Friday, November 12, 2010

Darwinism and Junk DNA

 
Robert Crowther has posted a criticism of Francis Collins on Evolution News & Views (sic): Francis Collins, Evolution and "Darwin of the Gaps".
Much of Collins’s case for Darwinian evolution is based on so-called “junk DNA.” This is the part of the genome that does not appear to code for the production of proteins. In mammals, the vast majority of DNA has been dismissed as “junk.”

Junk DNA, according to Darwinists like Collins, gives evidence of common descent—the idea that all life, including human life, branches off from a common evolutionary tree. As life evolved, according to this view, garbled, useless genetic information accumulated and has remained fixed—like dirt swept under a carpet—even as mammals, for example, diversified from a common ancestor.

But the argument from junk DNA—also called “ancient repetitive elements” (AREs)— depends on the premise that no function will ever be discovered for AREs. Collins’s faith in Darwinian theory would be severely hamstrung if the premise were shown to be wrong. It is a faith based on gaps in scientific knowledge. Hence, “Darwin of the gaps.”
I don't want to defend Francis Collins. I want to emphasize something else; namely that the concept of junk DNA is about as far removed from "Darwinism" as you can possibly be and still be an evolutionary biologist. If it has any meaning at all, "Darwinism" has to be a synonym for the belief in natural selection as the most potent mechanism of evolution. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory."

Why do creationists have so much trouble understanding this? It's not that hard.


94 comments:

  1. It is always so irritating to see Creationists entirely miss the point on "junk DNA" like this. Many elements we know a great deal about and that leads us to the conclusion that they are "junk." Other bits are inferred to be non-functional through the same approach that is used to identify protein-coding genes and other functional elements: by level of conservation. Then, of course there are the catch-all arguments such as mutational load and the c-value paradox (e.g. onion test) that Larry has posted on.

    Bottom line: We have positive reasons for believing that these things are "junk."

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  2. I'd heard that an experiment had actually been run using mice to see what would happen if the "junk DNA" was removed from their genome... if a fully-functioning mouse would still result... and I'd been led to understand that, in fact, it had. Isn't this exactly the kind of evidence that creationists say can't be produced? But of course, they'll forever ignore that fact and insist it hasn't, and couldn't be.

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  3. The experiment I mentioned is cited here, among other places...

    http://www.nature.com/news/2004/041018/full/news041018-7.html

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  4. The DI could learn an awful lot by simply listening to YEC biologists; Todd Wood: A primer on transposable elements

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  5. Robert Crowther's synopsis is so bad that it is Not Even Wrong. He is a non-starter.

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  6. Why do creationists have so much trouble understanding

    You could have stopped right there. Creationists have no interest in understanding anything. They merely wish to repeat written scripture and promote or impose their spotty interpretation of that scripture on everyone else.

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  7. I've always been irritated by the ridiculous fallacy that "you can't prove a negative," and here's another example why. "You can't prove junk DNA has no function, that's a negative!" And yes, I'm well aware there are certain kinds of universal negatives that really can't be proven, but obviously this ain't one of them.

    We should also clarify that when we say junk DNA has no function, we really mean that it has no non-trivial function that relates to its specific code sequence. This will prevent smartass creationists from claiming that God created junk DNA for some trivial function, like taking up space, or available segments for future front-loading, or as a buffer from random mutation (which prompts the question of why God would even permit random mutation in the first place if it's gonna mess up his design).

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  8. Anonymous writes:

    We should also clarify that when we say junk DNA has no function, we really mean that it has no non-trivial function that relates to its specific code sequence. This will prevent smartass creationists from claiming that God created junk DNA for some trivial function, like taking up space, or available segments for future front-loading, or as a buffer from random mutation (which prompts the question of why God would even permit random mutation in the first place if it's gonna mess up his design).

    I would call any statement of the form "This will prevent smartass creationists from claiming that God..." a fond but doomed hope.

    Just look at the claims. They could have been about actual problems for current evolutionary theory, or at least unresolved research questions. But instead they are notions like "front loading," the type of claim that can only be made in the absence of knowing or caring what the science actually says.

    If someone asked you, as a philosophical notion unconstrained by fact, what a Creator could have meant by loading up living things with genetic material that has no current function, "Planning for the future!" could well be one of the answers. But if you actually know the facts - that the structure of this material shows it consists overwhelmingly of defective copies of what has gone before, not new and unique stuff - then that, if you are being intellectually honest with yourself and others, negates the possibility of the "front loading" argument.

    When ID creationists make this sort of claim, it shows they either don't know the facts, or, knowing the facts, don't care to engage in intellectually honest discussion. And unfortunately, I doubt any amount of clarification on the part of real scientists or interested laypersons will change that.

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  9. At this creationist talk a couple weeks ago I was stupid (masochistic) enough to go to, the crook put up this horrible mangled tree of life, pointed to Amoeba and commented how we animals have so many more genes because we're so complex, therefore no junk DNA, blah blah blah...

    It was thoroughly amusing, considering the largest eukaryotic genome belongs to Amoeba dubia, etc. Of course, not like those people would let pesky things like "facts" get in the way of their libelous narrative...

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  10. I have a question regarding junk DNA. In the lac operon, there are DNA sequences between the operators and the promoter. Are those interstitial sequences considered junk DNA, even though they function as the DNA loop that is formed to block polymerase?

    Note that I am not arguing that most junk DNA is functional. Just narrowing down a definition for myself.

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  11. Kele, I believe that it is "junk" DNA if it lacks a function directly related to its sequence. If those sequences are merely repeated spacers, it would be considered "junk" DNA as far as I know, despite it having *some* use (this is part of why I put the term in quotes). Some "junk" DNA is useful for something, but the great majority isn't and none of it has a function related to sequence.

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  13. Larry writes: "Why do creationists have so much trouble understanding this? It's not that hard." And Luke thinks that Crowther is "missing the point."

    Well, you two are being way too generous to the sleazy Discovery Institute. The author of that post knows perfectly well that junk DNA has nothing to do with "Darwinism," and he knows even better that Francis Collins' "case for Darwinian evolution" does not rely centrally on junk DNA. (I'll grant that his idiotic equation of "junk DNA" with "ancient repetitive elements" suggests that he's an ignoramus.)

    No, kids, the disconnect here has nothing to do with "missing the point" or failing to "understand." It's just old-fashioned dishonesty, probably the only thing the DI will ever be remembered for.

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  14. I understand Prof. Moran's statement that junk DNA is antithetical to Darwin's line of thinking, but I do like how the cited article says that junk DNA is darwinian /because/ of its relationship with Common Descent.

    One can argue that Common Descent is not all there is to Darwinism, but its one of the really big things that differentiated Darwin's ideas from his contemporaries, yes no?

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  15. The idea of "junk DNA" is essentially an argument from intellectual laziness and personal incredulity.

    As I understand Larry's position, he accepts that much of non-coding DNA serves a function, but that the SINEs and LINEs that make up about 40% of the genome, really are junk.

    I would dispute this because of what we now know about how these retrotransposable elements can modulate gene expression when they are inserted into intragenic regions.

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  16. ^
    I've heard this argument before. To clarify what you're saying, the "function" of junk DNA is to increase the mutability of the small fraction of the genome that controls transcription?

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  17. @Reza C-value paradox. If transposon filler is so good for the genome, then why is there such incredible variation in the amount thereof often within a single small clade, and with not even the slightest correlation with complexity or anything else?

    Furthermore, why is it that genomes under strong selective pressure for size, such as nucleomorphs and genomes of intracellular parasites, tend to be so damn small and streamlined? Some microsporidian (single celled fungal intracellular parasites of...well, a LOT of things) genomes have something like 17 or 20 introns, and extremely reduced intergenic regions. This suggests that when selection does act, it seems to *dislike* transposons and other spacers.

