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Author Topic:   What is the mechanism that prevents microevolution to become macroevolution?
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 61 of 301 (345556)
08-31-2006 9:21 PM
Reply to: Message 59 by Faith
08-31-2006 1:39 PM


Re: Faith Logic
What is a fantasy -- utterly without evidence, simply assumed -- is this idea that mutation drives evolution.
It's no fantasy. It's trivial to construct an experiment where a population develops where the only source of alternate alleles is mutation. That evolution happens in these populations is proof that mutation is one of the driving forces of evolution and a true source of genetic novelty.

This message is a reply to:
 Message 59 by Faith, posted 08-31-2006 1:39 PM Faith has replied

Replies to this message:
 Message 62 by Faith, posted 08-31-2006 9:44 PM crashfrog has replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 62 of 301 (345566)
08-31-2006 9:44 PM
Reply to: Message 61 by crashfrog
08-31-2006 9:21 PM


Re: Faith Logic
You are talking about ONE kind of experiment with bacteria and ONLY bacteria, correct? Yes that one shows that mutation alone can bring about microevolution, but it also raises the questions just what mutation is {edit: Is it really a mistake?, is it really random?, is this one in bacteria really a mutation at all?} and whether the same kind of thing can be shown in any other organism.
In a population of chipmunks (thinking of a ring-species example from many months ago}, for instance, the main cause of phenotypic change from one population to another is the shuffling of already-present alleles brought about by a splitting or selection process, and often this involves the actual loss of some alleles to the population, even both old and new populations.
There are so many alleles already present in such a population there is no need for mutations to fuel microevolution {and how would you recognize a mutation in such a case anyway? If you breed a population from two chipmunks then you can control the number of alleles, but how often does a mutation show up to make your point in that case?}. The problem is, as always, identifying the ACTUAL action of mutations in such a population. You can't merely assume any particular role for them.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 61 by crashfrog, posted 08-31-2006 9:21 PM crashfrog has replied

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 Message 64 by crashfrog, posted 08-31-2006 11:00 PM Faith has replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 63 of 301 (345577)
08-31-2006 10:31 PM
Reply to: Message 47 by Quetzal
08-30-2006 4:04 PM


Re: Faith Logic
About the black and the brown socks, isn't it true that some genes have a LOT of alleles in some populations? So if the population splits a particular gene may lose some alleles. Also that one orange pair is probably left over from a previously larger number in a previous population, and may still exist in a large number in a cousin population, since splitting has no doubt already occurred to create any given population.
Beyond that, if the parent and daughter populations remain separated, they will both continue to generate new alleles. Mutation and recombination provide new variations/alleles, and differences in selection pressures or drift between the parent and daughter populations may emphasize or filter out these different alleles.
How do you KNOW that new alleles are generated, that is mutations that actually make a change and a change in a useful direction that gets passed on? There is no NEED for mutations for change to happen anyway. It's the natural result of the variety of alleles already present in the population.
Ultimately, the two populations - unless whatever barrier is removed - may differentiate enough that they can be identified as new varieties, subspecies, or even species. Even if there is some gene flow between the populations, it may be so reduced that the two populations follow separate or separating evolutionary trajectories. We see this in the existence of hybrid zones between different populations with limited gene flow (sort of "pre-speciation").
All of this happens merely with the given complement of alleles already in the population. There is absolutely NO evidence that any of this depends upon mutation, or that mutation even occurs at any rate that would contribute to the process.
Edited by Faith, : No reason given.

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 Message 47 by Quetzal, posted 08-30-2006 4:04 PM Quetzal has replied

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 64 of 301 (345582)
08-31-2006 11:00 PM
Reply to: Message 62 by Faith
08-31-2006 9:44 PM


Re: Faith Logic
You are talking about ONE kind of experiment with bacteria and ONLY bacteria, correct?
Bacteria experiments are the easiest, but it's not difficult to do with any kind of organism.
Yes that one shows that mutation alone can bring about microevolution, but it also raises the questions just what mutation is {edit: Is it really a mistake?, is it really random?, is this one in bacteria really a mutation at all?
I thought we were pretty clear on what mutations are, but, I mean, in an enclosed bioreactor, there's no outside influence; the bacteria are haploid so sexual recombination isn't happening; and they're all the clonal decendants of a single bacteria so we know that any alternate alleles that we discover in the population are the result of the only source left for them that we know about - mutation.
It could be, you know, mind beams from Alpha Centauri or something, but why don't we stick with the processes that we know occur? In the case of these experiments, that doesn't leave anything but mutation.
and whether the same kind of thing can be shown in any other organism.
The rules of genetics are the same for all living things on Earth.
In a population of chipmunks (thinking of a ring-species example from many months ago}, for instance, the main cause of phenotypic change from one population to another is the shuffling of already-present alleles brought about by a splitting or selection process, and often this involves the actual loss of some alleles to the population, even both old and new populations.
Yes. But we can structure the experiment to limit the alleles in our population. In the case of bacteria, which reproduce asexually, we can limit the number of alleles per gene to 1, because that's the maximum number of alleles an individual bacterium can have, and we can develop a whole population from a single individual. When we do that the population is called a "monoculture."
There are so many alleles already present in such a population there is no need for mutations to fuel microevolution {and how would you recognize a mutation in such a case anyway?
We recognize mutations after the fact when an individual presents with a unique allele that none of his ancestors had. Since mutation is the only natural source of new alleles, it's the only explanation for a new allele in the population. Further, gene sequencing analysis can show us the difference between the gene in the individual and the gene he should have inherited from its parents.
If you breed a population from two chipmunks then you can control the number of alleles, but how often does a mutation show up to make your point in that case?
In mammals, we expect roughly one point substitution mutation per every 3.2 billion base pair replications.
The problem is, as always, identifying the ACTUAL action of mutations in such a population.
Well, we know what mutations do - change gene sequences. And we know what genes do. (Many of them, anyway.) I don't see the major difficulty in perceiving the role of mutations, unless you mean to suggest that, contrary to the accepted understanding of biology for the last 100 years, DNA is not the molecule of inheritance of phenotype?

