Natural Limitation to Evolutionary Processes (2/14/05)

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But here is the important part, that I fear you are missing: Even though the success of the mutated allele drops "diversity" for its gene to zero, the organisms within the population have NOT reduced the allelic diversity for the other 20,000 genes in their genome. Thus, fixation of an allele for one gene generally has neglible effects on the allelic diversity for the other 99.99% of the genome. Genes coding for any other trait the population have retained their allelic diversity.

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Here's an example from close to home. People with ancestry from northern Europe are a little unusual in that they are probably able to digest milk as adults; for most people, lactose intolerance sets in after childhood. Lactose tolerance in Europeans is the result of natural selection acting on a single genetic variant on chromosome 2 sometime in the last five or ten thousand years. Selection did substantially reduce genetic variation around the gene in question (the gene for lactase), in a region about 1 million bases across. The remaining 99.97% of the genome is largely unaffected. Note that this was the result of a powerful selective pressure; weaker selection would have produced a smaller affected area. (Reference: Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene, Bersaglieri et al, Am. J. Hum. Genet., 74:1111-1120, 2004.)

Deleting this because I accidentally repeated it below.This message has been edited by Faith, 02-16-2005 15:47 AM

I wish I had more time. I had no idea how much time this debate would take. I appreciate all the responses but it can be a lot to deal with. Anyway I'm answering your latest post just because I think I can do it briefly as I'm not going to be able to get back to this for most of the day or longer, to all the posts that are accumulating unanswered.

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When this is drastic, as in the degree of natural selection that brings an antibiotic-resistant bacterium to the fore, or a poisonous newt, or bottlenecked creatures, some allelic frequencies are increased enormously, but the overall effect is a drastic decrease in allelic variation.

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Perhaps ...

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Only "perhaps?" Isn't it understood that variability is lost through drastic events because many alleles are lost, and that, overall, creatures inbreeding at this point are especially vulnerable to genetic diseases and even extinction?

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, but evolution does NOT only proceed by such drastic events that kill off the majority of the population. I tried to explain this to you on page one of this thread with a frog example, but perhaps you missed it. I'll try again:

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Sorry, no doubt that first post of yours is one I overlooked in my first general answer. I do hope to get back to all of them eventually unless I keep getting overwhelmed with new answers.

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An individual animal is born with a mutation that makes it slightly better at catching prey, and thus slightly more fit than the rest of the population. This does not mean that the rest of the population will now die off en masse. Instead, the frequency of that mutated allele may increase over generations in the population, since individuals carrying that allele are more fit and thus more likely to have offspring. As the frequency of the mutated allele increases, the frequency of the original alleles for that gene decreases. The mutated allele becomes fixed in the population, replacing previous allelic diversity for that gene with a single allele (a state which I'll call "zero allelic diversity").

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But here is the important part, that I fear you are missing: Even though the success of the mutated allele drops "diversity" for its gene to zero, the organisms within the population have NOT reduced the allelic diversity for the other 20,000 genes in their genome. Thus, fixation of an allele for one gene generally has neglible effects on the allelic diversity for the other 99.99% of the genome. Genes coding for any other trait the population have retained their allelic diversity.

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Is that clear?

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Yes, and helpful, but 1) how do you know "mutation" is the cause of the improvement in ability to catch prey rather than just a normal variation that normal Mendelian genetics operating on pre-existing genetic potentials could predict, that is, maybe a low-frequency allele's just happening to get expressed or perhaps a new combination of normally-occurring alleles at different loci, and 2) is this entirely theoretical or has it been observed?In any case my point has been that loss of diversity accompanies selection processes however caused and to whatever degree and in how ever many genes. If a trait is selected to the point that it works its way through a population, as you say the allele for that trait may become fixed without drastic events isolating it or otherwise selecting it. It's a tiny thing among 20,000 genes but it represents the pattern I'm talking about. The "processes of evolution" do tend toward loss of diversity, and ANY loss of diversity suggests the opposite of what the theory of evolution predicts.Or put it another way, the continuing diversity in the other 20,000 genes isn't producing evolution. Selection is what produces evolution, and selection reduces diversity.Again, the very processes that produce the improvements all the way out to actual "speciation" are accompanied by one degree or another of loss of diversity. As you are pointing out this doesn't have to be drastic, it is simply the way it happens at all levels. It is only when it is drastic that it becomes really visible and that's when you get "new species," not just a small improvement that works its way through a population but a whole new population based on many such improvements in many genes, or a type that is either selected for its fitness to its peculiar circumstances while others are destroyed by those same circumstances, or is accidentally created by bottlenecks and other disasters. In all cases the improvements /changes involve a reduction in diversity. It is just striking, it seems to me, that the "speciation" which is supposed to be the biggest proof of evolution, is in fact the case where the least diversity, least ability to change, adapt, continue to speciate, is possible.Now, apparently mutations counteract the effects of this process to a degree I am incapable of judging at this point, and I'm still very skeptical about that whole line of thought in any case.