    From the population genetic approach, there is strong support that genome size correlates negatively with effective population size (Lynch & Conery 2003 Science; Lynch 2007 PNAS). Large effective population size generally leads to a weakening of the effects of drift relative to selection; ie, selection becomes 'stronger'. I find it a pretty convincing argument that bacterial genomes are so efficient and relatively clean of junk due to their massive effective population sizes, where it is unlikely for drift to fix slightly deleterious changes. (basically, selection becomes 'stricter' under those conditions; selection in large mammals is particularly sloppy – I'd argue that is what enabled us to evolve in the first place!)

    Furthermore, the mutational coefficient µ correlates positively with relative efficiency of selection; the higher the mutation rate, the less likely it becomes for individual changes to fix via drift. Animal mitochondria have a substantially higher mutation rate, compared to their nuclear genomes; meanwhile, plant mitochondria have an unusually LOW mutation rate. Which would you guess has more introns and repeats and such? The plant mitochondria. Again, inefficient selection leads to bloated genomes, and higher genomic complexity. (data + story from seminar talk by M Lynch, OCT 2010)

    Lastly, I think the following recent Science perspectives piece by Gray et al. does a really nice job at explaining acquisition of complexity through non-adaptive means: "Irremediable Complexity" http://www.sciencemag.org/cgi/content/full/330/6006/920 (if you don't have access, my email's on my blog, I can send you a pdf). I think mainstream evolutionary biologists have not done justice to non-adaptive and neutral evolutionary processes, and I think that really needs to change in order to do evolutionary biology WELL.

    Summary: "junk" does not mean we're too lazy to figure out what it does and thus dismiss it. Objective molecular, phylogenetic and population genetic evidence does support that at least some part of genomes is there just because it can, and not for any particular adaptive/'useful' reason.

    -Psi-

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  18. PS: As for transposons participating in gene regulations: sure, you're bound to find previously-neutral things that later become useful, and even essential, for something (read that Science piece above). That does NOT mean they are therefore initially there "for" that reason. That's a teleological argument, and therefore a fallacy in evolutionary reasoning. A very common one, but evil nonetheless.


    Also, I'd like to ask you to take back the 'intellectual laziness' statement. I personally know some people who are hesitant and conservative in applying functional value to 'junk' DNA, and they are FAR from intellectually lazy, thank you very much.

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  19. Junk DNA is completely non-Darwinian and there's no way you could describe it as compatible with "Darwinian theory". Why do creationists have so much trouble understanding this?

    Junk DNA is perfectly compatible with "Darwinian theory". Why do you have so much trouble understanding this?

    Darwin, again:

    "I am inclined to suspect that we see, at least in some [cases], variations which are of no service to the species, and which consequently have not been seized on and rendered definite by natural selection.… Variations neither useful nor injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed.… We may easily err in attributing importance to characters, and in believing that they have been developed through natural selection;… many structures are now of no direct use to their possessors, and may never have been of any use to their progenitors.… [On the other hand,] we are much too ignorant in regard to the whole economy of any organic being to say what slight modifications would be of importance or not."

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  20. @Psi wave

    It IS an argument from laziness to *assume* that large swathes of ncDNA are useless junk because you can't be bothered to determine if they have a function.

    The fact is that ncDNA has increasingly been found to have some function - it was presumed that introns (25% of the genome) were simply "junk" until research showed that they play an important role in eukaryotic biology.

    As I said, retrotransposons serve to keep the gene expression dynamic. Rather than rant on about population genetics ,and the obvious point that selection is more effective in larger population sizes, I suggest you read this paper:

    Function of an LTR retrotransposon

    Stop *assuming* and start learning.

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  21. I'm a little confused by why the concept of "junk" DNA - even though much of what got that label smacked on may well be not junky - is not compatible with "Darwinian Theory". I'm wondering if the issue is partly semantic?

    I can't imagine that "much of" any case for natural selection would be the existence of remnant DNA. Isn't it more of an expected occasional aftermath of various accumulated mutational events over time? (especially if the species doesn't have the generation time of, say, bacteria, which seem to be quite lean) Or do I misunderstand the issue?

    Or is it more having to do with whatever the term "Darwinism" means which makes DNA issues not relevant. All through grad school and beyond, I never heard the word Darwinism applied to evolution. Either simple "Natural Selection" or, more often, "Evolutionary Biology" was used. So I take it from what you've written before that "Darwinism" implies something quite limited compared to what is actually done today.

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  22. @Reza

    "It IS an argument from laziness to *assume* that large swathes of ncDNA are useless junk because you can't be bothered to determine if they have a function."

    Agreed. If you see someone doing that, by all means explain it to them.

    However, it's irrelevant when addressing someone who actually presented evidence to support their position.

    Citing specific examples of (e.g.) retrotransposon elements having functions at long distances from genes is evidence that specific elements can have such functions. It doesn't show that all such elements have function, or refute evidence that some such elements are indeed junk.

    Being a dick does not make your argument more compelling.

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  23. @Psi Wavefunction
    “... I find it a pretty convincing argument that bacterial genomes are so efficient and relatively clean of junk due to their massive effective population sizes, where it is unlikely for drift to fix slightly deleterious changes...”,

    I thought the most plausible theory for why bacteria have such junkless genomes is the ratio of genome replication time to minimum generation time. Larry had a post a while back explaining that in bacteria, they are roughly the same, and that replication time was the major limit (assuming plentiful nutrients in the environment). Thus, if you junked up a bacterial genome as much as a human genome is, generation time would increase 20 fold, from 30 minutes to 10 hours. In a competition of two strains, one junky, one not, in the time needed for the junky one to double its size, the non-junky one would have increased by a factor of a million.

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  24. Reza, have you read Todd Wood's article? Here's a section;

    "With regard to the origin of the human species, when the chimp genome was sequenced, it was found to contain nearly all of the transposable elements that the human genome had. The transposable elements were arranged in the same places on chromosomes that were >95% identical in their sequences. I summarized these findings in a paper for OPBSG in 2006. The presence of many transposable elements in the human genome implied that they originated by transposition, and the presence of the same transposable elements in the chimp genome implied that humans and chimps shared a common ancestor. Why? Because of the staggering similarity.

    Let me offer a few closing observations. First, it is false to say that the connection between retroviruses and retrotransposons is just speculation or irrational. There is significant sequence similarity between the elements, which rules implies an ancestral connection. I discussed this in more detail when I discussed Liu and Soper's proposed "exogenization" of retrotransposons, an attempt to account for the similarity of retroviruses and retrotransposons.

    Second, it is misleading to say that transposable elements are "functional" or "essential." The vast majority of transposable elements in the human genome are nonfunctional copies that have been damaged(?) by point mutations. To my knowledge, there is no evidence of essential function for most of these transposable elements. Indeed, some eukaryotes (like baker's yeast) that have comparatively few transposable elements.

    Third, the argument for the common ancestry of chimps and humans depends in no way whatsoever on the functionality of transposable elements. The argument is more compelling if the sequences are purely parasitic, but the overwhelming similarity still implies that chimps and humans could have shared a common ancestor, even if transposable elements had an essential cellular function. In my chimp genome paper, I challenged myself and my fellow creationists to account for biological similarity in a creationist context. To date, the challenge has not been met.

    Fourth, McClintock herself proposed an important functional role for transposable elements. Functionality was not the exclusive prediction of creationists. It is definitely false to claim that evolutionists did not propose functions for transposable elements.

