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Author | Topic: How novel features evolve #2 | |||||||||||||||||||||||||||||||||||||||||||
zaius137 Member (Idle past 3439 days) Posts: 407 Joined: |
Dr. Adequate my friend
Do you know who Haldane is?
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Dr Adequate Member (Idle past 314 days) Posts: 16113 Joined:
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Was. Of course I do.
I am also familiar with his work in population genetics, and with the stupid fatuous mess creationists make when they try to misunderstand it. Edited by Dr Adequate, : No reason given.
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Tangle Member Posts: 9516 From: UK Joined: Member Rating: 5.1
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Zaius writes: I have a question; does every color change await a mutation of a gene? The first time it happens, it must do.
There must be an underlining adaptable mechanism built into the genome. Why? The theory tells us that it doesn't need one and the practice shows that it doesn't
If natural selection is the main mechanism of causation, there has to be a molecular interface between the resulting gene and environmental pressure. This interface should be discernable and explainable. As has been pointed out to you several times by all of us, natural selection is NOT the main mechanism of causation. It acts only AFTER a mutation has randomly occurred. The selection process has no connection to the mutation process.
Why is there heterozygosity of coloration remaining in the selected population of mice if say black mice are selected to be more fit? I think that's a question you have to ask yourself. If a designer was at work, he would make it so that dark mice living on dark rocks would always breed true. If the process of creation of new features/species involved random genetic error plus non-random selection, we'd expect to see what we actually see.Life, don't talk to me about life - Marvin the Paranoid Android
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Tangle Member Posts: 9516 From: UK Joined: Member Rating: 5.1
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Zaius writes: Thanks for your citation; was this linked in the last paper? . As it was written two years after the first, it wasn't referenced in the first paper :-;Life, don't talk to me about life - Marvin the Paranoid Android
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Tangle Member Posts: 9516 From: UK Joined: Member Rating: 5.1 |
I have a question for the geneticists.
How do we know that the genes involved in the dark mice colouration arose from a mutation of the genes coding for light mice? ie how can we distinguish which came first and/or that both haven't always been there?Life, don't talk to me about life - Marvin the Paranoid Android
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
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I think that's a question you have to ask yourself. If a designer was at work, he would make it so that dark mice living on dark rocks would always breed true. Actually the answer to this is very straight forward, there is considerable interbreeding between the dark and light populations. The second paper to have been referenced mentions this, indeed Zaius himself quoted a relevant extract in his very next post after he posed the question, Message 66, there are "high levels of gene flow between light and melanic populations." Indeed in yet another paper on this topic (Hoekstra et al., 2005) the authors note that "high levels of gene flow between neighboring melanic and light populations suggest the selection acting on color must be quite strong to maintain habitat-specific phenotypic distributions". TTFN, WK
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
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I've been rather halfheartedly drafting a reply to Zauis Message 44 for the past few days, but the discussion seems to have moved on quite a bit in that time and there were some sections relevant to the current direction, and particularly Tangle's question in Message 80, that I thought I would extract and present here.
We were discussing peripherally the action of the FGF4 retrogene insertion in short legged dogs and the fact that the genetic makeup necessary for such an insertion was not found in other modern dogs but rather in a grey wolf population. Zaius suggests that this may be a frequently occurring spontaneous mutation in the wolf population, which is merely strongly selected against, and so cannot really be considered novel.
Zaius writes: This does not sound unreasonable because if the retrogene appeared in a wild wolf that wolf might not be alive long enough to enjoy benefits of short legs. That is a perfectly reasonable argument and raises the question of how novel a feature can be considered when it has a low but significant rate of spontaneous appearance in a parent population, even if it is subsequently strongly selected against as in Zaius' example. Should we consider it novel simply if it was absent in the founding population? Taken to an extreme the alternative approach rapidly takes us to a position where our imperfect knowledge of the genetic makeup of previous generations makes it impossible to definitively consider any mutation novel as we can't confidently state that it never occurred transiently in any ancestral population. I'd say that for pragmatic purposes we would have to look at simply the extant variation that we can see and in the case of a line where we actually known the genetic makeup of the founders it is reasonable to consider a genetic feature novel that was not present in that founder population, I say a genetic feature rather than a phenotype since recessive traits could easily be masked for few generations. I think this is relevant of the discussion of the melanic mice because there are several other examples of adaptive colouration in other mouse species where the mutation has gone in the other direction from dark to light ( Hoekstra et al., 2006; Linnen et al., 2009; Steiner et al., 2009). Without a much larger scale phylogeny taking in the relatedness of these several rodent species, it is very hard to say which trait is truly ancestral and which derived and certainly not if the trait is novel in a broader sense. I would say that we can pragmatically determine given a certain depth of genetic information whether a trait is novel to a particular population as I outlined above. The above papers are also interesting as they touch on Zaius' challenge to me to show him some examples of adaptive mutations that weren't 'degradative'. As is often the case this is problematic as Zaius hasn't given us a clear definition of what he considers 'degradative', indeed he has made comments that suggest he might be using the term so broadly that any genetic change will fit it regardless of its effect. So within these various papers we have the initial example of the light to dark mutation set in the pocket mice. The function of the melanocortin receptor is to mediate the signalling from certain hormones which bind to the receptors, this mediation is done via the generation of cyclic-AMP (cAMP), the level of cAMP then determines whether the target cell produces eumelanin (Darker) or phaeomelanin (Lighter). So in terms of the genetic concepts of loss- or gain-of-function the melanic pocket mouse mutations in Mc1r are gain-of-function mutations giving rise to a more sensitive receptor balanced more towards eumelanin production (Nachman, 2005). However when we look at the other papers we see a light phenotype arising both from gain-of-function mutations increasing the expression of the Agouti gene, which inhibits the binding of melanocortin to its receptor, and through loss-of-function mutations where the binding specificity of the receptor for melanocortin is reduced and so is the level of cAMP, tipping the balance towards phaeomelanin production. So we have a very heterogeneous mixture of mutations, albeit all centered on one or two genes, some are gain-of-function mutations, some are loss-of-function, In some populations the derived mutations are those producing the light colouration, in others the dark and in some there are a mixture of derived alleles in both genes giving rise to a spectrum of melanic phenotypes. So given all this messy complexity how do we address Tangle's question, how do you distinguish the new, derived allele from the ancestral one? This usually comes down to being able to compare to another population considered to have common ancestry (which is undoubtedly an unfounded assumption in Zaius opinion). Polymorphisms/mutations which are found to be present in either of your populations of interest and your more distant outgroup are considered to be ancestral and those found in only one population to be derived. Since there is no way to be sure that you have captured the entire genetic diversity of a whole population in these sorts of cases these are always probabilistic inferences. TTFN, WK Edited by Wounded King, : Spelling Edited by Wounded King, : No reason given.