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Also - you seem hung up on the bacteria-mutation example, which is a good example because monoculture allows the experiment to begin with zero allelic diversity. However, that is not the only example of documented mutations (I gave you another one - the Baldwin mutation that appeared in a closed population several years ago and results in hairless (and I think darn cute) guinea pigs.)

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How do you know that this is a mutation rather than a normally occurring allelic variation, however rare in the guinea pig population? Do you know this from its DNA? As I understand it a mutation is an accident that happens in the ordering of the DNA, switching positions of segments or deleting them altogether and the like, which usually produces either something neutral that doesn't help the creature or something that hurts it. Does this question make sense? Already, knowing that what genes do is shuffle a few chemicals around, it boggles the mind to consider that such shufflings correspond to actual phenotypic traits anyway, but that being the case a mutation just sounds like another shuffling of chemicals, the question being whether it is a mistake or a normal possibility given whatever laws govern the whole process-- and it is usually defined as a mistake or an accident.

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I worked in mouse genetics for several years - mouse geneticists have established "inbred" mice that are homozygous for every gene, which means they have zero allelic diversity, not unlike bacterial monoculture. Mutations occur on a very regular basis in closed populations of these inbred, zero-allelic-diversity-mice. A simple example is an inbred mouse strain that happened to have black fur. One day white-furred mice began appearing in the population, and the mutation that caused this difference was identified. Examination of the DNA of the great-grandparents of the white-furred mice did not reveal the same mutation. There was no source of the white-furred gene except for mutation, since there was zero allelic diversity at that gene in the grandparents of the mice with the mutation.

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Fascinating. So even at the extremes of least genetic variability variation can occur. This and the bacterium example do raise questions about what variation is. The probabilities of anything nonlethal occurring through random "accidents" just "seem" astronomical to my untutored mind. I can't think they are accidents but are obeying some law. It just boggles the mind that an "accident" such as mutation is said to be, can have such a pinpoint nonlethal effect. Deleterious effects, of course, are easy to understand as the product of accidental changes.But in any case, again, if a particular mutation, or oddball normal allele, any change in a gene, is selected by any process whatever, from the gradual dispersion through the population you describe above, to allowing the naked guinea pigs or white mice to breed only with each other, again you have the reduction-in-diversity effect which always accompanies selection, and again the question for the sake of the theory of evolution is whether life-enhancing or at least nonthreatening mutations outstrip these effects or not.This message has been edited by Faith, 02-16-2005 15:42 AM

I would presume, though I'm not an expert, that we know its a mutation because none of the organism's ancestors possess the trait. Since it didn't inherit the trait, but its decendants have inherited the trait, we know that it arose through mutation. I don't percieve a difference between those two alternatives. Genetic sequences mutate because its impossible to completely prevent mutation, because of the laws of physics. Does that mean that DNA is "meant" to mutate? That's not really a question science can answer.I mean, DNA can't break the laws of physics. Anything that happens to a genetic sequence has to occur according to the laws of physics, including mutation. Why? Protein structures are often malleable to some degree. An inert polypeptide has no effect on cellular chemistry, beyond tying up some amino residues that could be better employed elsewhere. It seems to me that there's considerable room to play around with cellular protein chemistry. The really crucial stuff is often backed up by the very evolutionary precursors that allowed it to evolve. (For instance your cells have two separate metabolic pathways; the original anaerobic pathways that first evolved those billions of years ago, and the more modern, much more effective aerobic pathways that evolved subsequently. Which is not to say that you can survive without oxygen, but many of your cells can, at least for a little bit; that's why you get muscle cramps, for instance.) According to observation, this must clearly be the case. If you like, you could easily perform an experiment on bacteria in a chemostat; you could raise a monoculture to maturity and assess how quickly variation expands in a population experiencing as little selection as you could devise. In fact I should think this experiment has probably already been done.