    Fifth, peculiar examples like the transposable elements of Oxytricha and other ciliates do not provide a solution to the question of functionality of transposable elements. Such things only highlight the oddness of transposable elements and the idiosyncratic roles they play in certain cells. In other words, the occasional transposable elements that do some important job for their host cells emphasize the lack of a general "functional" role for transposable elements in other cells.

    Sixth, transcription does not equate to cellular function. It just isn't the same thing. It's interesting, but not even close to conclusive.

    Seventh, function does not equate to design. It just isn't the same thing."

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  25. @Clive

    Yes, Wood's argument is just an argument from personal stupidity.

    Little by little, we are finding more about the regulatory power of retrotransposons. I make a prediction: Larry Moran will have to recant his claims about "junk DNA" before he retires because the evidence will be so overwhelming.

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  26. Reza writes:

    "Yes, Wood's argument is just an argument from personal stupidity."

    There is indeed an argument from personal stupidity being made here, but not by Wood. Or Clive or Psi.

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  27. @Reza I love how you assume to be smarter than an entire freaking field of qualified experts on the subject. Those of us with bleaker intelligence must, unfortunately, resort to evidence and real data...

    By your argument, we just 'assume' there is no intelligent design behind evolution; the more we look, the more evidence for creation we will find. It is intellectual laziness to assume everything somehow just purposelessly evolved 'by itself', hah!

    Protip: Unsubstantiated assertiveness generally correlatives positively with personal ignorance. And/or obvious trolling...

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  28. @Psi

    Much of the the theory of evolutionism is based on a morass of assumptions. I am not surprised that Neo-Darwinists have taken an anti-scientific position and attempted to portray large swathes of ncDNA as "junk" to suit their own interpretation of "non-design" in Nature. But the more research that real scientists do, the more it becomes clear that this position is untenable.

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  29. Why do creationists have so much trouble understanding this? It's not that hard.

    In my experience, the problem with creationists 'getting this' is twofold.

    Firstly, and obviously, they are quite ignorant of the history of evolutionary thought and typically prefer to attack caricatures.

    Secondly, they like to claim the Darwinian stake (that junk DNA is probably functional, but the function is unknown) for themselves. That sort of stuff is all through the ID literature, and other creationist writing. Every time there any shred of potential junk is labelled as functional DNA, there are ID advocates claiming it as a nail in some sort of coffin for 'Darwinism', which is of course conflated with the whole of evolutionary theory. This is of course not merely a strawman but a wholesale reversal of a strong Darwinist position.

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  30. @Scott

    Yes, the issue is semantic. Larry (and many others with him) defines "Darwinism" as the idea that natural selection is the main driving force of evolutionary change. Since junk DNA is non-functional by definition, it cannot evolve by natural selection. You will find an explanation in Why I'm not a Darwinist.

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  31. Reza:

    "It IS an argument from laziness to *assume* that large swathes of ncDNA are useless junk because you can't be bothered to determine if they have a function."

    One of the first comments made on this post was that in which I pointed out that scientists haven't been lazy about it. They actually have done experiments to see if removing sections of "junk DNA" is detrimental to the organism in question -- in this case, a mouse; a substantially complicated organism -- and the conclusion is that the removal of non-coding sections is not lethal. It would seem that they're justifiably deemed "non-coding". I think we could all agree on point of demarcation: that if a segment is removed and the organism suffers, it's not "junk". But it's removed and the organism suffers no penalty, then clearly it's superfluous in any practical sense and qualifies as "junk". It's the equivalent of a bumper sticker... useless information along for the ride that makes no difference to the operation of the vehicle.

    It's easy to see that traits that are actively discriminatory to an organism's survival could be removed from the gene pool; we understand the process for that. But if a characteristic neither aids nor hinders a creature, by what mechanism would that characteristic be selected against, and thus removed? It would be every bit as successful as the organism as a whole. It's not difficult to see how useless segments could build up in a genome over time.

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  32. @Corneel
    Thanks! It's kinda what I figured.

    All this angst (most of this comment thread?) over differing definitions or labels being used in ways that (IMO) don't mean nearly as much as they used to mean.

    "Darwinism", whatever it's literal definition, seems to mean different things to different folks - to some it must mean natural selection with no reference to DNA, I guess, which is kind of a limited view of evolution. To others I guess the word is essentially equivalent to natural selection, which is a major component of modern Evolutionary theory.

    This impreciseness might be the reason I rarely heard the word "Darwinism" used during my time in the sciences. IMO, it's a word that has little use anymore and just leads to arguments over very little.

    Also, it leads to abuse by creationists, as we see here.

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  33. Also: "Junk DNA"
    I think this word (not the concept) needs to go as well - just a thought.

    It's both damning (it *implies* complete uselessness) and imprecise (useless, but how useless: non-coding? non-enhancer - positive or negative? just pure space-filler?).

    And, like "Darwinism," it appears to also create lovely fights and abuse by creationists.

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  34. Reza writes:

    I am not surprised that Neo-Darwinists have taken an anti-scientific position and attempted to portray large swathes of ncDNA as "junk" to suit their own interpretation of "non-design" in Nature. But the more research that real scientists do, the more it becomes clear that this position is untenable.

    The single article you cited found a function for a single transposon. With about one-and-three-quarter million copies of transposon elements in the human genome from just the two major transposon families, I'd say there's a bit of work to do before anyone could conceivably make a scientifically supportable statement that most (or even a significant proportion of) transposons are functional.

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  35. @psi,

    Large effective population size generally leads to a weakening of the effects of drift relative to selection; ie, selection becomes 'stronger'.

    This is (broadly) true within the model of allele substitution in a panmictic sexual population. The smaller your sample, the more any directional component can be influenced by the buffeting of drift. But I'm not sure Lynch is right in extending this to prokaryotes. To an individual prokaryote, every cell in its immediate vicinity, relative or not, is a competitor and a threat. It has to do better than them, and has no need to have offspring with them. Rather than an asexual 'population', effective or not, there is simply a large collection of asexual individuals, each of population 1. The 'motor' of mixing in a sexual population is sex itself - the only thing that can approach the pop-gen well-mixed ideal is iterated sexual union. It needs dispersal too, but mating acts as a 'vector force'. But there is nothing mixing a collection of asexual prokaryotes in an equivalent manner that would allow the 'signal' of selection to drown out the 'noise' of local drift, outside the lab.

    I'd argue that selection on genome size is strong in prokaryotes not because of gross population size, but because each clonal line will be swamped if it slows down. Eukaryotes discovered leisure - they can invest much more time per cycle in growth, with a correspondingly diminished relevance of DNA replication time-and-materials costs. What gave them this leisure - sex, mitochondria, multiple chromosomes, phagocytosis or something else - I don't know, but I'd see this, with the attendant N-independent relaxation of individual selection on genetic economy, as being more significant than population size/drift.

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  36. "As I said, retrotransposons serve to keep the gene expression dynamic. Rather than rant on about population genetics ,and the obvious point that selection is more effective in larger population sizes, I suggest you read this paper:

    Function of an LTR retrotransposon"

    It's amusing that IDC'ers point to examples like this and claim that this is somehow devastating to "Darwinism". All instances where retrotransposons are shown to have a function are examples of gain-of-function (dare I say, information) for the organism. Something that cannot happen, according to IDC'ers.

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  37. @Lone Primate and Others.

    You make a fundamental mistake in assuming that junk would inevitably accumulate in the genome when this poses an unnecessary burden on cellular metabolism - like what is the point of having introns if only to splice them out after transcribing them? Natural selection maintains biological efficiency.