This message is a reply to:
 Message 62 by Faith, posted 08-31-2006 9:44 PM Faith has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 65 of 301 (345591)
08-31-2006 11:44 PM
Reply to: Message 55 by Equinox
08-31-2006 12:46 PM


Re: Faith Logic
Faith wrote:
When it leads to a population that doesn't interbreed with the parent population this is called "speciation." The point is this speciation is brought about by the loss of allelic information. Without this loss there would not be any speciation at all because all the same alleles would continue to keep the phenotype the same as in the parent population. {Edit: OK I overstated this again. The change may be brought about without an actual loss of alleles, merely a change in frequencies, but often there is such a loss, as when the new population is appreciably smaller than the parent population.}
Um, you still have your mutation blinders on. Speciation could occur without any loss of alleles. Simply have enough mutations so as to prevent interbreeding.
Speciation could occur both without any loss of alleles AND without mutations it seems to me, simply with a change in frequencies caused by a population split that sharply reduces the effect of some of them in the new population, especially a small population. This alone will bring up new traits and distinguish one population (or "breed" or sometimes even "species") from another. And I really doubt that mutation is necessary to lead to inability to interbreed; I'm not sure what the mechanisms for this would be except that some allelic situations or the possible death of some genes could make interbreeding difficult or impossible.
These mutations could all be made by first copying genes, then only adding functions in the copies, thus the entire original genome is still there.
Why ignore this possibility?
This isn't being ignored so much as set aside in order to highlight the actual effect of the splitting and selecting processes in the general direction of reducing genetic diversity.
But when we do focus on it, questions about it do come up. The splitting processes are easy to recognize: Thousands of already-present alleles -- including very possibly quite a few alleles, a dozen or so or more possibly, for a given gene -- shuffling around and pairing up in many reproductive events is easy to picture. How mutation enters into this is not easy to picture. How mutation is even NEEDED is a question considering all the allelic possibilities there are in some large populations. And this is separate from whether the mutations known to happen make any kind of contribution in the form of new traits that get passed on.
What seems to be left out of the formula is this general tendency to allelic depletion and reduced genetic diversity over time.
Yes. That’s left out because it’s a fantasy. Speciation is a poor place to look for a “loss of genetic information”. Why? Because it only works if you put your creationist blinders on and look only at the little split off group that speciates, and then completely look away before accumulated mutations add more genetic information in the form of new alleles that weren’t in either starting population.
There is no need for such mutations to occur to bring about great changes in two separated populations simply from the change in frequency of alleles, and possible complete elimination of some alleles -- no need, and no evidence that mutation actually makes a contribution to this process. You can breed dogs to enhance particular EXISTING traits, you know, simply by combining existing alleles for the traits you desire, and a big factor in this process is the elmination of competing alleles.
There is no need to postulate the addition of anything new in the form of mutations in this process. MAYBE mutation is a part of it, but so far it sounds mostly hypthetical.
You need the blinders because if you look at both populations, the loss is little if any.
It depends. I'm talking about a TREND, as I've said.
Many, if not most speciation events happen with one small group leaving a big group. The big group hasn’t lost any genetic information, since it’s big. The little group has, but again, if you look at both groups, no loss.
I've grasped this just fine. I focus on the little group because it will express the greatest changes in the phenotype thanks to its depleted genetic diversity caused by the reduction in allelic possibilities. This is the trend I am trying to focus on here.
Then, both groups ADD genetic information through mutation, resulting in an overall increase in genetic information.
All theory, all fantasy. Again, mutation is not needed to produce new phenotypes. Reduced genetic diversity is what brings this about, the removal of some alleles so that others come to expression. A lot of genetic information is not needed for speciation. Reduction of genetic information and genetic diversity will do it quite efficiently. That's the point.
Now, of course you would like to have a lot of genetic information if the ToE makes sense. But no, speciation does not need a lot of genetic information. {EDIT: What this implies is that speciation and the ToE are at odds, exactly the opposite of what you claim, and the opposite of what must be the case if the ToE is true.}
Now that I’ve posted it twice, do you understand how one mutation can make an extra copy of a stretch of DNA, then later mutations can change that new stretch, resulting in new alleles without the loss of the one they came from?
Yes, but I'm very unsure of the actual character of these "new alleles."
Looking at the speciation process and claiming that speciation causes a loss (and not a gain) of genetic information seems difficult to me.
Well, but it's been explained how it happens and it makes sense. The problem is that evolutionists assign a great role to mutation that is really not justified. It isn't needed, as I've said, and it hasn't been demonstrated. It is merely assumed.
A better place to argue for the loss of genetic information is clearly the extinction of a species. No one argues that they happen, and that they happen a lot. After all, over 99% of the species that have ever lived are extinct. And when a species goes extinct, ALL of the genetic information that made them different from surviving species is gone.
Certainly. Extinction is the perfect example. What is not generally acknowledged is that it is those "processes of evolution" that lead to "speciation" that make species ultimately vulnerable to extinction when a certain number of splits have occurred or a drastic split like a bottleneck occurs. The cheetah is a prime example. The cheetah does pretty well considering its drastically allelically depleted condition.
The reason this is not recognized is that mutation is ASSUMED to take up the slack -- merely assumed, as far as I can see, without the kind of evidence needed to show that it could play that role, given the actual things mutation is and does, or certainly that it does.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 55 by Equinox, posted 08-31-2006 12:46 PM Equinox has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 66 of 301 (345630)
09-01-2006 2:20 AM
Reply to: Message 58 by Faith
08-31-2006 1:34 PM


