Adding information to the genome.

Please! No! Not another one, aaaaargh!!TTFN,WK

Maybe this would be a topic better suited to my New genes in the Human lineage thread where we started discussing this very issue. It looks like people here still want to focus on your understanding of neutral theory.TTFN,WK

An interesting recent paper in this regard is Pan and Zhang (2009) in which they look at changes in gene copy number in all the different gene families across 10 species. They calculate rates of copy number change associated with distinct families in each species and then identify groups of gene families with similar rates of change. They then tie these rate pattern groups (RPG) into the GO functional ontologies to address their actual biological significance. They identified 12 RPGs which were unique to 1 out of the 10 species, strongly suggesting species specific differences were a result of gene duplications in specific gene families.They also find that these characteristic patterns of change predominantly involve increases in gene copy number rather than reduction, undercutting one of the common creationist/ID mantras that we only ever see losses of information leading to adaptive evolution.TTFN,WK

You shouldn't need a subscription, try going through the link from the abstract.TTFN,WK

There is an interesting paper by Kondrashov et al. (2002) which casts doubt on the premise that the benefits of gene duplication are simply due to allowing novel variation as a result of neutral/nearly neutral molecular evolution.They compare rates of non-synonymous/synonymous substitutions between duplicate gene families within species (paralogues) and closely related genes between species (orthologues). They find that the rates are lower in paralogous groups than between species but that both paralogues appear to be subject to purifying selection and do not appear to experience a neutral evolutionary phase.They suggest that most duplications which persist actually impart an immediate short term fitness benefit to the organism, generally through a protein dosage effect, rather than the more hit and miss hopeful monster style scenario of the neutral hypothesis.The vast majority of duplications probably end up silenced and reduced to pseudogenes after a period of neutral evolution, but these aren't the genes we find in modern genomes as the result of duplications.The subsequent generation of novel function is still considered an effect of relaxed selection allowing a higher rate of evolution between the duplicates.TTFN,WK

When gene duplication and neutral theory come up together then addressing Ohno's original theory of duplication producing redundant copies allowing neutral evolution to produce neo-functionalisation is almost unavoidable.Given Kimura's emphasis on gene duplication, and molecular evolution in general, it is hard to argue that he wasn't also thinking along these lines.TTFN,WK

That makes relaxed selection a prerequisite for "a sudden increase or boom of neutral variation" not for the generation of any variation. In fact all it says it that one leads to the other not that it is a pre-requisite, there might be other explanations for a sudden increase in variation linked to underlying mutation rates.It seems inconsistent to keep repeating Kimura's words to us to support you misrepresenting what he said when if you actually read what you were quoting you should be able to easily see that it doesn't support your claim.*ABE* Sorry I was focusing on your second, emphasis added quote. I see where the 'pre-requisite' phrase was in the first quote. Although I would point out that evolutionary progress and variation are not synonymous as you conflate them to be.TTFN,WKEdited by Wounded King, : No reason given.

I think they are pretty clearly off-topic metacomments, given what bolder-dash did in his own thread it doesn't seem unreasonable to discourage him doing the same thing to someone else's thread. HGT has already been brought up in this thread and it was pointed out that while horizontal gene transfer can allow the introduction of genetic information from one genome to another it does not create novel genetic information. It simply pushes the question of how the functional genetic information originated back a step. As far as coherence goes this fails somewhat, could you maybe rephrase your question and make it a bit clearer what you actually want to know? I think you would have a hard time finding anyone in evolutionary biology who claimed this was the case. That is leaving aside that the most common genomes by far on Earth are still bacterial ones.TTFN,WK

I'd be happy to have a debate in [forum=-8] forum, if we could agree on a clear enough topic.TTFN,WK

You seem to be using 'coherence' to describe several different and disparate phenomena. In the case of the cilium you seem to be using coherence both to mean the straightforward Irreducible Complexity argument and to describe the cellular physiological processes which cause ciliary synchronisation.This just serves to make things very confusing. Please can we try not to just make up our own terminology for things. If you want to talk about irreducible complexity then say so. If you want to talk about something else then be specific.TTFN,WK

