Wednesday, April 03, 2013

Understanding the ENCODE Results

Josh Witten of The Finch and the Pea participated in a video discussion about the ENCODE results [see Decoding ENCODE]. The hosts are Rajini Rao, Buddhini Samarasinghe and Scott Lewis. The other guest is Ian Bosdet. The goal is to explain the controversy over ENCODE in a way that the general public can understand.

Post a comment and let me know what you think. Do you understand the issues after watching the video?



43 comments :

  1. I think it's quite a good discussion. Not sure why Scott Lewis was involved, but those with genomics/biology background had some insightful comments.

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    1. As a member of the general public it seemed to me that Scott Lewis was there to play the Everyman, to help keep the dialogue at a level that the general public could understand.

      I have to say that I did not find his use of metaphor and allusion very helpful.

      I thought Josh Witten struck the right balance of not dumbing down the information to the point where it was pablum but still somewhat comprehensible to folk like me.

      The distinction between biochemical activity and function was a good one and if I understood the conversation correctly, the mandate of the ENCODE project was to map out biochemical activity and the experimental protocols used did not allow for any sort of function (in the sense of being useful to the organism and conserved by evolution) to be inferred.

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  2. Josh Witten and Scott Lewis @BaldAstronomer? Is this some kind of april's fool prank. Or, is it a conspiracy?

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  3. I'm sure that getting the central dogma wrong at the beginning warmed the cockles of your heart.

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    1. You noticed that? :-)

      I also wasn't very happy with the explanation of genes in bacteria and in eukaryotes. The part about the evolutionary advantage of introns is very misleading (i.e. probably wrong). This is not the fault of Rajini Rao because I'm sure she is accurately repeating what she was taught.

      The graph showing genome composition at 9:36 was interesting but I think it would have been helpful to mention genes that don't encode proteins and functional regions that aren't part of genes. The "unsequenced region" is also a bit misleading since we know that it covers functional regions of the genome (i.e. centromeres) and we know that a lot of it is junk.

      I also like to emphasize in my talks that most of the "transposon" part of the genome is known to be nonfunctional "pseudogenes" or junk.

      I don't know how much of this is important for the general public.

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    2. Larry,

      did you do a post on what parts of the genome were NOT sequenced/ can't be compared with e.g. chimps?

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  4. I specifically have found very interesting Josh’s two comments:
    1. At about 55:00

    “Junk DNA is something that evolutionary biology actually predicts. If we didn’t have junk DNA, it would mean that there is something wrong with our understanding of evolutionary theory. …So the claim they (the ENCODE) are making (that 80% of our genome is functional or even more up 100)…That’s a very bizarre claim… which would mean that we would have to rewrite our evolution textbooks. “

    What’s wrong with rewriting textbooks if evidence points in that direction?

    Scott Lewis does not see a problem with that.

    Scott: “I’m down for rewriting textbooks.”

    Why?

    “I think this is the biggest point of science. You are discovering new things and you have to be willing to throw out an old paradigm if it’s not working anymore.(. ..) If we are finding it to be accurate… We should be willing to rewrite the rules because there are new rules involved…
    There is people who get stuck in there trench…”

    Anybody can guess why Scott is advocating for rewriting of textbooks? I tell you: his job and pride would not be affected by the rewriting of textbooks unlike the rest.

    Here is the best part of the show. Josh now is trying to take back his statement and attempts to convince us that he is not against rewriting the textbooks by going on how evolutionary theory predicts junk DNA. .. and ENCODE is complicating that…

    At 58:00 he repeats that ENCODE claim implies that there is something wrong with the theory of evolution…and so on… the shock evolutionists experience by the full functionality of DNA that “ Everything you know is wrong… That could be true (Josh says. Really???) but you need an extraordinary evidence (to prove this) but they (ENCODE) did not provide that.” Why?

    Because, ENCODE only had ordinary scientific proof.

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    1. Interesting that you quote the physicist that admits to not understanding science very well, and somehow you miss, for instance, the genomics researcher (i.e. one who understands the science) saying , at 45:01-45:04

      "and the experiments were never designed to actually answer that question."

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    2. Of course, while Dominic never intended to aswer Larry's question, the contents of his post amount to a resounding "no".
      No, Dominic does not understand the issues any better now, even after having watched this video.