    Deleting chunks of ncDNA may well have no phenotypic effect just as much as deleting whole genes may not - redundancy sees to that.

    As I say, the more research that is being done into repetitive elements, the more it is becoming clear that they do have a regulatory role. Sure, I have presented only one example - but there are many others in the literature if you care to look.

    This is a very new and exciting field: The killjoys are the Darwinists who want to poo-poo anything that contradicts their ideology.

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  38. Reza says,

    The idea of "junk DNA" is essentially an argument from intellectual laziness and personal incredulity.

    That's strange, because I think just the opposite.

    As I understand Larry's position, he accepts that much of non-coding DNA serves a function, but that the SINEs and LINEs that make up about 40% of the genome, really are junk.

    Nope. I think that 90% of our genome is junk DNA.

    I would dispute this because of what we now know about how these retrotransposable elements can modulate gene expression when they are inserted into intragenic regions.

    To me, that's an example of intellectual laziness and personal incredulity.

    Only a small percentage of retrotransposons are actually functional. They are the only ones capable of transposing.

    What you're saying is that there has been selection in favor of keeping this small percentage of active transposons because at some time in the future they might contribute to a mutation event leading to some benefit. That probability is something like one in a billion.

    Meanwhile, the probability that they will cause a detrimental mutation is about 1000-fold greater.

    I'd be interested in hearing more about this idea that you can have selection (function) for some future possibility. It sounds to me like an example of intellectual laziness.

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  39. El PaleoFreak says,

    Junk DNA is perfectly compatible with "Darwinian theory". Why do you have so much trouble understanding this?

    Darwin was a very smart man and he was careful to cover all his bases. Of course he recognized that some variation could be invisible to natural selection. You could also pick out examples of his writing that support the inheritance of acquired characteristics.

    However, to say that Darwinian theory is perfectly compatible with the inheritance of acquired characteristics would be mispresenting Darwin's theory of natural selection.

    Similarly, to focus on a few short passages in his writings in order to claim that Darwinian theory is compatible with fixation of nearly neutral alleles by random genetic drift is a serious misrepresentation of what he actually meant.

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  40. Reza says,

    The fact is that ncDNA has increasingly been found to have some function - it was presumed that introns (25% of the genome) were simply "junk" until research showed that they play an important role in eukaryotic biology.

    Nobody ever thought that all introns were junk. Statements like Reza's are not an example of intellectual laziness. They are examples of lying.

    We know that many introns have a function and we know that all introns contain essential regulatory sequences what control processing. On the other hand, we also know that most of the sequence of any particular intron has no function and can be deleted with no effect on the organism.

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  41. Larry says:

    We know that many introns have a function and we know that all introns contain essential regulatory sequences what control processing. On the other hand, we also know that most of the sequence of any particular intron has no function and can be deleted with no effect on the organism.

    The same could be said for many exonic regions, especially those that are not translated. And I can knock-out a duplicate of a gene and it will have no effect on the organism - it is called functional compensation (biological redundancy). What is your point exactly, Larry?

    Do you know that much of a peptide sequence could be seen as "junk" in your estimation because it contains no motifs that serve a crucial function?

    And what about centromeres and telomeres? Are they junk? Do they not serve any function in replication and mitosis?

    As I say, it is intellectually lazy and also dangerous to dismiss ncDNA as "junk" until all of the results are in.

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  42. Larry also remarks:

    What you're saying is that there has been selection in favor of keeping this small percentage of active transposons because at some time in the future they might contribute to a mutation event leading to some benefit. That probability is something like one in a billion.

    Except that the evidence *doe*s show that LTR transposons are subject to selective pressures.

    Retrotransposon evolution by natural selection

    You seem to not grasp the idea of selection being able to look into the future. Well, it does - certainly in the case of gene duplication. Those individuals with intact back-up copies are at a reproductive advantage over those that don't should a nullifying mutation occur in the future. In this way, selection prevents degeneracy and this is why redundancy is so widespread.

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  43. "until all of the results are in" is a dishonest tactic. It is in credibly unlikely that we will have "all of the results" since we keep finding out that the more we do know the more things we'd like to know. This is normal for science. But as Asmomov famous relativity of wrong essay points out, not knowing everything does not mean we don't know enough to state certain things.

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  44. @Reza,

    Your "wait for all of the data to come in" stance is a bit like denying gravity exists, because we have not yet observed a particle that confers the effect.

    In addition to the extensive postings on the topic here at Sandwalk, please go and read the history of the concept of "junk DNA". Another blog is documenting the ~40 years of work and discussion on the topic.

    I think ~40 years of discussion is the opposite of intellectual laziness.

    http://www.genomicron.evolverzone.com/2008/02/junk-dna-quotes-of-interest-series/

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  45. Reza says,

    The same could be said for many exonic regions, especially those that are not translated. And I can knock-out a duplicate of a gene and it will have no effect on the organism - it is called functional compensation (biological redundancy). What is your point exactly, Larry?

    My point was that you lied—or were intellectually lazy—when you said that introns used to be thought of as junk.

    There are many noncoding regions that are not junk and there are many non-transcribed regions that are not junk. I've written extensively about those essential noncoding regions but apparently you are too lazy to read the literature.

    Do you know that much of a peptide sequence could be seen as "junk" in your estimation because it contains no motifs that serve a crucial function?

    No, I didn't know that. Can you give me some examples where reputable scientists say that?

    And what about centromeres and telomeres? Are they junk? Do they not serve any function in replication and mitosis?

    Centromeres and telomers are not junk. I have never, ever, seen a scientist claim that they are. Have you?

    Centromere DNA

    Telomeres

    More Junk DNA Fallacies

    As I say, it is intellectually lazy and also dangerous to dismiss ncDNA as "junk" until all of the results are in.

    Tons of results are in and the evidence overwhelmingly supports the working hypothesis that most of mammalian genomes is junk. It is intellectually dishonest to ignore this evidence for the sole reason that you don't like the conclusion.

    Note that I said "dishonest," not "lazy." I have concluded that you are not lazy.

    ReplyDelete
  46. Reza says,

    This is a very new and exciting field: The killjoys are the Darwinists who want to poo-poo anything that contradicts their ideology.

    The "Darwinists" are those adaptationists who are committed to the belief that (almost) everything is the result of positive natural selection. They can't stand the idea that 90% of our genome may be junk so they fight back with silly arguments in order to defend their ideological stance.

    It's often referred to as intellectual laziness when a person can't adapt (pun intended) to new concepts such as Evolution by Accident.

    It's not really a big surprise that IDiots use adaptationists as their whipping boy. What's surprising is that IDiots can't see the difference between adaptationists and pluralists even on such a simple topic as the existence of junk DNA. The junk DNA debate has been going on for 40 years—that hardly qualifies as a "very new and exciting field."

    There are only two possible explanations for this IDiotic behavior. The IDiots are either stupid or liars.

    ReplyDelete
  47. Larry makes several succinct points directed at me.

    Let me get something straight:

    1) Darwinists *have* used 'junk DNA' as evidence for biological inefficiency for a long time now. John Avise, a committed Darwinist/adaptationist/selectionist, summarized it in a recent PNAS paper entitled "Footprints of nonsentient design inside the human genome"

    Aviseon junk DNA

    In the paper, Avise explicitly claims that introns are junk, be they vestigial or otherwise:

    "There are good reasons to think that cells might be better off without introns, in an ideal world. Introns impose energetic burdens on cells......Do introns
    otherwise provide evidence of optimal genomic design? No,
    because premRNA processing also has opened vast opportunities
    for cellular mishaps in protein production."


    So, I am not "lying" or being stoopid: scientists today think introns in eukaryotic genomes are basically a waste of space.