Re: Overly technical references
Yours on mutation was way over my head and not really focused on beneficial mutations
The whole point of that thread was that you asked questions so we could elaborate on the nature of mutations. Since you gave up on that idea without asking a single question just because a couple of other people had asked questions requiring more technical answers, the threads purpose was rather undercut.
TTFN,
WK

This message is a reply to:
 Message 58 by Faith, posted 08-31-2006 1:34 PM Faith has replied

Replies to this message:
 Message 69 by Faith, posted 09-01-2006 4:10 AM Wounded King has not replied

PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 67 of 301 (345633)
09-01-2006 3:12 AM
Reply to: Message 60 by Equinox
08-31-2006 1:58 PM


Re: Overly technical references
I have to partially disagree. While Faith would certainly be entitled to ask for further explanation, even a layman should be able to work out that the papaer does address the genetic evidence:
These are the 3rd and 4th sentences from the abstract:
This addresses the question of other, more recent, population size bottlenecks, and we review nonrecombining and recombining genetic systems that may reflect them. We examine how these genetic data constrain the possibility of significant population size bottlenecks (i.e., of sufficiently small size and/or long duration to minimize genetic variation in autosomal and haploid systems) at several different critical times in human history.
While a layman might struggle with the technical words I cannot see how they could read "We examine how these genetic data..." and come to the conclusion that the paper does not discuss the genetic data.
So I do not see that Faith can be considered to be right in rejecting the paper if she is not even prepared to read the first few sentences of the abstract. Her complaint here, while not completely invalid, is something of a red herring, raised to cover the fact that she is dismissing a source without even a cursory investigation of its contents.t

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 68 of 301 (345641)
09-01-2006 4:09 AM
Reply to: Message 50 by RAZD
08-30-2006 6:49 PM