      Unfortunately Larry's blog isn't followed by "the general public" who would otherwise benetif from watching a video such as this, but instead by creationist stormtroopers for doctrine who are only out to propagandize, and the few of us who already understood the subject before.

      It seems to me the "general public" is blissfully unaware of the ENCODE project, never mind the whole ID/Evolution "debate", and that's not to mention the whole thing about Junk DNA. If it weren't for the fact that I have come to this whole thing through an initial interest in biological evolution and the science of origins, I would have remained utterly clueless on these subjects, and this is coming from a lab-technician who is in some ways tangentially involved in genetics and disease related science.

      I think I can unambigously state that none of my technician colleagues, or any of the people I went to school with to become a lab technician, has even the slightes idea about these matters. The "general public" can only be even worse off.

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    3. @ Dominic

      I haven't watched the video, yet. So when I do, is that really they only argument made against the claim that most of the genome is functional? That this would mean rewriting the evolutionary textbooks? No other "ordinary scientific proof (sic)" to refute the claim? If so, I have a hard time understanding why Larry would promote a video that was so vapid. But I guess I'll just have to see for myself. There is the slight chance that you simply don't have the first clue what you're talking about....

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    4. Rumraket,

      It seems to me the "general public" is blissfully unaware of the ENCODE project, never mind the whole ID/Evolution "debate", and that's not to mention the whole thing about Junk DNA.

      Perhaps, but the good old BBC did run an interview with Birney in their national Radio 4 "Material World" strand (transcript on Genomicron), at the not-too-buried time of 4.30pm. The interviewer seems up on the issues.

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    5. A truly excellent but disturbing insight into the workings of a delusional and paranoid mindset.

      This video was obviously a carefully orchestrated effort by the presenters to hide the true story and it is only due to the inadvertent slip up by Josh Witten and the diligence and perspicuity of Dominic that the truth will finally be revealed.

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    6. @Dominic Nikel,

      It's true that Josh Witten says that "Junk DNA is actually something that evolutionary biology predicts." He is wrong. Evolutionary theory would not be refuted if all of our genome turns out to be functional. It's unfortunate that Josh puts so much emphasis on this incorrect idea.

      Also, there's nothing wrong with rewriting the textbooks when old hypotheses are disproved and new ideas gain acceptance. That's how science works. What you and the general public need to understand is that this is a very rare event because textbooks are usually very conservative. They don't incorporate fundamental principles and concepts until they have lots and lots of supporting evidence. These sorts of fundamental principles and concepts don't get changed very often.

      That doesn't stop people from claiming that their latest results are so revolutionary that the textbooks need to be rewritten. I can assure you as a textbook author that most of these claims turn out to be wrong.

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    7. Rumraket says,

      It seems to me the "general public" is blissfully unaware of the ENCODE project, never mind the whole ID/Evolution "debate", and that's not to mention the whole thing about Junk DNA.

      That's true but it misses the point. The death of junk DNA was widely advertised in newspapers and magazines and I think it's fair to say that most science writers were deceived by the ENCODE publicity campaign. This will influence their writing in the future and the net effect is that people who read about science will have an incorrect understanding of our genome.

      More importantly, science educators will read and watch these stories in the public media and they will read similar hype in the science journals. The result will be a generation of science students who will be incorrectly taught. They will grow up to be researchers, like those working on the ENCODE project.

      You can see the result in the video because we've already been through several iterations of this scenario. The proponents of massive alternative splicing and an evolutionary role for introns have been much more effective at getting their message out than the cooler heads who have looked seriously at the problem. We now have a generation of graduate students and young researchers who have never been told that these just-so stories are controversial.

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    8. @Larry,

      At one point in the video the synthetic organism being designed by Craig Venter was being discussed.

      It was claimed (I don't recall by which speaker) that the genome of this organism would be stripped down to just essential DNA and would contain no "junk".

      It was then claimed that this organism would be unable to respond to changes in it's environment as it would lack a "reservoir" of DNA that would allow it to be modified in response to changes in it's environment, the implication being, if I understood correctly, that since all it's DNA was already co-opted to functions necessary for survival, any changes to existing DNA would be immediately and fatally deleterious.

      Was this an accurate claim as to how the organism would respond (or not) to changes in it's environment ?