    Now, moving on...

    I know for a fact that the sequences of many untranslated exonic regions can be deleted or mutated with no real phenotypic effect. True, there are some important functional features in the 3'UTR (like for mRNA localization etc) but these are relatively small compared to most of it. You would have to conclude that there is junk inside exons.

    Proteins are remarkably flexible. For example, CCNG1 has lost a PEST sequence at its C-terminus (due to a premature truncation) but it still functions in large part because it contains the all-important cyclin box.

    CCNG1, a cyclin without a PEST C-terminus

    If you look at many gene duplicates, so long as they retain one or two essential domains, the rest of the sequence can be altered substantially. I am currently writing a paper on such a development in the Cdx "transcription factor" family. I would be happy to share my results if you are interested.

    ReplyDelete
  48. Notice that Professor Moran accepts that promoters, introns, centromeres, telomeres and other ncDNA elements are indeed functional. He just wants to give the false impression that the amount to about 6% of the genome.

    He also fails to see that non-functional "pseudogenes" are one of the best arguments used by Darwinists in suppport of their theory of common ancestry. For all the talk on "adaptation", the respite in purifying selection among duplicates can lead to degeneracy.

    Larry has obviously never heard of the term "relaxed selection" in evolutionist parlance before.

    ReplyDelete
  49. I am currently writing a paper on such a development in the Cdx "transcription factor" family. I would be happy to share my results if you are interested.

    lol

    For those not in the know, "reza" is mildly notorious internet troll atheistoclast. He's been writing papers, stalking researchers and generally being a bit of an arse for a couple of years now. Most papers have been rejected for being laughable pieces of shit, as the following rejection letters will testify:


    http://talkrational.org/showpost.php?p=961411&postcount=905

    http://talkrational.org/showpost.php?p=916841&postcount=1308

    http://talkrational.org/showpost.php?p=928402&postcount=57

    http://talkrational.org/showpost.php?p=954074&postcount=891

    But he finally managed to squeeze a paper into a journal last week. How you might ask? By targetting an obscure, multidisciplinary journal with evidently extremely poor standards of peer review:

    http://www.springerlink.com/content/q767h613177m34r1/

    Apparently there's another similarly shitty paper on its way, in a similarly shitty journal.

    I'm sure the scientific community is awaiting further "results" with baited breath.

    ReplyDelete
  50. SteveF:

    Thanks for bailing Larry out of jail: I was turning the screw before you arrived on the scene: I produced a statement from a Darwinist ridiculously claiming that introns were useless junk.

    I am still curious to know why Larry thinks that introns are *not junk* but that their DNA sequence apparently is random gibberish. As introns make up 25% of the genome, this is crucial to his argument.

    ReplyDelete
  51. Reza says,

    Notice that Professor Moran accepts that promoters, introns, centromeres, telomeres and other ncDNA elements are indeed functional. He just wants to give the false impression that the amount to about 6% of the genome.

    Please feel free to present evidence to the contrary. I've calculated the percentage of the genome that corresponds to the essential elements in centromeres (2%), telomeres (<1%), regulatory sequences (0.6%), essential RNA's (<1%), and the essential regions of introns (<1%).

    There are a few other sequences that I haven't addressed—such as SARs and origins of replication—but these don't account for more than 1% of the genome.

    Why do you think that the evidence I've presented is "false"? If you have a better scientific explanation then please tell us. Don't be lazy.

    ReplyDelete
  52. Reza says,

    Thanks for bailing Larry out of jail: I was turning the screw before you arrived on the scene: I produced a statement from a Darwinist ridiculously claiming that introns were useless junk.

    I'd like to reiterate Reza's vote of thanks. Until SteveF posted his comment I was about to crack under the pressure of Reza's amazing logic. Thanks again, Steve.

    For the sake of any readers who are still hanging on, let me summarize the point about introns. Contrary to what Reza said, there was never a time when the consensus among evolutionary biologists and molecular biologists was that all introns are junk.

    And there was certainly never a time when "Darwinists" believed that since it contradicts their main premise.

    Reza quoted John Avise as an example of a "committed Darwinist/adaptationist/selectionist" who says that introns are junk but that's a lie as can be easily seen from the quotation Reza used.

    First, Avise is a pluralist, not an adaptationist.

    Second, Avise is pointing out that the presence of introns is not a very good example of intelligent design and there's good reason to question whether introns were even necessary in the development of modern organisms. A good designer, according to Avise, could have easily designed a better genome without using introns.

    Nevertheless, given that evolution has produced split genes (introns) we are stuck with an elaborate system for coping with that evolutionary accident. Consequently, some of the intron sequence is currently essential for survival and mutations in those regions can be lethal.

    Avise makes this point in his PNAS paper, and several times in his book, by emphasizing that up to one-third of human genetic diseases are due to mutations in splicing. That's not evidence of junk.

    Avise also points out in his book (Inside the Human Genome: A Case for Non-intelligent Design) that alternative splicing is an important and essential process in eukaryotes. Since that process requires introns, it follows that at least some introns are essential in the opinion of John Avise.

    Reza does not appear to be very efficient at reading for comprehension.

    ReplyDelete
  53. Reza asks,

    I am still curious to know why Larry thinks that introns are *not junk* but that their DNA sequence apparently is random gibberish. As introns make up 25% of the genome, this is crucial to his argument.

    Some intron sequences are essential for survival. These include the 5' and 3' splice junction sequences and the branch site. We should also include small regulatory sequences that control alternative splicing [RNA Splicing: Introns and Exons].

    Some of rest of the intron sequence is necessary in order to form the loop required for formation of the spliceosome. Thus, the minimum size of an intron is about 100 bp. The rest of the DNA for introns is dispensable and the sequence is not conserved [Junk in Your Genome: Intron Size and Distribution].

    Reza, you're welcome to contest any of the statements I've made. The only criterion is that you have to support your statements with evidence.

    Good luck.

    ReplyDelete
  54. Larry,

    If Avise recognizes that introns serve as important spacer sequences to facilitate alternative splicing /exon skipping then why does he assert that eukaryotic cells would do better without them? That is an extraordinarily stupid statement for Avise to make. He hasn't shown how a "designer" could have built a genome with no introns in the case of eukaryotes, so why should I accept his argument?

    Adaptationists (like Avise, Ayala or Dawkins) are OK with the idea of pseudogenes and other junk can result from a relaxation of selective pressures - like during a population bottleneck when random drift is a much bigger force than selection.

    Now, I want to know why you think that "non-essential" parts of introns - i.e. those which do not contain regulatory motifs - should be seen as "junk"? What if their function is just to separate exons or to contribute to mRNA stability as research shows?

    Introns and mRNA stability

    You continue to avoid answering my point concerning "essential regions" of proteins. In the FOX gene family, the forkhead box is essential to function - the rest of the peptide can be significantly altered or deleted. In the Cdx family, the homeodomain is essential but the rest is not.

    You are offering a minimalist dogma - that there exists a minimal amount of DNA which is absolutely essential to life. I would agree with you - but I don't think the rest can be categorized as "junk" - that is nonsense.

    ReplyDelete
  55. Larry,

    I am really curious. Have you ever heard of the term "biological redundancy" before? You do know that the information in a data file can be compressed to ensure a "minimal redundancy". This does not mean that it contained any "junk" as such.

    You need both essential and non-essential regions of DNA to make life function optimally. Naturally, the non-essential regions are liable to mutate more freely than the essential bits.

    This must come as a surprise to you....but not to myself.

    ReplyDelete
  56. Reza, is it true that you are Joseph Esfandiar Hannon Bozorgmehr from Manchester UK?

