the phylogeographic challenge to creationism

One unreplicated verified test with bacteria proves absolutely nothing, and since I don't understand bacteria I refuse to give it a second thought. I've made my case and you can't answer it so glibly with one lousy vague experiment.

I don't have anything so rarefied in mind. For purposes of this discussion I'm not even taking mutation into account, let alone postulating a condition of extremely high rates of mutation. I'm talking only about the natural tendency of the (misnamed "evolutionary") processes that decrease genetic diversity through the splitting of populations, with the idea that beneficial mutation would be one of the processes that slows this tendency and may or may not reverse it (I doubt it does). These processes may occur speedily under certain situations, or hardly at all where there are many generations of relative stability, but the overall trend in the end is always toward a decrease. It's interesting that hypothetically there could be the situation you are talking about, where "garbage" mutations can't be cleared out (?) but I don't see that it's related to what I'm saying.

Sorry, yes you were answering the OP. No, variation is the result of normal reproduction which shuffles alleles into new combinations, at least in the case of sexual reproduction. Mutation does not have to enter into it.(I started calling these processes subtractive and additive to make my basic point about them clear).This message has been edited by Faith, 12-08-2005 02:39 PM

Yes, so I understand, but when I am using the term I'm not thinking of mutation, merely the usual Mendelian process of variation. I hope to have time to answer your post more fully later. Just wanted to make that one correction as I saw it.

May I ask what this entire sequence of posts on mutation and retroviruses etc. has to do with the phylogeographic challenge to creationism which was Mick's OP?

It's been hard to get back to this post because it's SO long and the thread went off topic and now SO much time has elapsed but maybe I'll try a short response. It's a logical inference from the processes in question, nothing so grand as an unsupported assertion. The question that keeps being raised about mutations here at EvC is whether or not they are random events as opposed to law-abiding processes that are predictable. To the extent they are the latter they can't be said to be bringing anything new into the species picture, but merely contributing to the built-in variability that all living things exhibit through Mendelian processes, dominance-recession and so on. But this is off the topic of the OP so I won't be tracing it with you. I believe speciation has a natural limit defined by the fact that most of the processes that lead to speciation, from genetic drift to natural selection to bottleneck, produce new phenotypes BY reducing genetic variability. Mutation keeps being added in without the slightest attempt to explain how it might overcome this effect, rather it appears to be assumed. That is merely the ToE faith. The processes I am discussing tend to limit speciation past a certain point call this faith into question. My statement was logically correct and I suggest you review it.I'll have to get back to this as it's taking too long and I have to go to church.

It has not been proven. Many speculations, no proof. Others, not just creos, have said things that disagree with you. In a complex system with one factor increasing diversity and half a dozen decreasing it so much is possible that you need to say more than this. And that one factor that increases it does so sometimes in a random way, often in a lethal way, sometimes in a neutral way, rarely in a positive way, and a lot of it doesn't look random at all but predictable.This message has been edited by Faith, 12-18-2005 05:23 PMThis message has been edited by Faith, 12-18-2005 06:01 PM

Come on, crashie, you simply need to REALLY prove it SO carefully to li'l 'ol ignorant me. Surely you know that it takes much repetition and careful explanation and many different approaches to educate a person in the complexities of genetics. Patience.This message has been edited by Faith, 12-20-2005 12:45 AM