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    9. Oberski,

      if you precis of the conversation is accurate, that is a gross misrepresentation. Bacteria do not have junk DNA.

      Secondly, we know that the ratio of deleterious to beneficial mutations (ignoring the changes that make no functional difference, which is the majority) is 10:1.

      With large population sizes, bacteria can tolerate a 10:1 ratio of deleterious to beneficial mutations, in the subset of changes that make a functional difference.

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    10. You can see the result in the video because we've already been through several iterations of this scenario. The proponents of massive alternative splicing and an evolutionary role for introns have been much more effective at getting their message out than the cooler heads who have looked seriously at the problem. We now have a generation of graduate students and young researchers who have never been told that these just-so stories are controversial.

      I didn't have time to watch the whole thing but I made it the 15th minutes and within those 15 minutes one of the most cringeworthy things I heard was how introns are there for adaptive reasons. No mention of group II introns at all even if they did talk about how TEs are there because of inefficient selection in humans a bit after that

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    11. ...that since all it's DNA was already co-opted to functions necessary for survival, any changes to existing DNA would be immediately and fatally deleterious


      Not sure, but I suspect the comment you reference is referring to the organism having a much reduced genome relative to many other "wild" bacteria and that most of the genes present are essential genes required for basic cellular processes only. It would be true that such a stripped down genome (which is of the sort that might be found in endosymbiotic bacteria by the way)would generally permit survival only under relatively stable environmental conditions. The junk reference you heard should not be confused with the normal meaning of term junk DNA. In this case the speaker probably meant any genes not unconditionally essential to survival. If the speaker used to the term junk DNA in this context, it was a very poor choice of words.

      As for lethality of changes occuring, most mutations would still be neutral even though all or nearly all the genes are essential. The most you can say is that, since every gene is essential, any mutation that does knock out gene/protein function will be lethal...which is obviously not the case in most bacteria which carry many non-essential genes in addition to the core essential ones.

      As for adapting to changing conditions, it simply no longer has the broad repetoire of non-essential genes useful for survival under diverse and changing environmental conditions.

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    12. Giorgi Marinov: No mention of group II introns at all even if they did talk about how TEs are there because of inefficient selection in humans a bit after that”

      In a previous comment about group II introns ( http://sandwalk.blogspot.com/2013/03/on-meaning-of-word-function.html#comment-form ) you said:

      “Spliceosomal introns indeed evolved from group II introns - but it wasn't because this was beneficial, it was because it was either that or extinction, due to the deleterious effect of those same group II introns”

      My understanding is that you are saying that spliceosamal introns evolved as a protective or defensive mechanism because “it was either that or extinction due to the deleterious effect of those same group II introns”. Is that correct?

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    13. @steve oberski,

      It was then claimed that this organism would be unable to respond to changes in it's environment as it would lack a "reservoir" of DNA that would allow it to be modified in response to changes in it's environment, the implication being, if I understood correctly, that since all it's DNA was already co-opted to functions necessary for survival, any changes to existing DNA would be immediately and fatally deleterious.

      I don't think that's correct and I also don't think that junk DNA has a function; namely, to act as a reservoir for future change. I'm not sure what was meant. Josh (see below) seems to be suggesting that "truly non-functional" DNA might not exist. He seems to be saying that junk DNA is adaptive—therefore functional.

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  5. This comment has been removed by the author.

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    1. Oops, I didn't notice that Ryan had a much better transcript of Birney's BBC interview on Genomicron. Thus; I've deleted my prior post.

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    2. Oh sorry, I just noticed your post ... I duplicated the info!

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  6. Unsurprisingly and ignoring the recent critiques ENCODE finds support in more industry related web sites. E.g, R. Grayle ENCODE and the Truth, Hank's SciShow WATCH: What's Your Junk DNA Worth? and Ian Dunham ENCODE-ing the Future

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  7. I'm going to respond to several different comments here in one fell swoop rather than in several replies.

    Scott Lewis, an astronomer, was there to provide an "everyman" filter to prevent use of obscure language or assumptions of base knowledge. He was also there because he regularly hosts ScienceSunday and provides technical "know how" to make things work logistically.