    Is it true that you are also known as "Atheistoclast" and that you have created up to 95 different accounts on RichardDawkins.net in order to avoid being banned from that site?

    You claim that you "went back to the UK to start a business selling components - just nuts and bolts - to the Iranian nuclear and missile industries." Is it true that this business was shut down because it broke international law?

    ReplyDelete
  57. @Larry

    To all of your intrusive and personal questions:

    Yes, that is my proper name.

    I was repeatedly banned on the RD site for arbitrary reasons and so kept "re-introducing" myself to avoid the censorship. Dawkins himself closed down the site because of the disgraceful behavior of the members and the poor standards of moderation. I cannot be faulted.

    I was involved in *legally* selling specialized CNC-made parts to the Iranian aerospace and power industries but the imposition of sanctions prevented the business from succeeding. I broke no laws. I know that in Canada you lot are very strict on trade with Iran.

    Now, I write scientific papers that dissent from Darwinism.

    Anything else?

    ReplyDelete
  58. Reza, aka Joseph, aka atheistoclast also claims that the Holocaust isn't true and holds to major conspiracy theories conspiracy concerning the "British Establishment". He's also banned at Pharyngula - part of the banning note refers to the multiple rejected papers. I suppose that part at least should now be altered, after the idiots at Journal of Bioeconomics dropped the ball.

    TBH, it's rather difficult to know exactly what he believes and I'd caution against taking anything he writes at face value. Part of me thinks that the whole thing, including the crappy paper published above, is a troll of truly epic proportions. More likely, he believes some of this stuff and not others and delights in winding people up.

    Oh and judging from the PM that just appeared in my inbox, he isn't very happy with my post above.

    ReplyDelete
  59. Larry writes:

    Is it true that....

    Judging from the quote below, I'm thinking he may have a somewhat different concept of "truth:"

    "As with holocaust revisionism, evolutionism revisionism is important in establishing the truth."

    ReplyDelete
  60. SteveF:

    Why all the vitriolic and ad hominem remarks directed at me?

    I have been nothing but polite here on Sandwalk, and have responded to all of Larry's points and those of the others.

    The fact is that Prof. Moran's blog is ***massively*** better than PZ or Jerry's. He talks about real science, whereas they discuss just about any old nonsense.

    You *hate* the fact that I have had a paper published in a Springer journal because you know that you could not do the same. Publishing in a mainstream academic journal is *not easy*.

    Sure, my criticism of the orthodoxy goes beyond evolutionary theory - I question many things where censorship is widespread.

    The 'right to oppose' is fundamental to any kind of progress in science and society as a whole.

    ReplyDelete
  61. Steve F,

    Thanks to your thread derail I missed the kill: Larry got away.

    Anyway, ncDNA is not my area of expertise: gene duplication is.

    ReplyDelete
  62. Reza:
    I am really curious. Have you ever heard of the term "biological redundancy" before? You do know that the information in a data file can be compressed to ensure a "minimal redundancy". This does not mean that it contained any "junk" as such.

    "Redundancy" - it's the new "complexity"! :D

    Oh well, let's feed the troll.

    Your analogy is flawed. A Kolmogorov random string has maximum entropy and is thereby incompressible. Thus the more random the data, the worse they can be compressed.

    Also if your argument is the functionality of redundancy why don't you prove it? You can easily control for the Shannon entropy of the alphabet and then define a metric (e.g. Damerau-Levenshtein) of the code to measure. And it's very straight-forward to just do what LM advised: I.e. cut away any redundancy your current understanding assigns no functionality to and observe the results.

    I'm no biologist caveat: I have no idea if it is technically feasible to "cut away" redundancy in the genome. I think I remember something about LM saying that you can infer redundancy by the statistical change to the respective regions. That certainly sounds doable.

    So if you're so convinced of your ideas: Do it! You'll be quite famous if you succeed. Even if you fail honestly, i.e. we can salvage the negative from your excellent scientific procedure, I'm sure we can get PZ Myers to unban you. ;)

    ReplyDelete
  63. Larry: "It's not really a big surprise that IDiots use adaptationists as their whipping boy."

    What's weird is that they turn around and use adaptionist arguments to promote the idea that most (all?) DNA must have function. After all, why would an ID create a species with a bunch of junk in its genome -- It must all be functional!

    ReplyDelete
  64. Reza says,

    Anyway, ncDNA is not my area of expertise ...

    That was pretty obvious. It was also obvious that you don't understand the difference between non-coding DNA and junk DNA.

    Too bad Steve derailed the discussion or I would have had time to educate you—although I'm told that many other have made the attempt and been unsuccessful.

    ReplyDelete
  65. Larry,

    You need to understand coding DNA in order to fully understand the importance of non-coding DNA.

    1) You don't get how much of coding DNA contain no biochemical motifs and any major function.

    2) You don't seem to understand that the "function" of large amounts of DNA is just to contribute to stability and or redundancy.

    I repeat, you are a *reductionist* and a *minimalist*. You fail to comprehend that being "non-essential" does not necessarily mean "junk".

    ReplyDelete
  66. Reza says,

    You need to understand coding DNA in order to fully understand the importance of non-coding DNA.

    And you're going to teach me, right?

    1) You don't get how much of coding DNA contain no biochemical motifs and any major function.

    I'm all ears. As it happens, your timing is perfect 'cause right now I'm writing up a section for the next edition of my book. The section is on "Intrinsically Disordered Proteins" and I was having a great deal of trouble with it—it didn't make sense because of my mistaken belief that every single amino acid was necessary for function.

    Thanks for pointing out my error.

    2) You don't seem to understand that the "function" of large amounts of DNA is just to contribute to stability and or redundancy.

    I think I get the "stability" part. If you read my articles on junk DNA you might see a few glimmers of understanding.

    "Redundancy" also seems pretty simple. I don't think anyone says that extra copies of a protein-encoding gene are junk. Besides, it's a trivial part of the problem.

    With respect to "stability" and "redundancy" where, exactly, did I go wrong?

    I repeat, you are a *reductionist* and a *minimalist*. You fail to comprehend that being "non-essential" does not necessarily mean "junk".

    Thank God you were able to discover that fatal flaw in my defense of junk DNA.

    ReplyDelete
  67. Stealing from Monty Python's 'Meaning of Life':

    'Every amino acid is sacred.
    Every amino acid is great.
    If a amino acid is wasted,
    God gets quite irate.

    [...]
    Every amino acid is wanted.
    Every amino acid is good.
    Every amino acid is needed
    In your neighbourhood.
    '

    ReplyDelete
  68. Larry,

    You're already getting your free education, and have been forgiven for your sinful remarks.

    Many residues in a peptide sequence can indeed be altered with no consequence. It depends on the protein - those involved in translation initiation, for example, are going to be stringently preserved by purifying selection. However, as a general rule, there exists a conserved motif which represents the essential function, and the rest of the sequence is ancillary.

    The crucial homoeodomain consists of about 60 amino acids, but most Hox genes are 300-400 residues long. So, only abut 20% of the protein sequence is "essential" for DNA-binding in developmental regulation. It doesn't mean the rest is "junk" - it is just more "flexible" in sequence.

    Regarding stability, I cited in a previous post some research into introns which shows that they appear to have a role in mRNA stability - like with the 3'UTR.

    Redundancy is not limited to coding DNA - 80% of eukaryotic genomes are made up of duplicates -
    but this may also be the case for many SINES and LINEs to ensure against degeneracy and the inactivation of retrotransposons. The more redundancy you put into a system, the more "robust" it is, albeit inefficient in terms of space. This is not an argument in support of ID since evolutionary processes have been observed to be responsible for maintaining robustness in the genome.

