Are Selfish Genes Selfish? Are Retro-transposons Junk?

_{January 12, 2012

'Junk DNA', Darwinism}

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At PhysOrg.com, they have an article dealing with the CTCF protein and its binding sites. It turns out that the CTCF has both binding sites that are common to all mammalian lineages, and thus “conserved” and “ancient”, as well as binding sites found only in particular lineages. The binding sites found only in particular lineages are embedded inside “retro-transposons”, which “use a copy-paste mechanism to spread copies of themselves throughout the genome.”

However:

The retro-transposon’s copy-and-paste behaviour has long been considered totally self-serving. However, the study showed that when a retro-transposon containing a CTCF-binding sequence spreads around a mammal’s genome, it can deposit functional CTCF binding sites in novel locations, altering the activity of distant genes.

Further:

We looked at six mammalian species representing primates, marsupials, rodents and carnivores, and discovered a simple mechanism that they all use to remodel their DNA . . . ”

Another day; another bad day for Darwinism. It looks like “junk” isn’t “junk” after all. FYI, here’s the link.

Comments

Chas D:
Viable transposons code their own transposition, ’tis true. That itself is curious. If they were ‘for the benefit of the genome’, one would not expect to see them acting like viruses.
Nice strawman.
But MUCH more important to note is that the vast majority of transposon sequences in the genome are broken.
They have done their job- finished, no need to jump around. But anyway how does your position explain transposons? Or was I right...Joe_{January 15, 2012
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Transposons carry within its DNA sequence the coding for two of the enzymes it requires to “jump around”, meaning your position doesn’t have any explanation for them beyond “looky thar at them tahr thingies!”
Not one of most incisive pieces of argumentation, Joe. Viable transposons code their own transposition, 'tis true. That itself is curious. If they were 'for the benefit of the genome', one would not expect to see them acting like viruses. An organism-controlled transposable sequence could be operated on solely by genes outside it - the sequence itself does not have to possess any genes at all. And better it doesn't, because these things can rapidly get out of hand. Yet it does have genes - those genes benefit, first and foremost, the transposon. Having jumped, provided it does not break, a viable transposon can jump again. And again. And again. Each new viable copy can spawn new copies - an exponential process. Sometimes - it could not be otherwise - a transposon lands in a gene. This is much the same as a mutation. The sequence added is pretty 'random'. Sometimes the result is detrimental, sometimes it is neutral. And sometimes it is beneficial. But MUCH more important to note is that the vast majority of transposon sequences in the genome are broken. They do not have viable copies of the enzymes required to jump around - which is a damn good job because these things can spread like wildfire when they get out of hand. It is, on the surface, a crap, scattergun way of generating novelty. "RM+NS" cannot do nuffing, but spraying transposons round like schrapnel can? Even if active transposons serve a 'purpose', there is no reason to suppose that inactive ones do by association. Their purpose cannot be to transpose, since they cannot transpose. One could argue that damage to transpositional ability is a designed 'fail-safe' to limit over-infestation. But nothing is sweeping up this debris. Dead transposons are, as far as can be told, junk, whatever their active or gene-inserted cousins may be up to. And there are millions of 'em!Chas D_{January 15, 2012
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Transposons carry within its DNA sequence the coding for two of the enzymes it requires to "jump around", meaning your position doesn't have any explanation for them beyond "looky thar at them tahr thingies!"Joe_{January 15, 2012
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I honestly believe that it takes blind faith on the part of evolutionists to believe that known Darwinian processes can account for macro-evolution. This is the challenge for Darwinism; and it can’t rise to meet it.
To respond, I need your definition of "macro-evolution". If you have already given it, apologies, but could you repeat it?Elizabeth Liddle_{January 15, 2012
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IOW, “evolutionist” is too vague. Darwinist is much more specific and accurate, as it identifies the person’s reliance on random variation and selection (environmental change).