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jar Member (Idle past 424 days) Posts: 34026 From: Texas!! Joined: |
Remember that it really doesn't matter which came first.
Mistakes happen. Mutations continue. Pick a population and there will still be mutations.Anyone so limited that they can only spell a word one way is severely handicapped!
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Taq Member Posts: 10085 Joined: Member Rating: 5.6
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Your scenario is right in line with most evolutionists’ beliefs (that is the good news) but those suppositions do not hold up under scientific investigation (that is the bad news).
The paper we are discussing is the scientific investigation, and it does hold up. You can lead a horse to water . . .
The problem is it has never been observed
It is observed in the paper we are discussing.
Do you know who Haldane is? Major evolution calculations are based on Haldane’s work. Do you know the problems with Haldane's work? Such as his calculations did not correctly model the fixation of two alleles, nor did it take into account selective sweeps?
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Taq Member Posts: 10085 Joined: Member Rating: 5.6
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How do we know that the genes involved in the dark mice colouration arose from a mutation of the genes coding for light mice? ie how can we distinguish which came first and/or that both haven't always been there? You do this by comparing the synonymous and nonsynonymous mutations. From the paper:
quote: There has been more time for sequence variation (aka neutral mutations) to build up in the light variant than in the dark variant demonstrating that the dark variant is more recent. This also jives with the recent appearance of the dark lava (<1 years).
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Dr Adequate Member (Idle past 314 days) Posts: 16113 Joined:
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Do you know the problems with Haldane's work? Haldane knew the problems with Haldane's work. But the major problem with creationist gibberish about Haldane is, in my opinion, more fundamental than that. They take Haldane's original calculations as gospel. Then they say that based on these calculations there can't be more than (IIRC) ~1600 adaptive mutations between more basal apes and modern humans. Then they maintain without any evidence that this would not be enough adaptive mutations to make the difference, and that therefore this couldn't have happened. Now this is just something that they've pulled out of their hind ends. As with every creationist attempt at a quantitative argument, one of the figures involved is just something that they've made up. Or, indeed, not even specified. They don't even say how many adaptive mutations they think would do the trick, they just naively apply Haldane to set a maximum on how many have occurred, and then declare for absolutely no reason that it must have been more than that.
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Tangle Member Posts: 9516 From: UK Joined: Member Rating: 5.1
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Thanks Taq, so we can now say with a very high level of certainty, backed up with real hard evidence, that the gene for light colouration preceded those for dark and that the dark mice genes are a mutation of the light mice genes.
We can also show natural selection working on both the light and the dark mice based on their survival chances in their different environments. We have therefore demonstrated the Theory of Evolution in practice. But of course, they're still mice....Life, don't talk to me about life - Marvin the Paranoid Android
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Taq Member Posts: 10085 Joined: Member Rating: 5.6
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Thanks Taq, so we can now say with a very high level of certainty, backed up with real hard evidence, that the gene for light colouration preceded those for dark and that the dark mice genes are a mutation of the light mice genes. Yep. The invariance of the dark allele is consistent with a single, recent founder for the gene lineage, at least from my understanding.
But of course, they're still mice.... As they should be, if evolution is true.
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Taq Member Posts: 10085 Joined: Member Rating: 5.6
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But the major problem with creationist gibberish about Haldane is, in my opinion, more fundamental than that. They take Haldane's original calculations as gospel. Then they say that based on these calculations there can't be more than (IIRC) ~1600 adaptive mutations between more basal apes and modern humans. Then they maintain without any evidence that this would not be enough adaptive mutations to make the difference, and that therefore this couldn't have happened. It's like the story of the engineers and the bumblebee. The engineers wrote a computer program that attempted to model the aerodynamics of the bumblebee. What did their model show them? That the bumblebee should not be able to fly. At this point we have two choices. On one hand, this could indicate that the bumblebee uses supernatural powers to stay aloft. On the other hand, the model is wrong since obviously, bumblebees can fly. Science opts for the latter, and creatoinists the former. They just can not understand the simple concept that the map is not the territory.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined:
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Honestly, I'd quibble with this argument. The synonymous/nonsynonymous ratio tells us more about selection and the timing of the selective pressure rather than the relative temporal origin of the alleles' necessarily. So while it is consistent with a recent origin I'd suggest it is equally consistent with a strong selective pressure bringing an already existent low frequency allele up to near fixation levels. I'd be careful of treating this as some sort of slam dunk for the timing of when the allele first arose.
I'd say that the fact that there is a different basis for melanism in the other dark population of the same species is better evidence for the dark alleles being a derived trait than the variation levels. If there was an already existing melanic trait in the species it would be reasonable to expect that it would be the selected melanic form in both populations. TTFN, WK
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