this is occurring at such a rate, yet should be so harmful in your model.

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    20. @TheOtherJim...

      First, I'm not suggesting a “hyper-selection model”, to the contrary, I'm assuming that much of the genome is open to insertion of otherwise harmless chunks of DNA. Some (probably small) fraction of possible insertion points would result in inappropriate transcription, for instance at high levels along with pre-existing genes. These would be selected against when they occurred, although I would expect the level of down-selection to vary from near-zero to fairly extreme.

      Assuming this RNA machine is so finely tuned, how can we stick these enormous gene constructs (which would locally mess with transcription by virtue of their own promoters and enhancers) at random into the mouse genome, and get viable mice indistinguishable from wildtype? You would expect in a highly tuned transcriptional background there would be relatively few sites available for insertion, but they go all over the place.

      I'm not sure where the communication breakdown occurred here, but what I'm suggesting is that much of the supposed "junk DNA" may actually perform a "useful" function. Probably not as "useful" as promoter and TF logic, or protein coding, and perhaps more "useful" for population-level functions such as helping to maintain genetic diversity.

      What I'm not suggesting is a “tightly regulated transcription machine”, that is either vulnerable to interference at most points, or capable of detecting an insertion at any but specially available points. Trans-acting functions at many, perhaps most, points would likely be unaffected by insertions anywhere outside their own limited sphere of activation.

      While I've done considerable reading on the subject, I would describe it as sparse and scattershot at best compared to what's available. For all that, what I perceive is a growing recognition of substantial redundancy in the genome and its associated developmental control logic, which contributes to substantial redundancy. Or, more recently:

      To date, deletion of most individual miRNAs in mice failed to cause an obvious defect; however, important phenotypes often emerge when compound miRNA knockout mice are generated, thereby partially or completely removing the redundancy in the mouse genome (Tables 1 and ​and2).2). These findings suggest that mammals are generally resistant to moderate perturbation of individual miRNA expression. The unique gene structures, genomic organization and expression regulation of miRNAs all contribute to the molecular basis for their functional robustness, thus careful experimental strategies are required to elucidate their biological significance. Here, we will discuss how genomic redundancy, polycistronic gene structure and expression regulation all contribute to the unusual functional robustness of some miRNAs.

      My point (part of it) is that just because a small region of DNA can be knocked out without “an obvious defect” doesn't mean it's "junk". The redundancy it provides is "useful", at the population genome level if not the individual.

      Delete
    21. I may have read too much into your comment "inappropriate transcription would be selected against.", then. I'll end it here, then.

      And to save the blog from clutter, I'll resist commenting on the evolutionary problem with "redundancy". Another hotly discussed topic. ;-)

      Delete
  14. AK, Several points.

    1. Various useful bits of DNA you listed (e.g.attachment points for proteins) are useful and therefore are NOT junk DNA.

    2. In any given type of cell, certain genes are transcribed at high rates, others a somewhat lower rates, and then any other parts of the DNA may get transcribed at a rate of one copy or less per cell. Among the thousands and thousands of RNA's and proteins in the cell, that one copy isn't going to have an effect, even if it can do something before it is broken down and recycled.

    3. It looks like 44% of the human genome consists of transposons and their mutated remains. Another 8% consists of mutated viruses. Other sequences are mutated, useless, former protein-coding genes. In other words, we know what much of the junk DNA is, and it's not useful to us humans. Our calling it "junk" does not indicate a lack of knowledge about what it is.

    4. Natural selection is a near-sighted process. If individuals with certain genes reproduce more than others with different alternatives, the frequency of those genes increase in the very next generation. If a particular stretch of DNA would be beneficial 500 generations from now, it will nonetheless mutate and change and perhaps even be lost for the next 499 generations.

    5. Populations evolve mainly through changes in their useful DNA (protein-coding, RNA-coding, regulatory, or structural DNA). Organisms don't need to carry around all that junk DNA in order to be able to evolve in the future. True, occasional new pathways open up if a bit of junk DNA mutates in such a way that it produces a useful product or performs some other useful process, but such events are very few.

    6. Some organisms (e.g. fugu and bladderworts) have minimal junk DNA and they seem to be living and even evolving just fine.