IOW, you completely misunderstand the point. I wasn't proposing an alternative, merely pointing out the inaccuracy of the "darwinist" label. You can call me what the hell you like, to be honest, but simply in the interests of accuracy, calling all advocates of 'unintelligent' evolution darwinists because it "identifies the person’s reliance on random variation and selection" is precisely why you CANNOT call all such people darwinists! Inasmuch as you see it as a political movement or a religion, or need a handy label to lump together the heathen herd, knock yourself out. "Evolutionist", to me, is like "geneticist" - one who studies evolution: mechanism, cause, consequence. And I guess I am neither, professionally. But no-one is a "Newtonist", or a "Mendelist" or "Morganist" or "Fisherist". One immediately finds oneself wondering which of Darwin's many views (some accurate, some not) one is being associated with. It provides a useful means for the lazy to attack the subject, I suppose. Common descent preceded Darwin, and Natural Selection was independently elucidated both prior to and contemporary with his formulation. He was uncannily prescient on a huge amount of the modern theory, but ... Even in your terms, it is difficult to determine why the discovery of a previously unknown functional role for some instances of a transpositional sequence should be a bad day for those who consider the mechanisms underlying evolution to be neither goal-directed nor demanding of intelligent tweaking.Chas D_{January 15, 2012
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Chas D: Darwinism can mean several things: 1) Common Descent 2) Gradualism 3) Natural Selection as the prime reason populations change. And being an "evolutionist" can also mean several things: 1) Life evolved 2) Life evolved through random processes 3) Life evolved through random processes and common descent. Hardly anyone outside of the odd popular science writer calls themselves a “darwinist” these days. He did write in 1859, after all, and things move on. However, it was Darwin who proposed his putative "theory of evolution". And to call yourself an "evolutionist" fails to distinguish between those who, unlike YEC, believe that life forms developed over a time frame witnessed to by the fossil record. This is the same failure that marks the imprecision of equivocating that "evolution is a fact" and "I believe evolution occurred through Darwinian processes." IOW, "evolutionist" is too vague. Darwinist is much more specific and accurate, as it identifies the person's reliance on random variation and selection (environmental change). An over reliance on neutral drift renders NS an almost invisible force, and so I'm not sure what that makes someone. I guess I'll call them "drifters"! ;)PaV_{January 14, 2012
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Elizabeth: Here's another metaphor. Imagine a computer programmer who, having built his software and the computer to run it on, writes a program to carry out a specific function. Then imagine this programmer writing other such programs, and then stringing them together so that in the end, an incredibly complex level of functioning is made possible. I like my metaphor better than yours.PaV_{January 14, 2012
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Chas D and E Liddle: Neutral theory was proposed by Kimura because of the high degree of polymorphisms found in proteins. Because of genetic load, directional selection could not be taking place at so many loci all at once. Kimura promoted the idea of neutral drift coupled to positive selection way back in the 80's. To this point, this is all just history. Yet, the problem remains that of a realistic time-frame. Yes, neutral drift happens, but it happens extremely slowly, not allowing realistic time-frames for significant genomic change. [The "infinite allele" model of Kimura is based on the fact that if an allele (whatever exactly this means) mutates, that the probability of it mutating again is so remote that it's as if this allele goes on as it is forever.] And positive selection still has the problem of genetic load, a problem exacerbated by the greater degree of polymorphism discovered through WGA. I honestly believe that it takes blind faith on the part of evolutionists to believe that known Darwinian processes can account for macro-evolution. This is the challenge for Darwinism; and it can't rise to meet it.PaV_{January 14, 2012
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No, the other way round: there is always drift, and sometimes bias to that drift, aka "natural selection". The metaphor goes like this: The imagine a bottle bobbing about on a choppy lake. If there are no currents (and no prevailing wind direction), it will take a "random walk" - it is likely to end up far from where it was first dropped, but there's no way of knowing where, apart from knowing that the longer you've left it, the further from the start it is possible for it to end up. Now add a current. The thing will still do its "random walk" but there will be a bias to the probability of where it ends up - it's more likely to end up downstream than in any other direction. The weaker the current, the less the probability that it will end up downstream in preference ot any other direction. The stronger the current, the greater the likelihood it will end up downstream. Or, my more potent metaphor: Imagine losing a toddler in IKEA. The longer he's missing for, the further he could have got to, but there's no way of knowing in which direction he's likely to be (although he'll never be far from where he was half a minute ago). However, if there is a hot dog stand in the store, there's more chance his next move at any given time will be in the direction of the hot dogs. So your best bet (though it is still a remote one) is to head there. The maze of aisles in IKEA are drift. The hot dog stand is natural selection. The toddler is the population.Elizabeth Liddle_{January 14, 2012