This remains to be proved. It's when there is very little diversity left that the phenomenon I'm talking about is on display as it were. At this point we have speciation to the max. There is no further variation possible, unless mutation can increase the diversity to the point that further speciation is again possible. Otherwise it is at this point that extinction becomes a real possibility if the environment requires a change that can't occur. The opposite of what evolution would predict. If extinction doesn't occur. If extreme bottleneck doesn't occur. What is needed is some real conjuring with actual facts and possibilities. But doesn't death itself reduce diversity over time? Every individual that dies without reproducing would either make no difference or makes a small difference -- in the direction of reducing genetic potentials. It represents some genetic potential that is no longer available in the gene pool, to however small a degree. At least even a single death changes frequencies in the population as all these factors I've been talking about do. Interesting point. This of course means that mutation in this situation becomes a factor not of increased diversity but of decreased viability and therefore eventually decreased diversity, if it is true that any death before reproduction, if it has any effect at all, will have an effect in that direction. It is even possible at an extreme for a death to remove from a very small population the last remaining alternate allele for a particular trait, leaving that population totally homozygous for that trait and incapable of variation unless a truly useful mutation can be counted on. Some have said that this kind of mutation is actually rather common. In which case I don't think we're talking about mutation but some kind of built-in mechanism that contributes to variation in a nonrandom way.There's a lot I need to learn I know, but everything in its time. If these processes aren't acknowledged I'm not going to be able to learn the processes that supposedly oppose them as it's like denying that this is going on at all, and I simply have to repeat it. What you mean by "beneficial" seems to be merely that they will more likely produce a change that will be expressed phenotypically, but what's to guarantee that the new trait will be useful in some adaptive way?And what in reality is actually seen? This is pretty speculative.

The same factors that lead to speciation lead to the lack of genetic diversity. These are the processes that divide populations and aplit them apart. If there is a causal relationship it is in the other direction - a reduction in genetic diversity is usually what has to happen to develop a new trait in a population. Which is exactly what I've been talking about for months, exactly the result of all the processes that divide populations. They all lead to a reduction in genetic diversity for the reasons you are talking about. If you didn't get that this is what I was talking about, no wonder nothing you've been saying has made any sense. Gee, he finally gets it. Depends. Often something similar is exactly what gets called speciation, only less dramatic than the extreme of a clone.

Here's a question for the expert as this thread winds to an end.So in the case of say the cheetah, or any creature which has been reduced to homozygosity at many loci, this has come about through the removal of alleles from the population by one process or event or another such as migration or natural selection or the like, right? The cheetah's having suffered the severest kind of bottleneck, even reduction to a single female, is the usual explanation in that case I believe.But there may be many degrees of removal of alleles from a population by these same processes, depending on the genetic potentials in the original or any given parent population, and the severity of the population reduction, so that it could take many such processes to affect the genetic diversity appreciably, so that a state of stability or equilibrium could be the case for many generations. Or on the contrary only one migration, certainly a bottleneck, could even remove half a dozen possibilities for one loci from the population, or more or less, but that in any case through many splittings over many years or centuries, and leaving mutation aside for the moment, we are talking about a progressive reduction in genetic diversity in each of the new populations from the old.And this may at times involve such changes as amount to speciation, so that a new population may in fact diverge so appreciably from the original or even the previous parent population that we have what is called a new species. Isn't this what Mick was describing in his OP?Am I also right that simple death of individual immature (nonreproducing) organisms over long periods of time would also contribute to the overall reduction of genetic diversity in ALL populations as surely alleles are removed from the population by this means too, though much more gradually than population splits or massive numbers of deaths would bring it about of course.Further, doesn't this progressive gradual depletion imply a previously much much greater genetic diversity in an original population back oh a few thousand years or so?And, what kind of further change may occur at a particular locus after it has been reduced to homozygosity in a given population? What if a bad mutation simply wipes out that allele in an individual rather than producing a viable chemical alternative? I assume this could happen and if it is not lethal to the creature it would be passed on, this complete absence of an allele or a whole locus, no? If other factors favored this particular strain, even perhaps by some toxic agent's being foiled by the absence itself, this complete absence of a gene could even come to dominate in a population, couldn't it?What would this dead locus look like in the genome? Might it look like junk DNA?Yes, I understand that mutation supposedly counteracts the processes of reduction and removal of alleles from populations, but as usual I would like to focus on these processes apart from it if you would.This message has been edited by Faith, 12-20-2005 03:44 AM

Crash, I'm sure you've said some useful things somewhere in all your attempts to educate me, but I don't relate to your way of expressing youself or relating to me and it ends up being counterproductive, so until further notice I will refrain from addressing your posts, and please don't answer my posts on this subject. I would really appreciate it. Thanks.This message has been edited by Faith, 12-20-2005 11:26 AM

It won't interest me if it doesn't acknowledge the point I've been trying to make here. If it does, and you want to discuss how mutation alters that picture, that could be interesting.