    I don't know whether you are aware of research into ncDNA in Drosophila: The authors of a 2008 paper talk of a "large fraction" of ncDNA being functionally important.

    ncDNA in Drosophila simulans

    "Overall, these results support recent claims that a large
    fraction
    of noncoding DNA in Drosophila is functionally
    important (Bergman and Kreitman 2001; Andolfatto
    2005; Haddrill, Charlesworth, et al. 2005; Bachtrog and
    Andolfatto 2006; Halligan and Keightley 2006)."


    But you insist that only 5-6% of ncDNA could possibly be useful.

    ReplyDelete
  69. Oh, come on LM, even someone as uneducated as you can't believe Reza wrote 5 times about something as minimalistic as error failsafes when invoking the power of "redundancy". How lamely reductionist of you. Have you learned nothing of Master Chopra?

    Obviously even if error correction (and alphabet [codon?] redundancy) is accounted for there is another holistic functionality to redundancy which we just haven't caught on to.

    Alas, we probably never will, since it is so redundant. At least not with this dogmatic narrow-mindedness called "science".

    ReplyDelete
  70. Btw, here's a serious (algorithmic information theory) paper on logical depth and fault-tolerant evolution:
    http://www.cs.bu.edu/faculty/gacs/papers/self-correcting-2d.pdf

    Note the subtle difference in depth to ... "redundancy".

    ReplyDelete
  71. Btw, for junk to accumulate in the genome, the rate of production must exceed the rate of deletion. Evolution tends to delete stuff as well as copy stuff.

    The reason why many duplicate coding genes have been retained is because they serve a redundant function - they compensate for loss of function mutations. They have been preserved by selection for this biological utility.

    If there is real "junk" in the genome then selection would try and whittle it down because of the energy costs of having to replicate it when it serves no use.

    There is a method in the madness of having large swathes of ncDNA.

    ReplyDelete
  72. The problem is that Larry is old school. His generation preceded the "information age" and he is incapable of understanding the relationship between genetics and information & communication theory.

    ReplyDelete
  73. Reza says,

    The problem is that Larry is old school. His generation preceded the "information age" and he is incapable of understanding the relationship between genetics and information & communication theory.

    Yeah, you're pretty much right about that.

    I didn't write my first biochemistry computer programs (in FORTRAN) until 1968 and they ran on an IBM360/91. That was already a third generation computer—computers had been around for twenty years by then.

    Some of my friends had been programming for years before I ever started. So I was late to the party and never really caught up.

    ReplyDelete
  74. Reza says,

    If there is real "junk" in the genome then selection would try and whittle it down because of the energy costs of having to replicate it when it serves no use.

    [Slaps hand on head!]

    Now, why didn't I think of that? I must be really stupid!

    Thanks, Reza, for showing us how knowledgeable you are about evolution and information theory.

    ReplyDelete
  75. No problem, Larry.

    I knew you had overlooked the fact that life aims to be as efficient as possible. I now offer you a way to TEST which one of us is right.

    The Neanderthal genome has been sequenced. Now, if we accept your theory of inexorable junk accumulation, there should be *less* junk in the Neanderthal genome than in modern humans (since 50,000 years and over 2000 generations or so separates us).

    We might also look at T-Rex DNA that was recovered a few years ago.

    Btw, do you envisage junk accumulating ad infinitum? Are we destined to have enormous genomes full of junk sequences?

    ReplyDelete
  76. Reza asks,

    I now offer you a way to TEST which one of us is right.

    The Neanderthal genome has been sequenced. Now, if we accept your theory of inexorable junk accumulation, there should be *less* junk in the Neanderthal genome than in modern humans (since 50,000 years and over 2000 generations or so separates us).


    Boy, you ask some tough questions that really put me on the spot!

    Let me try and answer—I hope the result won't be any more embarrassing for me that your previous questions.

    First, I wasn't aware of the fact that I had a theory of inexorable junk accumulation. How perceptive of you to have noticed that this was an important part of my position.

    According to Ryan Gregory's database on primate genome size, humans have a genome size of 3.50 pg. For chimps it's 3.68 pg and in the cases of gorillas and orangutans their genome sizes are 3.75 pg and 3.79 pg respectively.

    It looks like humans are losing DNA so there goes my theory up in smoke! Damn.

    I guess Neanderthals should have a tiny bit more junk DNA based on these numbers. Does that mean you are right .... again?

    ReplyDelete
  77. Not really, Larry. Junk accumulation should increase with generational time and not evolutionary lineage.

    The Neanderthal genome represents Homo sapiens DNA from as much as 100,000 years ago. It is an insight into an ancient human.

    I am concerned that you have no way to test for and verify/falsify junk accumulation. If something cannot be tested for, why should it be regarded as scientific?

    Also, have you calculated the metabolic cost of all 60 trillion cells in our body having to replicate so much junk? Could we all be much more energetic and healthy if we dispensed with this evolutionary garbage?

    ReplyDelete
  78. What Reza keeps referring to as "redundancy" is far closer to "degeneracy". Large amounts of structurally different entities serve the same essential function. At the very least I fail to see this is a compelling argument for intelligent design.

    ReplyDelete
  79. Tyler,

    The use of redundancy - that is a fail-safe against degeneracy - is in fact part and parcel of good design. Always have a backup. Of course, stoopid biologists (they are not scientists in the true sense) are realizing this now.

    However, the genome seems to be designed to be prone to duplicate and so add to biological robustness at the cost of efficiency.

    If we removed all the ncDNA that Larry regards as "junk" you would find that life might just about be possible, though it would be at breaking point and extinction would be far more probable.

    ReplyDelete
  80. Reza says,

    Not really, Larry. Junk accumulation should increase with generational time and not evolutionary lineage.

    I'm just about finished playing with you, Reza, but I'd like to add a few comments just to set the record straight.

    Nobody, especially me, says that the amount of junk DNA should increase with time. The data is all over the map. Junk DNA accumulates in some lineages and appears to be lost in others.

    I am concerned that you have no way to test for and verify/falsify junk accumulation. If something cannot be tested for, why should it be regarded as scientific?

    We have tons of data on genome sizes in thousands of species. The data says that junk DNA accumulates in some and not in others. The data says that there's no correlation between complexity and genome size.

    What other kinds of tests are you looking for?

    Also, have you calculated the metabolic cost of all 60 trillion cells in our body having to replicate so much junk? Could we all be much more energetic and healthy if we dispensed with this evolutionary garbage?

    We can do some rough, back-of-the envelope calculations. First, very few of your cells are replicating DNA but you would have to study a bit of biology to know that.

    For any given human cell you can assume that 10,000 genes are active and they produce, on average, 100 primary transcripts per generation (one day). That's already more expensive than the cost of replicating the entire genome. Add in the cost of making proteins from these active genes and the cost of replicating the genome drops to less than 10% of that total—and that's being generous.

    Now, when you start adding up the cost of making lipids & membranes, carbohydrates, and other cell component, the relative cost of DNA synthesis drops even further. And we haven't yet factored in transport—that's a biggy.

    I'd estimate that for rapidly dividing human cells the cost of replicating junk DNA can't be more than 1% of the total cost of cell metabolism. It will be much less for cells that don't replicate every day.

    The available data indicates that about 90% of our DNA is junk. This strongly implies that whatever energy cost this entails it isn't sufficient to affect fitness. That, in turn, strongly suggests that biology is sloppy and no organisms are optimally fit. In other words, natural selection is much less potent than most people believe.

    ReplyDelete
  81. It seems Larry has proposed *no formal test* to determine the "junkiness" of most of the genome.