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"in which “selection” is simply a bias to the stochastic sampling of alleles in each generation, in favour of what increased reproductive success in the parent generation." Then, there is always "natural selection? never genetical drift?Blas_{January 14, 2012
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Changes in genotypes is not what evolution is broadly concerned about
OK, as an explanatory framework for changes in phenotypes, that makes some sense. But at base, the underlying mechanism by which phenotypes change is by population and lineage changes in genotype. That may be mediated via phenotype; it may not.Chas D_{January 14, 2012
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Although to my mind it makes more sense to combine them in a single concept, in which “selection” is simply a bias to the stochastic sampling of alleles in each generation, in favour of what increased reproductive success in the parent generation.
Absolutely. It's all about sampling. When selection is 'off', it's all drift. Turning up the selective 'heat' diminishes, but does not eliminate, the role of drift. The compartments are historic - Selection, then Neutral Theory, then Near-neutral theory. The reality is a continuum, dependent on the intensity of selection.Chas D_{January 14, 2012
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Changes in genotypes is not what evolution is broadly concerned about
I'm afraid you are mistaken. You are telling 'evos' what it is they study? Genotype is all that is inherited (you may shout "epigenetics!", but epigenetic factors ultimately trace back to genetic ones). And to declare that evolution is only interested in limited 'types of change' is hogwash. Genotypes are sorted (by selection) according to some phenotypic effect that they have on the lives of organisms built from them. To that extent, yes, phenotype is important. They are also sorted (by drift) completely independently of their effects on phenotype. Either way, what gets squirted into the next generation are genes, functional and nonfunctional alike.
Evolution must predict ‘a whole lot’ of junk, if it made real predictions, but will accommodate any amount.
It really, really, depends on circumstances. Sorry. Evolutionary theory is about the regularities dictated by the central processes (replication in a finite world). The causes of any differential are necessarily circumstantial. The distributions of junk across various taxa are raw data, not predicted results - though the existence of junk was indeed predicted by an 'evo' (Ohno). I wasn't aware he had been in your face about it. What 'real predictions' do you have in mind? Lottery numbers? The winner of the next Derby? What predictions do other sciences make? "If I hold a rock out and let go, I predict that it will fall". "Suppose you are deep in space with no planet or star anywhere in the vicinty". "OK smart-arse, if I hold a rock out and there is a massive body nearby it will fall". "OK, exactly where on the surface will it end up?" "Ummmm...". "Aha! Your so-called science fails to make a prediction. Nya-nya-nya-nya-nya" It is not the fault of evolutionary theory that the entities produced by the stochastic processes of evolution are divergent wrt this or that characteristic. "If being a giraffe is so great, how come everything on earth isn't a giraffe?". Junk was 'predicted' by an evo. No-one believed him, because 'evos' felt, like ID-ers, that such wastage would not be retained. There was a debate. 30 years later, and refined by widely available genome databases, it looks like the 'selectionists' were wrong ("a bad day for evo!"). The greater part (ie >50%) of most eukaryote genomes appears to be nonfunctional. Allowing for cryptic function (and being 5 times more generous than I am inclined to be) it is unlikely that we will see functional sequence in humans getting past 25%. That is not based upon evolutionary theory, it is based upon functional analysis. I could be wrong. And so bloody what if I am? What would that mean for evolutionary theory (as opposed to Ohno's theory)? Another bad day for evo, of course. How do we cope?Chas D_{January 14, 2012
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No citation needed, we've had to endure evos hopped up on 'junk' for too long. Changes in genotypes is not what evolution is broadly concerned about, an imaginary and impossible type of change is what evolution is 'concerned' with. Evolution must predict 'a whole lot' of junk, if it made real predictions, but will accommodate any amount. I don't think anyone can speak with authority on the inner workings of life, we're at the observe and wonder stage at best.butifnot_{January 13, 2012
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ToE is all mechanisms by which replicators change in population frequency and in lineages, and the consequences of this for populations and lineages. Neutral Theory is evolution in the absence of selection – the background process.