    So, biologists who argue that most of the human genome aren't doing so from ignorance. Exactly how much of our genome is junk? People who understand the issue argue about it. However, reasonable hypotheses are in the range from "a lot" to "a whole big lot."

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    Replies
    1. @bwilson295... (part 1)

      2. In any given type of cell, certain genes are transcribed at high rates, others a somewhat lower rates, and then any other parts of the DNA may get transcribed at a rate of one copy or less per cell. Among the thousands and thousands of RNA's and proteins in the cell, that one copy isn't going to have an effect, even if it can do something before it is broken down and recycled.

      Just because it isn't transcribed doesn't mean it isn't useful:

      Noncoding RNAs and the borders
      of heterochromatin
      by Allison L. Cohen and Songtao Jia WIREs RNA 2014. doi: 10.1002/wrna.1249

      Eukaryotic genomes contain long stretches of repetitive DNA sequences,which are the preferred sites for the assembly of heterochromatin structures. The formation of heterochromatin results in highly condensed chromosomal domains that limit the accessibility ofDNA to the transcription and recombination machinery to maintain genome stability. Heterochromatin has the tendency to spread, and the formation of boundaries that block heterochromatin spreading is required to maintain stable gene expression patterns. Recent work has suggested that noncoding RNAs (ncRNAs) are involved in regulating boundary formation in addition to their well-established roles in chromatin regulation. Here, we present a review of our current understanding of the involvement of ncRNA at the boundaries of heterochromatin, highlighting their mechanisms of action in different settings.

      This cite suggests (to me, anyway) that in some circumstances, perhaps many, it's simply the length that matters, or perhaps the number of repeats of a certain sequence. Adding a repeat might have a small effect, adding another might have a slightly larger, and so on. So the rapid addition of a few hundred repeats might have the effect of turning one small knob in a complex analog computer. If it provided a minor adaptive advantage, it could easily be worth the slightly increased cost of maintaining that larger genome.

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    2. @bwilson295... (part 2)

      3. It looks like 44% of the human genome consists of transposons and their mutated remains. Another 8% consists of mutated viruses. Other sequences are mutated, useless, former protein-coding genes. In other words, we know what much of the junk DNA is, and it's not useful to us humans. Our calling it "junk" does not indicate a lack of knowledge about what it is.

      Well, I won't dispute that, depending on your definition of "junk". But if it's left over from a process that is, or has been, adaptive during previous evolution, it's only "useless" in a narrow sense. That is, its presence may be part of the cost of some other process that is, or was in the past, adaptive.

      5. Populations evolve mainly through changes in their useful DNA (protein-coding, RNA-coding, regulatory, or structural DNA). Organisms don't need to carry around all that junk DNA in order to be able to evolve in the future. True, occasional new pathways open up if a bit of junk DNA mutates in such a way that it produces a useful product or performs some other useful process, but such events are very few.

      Just because they're few doesn't mean they can't have value according to their rarity. See the Crisp, Boschetti et al. paper referenced above. The chordate lineage gained a number of genes through HGT that might well have made a critical contribution to their success.

      Exactly how much of our genome is junk? People who understand the issue argue about it. However, reasonable hypotheses are in the range from "a lot" to "a whole big lot."

      Fair enough. But my question had to do with the statement:

      We need to preserve these comments for posterity just in case our genome actually turns out to be full of junk as most knowledgeable scientists believe.” [my bold]

      Making “full of junk” a favored hypothesis is one thing, such a strong theory as to warrant "belief" is another.

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    3. AK, you need to go back and read Larry's previous posts about junk DNA, especially the arguments that tell us it's junk: mutational load, lack of sequence conservation, c value paradox (the onion test). Did I forget any?

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    4. @John Harshman...

      I've been reading the primary literature on that subject for years. Along with studies of the mechanisms of DNA "repair" and other types of recombination. As a result I'm very skeptical of arguments about "junk DNA".

      Of course, there's a semantic quibble. "Junk" could be taken to mean stuff that you don't need right now, but (in a community sense) might be good for something somewhere/somewhen else. But in that case, the analogy sort of falls apart, because how it's interpreted depends on the precise meaning of "junk".

      "Junk" isn't a scientific term, in the sense of having a precise, well-defined meaning that can be fed into rigorous models. Perhaps it shouldn't be used in science.