    We were time limited to about 75 minutes. Therefore, some decisions about prioritizing discussion of ENCODE versus addressing issues in the introductory material had to be made. For example, I was not happy with the discussion of introns, especially the idea of rearrangable "LEGO blocks". This creates an inaccurate impression of alternative splicing and ignores linear constraints on possible isoforms. In favor of conserving time later for other topics, I let that slide. You may disagree with the prioritization that went into that decision making, but bear in mind that, given non-infinite time, not all errors are made from ignorance or incompetence.

    Regarding synthetic organisms, we were responding to a listener question about if it would be easier to build an organism without "junk DNA". Ian and I both seemed to interpret that as meaning truly non-functional DNA. To my mind, the difficulty of adding truly neutral DNA sequences would argue against the effort & the ability of microorganisms to brute force their way through the unfavorable ratio between deleterious and beneficial mutations would negate the benefit a neutral space for evolutionary tinkering (if one deems that to actually be an adaptive advantage).

    My statement that "evolutionary theory predicts junk DNA" was directed at the widely adopted concept in writing about ENCODE's claims that "junk DNA" is a problem for biology that needs to be resolved. It is interesting and worthy of study, but it is not a problem.

    Evolutionary theory tells us that natural selection is unlikely to be able to eliminate non-functional sequences in species with population structures and life histories like those of humans. While evolutionary theory may not predict the precise details of junk DNA in the human genome, the existence of junk DNA fits comfortable into that theory. No junk DNA in humans would not. I used "predicts" in this sense. I think the weakness in my statement was that I did not make clear the particular usage of the word "predicts" as well as I might have. It may not be the best use of the term, but it wasn't like I scripted my comments either. The lack of any conservation signal at supposedly "functional" sites also suggests that ENCODE's claim flies in the face of our understanding of evolution.

    As I stated, I have no objection to rewriting textbooks. I do have an objection to rewriting them based on bad evidence.

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    1. Josh: “ While evolutionary theory may not predict the precise details of junk DNA in the human genome, the existence of junk DNA fits comfortable into that theory. No junk DNA in humans would not”

      I think this is a very interesting concept that is somewhat similar to Doolittle and Sapienza concept of non-phenotypic selection for "junk DNA", but worth future development from both evolutionary and philosophical perspectives.

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    2. Josh,

      Thanks for clearing up your use of the word "predict." The problem stems from the fact that the creationists DO claim (incorrectly) that evolution predicted junk DNA. They claim that since junk DNA has been refuted this means that evolutionary theory is wrong. I was hoping that you weren't using "predict" in that sense.

      However, when you say ...

      While evolutionary theory may not predict the precise details of junk DNA in the human genome, the existence of junk DNA fits comfortable into that theory. No junk DNA in humans would not.

      It still sounds confusing. Why do you think that vertebrates without substantial amounts of junk DNA would not fit comfortably into evolutionary theory? Does the genome of pufferfish worry you?

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    3. Larry

      I was addressing the idea that junk DNA is a problem. I understand the confusion with the creationist approach, but I frankly am disinterested in dumbing down evolution in a Dawkins-esque adaptionist way to score points against them. While continually annoying, they have lost the war in the courts.

      You will note that I was careful to say "in humans". While I know essentially nothing about the population structure & life history of the pufferfish, I am well aware of its genomic efficiency (as well as the genomic inefficiency of many other teleosts). This does not trouble me because I presume the species does not have the same population history and structure as humans. I think your inference that vertebrates without junk DNA pose more of a challenge than those that do, but I rest comfortably and, perhaps, naively in the confidence that those without possess extremely odd and interesting histories. We have invested a lot of time and energy into researching our hominid ancestors and the constraints of those parameters inform my opinion.

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    4. I think it is relevant to clarify that puffer fish genome contains substantial amounts of the so called ‘junk DNA’ (jDNA); in fact, it appears that most of the puffer fish genome is composed of jDNA (see: http://www.ncbi.nlm.nih.gov/pubmed/12727902); http://www.ncbi.nlm.nih.gov/pubmed/12142439

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    5. @Josh,

      Okay, I think I understand where you are coming from. Back in the 1970s when it first became apparent that mammalian genomes contained lots of junk DNA we interpreted that in light of populations genetics. Most experts understood that if the deleterious effects of extra DNA were small then, given the population structure of mammalian populations, it is quite reasonable that their genomes accumulate junk. Junk DNA is consistent with evolutionary theory but not predicted by it.