Although to my mind it makes more sense to combine them in a single concept, in which "selection" is simply a bias to the stochastic sampling of alleles in each generation, in favour of what increased reproductive success in the parent generation.Elizabeth Liddle_{January 13, 2012
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Then ToE is darwinism, Neutral Theory, both, none?
ToE is all mechanisms by which replicators change in population frequency and in lineages, and the consequences of this for populations and lineages. Neutral Theory is evolution in the absence of selection - the background process. Darwinism can mean several things: 1) Common Descent 2) Gradualism 3) Natural Selection as the prime reason populations change. Hardly anyone outside of the odd popular science writer calls themselves a "darwinist" these days. He did write in 1859, after all, and things move on. 1) Common Descent must be extended to include non-vertical means of gene transfer 2) Gradualism dominates, but larger changes are more prevalent than he was aware. 3) Natural Selection is now seen as a bias within the background process (population sampling) rather than the central mechanism. It remains important, but Drift (ie chance) is much more important than was once thought. One reason for this is the prevalance of neutral sequences - eg junk. A bad day for darwinism when Drift came along, I can tell yer. Ah yes, I remember it well ...Chas D_{January 13, 2012
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No one can pretend that evolutionists didn’t throw junk DNA in everyones face for decades and even give the impression that they had predicted it.
Citation, please. There is a lot of apparent junk in most eukaryotic genomes and hardly any in most prokaryotic; masses in the onion and barely any in the pufferfish. I am not aware of any retrospective claim of prediction for any of this.
But now that it’s been explained, after the fact of course, the theory is tied to all the junk producing mechanisms posited to have been acting over eons. ‘Non coding’ DNA must accumulate? So when non-coding DNA turns out not to be non-functional it is not consistent. While ID would predict degradation, evolution surely predicts more ‘junk’ and so as it decreases – bad for evo.
One of the more convoluted ways to get to the slogan 'bad for evo' I have encountered. What's this new find shifted the percentage by? 0.01%? 0.02%? To what extent do you think evolution 'predicts more junk'? Another 100 bases? an ounce? a ton? Still, when the amount of DNA does not change, as here (just relabelling), that is irrelevant anyway. Here's the news - evolutionary theory is broadly concerned with changes in genotypes. Some genotypes have phenotypes, which influence genotype survival, and some don't. Neutral or non-existent phenotypes (eg individual 'true' junk sequences) and non-neutral phenotypes both evolve. The total cost of all DNA is a phenotype of sorts, which I predict limits its indefinite expansion. Evo fine.Chas D_{January 13, 2012
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Then ToE is darwinism, Neutral Theory, both, none?Blas_{January 13, 2012
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No one can pretend that evolutionists didn't throw junk DNA in everyones face for decades and even give the impression that they had predicted it.
Up until 1980, junk was undreamt of.
But now that it's been explained, after the fact of course, the theory is tied to all the junk producing mechanisms posited to have been acting over eons. 'Non coding' DNA must accumulate? So when non-coding DNA turns out not to be non-functional it is not consistent. While ID would predict degradation, evolution surely predicts more 'junk' and so as it decreases - bad for evo.butifnot_{January 13, 2012
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Guys it’s a bad day for darwinism because it is another layer of information it cannot account for.
Crikey. A bad day for music theory as well then. ('True' junk, incidentally, would fall under the Neutral Theory. This is a central part of evolutionary theory but not, for historic reasons, "darwinism". So it's actually a good day for darwinism if it has a function!).Chas D_{January 12, 2012
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Guys it's a bad day for darwinism because it is another layer of information it cannot account for. Not that it matters because that is just another promissory note...Joe_{January 12, 2012
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It's a sign of how desperate ID proponents are for a confirmed 'prediction'. Unfortunately, ID does not predict that junk DNA has a function. That would be true only if we assumed that the designer would not have put nonfunctional elements into his design. As ID proponents are fond of saying, intelligent design is not optimal design. They can't have it both ways.champignon_{January 12, 2012
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A bad day? Why? Does evolutionary theory care about the extent of junk in genomes? Up until 1980, junk was undreamt of. I suspect that Ohno's 1980 paper would have been reported then as "a bad day for Darwinism" - all this junk and no selective explanation! 30 years later we get a little function for some previously misclassified junk - and it's a "bad day for Darwinism"!.Chas D_{January 12, 2012
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