I don't know the specifics of the examples you gave, so I didn't give a specific answer. Yes. Inbred creatures are more vulnerable to drastic environmental change and extinction.However, like the title of the post says - evolution does not proceed solely by drastic events. In other words, drastic events that result in severe genetic bottlenecks only represent a small portion of evolutionary change. My guess is that most populations that pass through a severe genetic bottleneck go extinct. But again, evolution doesn't proceed only through bottlenecks. See message #43 in this thread. Then you should stop making concrete statements like the following: Again, you are discussing relative rates when you haven't presented the actual rates. Also, evolution theory itself requires some loss of diversity, so ANY loss of diversity does NOT suggest the opposite of the theory.Also, "diversity" is subject to positive selection in most cases. That is, natural selection maintains diversity of some alleles. Yes it is! Evolution does NOT proceed by natural selection judging one gene at a time - an organism's phenotype is the sum of all of its genes, and all of its genes undergo selection. False. Evolution proceeds by mutation and selection, not just selection. In some cases selection reduces diversity; in other cases selection maintains diversity. I'm not sure if the mutation has been mapped to a specific gene in the guinea pig, (though it has been in the mouse mutation I mention.) How do we know it is a mutation? Well, like the curly-eared cats mentioned above, humans in general, and specifically animal breeders, would have noticed a hairless guinea pig or a curly-eared cat in the past few thousand years, especially these mutation, both of which are simple single gene mutations, and NOT the result of complex multi-gene interactions. And the curly-ear mutation is a dominant mutation (all cats with a single copy of the mutation have curly ears), so it would have been seen if it existed prior to 1981. Variation produced by mutation-I'm not sure if you understood the point of the mouse example or not. It is a case where it is absolutely known that mutation increased genetic variation. Offspring had an allele that their grandparents did not have. The mouse example refutes the idea that genetic variability can only decrease.
That is, the inbred mouse population went from zero allelic diversity to some allelic diversity when the mutation arose.A population with only the genetic capacity to produce black mice developed the capacity to produce black mice and white mice. It seems like your underlying assumption is that the moment the white mice appear, all of the black mice die. This isn't the case - a mutation created allelic diversity that now produces two coat colors in a population that previously could only produce one. You've said this dozens of times, but you've yet to begin to support it. Perhaps you should stop using such absolute language until you have some evidence to back you up.

Just snatching a moment to answer this:

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Now, apparently mutations counteract the effects of this process to a degree I am incapable of judging at this point,

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Then you should stop making concrete statements like the following:

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The "processes of evolution" do tend toward loss of diversity, and ANY loss of diversity suggests the opposite of what the theory of evolution predicts.

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No, because this is an independent process that is always true whether mutation occurs at a rate that can overcome it or not. ALWAYS selection decreases diversity. I haven't yet seen anything that contradicts it. Whether it is one allele that is becoming dominant in a population due to sexual selection, or multiple alleles of multiple genes altering the character of a whole population even more noticeably, or the reductions in population that are caused by natural selection or events such as bottleneck, ALWAYS selection processes decrease genetic diversity.The only question is whether mutation increases genetic diversity enough to keep the theory of evolution afloat.

The process of natural selection works on the phenotypes. This can cause a reduction in variation but you mustn't forget that there is still hidden variation within the genotype which can continue on in later generations and not be expressed.

Mutation is a "process of evolution"; it is not independent from it. It is independent of selection, but not independent of evolution. Do you have any sort of reference or source to support this absolute statement? Off the top of my head - hemaglobin allelic diversity is maintained by selective forces. If an individual is homozygous wild-type, they are susceptible to malaria (the selective force); if they are homozygous for the sickle-cell allele, they have anemia. Thus the allelic diversity of having two hemaglobin alleles is maintained in the population, because heterozygous individuals are positively selected for.There it is - an example of selection maintaining diversity.You can take the "ALWAYS" off the front of your statements. Why do you think selection acts faster than mutation? You are so adamant about it, but you haven't provided any evidence for why you think the rate of the former is higher than the rate of the latter.

How do you think that that adaptive trait came about in the first place? This, I think, is a fundemental problem that you are falling under. Mutation had to have happened at one time or another. This mutation may already have been present in the population but not expressed, until some selective pressure made it beneficial to HAVE that mutation. How do you think you get variations in allele's??

As I've pointed out the rate of mutation is almost certainly in a dynamic equilibrium with the rate at which alleles are lost. The rate of mutation is typically constant for a given population size while the rate at which alleles are lost is subject to negative feedback.To the best of my knowledge there is no evidence that the rate of loss is so high as to force the level of variation down to near zero. On the face of it even the examples discussed so far indicate that this is false - clonal bacteria cultures are able to gain new variation, and the cheetah's - as well as being an unusual case - have also recovered a degree of variation (this is how we can estimate the date of the severe bottleneck).

Isn't the Hardy-Weinberg Equilibrium equation often used as an indicator that evolution is happening? You can compare allelic frequencies from the equation to actual allelic frequencies in the population to show that/if evolution is happening.