    Of course, "junk" should accumulate over time! Evolution is a time-related process for goodness sake! Accumulation may vary according to each species, but one should expect there to be more junk DNA around now than 500 million years ago.

    I have cited numerous papers which all attest that much of the sequences found in introns, UTRS, retotransposable elements and other ncDNA is in fact functional, although maybe not essential, and is subject to selection. If you want to ignore the evidence and live in abject denial - fine.

    Even a 1% metabolic energy cost would be critical in an environment where food resources are short or where climatic conditions are harsh - natural selection would therefore aim to whittle the "junk DNA" down.

    I confidently predict that your analysis will soon be consigned to the ash heap of history, like so much of the claims associated with evolutionary biology.

    ReplyDelete
  82. Assuming Larry has had enough and knows he is well-beaten,I am declaring myself the winner of this debate.

    It is a victory of science and rationalism over ideology and superstition.

    ReplyDelete
  83. Reza states:"Of course, "junk" should accumulate over time! Evolution is a time-related process for goodness sake! Accumulation may vary according to each species, but one should expect there to be more junk DNA around now than 500 million years ago."

    Well, if we accept Lynch's (2007) well-evidenced line of thinking, there is a pretty clear, general link between effective population size and 'junk' accumulation. I know of no one that posits some kind of general and continual accumulation of 'junk' without consideration for factors like Ne.

    Incidentally, in the human lineage, there has of course been massive population expansion, and orresponding evidence for increased selection. Thus there is no reason at all that I know of to expect a linear increase in human 'junk' DNA continuing to this day.

    ReplyDelete
  84. I've said elsewhere, I've you've got enough energy to play Nintendo, you've got enough extra energy to evolve. Now I'll have to append: '... and carry junk in your genome'.

    I mean, we cycle through over our bodyweight in ATP every day.

    ReplyDelete
  85. Paul,

    Lynch refers to the fact that the probability of fixation for a neutral allele is 1/2N in a diploid population. So, in smaller populations, junk should accumulate more rapidly than in large populations. However, Lynch ignores the fact that neutral variation can still be effected by selective forces due to genetic linkage and other factors.

    Larry believes junk has accumulated in the genome. Such junk must have accumulated *over time*. It didn't just suddenly come into existence. As such, if we extracted DNA from an ancient fruit fly, we would expect it to contain *less junk* than in contemporary species.

    That is my argument.

    ReplyDelete
  86. Reza states:"Lynch refers to the fact that the probability of fixation for a neutral allele is 1/2N in a diploid population. So, in smaller populations, junk should accumulate more rapidly than in large populations. However, Lynch ignores the fact that neutral variation can still be effected by selective forces due to genetic linkage and other factors."
    Of course neutral variation can - and is - affected by linkage. This does not constitute any sort of a argument against Lynch's position. After all, linkage does not increase the amount of neutral variation that gets fixed in a population (Birky and Walsh, 1988).

    "Larry believes junk has accumulated in the genome. Such junk must have accumulated *over time*. It didn't just suddenly come into existence. As such, if we extracted DNA from an ancient fruit fly, we would expect it to contain *less junk* than in contemporary species."
    Ah yes. I see the reason people have used the word "troll" in this thread. Will you just keep repeating yourself in spite of any evidence presented to the contrary?

    Once again, yes junk accumulates, but there is not some linear increase with time. The ability of populations to purge junk relates to Ne. If the species of fruit fly you have in mind was once marginal or fragmented and now widespread and ubiquitous, it is possible that the ancient genome would have more junk that the contemporary one.

    "That is my argument.
    You're right there. It's your argument with yourself, because you're only addressing strawmen of your own making.

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  87. Atheistoclast:
    "Anyway, ncDNA is not my area of expertise: gene duplication is."

    Really? Expertise? By what criterion are you an expert?

    What are your publications on the subject such that you deserve such a moniker?

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  88. @Reza,

    You seem to have missed this on another thread.

    I think you really should check out this posting...
    http://pandasthumb.org/archives/2010/11/dont-know-enoug.html

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  89. Paul,

    I never stated there was a *linear increase in junk accumulation - stop trolling. Maybe it accumulates in fits and starts. But accumulate it must *over time* if Moran is right. At one point there must have been little or no junk in eukaryotic genomes.

    Irrespective of population dynamics, we should expect there to have been *less junk* around 500 million years ago than today.

    That is why I am proposing, if feasible, extracting DNA from the remains of ancient species ( we did it with T-Rex) and determining how much ncDNA is present.

    Anyway, I dispute that there is much junk at all in the genome...and most scientists are coming round to my thinking.

    Not so junk DNA

    I really wonder whether Larry actually reads about any of the research conducted into ncDNA in the past few years. I think "junk DNA" has become an article of faith for him - a kind of religion.

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  90. Reza said

    That is why I am proposing, if feasible, extracting DNA from the remains of ancient species ( we did it with T-Rex) and determining how much ncDNA is present.

    Umm... you do know that was a movie, right?

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  91. Hey, Reza, it gets worse –the following piece in Science that may offend you greatly ;-)

    http://www.sciencemag.org/cgi/content/full/330/6006/920

    That's right, we think perhaps much of cellular complexity itself may be "junk". Genome 'junk' is trivial by comparison, ha!

    Then again, those authors know way more about the diversity of eukaryotic genomes and molecular biology than you could ever dream to – most of you think animals, fungi and plants are all there is to eukaryotic diversity, and ignore the other 90%. And pretend like your special cases apply to the rest of life. Good luck with that.

    * Just so you're aware, I'm no less convinced in my stance than you are in yours, so there's no point in you arguing with me unless you bring solid facts and data on the table (eg, verifiable examples, primary research papers – not review literature – that shit's heavily opinionated anyway)

    Anyway, I'm pretty much convinced you're a troll anyway, but I felt like being snarky and you're a very appropriate target for that.


    Oh, and if you decide to ad hom attack any of the authors on that paper, the level of snark in this comment will be peanuts compared to what will come at you then. I know some of those people personally. You've been warned.

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  92. @Reza,

    One 'function' of maintaining junk is that it enables paired haploid genomes to perform a successful meiosis. You are constrained by what everyone else in the population has. There might be a metabolic cost to replicating it; it could be huge, but if getting rid of a large chunk of it renders your gametes sterile one generation on, there is a balancing pressure against that. If we all agreed to get rid of the same bits, we might become a super-race of super-organisms, but eukaryotes are doing OK as they are, to be honest.

    Additionally, any individual losses can only be piecemeal. If (try accepting the position for argument's sake) we really do have a vast amount of unnecessary genome baggage, you can only shed it in small chunks (otherwise you will shed real genes along with it, even setting meiosis aside). The evolutionary advantage associated with such cheese-paring is likely to be minuscule, as a selective advantage in terms of additional offspring produced.

    It has also come to play a role in development - if it takes extra time to replicate it, that time is factored into the tuned developmental pathway. Get rid of it, and we might develop quicker; we might also develop in some decidedly odd ways. Just because something like junk was not selected 'for' does not mean it can be dispensed with at a later date without impact.

    I know you won't accept these points, because you clearly have a strong emotional investment in an adaptive/design reason for the genomes that we have, but it strikes me that the 'junk' hypothesis - eukaryote genomes are bloated because the pressure towards reduction is weak at best - is the likeliest position, pending a demonstration of a direct sequence-dependent functional role within the individual.

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  93. Just a clarification – in my above comment, the "we" in the first paragraph makes it sound like I'm involved in that paper – I'm NOT. I changed the preceding sentence a few times and only now realised that 'we' doesn't convey what I initially meant it to...

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