      And as for “mutational load, lack of sequence conservation, c value paradox (the onion test)”, AFAIK I've addressed all these in comments above.

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    5. bwilson295; Saturday, June 06, 2015 5:09:00 PM:

      "It looks like 44% of the human genome consists of transposons and their mutated remains. Another 8% consists of mutated viruses. Other sequences are mutated, useless, former protein-coding genes. In other words, we know what much of the junk DNA is, and it's not useful to us humans. Our calling it "junk" does not indicate a lack of knowledge about what it is.

      I agree with some of your points. However, as you probably know, some of us here at Sandwalk have presented alternative views, pointing to the possibility that the so called 'junk DNA' (all of it) serves essential non-information functions, such as protection against insertion mutagenesis by endogenous and exogenous DNA viral elements, particularly in the somatic tissues. Please read my recent brief paper discussing this theory, which is available for free at: http://biorxiv.org/content/early/2013/11/18/000588

      If you have any questions, I'll be happy to address them.

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    6. Claudiu, I have read all your Sandwalk comments about junk DNA as protection against transposons and viruses. I personally doubt that such a role is consistent with the great amount of apparently junk DNA observed in some genomes (that's expensive protection!) or the tremendous variation in DNA content among species. However, I personally cannot rule this hypothesis out. It's in my "probably not but maybe possible" category.

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    7. @bwilson295...

      “[...] the great amount of apparently junk DNA observed in some genomes (that's expensive protection!) [...]

      Is it. My understanding was that the actual metabolic expense of that extra DNA was pretty small. Certainly, some hard numbers would be useful. Do you have a study, or do I have to play with Google?

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    8. @Claudiu Bandea...

      I've only started reading your paper, but I have to comment about this:

      However, Graur et al. limit their evaluation of genomic DNA’s biological functions to its informational roles (iDNA), which are based on sequence specificity. Although the authors recognize, apparently as an afterthought, that: “It has been pointed to us that...some parts of the genome may be functional but not under constraint with respect to nucleotide composition”, they sidestep the significance of non-informational roles for DNA (niDNA).

      I'm not sure where you are WRT the issue of “sequence specificity”, but even in coding DNA it's not an absolute. Roughly 1/3 of the bases in any ORF are open to 2-4 bases without changing the target protein, although they may well impact the tertiary structure of the transcribed DNA. But I suspect the latter impact is much smaller, an analog decimal point compared to the sequence dependency of the amino acid units.

      Which latter themselves aren't completely obligatory. In many proteins, only a small subset of the residues are actually required to be unique. For many others, especially in signalling parts of the protein sequence, only their hydrophobicity matters.

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    9. Barbara,

      Thanks for reading my comments. It would be better, though, to read to paper, which offers a more complete story; it is a relatively short, straightforward and enjoyable to read, I heard -:)

      Regarding your concern about the protective mechanism being rather "expensive", as mentioned by AK the metabolic expense on jDNA are small compare to other metabolic expenses in organisms with high C-value, such as in humans and onions [hint, hint; -:)].

      However, I think you will agree with me that jDNA is "expensive" whether it has, or it doesn't have a biological function, anyway.

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    10. @ AK,

      You are absolutely right.

      In my paper, I use the terms 'sequence specificity' and "informational DNA" in the way they are usually understood in the field of genetics and evolutionary biology: sequences that are under evolutionary constrains.

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    11. Sorry, Claudiu, but this is my busy season. Sandwalk is about as far outside necessary reading as I go right now.

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    12. No problem Barbara, but until you find the time to read the paper, you might want to reflect on the following evidence supporting my theory (see: http://biorxiv.org/content/early/2013/11/18/000588):

      "One of the most bizarre, but highly intriguing genome defense systems against invading inserting elements is found in ciliates, a highly diverse group of protozoans [29]. These organisms have two genomes: a germ-line, diploid genome, which is transcriptionally silent and carries tens of thousands of mobile elements, and a transcriptionally active polyploid genome, which originates from the germ-line genome by programmed DNA rearrangement and elimination of mobile elements. In some groups of ciliates, such as Oxytricha, over 90% of the germ-line genome is composed of jDNA, which is eliminated during the programmed DNA deletion. Apparently, in these single-cell organisms, maintaining the jDNA as a defense system against insertional mutagenesis in the germ-line genome was under very strong positive selection."