Codons can often have a change in the last base without affecting the amino acid it codes for. There are 20 amino acids in biological systems and DNA has 4 base pairs arranged in complementary pairs. That gives us, what, 64 different combinations for the codons. As you can see, those 64 different combinations code for 20 amino acids. As an example: GCT, GCC, GCA all code for alanine. A point mutation can affect the last base of the codon and this would essentially be a neutral mutation. It wouldn't change the code for the amino acid.Now, if you look at which parts of the DNA strand actually used to code for the proteins produced you would see that often there is much of the strand that is no longer used or codes for nothing. Any change to this portion of the code, via point mutation, would again be neutral. In fact, often mRNA is "snipped" of portions of its chain before it is sent out of the nucleus to be read by the tRNA. (Obviously it is more complicated than this but I hope you get the picture.) That snipped portion might have had a mutation but is ignored because it doesn't pass through.So you can see that DNA has such redundancies to it, that mutations (specifically point mutations), may not even affect the survival of the organism.

Which explains why this mutation is NOT selected against even though having homozygous allele's for sicke-cell is VERY deleterious. I don't think they even live to reproductive age, correct? Having this allele in populations exposed to malaria carrying mosquitos is a positive thing. If you're heterogenous for this trait, you have some resistance to the disease and are able to pass YOUR gene to your offspring. You have a reproductive advantage over the homozygous normal carrying individual in THAT environment.(I hope you don't mind me adding my comments here. Just hoping he reads through the posts and isn't selective I guess.)Which reminds me. The change in the gene is a point mutation. IT can be deleterious when you are homozygous for the trait, but heterozygous individuals have a reproductive advantage.

Faith, isn't this a very odd way to come at this?You've jumped into the kind of details that researchers like to deal with: thinks that might be called "computational evolution". (I'm makin g that up.).You've jumped in while admitting you know pretty much nothing about the topic at all. Why would you do that? Why not build a base of understanding before you dive into the deep end? There is no pedagological approach that I'm aware of that suggests that yours is a good way to go at it.There may be many other things that you need to clarify first. You haven't as yet made it clear what else you understand or accept.For one thing, separate from the theory of how evolution occured, there is the fact that evolution has occured. If you wonder if the current theory can explain how you need to come up with another one explaining that it has.If, on the other hand, you think that it hasn't happened at all. You need to forget about the theory and get back to the underlying evidence that shows that it has occured (by whatever mechanisms). At the extreme this means backing up and recognizing what has been called "deep time". The evolution of life on earth has occured over a period greater than 3 billion years. You willingness to accept that evolution could happen is bound to be affected by your acceptance of the time scales. If you don't accept them then why would you worry about mutation rates? Or even if evolution occured. All you have to do is show that the 3 billion years value is wrong.How about one step at a time.If you wish to stick to this then you need to show the math that shows that various selective pressures will reduce variation under specific mutation rates.This kind of work is done by evolutionary theorists (though I don't know enough to be able to point to the publications). If you want to suggest that your ideas are right then you have to start with numbers. Produce models showing what happens with various rates of mutation and selection.It seems you haven't the tiniest bit of reason to support what you are suggesting. The only reason you are bringing it up is because you don't like the idea of evolution itself. How about being a bit honest and admit that you are not either going to believe what you are told or do the enormous amount of work necessary to understand the science at the level of detail you are attempting to discuss.

Here is an example of numbers being applied. I'm not spending long at it but I'm throwing it out to allow others to attack it and hopefully produce a better model.Here is my scenario:I have a population of 1 million individuals. This is the carrying capacity of the available resources.These animals live 5 years producing two surviving pups per female per year from the end of their first year.They have 30,000 genes. There is no junk DNA. There are therefore 30,000 alleles in the whole population.Each individual has 10 mutations randomly scattered in it's genes.Half of these are fatal and the pups carrying them are still born or not even carried to term. This gives 5 mutations per individual.The entire population has exactly the same genome at the beginning of the process.What happens?Since there are 1,000,000 new individuals born per year and only 200,000 dying of old age in a year a stable population requires that 800,000 individuals die either by selection or randomly each year.Assume half are randomly killed and half are selected against.In each generation there are 5 million new genes. One way or the other 4 million do not get passed on. This gives us 1 million new alleles added each generation.This means about 1 out of 30,000 genes becomes new in a generation per individual on average. At first, the new ones will be scattered and probably not be on top of a previous one. As the generations go by this will start to happen and there will some of the so-called new ones will be replaced at random.In one year we go from 30,000 alleles in the gene pool to 1,030,000 alleles. Then to 2,030,000 and so on. This is before we allow for selection.The assumptions above have about 100,000 alleles being selected for in some way. Now we have to apply the degree to which they are selected. Let's assume very strongly so they will become fixed very quickly. This means that they drive out all the alleles that are at the some location. At first there aren't many collesions so the number of alleles goes up sharply.Now what I need to do is figure out what the equilibrium diversity will be.