Re: are bottlenecks tied to speciation?
THAT'S WHAT SPECIATION DOES, IT SEVERELY REDUCES GENETIC DIVERSITY. That's what a bottleneck is, severely reduced genetic diversity.
I don't think these - speciation and bottlenecks - are necessarily related.
What I'm saying is that a bottleneck is simply an extreme version of a number of the selecting and population-splitting processes that cause new traits to appear in the phenotype. As I've been explaining, and so has MJFloresta, sometimes the process is subtle, not involving actual loss of alleles to a population but simply changing their frequencies so that some that predominated in the combined population before the split may no longer be expressed as much or at all, while others will be. Phenotypic change is the product of these changes. When the population split or selection process is drastic and reduces a new population to very small numbers then the changes may be dramatic, and what has happened then is that a LOT of alleles have been lost and the ones left are coming to expression and creating a new phenotype that characterizes the new population. There are degrees of this between the very subtle and the very dramatic.
Speciation may cause a bottleneck, if it is of the founding population variety and the population is small.
But a founding population IS like a bottleneck and it's the bottleneck or founder effect that is causing the speciation, not the other way around. That is, the bottleneck or founder effect eliminates a great many alleles so that now the alleles that are left define the new small population. This brings about a new phenotype, even a new species. Reduced genetic variability = phenotypic change or speciation.
A bottleneck event may cause speciation, as in the Yucatan meteor extinction event and the subsequent rapid speciation of many types to fill the voids left by extinct species (most well know would be foraminifera)
Yes, that's an example of a drastic bottleneck, but the speciation is brought about simply by the reduced allelic possibilities in the new population, allowing the few that remain to be expressed as new traits in the phenotype.
But does one necessarily follow from the other?
Well, I suppose it's possible that the bottleneck simply might select out the very alleles that are already most expressed in the population and there would be little phenotypic change. I can't think of another way this might happen.
If the bottleneck is caused by a random event that does not select one set of genes over others, it could leave behind nearly as much diversity as there was before, diversity that would be quickly recirculated into the population as a whole ..
Yes, nearly as much if there is no loss of alleles or the loss is minor. But any loss of alleles is the same thing as a reduction in genetic diversity. That is, there are that many fewer allelic possibilities for the population as a whole. Must have misread you here. It doesn't matter what the cause is, a bottleneck is an extreme reduction in population which involves an extreme loss of alleles from the original population, and this great reduction in alleles allows the fewer number of alleles in the bottlenecked population to be expressed in the phenotype. If these alleles include some that didn't get expressed in the original population then the new traits will comprise a dramatically new phenotype.
But I don't see that it matters a lot whether the cause is random or not, although the targeted selection of particular alleles over others would certainly be a more dramatic case. But even in a random situation, if the overall number of alleles is severely reduced by the event, whether it's the geographic separation-plus-loss of inbreeding ability over time, or natural selection by which a very few adaptive traits are selected from a population in which the vast majority die, overall there will be this tendency to reduction in number of alleles which is the same as decrease in genetic/allelic variability, and this can bring new traits out in a population. Again, the more drastic the population reduction, the more dramatic the loss of genetic variability and the greater the phenotypic change -- on out to speciation. Since you are talking about a bottleneck all these thoughts are out of place.
....and the missing amount made up with subsequent mutation rates, but the population could still be the same species generations after the bottleneck event has passed.
With a large number of alleles no longer available to the bottlenecked population there is simply a great loss of diversity right there. Even if there is a striking phenotypic change you may still not want to call it a new species. It depends, but it is certainly change in the direction of speciation.
You think mutation could make this up, but mutation's role is being questioned here. It hasn't made it up for the cheetah yet. How long should it take?
If speciation occurs in a whole population through drift over time then there is no bottleneck involved and the amount of diversity in any one generation is the same as the one before and after.
Yes, drift is the situation of no population split which we've been acknowledging may change the phenotype without reduction in diversity. It's the natural playing out of changing allelic frequencies in the population that brings this about in this case. Nothing new is added, only the frequencies change. That's all it takes to change a phenotype, the shuffling of allele frequencies.
Or speciation where a population divides into two or more subpopulations that no longer mate -- there is no loss in diversity there, as it is divided between the two populations.
But there is definitely a loss of diversity IN the subpopulations and this is what we are talking about. If they can't interbreed then they can't recombine their alleles so the diversity they share between them is meaningless. Meanwhile, within the smaller new populations you have new allelic frequencies, and some alleles from the former combined population may be completely lost. In both these cases you will see over time a change in the phenotype, but if alleles are actually lost, then you'll see both a reduction in genetic variability and the expression of new traits or phenotypes. Reduction = Speciation, as a trend over time.
There are other factors involve that make a strict relationship problematical, imh(ysa)o.
Only mutation. Nothing else.
==================LATE BREAKING EDIT:=====================
{EDIT: Just realized that probably that paper that Wounded linked to meant what you seem to mean, where they say:
There are many reasons to believe that there may have been a number of severe population size bottlenecks on the lineage leading to living humans, principally because of the many speciation events that must have occurred.
which in my Message 32 I answered:
quote:
Yes, of course. THAT'S WHAT SPECIATION DOES, IT SEVERELY REDUCES GENETIC DIVERSITY. That's what a bottleneck is, severely reduced genetic diversity
So there does seem to be this idea that speciation CAUSES bottlenecks. So the idea is that mutations occur that get selected, this being the evolutionist idea of how evolution happens, which of course means that speciation happens this way, and this causes a bottleneck during the phase that the selected mutations are forming a new population.
Some thoughts:
This implies that these supposed mutations replace other perfectly viable alleles in the population, based on some posited advantage that causes them to be selected over the others, in some particular area of function.
I'm going to have to ponder this some more, but maybe I finally figured out what is generally thought. Seems like it can't possibly work if you think about the whole supposed history of evolution.
Also odd, it seems to me, that this notion seems to have so completely eclipsed the obvious normal way new phenotypes are created, by the changing of the frequencies of alleles already in the population. That is you just select what is already there, and has perhaps always already been there, not something new. You just pick the best version of it to see if you can breed a yet better version of it.
But it's probably too early in the morning after another night of insomnia to try to think so hard.
MAYBE IT WOULD HELP IF SOMEBODY DID GO TO THE TROUBLE TO TRANSLATE THAT ARTICLE FOR ME. I'D APPRECIATE THE EFFORT.
Edited by Faith, : No reason given.
Edited by Faith, : punctuation, grammar
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 50 by RAZD, posted 08-30-2006 6:49 PM RAZD has replied

Replies to this message:
 Message 88 by RAZD, posted 09-01-2006 9:30 PM Faith has replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 69 of 301 (345642)
09-01-2006 4:10 AM
Reply to: Message 66 by Wounded King
09-01-2006 2:20 AM


Re: Overly technical references
You are right, and I suppose I could still try to turn it in that direction. I got discouraged somehow.