      With that background, it would have been a real shock to find that humans had no junk in their genome.

      However, if we had discovered back then that mammalian genomes were ten times smaller then we would have assumed that the deleterious effects of extra DNA were too severe to survive even in species with small population sizes. In this hypothetical case, the lack of junk DNA in mammals would not have conflicted with evolutionary theory. Lack of junk is consistent with evolutionary theory.

      Do you agree?

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    6. Claudiu - I believe approximately 100Mb (~1/3) of the pufferfish genome is gene-coding, which is in the same general ballpark as the human transcriptome. Of the remainder only a small fraction is repetitive and the rest is single-copy something. I think this is another problem with using the overly-broad term "junk".

      Thanks everyone for taking an interest in out discussion. I think that Josh did a good job of filling in some details above.

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    7. Larry, I absolutely agree. The expectation is based on what we know about effective population size, life history characters, selection pressure, and mutation rate. So, junk and no junk DNA are both consistent with evolutionary theory. The predictions would differ based on these conditions. In humans, we have information about these things from areas other than reference genome sequencing. So, I think it is fair to say that given what we know, junk DNA is predicted in humans. I'm wary of drawing strong inferences about the values of multiple parameters in species like the pufferfish from the DNA alone (gets circular).

      I would reiterate that my comment was addressed at the rhetorical idea, which does have traction among biologists, that "junk DNA" is a problem - not to make a historical comment about what people actually thought before I was born. :)

      As Ian notes, "junk DNA" is a problematic term because everyone uses a slightly different definition.

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  8. Claudiu BandeaThursday, April 04, 2013 2:34:00 PM

    My understanding is that you are saying that spliceosamal introns evolved as a protective or defensive mechanism because “it was either that or extinction due to the deleterious effect of those same group II introns”. Is that correct?


    No, you are misrepresenting what I said in an absolutely horrifying way. I said spllecosomal introns evolved from group II introns. Group II introns are selfish elements that do not good to the host genome, exactly the opposite, they disrupt its mRNAs, and their self-splicing ability is an adaptation on their part so that they don't end up killing their host and going extinct with it. Still, there is very very little of them in prokaryotes, and there's a reason for it - they are not beneficial and selection in prokaryotes is strong (due to the large Ne) so they're kept in check. In eukaryotes, it's a very different situation. Read these papers, among many that discuss that:

    Martin W, Koonin EV. 2006. Introns and the origin of nucleus-cytosol compartmentalization. Nature. 440(7080):41-5.

    Koonin EV. 2006. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate? Biol Direct. 1:22.

    Also, in general, it is not at all controversial that selection is much stronger in prokaryotes than in eukaryotes. You don't accept the "high Ne => strong selection, low Ne => weak selection" theory. But if you don't accept that, then there would be no reason to think there would be any differences in the strength of selection between the two groups and we would expect to see equal levels of adaptation. The wouldn't you think that if introns and alternative splicing were of such benefit to organisms prokaryotes would have evolved those too, given how highly adapted they are, often down to truly minuscule details, given how prevalent LGT is among them, and given the fact that they already have self-splicing introns? That's not what is observed though

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    1. Georgi Marinov says: “I said spllecosomal introns evolved from group II introns. Group II introns are selfish elements that do not good to the host genome, exactly the opposite, they disrupt its mRNAs, and their self-splicing ability is an adaptation on their part so that they don't end up killing their host and going extinct with it

      So, the “self-splicing ability is an adaptation on their part so that they don't end up killing their host and going extinct with it”. From an evolutionary perspective, don’t you think that the co-evolution of group II introns with their hosts was a protective mechanism that helped both of them to survive?

      Also, what do you think about the spliceosomes, which are rather complex machineries. Why did they evolve, to protect the ‘introns’ or the host? Or were they just an evolutionary co-option to protect the host?

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    2. You obviously didn't read the papers I listed

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    3. Also, in general, it is not at all controversial that selection is much stronger in prokaryotes than in eukaryotes. You don't accept the "high Ne => strong selection, low Ne => weak selection" theory. But if you don't accept that, then there would be no reason to think there would be any differences in the strength of selection between the two groups and we would expect to see equal levels of adaptation.