Hi Kaichos Man,To try and stop the derailment of the Wright thread I am responding here where we have already been discussing Neutral Theory. Except of course that Kimura himself had elucidated one of those methods and the other was well established. As I have often repeated in this thread the open question is the balance between drift and selection, in this case whether the balance is different between evolution of the genotype and that of the phenotype. The genotpye and phenotype are not isomorphic but neither are they independent, the degree of 'gearing' between the two varies depending on what system is being studied. Looking at RNA enzymes there is a high degree of 'gearing' as their functionality directly relates to their secondary structure which is determined by the primary sequence. In proteins the connection is less close as there is degeneracy in the translation between genetic sequence and amino acid sequence. From metazoans there are many possible genetic variations which will have no discenible phenotypic effect at the larger scale and a subsequent reduction in the 'gearing' between the two. I fail to see how this example would in any way make Kimura wrong, his argument was that the vast majority of molecular/genotype level mutations were neutral and their propagation determined largely by chance, he never said that beneficial molecular mutations did not occur or that selection could not act upon the genotype. If adaptive phenotypes are fixed by selection it does indeed follow that a causative adaptive mutation at the genetic level similarly becomes fixed. Kimura had no problem with that, he merely proposed that such a course did not explain the vast majority of the genetic diversity that we see. You are wrong on both counts, deleterious mutations can indeed endure and become fixed in a population, in fact genetic drift is one of the reasons why this occurs, the random factor can overcome selection. The last part of course is the same canard you have been pushing for this entire thread under the guise of 'genomic information'. That is indeed poppycock, and it represents neither the view of Kimura nor even the adaptationists he was arguing against. Once again you treat the neutral and selective modes of evolution as mutually exclusive and arbitrarily insist only one can pertain to any given level. In actual fact there are mixtures of both neutral and selective/adaptive evolution at all levels. Nowadays Kimura's contention that the majority at the molecular level is neutral is widely accepted and while at the phenotypic level things are less clear cut, as there are still some strong adaptationists out there, the existence of mutations producing nearly neutral changes in phenotype is certainly accepted.Kimura Saying that he considered some phenotypic changes to be nearly neutral is a far cry from saying he considered all phenotypic change to be neutral or deleterious, clearly only someone with your peculiar ability to interpret Kimura's meaning could have gleaned that from anything he said. None of this is true and you have not a shred of evidence to support it. Your final quote speaks to Kimura's ignoring the place of adaptive mutations in his mathematical approach to calculating the rate of evolution, as genetic change, per generation. To take it as meaning that Kimura believed beneficial mutations did not occur is the most blatant sort of quote mining.TTFN,WK

I have never said that they evolve by different processes. I have consistently maintained that the same processes pertain to both, but that the balance of drift/selection on each is different depending on precisely what one is studying as the phenotype. But a non-selective evolution of the genotype may have absolutely no effect on the phenotype which is where the disjunction between the 2 can arise allowing the balance of drift/selection to vary. I agree that amount of selection is maintained between the 2, since it is effectively the phenotype which is being selected, but the amount of neutral evolution is where the discrepancy arises.So any example where portions of the genetic sequence diverge through drift while a few bases are maintained or propagated by selection should be sufficient. Such examples are present in virtually every single comparative genetic study ever done which identified even 1 nucleotide under selection, because such studies are likely to find many sites which are not being constrained by selection.You say ... ... but you neglect the fact that there is no corresponding phenotypic expression of many neutral mutations. My entire point was that the extent to which this is true varies depending on what you are considering as the phenotype. If you consider the protein product to be the phenotype it is less true than when we consider the gross morphology to be the phenotype of interest.I don't believe it is meaningful to talk of neutral evolution of the phenotype when the phenotype has not in fact undergone any change. Would you agree with this? If so then you must concede that the rate of neutral evolution between phenotype and genotype is partially decoupled.TTFN,WK