This message is a reply to:
 Message 66 by Wounded King, posted 09-01-2006 2:20 AM Wounded King has not replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 70 of 301 (345643)
09-01-2006 4:17 AM
Reply to: Message 67 by PaulK
09-01-2006 3:12 AM


Re: Overly technical references
So I do not see that Faith can be considered to be right in rejecting the paper if she is not even prepared to read the first few sentences of the abstract. Her complaint here, while not completely invalid, is something of a red herring, raised to cover the fact that she is dismissing a source without even a cursory investigation of its contents.t
You are right that I did initially reject it before reading much of it, just bogged down after the first few sentences. But now I have the whole thing in Word and have really struggled with it and can say that it is absolutely definitely a lost cause. If such a paper really has useful information to offer, it should NEVER be presented to a nonscientist untranslated and undigested like that.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 71 of 301 (345678)
09-01-2006 9:16 AM
Reply to: Message 18 by qed
08-27-2006 10:25 AM


Re: Cheetahs??
I have no idea why Cheetahs are such a popular creationist pick.
Maybe I can explain.
They are living proof of how fragile a species becomes when evolution is halted by an extreme population bottleneck, resulting in a limited gene pool.
This is becoming an extremely interesting problem now that I'm finally getting how evolutionists think about this stuff. Halted by the bottleneck. Hm.
Now the article that Wounded King linked, and a few things RAZD said, suggest that speciation itself, or the very stepping stone of evolution itself, *creates* a bottleneck.
So now we have that evolution both creates a bottleneck and is halted by a bottleneck. Interesting.
No wonder mutation is treated as so necessary to explain everything.
African Cheetah population was only reduced to hundreds... Interestingly the cheetah population of today has an exceptionally high mutation rate.
Well, now, have any of those mutations provided some allelic alternatives exactly in the places where the cheetah has been making do with just one for so long? -- that is, at many loci, not just one, not just a few, but many. The only mutations that could help the creature would be very functional beneficial ones at those particular loci. Could we please have some evidence of this?
Me, I'd worry about that high mutation rate in such an allelically depleted creature on the verge of extinction. But that's because I tend to look at mutation with a bit of a jaundiced eye, as rarely friend and largely foe.
Taking this to the next level the tiny gene pool caused by God's flood would make us all a lot less diverse than cheetahs (or more likely dead).
Not according to Creo Theory it wouldn't, because we have the reverse model from the ToE. We postulate that all living things started with a large genetic potential in the genome that has gradually played out over the millennia, and that it was still very large on the ark {edit: And is still surprisingly large even now, except for some species going or gone extinct}. On this idea Adam and Eve alone had the genetic potential built into just the two of them for all humanity to descend from them -- and since Eve was taken from Adam I think we can assume their genomes were identical. By the time we get to Noah and his three sons there was still enough genetic potential to beget every human being who has lived since then and lives now --from just those three sons and their wives.
But to answer your first question. According to Creo Theory, the allelic starvation of the cheetah caused by a bottleneck is an illustration of exactly the opposite of what you are saying and what evolutionists in general think. The cheetah IS the new species, brought about the way all new species are brought about, by the elimination or suppression of some alleles while others are expressed in the phenotype. In the case of the cheetah all the competing alleles are simply gone and its depleted condition even prevents it from being interbred with other cats so as to improve its health.
In other words, in a maximal irony, it is the very process of speciation itself that brings evolution to a halt -- and provides that barrier that defines a Kind. Which I've been arguing for months now.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 72 of 301 (345694)
09-01-2006 10:14 AM
Reply to: Message 64 by crashfrog
08-31-2006 11:00 PM


That one bacterium again
In the case of bacteria, which reproduce asexually, we can limit the number of alleles per gene to 1, because that's the maximum number of alleles an individual bacterium can have, and we can develop a whole population from a single individual. When we do that the population is called a "monoculture."
I'm still hoping to get to your post here, but right now I seem to have forgotten again what this bacteria example is supposed to demonstrate and must ask that you explain it again.
You get a whole population from a single bacterium with its one allele -- a whole population of that one kind of bactera with that one allele. And does this allele then mutate somewhere in that population, is that what this is all about? Does it mutate in a beneficial way? I'm probably punchy from being up all night, but I would appreciate getting this explained again. Thanks.

This message is a reply to:
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Replies to this message:
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Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 73 of 301 (345698)
09-01-2006 10:43 AM
Reply to: Message 63 by Faith
08-31-2006 10:31 PM


