Adding information to the genome.

Just to return to the OP, I assume there are people on this forum that would concede that somewhere along the line, evolution must have created a new gene.Anyone care to suggest how that might happen?

---

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

Hi Kaichos Man,Where are you getting your quotes from so that I may place them in context? I think you're having trouble understanding simple English. Where in the quoted passage do you interpret Kimura as denying a role for natural selection? AbE: And as we've told you over and over and over, natural selection doesn't generate variation. It acts as a filter on variation. Variation survives to the next generation as a result of natural selection operating to select that variation, not because it was generated by natural selection. It doesn't take any genius to understand this simple division of responsibility. Artist generates various types of art, the public selects the art. The art that survives was not generated by the public. In the same way, variants that survive were not generated by natural selection.How many times does this have to be explained to you? No sane biologist would ever deny a role for natural selection because it's responsible for all adaptation. Drift is random without regard to the environment and cannot produce adaptation to that environment outside of sheer luck. Only natural selection can produce adaptation to the environment, and the evidence for adaptation is in all life everywhere.--PercyEdited by Percy, : Add clarifying couple sentences.Edited by Percy, : Grammar.

I think the many ways have already been enumerated in this thread, and your recent Kimura quote mentioned one of them, gene duplication: After one gene becomes two through gene duplication the two genes will experience different mutations over time and gradually become more and more different.--Percy

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

Like this.

Might accessing that link require a subscription to Molecular Biology?--Percy

Hi Kaichos Man, No. He. Did. Not.The relaxed selection does not cause the increase in variation, it allows more naturally occurring random mutation variations to survive to following generations, the variations are still caused by mutations. He points out precisely where the variations come from: "In this stage, gene duplication in addition to point mutation must play a very important role in producing genetic variations." Mutation causes variations, low selection pressure allows more marginal random mutation variations to survive.In addition, under low selection pressure genetic drift plays a more dominant role than natural selection. IOW, under low selection pressure natural selection plays LESS of a role in evolution than it does under high selection pressure, with the result that more naturally occurring random mutation variations survive. Natural Selection allows some variation/s to remain, depending on how much they do not disadvantage the organisms to survive or breed, and weeds out the ones that do, in a given ecosystem. With high selection pressure more are weeded out, with low selection pressure more marginal variations survive because they CAN under less sever selection pressure. The variations are already in the population.Enjoy.

---

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

I've been avoiding taking the "hopeful monster" interpretation of neutral theory. When Kimura talks of relaxed selection I thought he had in mind an environment of plentiful resources resulting in broader ranges of variation within species categories than is typically the case, thereby increasing the likelihood of dealing successfully with eventual environmental change.--Percy

I will assume you did mean "genotypic level" in Message 234. Which is why Kimura said this:"I have proposed ``Survival of the Luckiest'' as a phrase that best characterizes my Neutral Theory. (Kimura, 1990a)and this:"I think chance plays a much greater part in evolution, and natural selection a lesser part, than biologists supposed a few years ago."(BBC documentary transcript) No it doesn't. No careful, credible, step-by-step, dawkins-weasel-style building of variation through natural selection. Kimura understood that that was impossible. Selection needs something to select, and that had to be generated by a stochastic process. Duplicate genes cobbled into something useful by drift alone. Pure chance. The hopeful monster.Kimura clearly feared illogicality more than improbability.

---

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

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

"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress."Kimura 1991and:"(i) A population is liberated from the preexisting selective constraint. (ii) Thereis a sudden increase or boom of neutral variations under relaxed selection."Emphasis. Added.

---

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

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.