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    13. Meanwhile, contemplate the fugu and the bladderworts, organisms that virtually lack junk DNA and yet seem to do well in their own ecological niches.

      Hmm. The Oxytricha genome undergoes serious rearrangement each time the cells undergo their version of sex. The bladderwort genome seems to have undergone serious rearrangement during its evolutionary history. Maybe junk-free genomes are more efficient, but getting rid of the junk is difficult and involves massive shuffling (and loss) of DNA?

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    14. Apparently, in these single-cell organisms, maintaining the jDNA as a defense system against insertional mutagenesis in the germ-line genome was under very strong positive selection."

      Or, having a genome editing mechanism renders the germ-line genome susceptible to massive invasion by mobile elements, which suffer less selection-against in such an environment.

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    15. Barbara,

      In a previous comment you raised the point about the putative "energetic costs" of protective DNA; "...I personally doubt that such a role is consistent with the great amount of apparently junk DNA observed in some genomes (that's expensive protection!) or the tremendous variation in DNA content among species". Part of my response was that: "I think you will agree with me that jDNA is "expensive" whether it has, or it doesn't have a biological function, anyway."

      Do you agree that the so called jDNA is "expensive" whether it has, or it doesn't have a biological function, and therefore the argument is mute?

      Barbara: "Meanwhile, contemplate the fugu and the bladderworts, organisms that virtually lack junk DNA and yet seem to do well in their own ecological niches".

      Indeed, some species have adapted to their specific ecological niches (which include putative inserting elements, such as retroviruses), by adjusting to amount of jDNA, which I prefer to refer to as 'symbiotic DNA' (sDNA).

      For example, as pointed out in my paper (see Supplementary material) there is strong evidence that in humming birds, there is a strong selection pressure on the genome size based on metabolic costs. Possibly, there is a similar situation in some species of carnivorous plants. Alternatively, some of the species with low C-value have evolved other mechanisms for suppressing insertion elements, or just happen that there are not susceptible to the inserting elements in their particular ecological niche.

      A good example of this situation, also presented in the paper (BTW, this is why it would make sense to read the paper), is the evolution of genome size in algal endosymbionts found in cryptophytes and chlorarachniophytes.

      "Perhaps one of the most revealing examples of genome size evolution is found in cryptophytes and chlorarachniophytes, which contain 4 evolutionary distinct genomes [26]. The algal endosymbionts of these species have a small nucleus (called nucleomorph) with a genome ranging from ~330 to 1,030 kilobase pairs, which is within the range of viral genomes. Compared to their ancestors, the genomes of these endosymbiotic algae have been reduced more than 200 fold. Remarkably, the number of their introns and their size have undergone drastic reductions, culminating with elimination of all introns and most, but not all, components of the spliceosomal machinery in at least in one species, H. andersenii [27]. The evolution of these remarkable endosymbiotic algae support the notion that deletion mutagenesis and the selection forces for eliminating jDNA, including introns, can be highly efficient in eukaryal genomes. In the context of the model discussed here, it is important to emphasize that, unlike the genome of their free living ancestors or that of most other eukaryotic cells, the genome of these endosymbionts is separated from host cytoplasm by several membranes (the nuclear envelope and the cellular and phagosomal membranes [26]), which constitute an effective ‘physical’ barrier and defensive system against exogenous inserting viral elements [18]. In the absence of newly introduced viral elements, the selective pressure associated with insertional mutagenesis had diminished, which led to the elimination of introns and of most jDNA, which are no longer needed as protective mechanisms"

      As concluded in the paper, the evolution of genome size is obviously a complex multi-factorial process:

      "As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size."

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    16. Allan Miller; Sunday, June 07, 2015 9:55:00 AM:

      ""Apparently, in these single-cell organisms, maintaining the jDNA as a defense system against insertional mutagenesis in the germ-line genome was under very strong positive selection."

      Or, having a genome editing mechanism renders the germ-line genome susceptible to massive invasion by mobile elements, which suffer less selection-against in such an environment."