Re: Faith Logic
About the black and the brown socks, isn't it true that some genes have a LOT of alleles in some populations? So if the population splits a particular gene may lose some alleles. Also that one orange pair is probably left over from a previously larger number in a previous population, and may still exist in a large number in a cousin population, since splitting has no doubt already occurred to create any given population.
Analogies are often unfortunately pushed beyond the limits of what they are intended to illustrate. In this case, my socks example was simply intended to demonstrate how a random selection of alleles statistically could end up in a new population. It's quite probable that you wouldn't end up with your orange socks in your bag - leaving that particular allele in the initial "sock population" - meaning no loss of "sock diversity".
Yes, most populations can have a whole bunch of different alleles for particular traits (depends on what the selection pressures might be). Much of the diversity in alleles is likely due to recombination - although there's more than sufficient evidence to indicate that many novel alleles arise through mutation - the Frog's bacteria examples show empirical proof of this. If there's no particular advantage or disadvantage provided by a particular allele or suite of alleles ('cause you really can't consider one allele in isolation as most genes have multiple, often synergistic effects), the frequency of the particular alleles varies mostly via drift. In fact, even disadvantageous alleles may be retained in a population if they are linked to other normal or even advantageous alleles. It's kind of a trade-off. An allele or suite of alleles may be retained in a population in what is called ecological polymorphism (a discussion of which will take us beyond this thread).
Anyway, when a population splits, an assortment of the existing alleles is contained in the new population. This could be a really skewed distribution (like the orange socks), or simply (like the brown/black socks) a representative sample of the existing alleles. If there's a normal representative sample in the new population, then the amount of divergeance between the two parent and daughter populations over time will depend on the relative level of gene flow between the two populations which is in turn based on several factors (which I don't think we need to get into unless you want).
How do you KNOW that new alleles are generated, that is mutations that actually make a change and a change in a useful direction that gets passed on? There is no NEED for mutations for change to happen anyway. It's the natural result of the variety of alleles already present in the population.
Well, there may not be any need for mutation to create new alleles, but nonetheless that's what happens. We see this in the existence of hybrid zones between two related populations. You mentioned ring species, and this is a critical issue in the formation of those rings. Adjacent populations - which start out with the same assortment of alleles prior to the split - diverge from each other, but generally remain "in contact". The hybrid zone between these populations gives an indicator of how much gene flow there is between them. Selection can cause linkage disequilibrium, but doesn't have to.
One of the really good examples of ring species that has been extensively studied in this context is the Ensatina salamander complex. Since you've consistently complained that technical references are a bit much, I'll just cite one for others who might be interested: Alexandrino J, Baird SJ, Lawson L, Macey JR, Moritz C, Wake DB, 2005, Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications, Evolution, 59:1334-1347. The interesting thing about this article, although the overall research was not directly related to my point, is that they were able to go back through 20 years of genetic data (as well as performing their own analyses), that showed divergeance between two subspecies populations (E. eschscholtzii xanthoptica and E. eschscholtzii platensis). The further apart geographically the populations of these two subspecies were, the greater the genetic divergeance. However, there was a well-defined hybrid zone between the closest populations. The researchers were able to show linkage disequilibrium due to differential selection pressures on either side of the zone. The selection pressures against the hybrids permitted the researchers to demonstrate a gradual increase in incompatibility between the two subspecies at the ends of the species' range. In other words, we're looking at incipient speciation between E. eschscholtzii xanthoptica and E. eschscholtzii platensis - and where we draw the line is kind of arbitrary. A taxonomic "splitter" could conceivably declare the populations at the extreme ends of the range separate species.
Making a long story short, there is sufficient genetic divergeance between the two "ends" of the E. eschscholtzii chain to indicate that a) the most distant populations do not simply represent a statistical assortment of existing alleles, and b) genetic diversity has not only not decreased, but has actually increased over the range of the species.
Hope this clarifies why you might be mistaken concerning both what happens in speciation and why mutation - in the case of the example provided - is the only realistic option for how the genetic incompatibility arose at the ends of a chain of populations leading to speciation.

This message is a reply to:
 Message 63 by Faith, posted 08-31-2006 10:31 PM Faith has replied

Replies to this message:
 Message 74 by Faith, posted 09-01-2006 11:48 AM Quetzal has replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 74 of 301 (345704)
09-01-2006 11:48 AM
Reply to: Message 73 by Quetzal
09-01-2006 10:43 AM