      Well, there is another possibility - it's not difference in Ne that's the prime causal factor, but difference in s. These are organisms of very different size, ecology and nutritional constraint.

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    4. Giorgi,

      In context of our discussion, I was interested in your thoughts and ideas, not those of other people, particularly when they do not participate in open discussions here at Sandwalk or other blogs.

      However, if you don’t want to address the questions from my previous comment, that’s fine.

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    5. 1. I am completely baffled by the statement "I want your thoughts and ideas, do not give me papers to read" - do you have any idea how science and scholarship work?

      2. I did not address you questions because they make zero sense and are either based on lack of understanding of what I posted, or worse, you not bothering to read it to begin with. I don't have much time to spend explaining the same thing again and again (which is another reason why referring to the literature is such an useful thing to do). Repeatedly ignoring what people explain to you then forcing them to explain it again, only to once again ignore it is a classic creationist tactic and I refuse to play that game.

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    6. @Giorgi

      Hopefully, you had some time to ‘cool off’ and reflect on our discussion. Here are excerpts from one of the papers you suggested and a more recent one from the same group:

      (http://www.ncbi.nlm.nih.gov/pubmed/16907971):

      “The beginning of eukaryogenesis was marked by a massive invasion of group II introns escaping from the mitochondrial endosymbiont into the host, archaeal chromosome that formed the basis of the emerging eukaryotic genome. This intron invasion triggered the formation of the signature features of the eukaryotic cell including the spliceosome, the nucleus, the linear chromosomes with telomeres, and the systems of nonsense-mediated decay and ubiquitin signaling, either as devices for direct defense against introns or as inevitable consequences of the invasion”

      (http://www.ncbi.nlm.nih.gov/pubmed/22507701):

      “Indeed, it has to be emphasized that Group II introns are typical mobile elements that actively spread around the host genome when given a chance by weakness of purifying selection pressure. However, at the mechanistic level, the adaptation of the early eukaryotes to the swarms of genomic parasites (if this is what introns are, Figure Figure9),9), which severely compromised the integrity of their genomes, an adaptation that apparently involved rapid evolution of the dauntingly complex spliceosome, remains an intriguing enigma.

      And, a reviewer comment from the same paper:

      “The authors actually touch on this notion, when they speculate as to whether introns are genomic parasites and how the host may have evolved the spliceosome as an adaptive response to intron invasion”

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    7. Why are you quoting these sentences as if they support your view when they in fact completely demolish it (which is why I referred to those papers)?????????????????????????

      I am completely baffled

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  9. Diogenes said:
    "Bacteria do not have junk DNA."

    Some bacteria do have junk DNA

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  10. @ Josh

    Thanks very much for your response.

    It has become clear to me, and perhaps others, that you and Larry differ in opinions as to whether human genome could turn out to be fully functional in the future and what effect this would have on human evolution. You simply seem to believe that fully functional human genome would mean that your knowledge of evolution is totally wrong, and Larry doesn’t not seem to see it to be a problem, if it does turn out to be fully functional. It may very well boil down to the definition of function, as it was suggested in the video by Rajini Rao.I will try to comment on that issue; what function could mean, later.

    However, I would like to bring to your attention and others the latter part of the video, that I have found quite interesting as well. I would like to hear your and others comments on this piece. Here is a transcript of more or less what you said at about 1:05 min mark.
    Josh Witten said:

    “The lab I did my graduate work in and bunch of other labs have been doing a lot of research...
    …where they synthesize random strings of DNA to try to analyze regulatory functions and other things like that….
    This actually plays directly into the ENCODE results of the junk DNA….
    It is actually very difficult to generate a random string of DNA of any length…
    …10 base pairs that doesn’t have biochemical activity…
    It could be hard to make a random piece of DNA that "doesn’t do something", if your assay is sensitive enough...
    …You might want to put it into junk DNA that is neutral and your synthetic organism…
    It is actually could be very difficult to find stuffs that don’t do anything, unless you are taking wholesale perhaps form junk DNA in a human genome…
    In the human genome actually, there are a lot of processes that go to make some those repetitive elements and that junk DNA and transposable elements stay junk and stay neutral…
    The DNA can’t really put it into a “neutral” on its own devices…
    The human genome kind of fights back against the junk, to keep it in check…
    To keep the junk yard in order...

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