      I think your making a highly relevant point, but can you please elaborate so I can better understand what you mean?

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  15. @Claudiu Bandea...

    The algal endosymbionts of these species have a small nucleus (called nucleomorph) with a genome ranging from ~330 to 1,030 kilobase pairs, which is within the range of viral genomes.

    These “algal endosymbionts” are more commonly referred to as former algal endosymbionts, AFAIK.

    In the context of the model discussed here, it is important to emphasize that, unlike the genome of their free living ancestors or that of most other eukaryotic cells, the genome of these endosymbionts is separated from host cytoplasm by several membranes (the nuclear envelope and the cellular and phagosomal membranes [26]), which constitute an effective ‘physical’ barrier and defensive system against exogenous inserting viral elements [18].

    In the context of an alternative explanation, AFAIK there is no sign that these former endosymbionts engage in sexual reproduction, with its attendant recombination. Thus a great advantage accruing to free-living relatives is lost: the ability for long stretches of non-coding intron to provide sites for recombination between functional protein units, while reducing the chance of recombination within them.

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    1. Hi AK,

      I have no problem in refereeing to “algal endosymbionts” as "former algal endosymbionts", and I agree with your point about 'sexual reproduction/recombination.'

      I also agree with your points about sDNA providing protection against deleterious indels associated with sexual recombination, as well as with the critical role of sDNA in increasing "genome fluidity" and providing mechanisms and material for enhanced "evolvability", which are consistent with my theory on the evolution of genome size and genome functionality in species with relatively high C-value, such as humans.

      BTW, how is the reading going?

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    2. Finished it last night. Still thinking about it.

      Specifically, the possibility that "junk" portions of viral or bacterial genomes might serve as attraction points for insertion of mobile elements. The cellular machinery involved in producing deletion mutations (assuming they're not simply random) would have no way of recognizing such an attraction point, so the overall level (of deletion mutations) would optimally be reduced until the benefit of reducing the genome size (small, AFAIK) balances the loss of potential attraction points.

      But this brings up another issue, closer to my interest: an attraction point for mobile elements, with signal points close together on each side, might serve as a "honeypot" trap for mobile elements: when such an element inserts itself, the signal points are much farther apart, and some DNA editing machinery could then respond by cutting out the whole section of DNA between the signal points.

      Such a mechanism would, IMO, be unlikely to be discovered unless/until somebody went actively looking for it. So it's conceivable that such things exist, waiting to be found.

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    3. Thanks for reading the paper.

      In regard to 'attraction points' for the insertion of mobile elements, as you know, they are the dominant protective mechanism against insertion mutagenesis in organisms, such as bacteria, that can't 'afford' large quantities of protective, symbiotic DNA (sDNA). However, as emphasized in the paper, even the organisms with elevated amount of sDNA might have enhanced protective mechanisms in form of preferred integration sites, whether based on sequence specificity, such as is the case with the site specific integration of chromoviruses, or based chromosomal 'architectural feature' (e.g. heterochromatin vs euchromatin). However, overall, the integration of viral elements in these genomes occur more or less random, which explains the presence of large quantities of sDNA, both in the intergenic and intragenic space.

      As also emphasized in the paper, there is strong evidence that the spliceosomes and the introns have evolved as a protective mechanism against insertion mutagenesis, just as proposed in my theory.


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    4. Mechanisms that insert (or allow insertion of) bacterial genome fragments into eukaryotic DNA can't "know" which points in the inserted fragment (if any) are useful attraction points. But they can allow the insertion, and if it contains such an attraction point, it will be positively selected.

      But once it's there, with an actual working attraction point, I suspect the cost of the rest of the added "junk" DNA would be small compared to the cost of losing the attraction point.

      So, within certain limits, and subject to many conditions that will (would) have to be researched, incorporation and retention of "random" fragments of bacterial genome might well be adaptive.

      When it comes to spliceosomes and introns, I'm much more skeptical. I see the whole intron thing as a very ancient adaption for evolution through recombination.

      Of course, I'm extremely skeptical of all the popular models that purport to explain how the three existing "empires" of life came to be. I have a number of alternative scenarios in mind, many of which seem much more plausible to me than the popular ones about bacterioforms first. But that's pretty much off topic here.

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