Re: Faith Logic
About the black and the brown socks, isn't it true that some genes have a LOT of alleles in some populations? So if the population splits a particular gene may lose some alleles. Also that one orange pair is probably left over from a previously larger number in a previous population, and may still exist in a large number in a cousin population, since splitting has no doubt already occurred to create any given population.
Analogies are often unfortunately pushed beyond the limits of what they are intended to illustrate. In this case, my socks example was simply intended to demonstrate how a random selection of alleles statistically could end up in a new population. It's quite probable that you wouldn't end up with your orange socks in your bag - leaving that particular allele in the initial "sock population" - meaning no loss of "sock diversity".
I think I got it and characterized it correctly although maybe my terminology is different enough to be confusing.
Yes, most populations can have a whole bunch of different alleles for particular traits (depends on what the selection pressures might be). Much of the diversity in alleles is likely due to recombination - although there's more than sufficient evidence to indicate that many novel alleles arise through mutation - the Frog's bacteria examples show empirical proof of this. If there's no particular advantage or disadvantage provided by a particular allele or suite of alleles ('cause you really can't consider one allele in isolation as most genes have multiple, often synergistic effects), the frequency of the particular alleles varies mostly via drift. In fact, even disadvantageous alleles may be retained in a population if they are linked to other normal or even advantageous alleles. It's kind of a trade-off. An allele or suite of alleles may be retained in a population in what is called ecological polymorphism (a discussion of which will take us beyond this thread).
Yes, this is all clear to me at least in a very general way, though I may not grasp all the technical aspects of it. I've assumed without stating it that a number of genes will be affected at once.
Anyway, when a population splits, an assortment of the existing alleles is contained in the new population. This could be a really skewed distribution (like the orange socks), or simply (like the brown/black socks) a representative sample of the existing alleles.
All implicit or explicit in what I've been saying I believe, although perhaps I said it in some other posts than mine to you, I don't remember.
If there's a normal representative sample in the new population, then the amount of divergeance between the two parent and daughter populations over time will depend on the relative level of gene flow between the two populations which is in turn based on several factors (which I don't think we need to get into unless you want).
The less gene flow the more divergence I would assume.
How do you KNOW that new alleles are generated, that is mutations that actually make a change and a change in a useful direction that gets passed on? There is no NEED for mutations for change to happen anyway. It's the natural result of the variety of alleles already present in the population.
Well, there may not be any need for mutation to create new alleles, but nonetheless that's what happens. We see this in the existence of hybrid zones between two related populations. You mentioned ring species, and this is a critical issue in the formation of those rings. Adjacent populations - which start out with the same assortment of alleles prior to the split - diverge from each other, but generally remain "in contact". The hybrid zone between these populations gives an indicator of how much gene flow there is between them. Selection can cause linkage disequilibrium, but doesn't have to.
The bolded sentence alerted me to look for the evidence that mutations are involved in this, and I haven't seen it. I don't know what "linkage disequilibrium" means, but the main thing is I don't see any reason at all from what you've described here how mutation is necessary to explain anything about this hybrid zone. The usual combining of alleles, different sets of them from the populations at both ends but affected by the different frequencies in both caused by the original split would do it I would think.
One of the really good examples of ring species that has been extensively studied in this context is the Ensatina salamander complex. Since you've consistently complained that technical references are a bit much, I'll just cite one for others who might be interested: Alexandrino J, Baird SJ, Lawson L, Macey JR, Moritz C, Wake DB, 2005, Strong selection against hybrids at a hybrid zone in the Ensatina ring species complex and its evolutionary implications, Evolution, 59:1334-1347.
I'd really appreciate it if instead of merely citing a technical paper a poster would give a brief abstract of it in nonscientific language. But at least you do go on to discuss an aspect of it:
The interesting thing about this article, although the overall research was not directly related to my point, is that they were able to go back through 20 years of genetic data (as well as performing their own analyses), that showed divergeance between two subspecies populations (E. eschscholtzii xanthoptica and E. eschscholtzii platensis). The further apart geographically the populations of these two subspecies were, the greater the genetic divergeance.
As I would expect. Less likelihood of gene flow between the two original populations plus more time for the differing allelic frequencies to manifest in the populations as a whole.
However, there was a well-defined hybrid zone between the closest populations. The researchers were able to show linkage disequilibrium due to differential selection pressures on either side of the zone.
I THINK I intuited what this means above although I don't know what "linkage disequilibrium" means. The differential selection pressures refers to the different allele frequencies on either side of the zone, which were brought about by the original split between them but became characteristic or more or less evenly spread in each population over time, and the new frequencies now produce a hybrid zone that reflects these new characteristics on either side of it rather than the original characteristics. All easily explained from the original given set of alleles without anything new added.
The selection pressures against the hybrids permitted the researchers to demonstrate a gradual increase in incompatibility between the two subspecies at the ends of the species' range. In other words, we're looking at incipient speciation between E. eschscholtzii xanthoptica and E. eschscholtzii platensis - and where we draw the line is kind of arbitrary. A taxonomic "splitter" could conceivably declare the populations at the extreme ends of the range separate species.
Again, what I would expect and have been describing in various posts here. I don't really get this point about the selection pressures against the hybrids and how it figures in this, but I would expect the incompatibility-unto-speciation effect based on what I've been saying.
Making a long story short, there is sufficient genetic divergeance between the two "ends" of the E. eschscholtzii chain to indicate that a) the most distant populations do not simply represent a statistical assortment of existing alleles,
I haven't assumed they would.
and b) genetic diversity has not only not decreased, but has actually increased over the range of the species.
And what demonstrates this? I haven't seen anything in the above that shows evidence of an increase in diversity, but most likely the opposite. That would imply an increase in alleles and that hasn't been shown. It is probably assumed, but it hasn't been shown.
Hope this clarifies why you might be mistaken concerning both what happens in speciation and why mutation - in the case of the example provided - is the only realistic option for how the genetic incompatibility arose at the ends of a chain of populations leading to speciation.
Oddly enough, given your certainty that these things are demonstrated in your post, I see only confirmation of what I've been saying. You haven't given any evidence of mutation for anything you've described, and as I've been postulating all along here, the genetic incompatibility at the ends of the chain of populations can most likely be explained by the decreasing "fit" between the genomes as they've differentiated over time based on their differing sets of alleles, maybe even merely differing frequencies of the same alleles. I see no reason to assume mutation in this process. So what I see here is what I've been describing: speciation or approach to speciation as the result of a reduction in genetic diversity / number of alleles.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 73 by Quetzal, posted 09-01-2006 10:43 AM Quetzal has replied

Replies to this message:
 Message 75 by Quetzal, posted 09-01-2006 12:56 PM Faith has replied
 Message 78 by Ben!, posted 09-01-2006 1:38 PM Faith has not replied
 Message 80 by EZscience, posted 09-01-2006 2:20 PM Faith has replied

Quetzal
Member (Idle past 5872 days)
Posts: 3228
Joined: 01-09-2002


Message 75 of 301 (345727)
09-01-2006 12:56 PM
Reply to: Message 74 by Faith
09-01-2006 11:48 AM


Re: Faith Logic
think I got it and characterized it correctly although maybe my terminology is different enough to be confusing.
Okay, as long as we're clear on what the original analogy was intended to illustrate.
Yes, this is all clear to me at least in a very general way, though I may not grasp all the technical aspects of it. I've assumed without stating it that a number of genes will be affected at once.
Yeah, but this wasn't the main point of the paragraph. As I noted, if we see a bunch of novel alleles appearing in separated populations, there's only two possibilities: recombination in sexually reproducing organisms, or one or another form of mutation. The discussion Froggie has had on bacteria shows pretty unequivocally that mutation can produce novelty. I suppose you can still argue that recombination is a more important factor, but the salamander article I linked to shows that the differences in the most divergeant populations is NOT due to simply reshuffling existing alleles, and therefore MUST (unless there's some other mechanism you haven't revealed yet) be due to mutation.
The less gene flow the more divergence I would assume.
Precisely.
The bolded sentence alerted me to look for the evidence that mutations are involved in this, and I haven't seen it. I don't know what "linkage disequilibrium" means, but the main thing is I don't see any reason at all from what you've described here how mutation is necessary to explain anything about this hybrid zone. The usual combining of alleles, different sets of them from the populations at both ends but affected by the different frequencies in both caused by the original split would do it I would think.
The hybrid zone is the area where the gene pools of the populations are mixing. As far as it goes, you're correct on the combining of alleles bit. That's what a hybrid zone is, after all. However, "linkage disequilibrium" is a fancy term that basically means alleles in one population are not necessarily found in the second population. The greater the degree of disequilibrium, the more divergeant the two populations are genetically. When you have differential selection pressures operating on the two populations - and especially when you have selection pressures more greatly effecting the hybrids between them than either of the two source populations - you get disequilibrium. It's kind of like a "tightening of the gene flow pipe" to use another analogy. It reduces the gene flow between source populations. Since neither of the two populations in my example have reached the stage of true "species" yet, we would expect the two populations to have quite a bit of allelic overlap between them. However, the choking off of gene flow caused by selection disfavoring the hybrids means that the two populations are becoming more and more divergeant over time. From where did this diversity arise? Recombination can't explain it entirely. Gene flow from one to another can't explain it entirely, because the gene flow is being choked off. What's left? For biologists, what's left is mutation giving rise to novel alleles.
I'd really appreciate it if instead of merely citing a technical paper a poster would give a brief abstract of it in nonscientific language. But at least you do go on to discuss an aspect of it:
I thought I did that. I'm at a loss as to how to address this. The mutation data including the specific loci the research addressed is contained in the article. For whatever reason, you have consistently stated that the articles we generally cite as reference for our claims are too technical, and you want a sort of "reader's digest condensed version". I have no problem with that request - and in fact discussed the relevant portions of the article in layman's terms. However, given that, I can't see how you can demand a simplified version that covers the relevance and at the same time demand the detailed technical evidence. It's there, in the article. I've simplified things about as much as I can. If you want the hard data, feel free to peruse the article itself. Otherwise, you're just going to have to take my word for it .
Faith writes:
Quetzal writes:
and b) genetic diversity has not only not decreased, but has actually increased over the range of the species.
And what demonstrates this? I haven't seen anything in the above that shows evidence of an increase in diversity, but most likely the opposite. That would imply an increase in alleles and that hasn't been shown. It is probably assumed, but it hasn't been shown.
Demonstrated, as noted in the article, by the fact that there is a somewhat different set of alleles in each source population. That's what makes them distinct subspecies in the first place.
Oddly enough, given your certainty that these things are demonstrated in your post, I see only confirmation of what I've been saying. You haven't given any evidence of mutation for anything you've described, and as I've been postulating all along here, the genetic incompatibility at the ends of the chain of populations can most likely be explained by the decreasing "fit" between the genomes as they've differentiated over time based on their differing sets of alleles, maybe even merely differing frequencies of the same alleles. I see no reason to assume mutation in this process. So what I see here is what I've been describing: speciation or approach to speciation as the result of a reduction in genetic diversity / number of alleles.
Make up your mind, Faith. Either you want the technical details, or you want a simplified version. Maybe Percy can make sense of this - he's generally very good at that - much better than I am. The mutation evidence is contained in the article. If you don't want to get technical, I'm not sure how you can accuse me of failing to provide evidence. In point of fact, I DID provide the evidence. My discussion was - at your request - simplified and as non-technical as I can make it. I'm really not sure how you think you can have it both ways. The evidence is there. I've provided the layman's explanation. I guess it's up to you to make the connection.

This message is a reply to:
 Message 74 by Faith, posted 09-01-2006 11:48 AM Faith has replied

Replies to this message:
 Message 77 by jar, posted 09-01-2006 1:08 PM Quetzal has replied
 Message 86 by Faith, posted 09-01-2006 7:08 PM Quetzal has replied

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