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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 63 of 87 (555208)
04-12-2010 4:34 PM


I'd like to see Bluejay's summary and ZenMonkey's opening post before I decide what I want to do.

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 65 of 87 (555249)
04-12-2010 7:45 PM
Reply to: Message 64 by ZenMonkey
04-12-2010 5:40 PM


Re: Picking up from the other thread.
There are a couple of points in this last exchange that I'd like to clarify, and then we can push on.

...I should be more precise here. If an allele for a particular trait is actually elimnated, then under your model it would necessarily never reappear in a given population. Whether by natural selection, genetic drift, of some other cause, once the last black fur allele is gone, then there will never be another black rabbit.

Yes.

If that's the case, then it should also be very likely if not certain that alleles for certain traits have already gone extinct for any number of populations, and we might never know about it. For example, there could very well have been a population of red-furred rabbits at one time, but that allele has now gone extinct. (Of course, I'm referring to rabbits having red fur in the same way that other creatures have red hair, not fire engine red.)

Yes, quite possible. I almost made this point myself in answer to your remark about purple fur. Yes, there could be other fur colors and patterns that no longer appear in any population of rabbits anywhere.

So we should agree if fur color is a neutral trait that confers no reproductive advantage, then if some accident reduces the frequency of a given allele at some point, but doesn't eliminate it, then it's highly probable that eventually the allele will reestablish itself in the population and regain its former standing, so to speak.

I don't see why this is "highly probable." It COULD regain its former standing, but it doesn't seem to me to be "probable" that it would come back to that extent from its highly reduced position. I would think something would have to favor it, some sort of selection for that to happen -- yes, reproductive advantage of some sort.

This assumes that the event that reduced the allele was only a one-time effect and not a continuous pressure. Otherwise we have a case of natural selection over-riding dominance in establishing the frequency of an allele.

OK, you apparently have in mind a dominant, the dominant black fur then. OK, if it's a one-time event that reduced it and it's dominant, eventually it would come back but it could be a VERY long time, longer than most of my scenarios allow for. {abe} Seems most likely to me that whatever selection pressure reduced it wouldn't let up. But the main thing to say here is that there are many ways variability can be increased, such as by populations rejoining, gene flow resuming, and previously reduced alleles being restored over time as in this example -- and of course also if mutations do anything remotely like you all believe they do -- but when all that is going on you aren't getting the phenotypic definition that is along the way to speciation, which is the necessary stepping stone to macroevolution, which therefore is prevented from happening.

But so long as an allele still exists, and so long as it remains neutral and not subject to natural selection pressures, then the dominance relationships of the various alleles should be the prime determinant of how often the traits they produce will appear in the population.

If no selection pressure, yes.

So just to be clear, if your model says that genetic diversity will always decline and never increase, then we should see a consistant decline not only in traits but also in species. There can't be any new species, only changes brought about by the elimination of alleles and shifts in their frequency in various populations.

Not at all. The opposite. This is the WAY you get new species is my claim.

It is the processes that reduce genetic diversity that bring out new traits, which is the essence of evolution after all, and there is no reason except accidental factors (size of population, environmental benevolence) that these processes must stop until the genetic diversity is depleted to such an extent that further evolution is at an end. At that point most likely you will have speciation. Any population that reaches that extremity will probably be a species, but the trend alll along has been in that direction. It's not too often reached, fortunately, though some populations do fine in that condition (the seals) and there will most likely be plenty of other lines of the same organism it's closely related to that aren't close to speciation, but that is the direction that selection, drift, migration, and so on ALWAYS take populations according to my understanding.

Or do you believe that by eliminating certain traits you can create a daughter population that can no longer breed with its parent? How much change do you think the elimination of traits can bring about?

All the change needed for speciation , speciation based on genetic mismatch anyway, yes, but only from a population that is already genetically depleted, very likely the end population in a ring series as I have been presenting it, for instance. Otherwise you get populations with new variations and SOME reduced genetic diversity but not necessarily extreme.

The argument is that there is a continual trend in this direction in all populations, though very slow in any that remain numerous AND various, even apparently not operating at all in some of those cases, and only seen at the extremes after many selecting, reducing or isolating events OR a one-time major event like a bottleneck or founder effect.

It appears that you agree with at least some of the Theory of Evolution, that the frequency of alleles in population does change over time and that natural selection as well as genetic drift and other causes, are what change that frequency.

Of course. Evolutionists do valid science most of the time and are able to describe phenomena in a way one can work with, WHEN they aren't just assuming stuff like mutations that they can't prove. There is no problem with the mechanisms of change, it's the assumed and unproven claim of OPEN-ENDED change that is false.

Where you appear to disagree is that alleles can be changed in such a way that new, viable alleles and new traits can ever be produced.

Yes. Feel a need to qualify this a bit now just for a reminder that while I'm now convinced that if you ever get an occasional "beneficial" -- I prefer "normal" or "functioning" -- allele from mutation, it's only a chemical fluke, I started out accepting the creation of new alleles through mutation and I'm willing to go back to that position. It really doesn't matter at all what the source of variation is, the processes of reduction and selection that are necessary to forming new varieties, and speciation itself, will eliminate most of it. Because getting whole new breeds and populations with a particular character depends on this process of reduction.

Your position also assumes the standard conditions of Young Earth Creationism.

Actually I don't start from that assumption. I think it is important to emphasize this. I do not argue FROM myYEC position at all on this topic although many insist on assuming I do. The argument about reducing diversity to get new traits could come from any position at all.

I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path. ALL evolving paths would ultimately lead to that end, but they aren't all doing it at the same rate. It DOES of course seem like it would fit into a YEC framework better than any other.

For one, the creation event must have been relatively recent for there still to be so many species of plants and animals to still be around.

It would seem so, but as I said, although it appears to be most compatible with YEC dating, the argument doesn't derive from a particular notion of the age of the earth, it stands on its own. If you have a built-in cache of alleles that doesn't change, then it is all running out to speciation where it must stop. It's not derived from theory or belief, it's completely empirical and ought to be testable somehow or other.

I still claim that if you add in mutations you'll end up at the same point anyway, just delayed and by a more complicated route full of starts and stops, because you simply do not GET speciation without the reduction in genetic diversity that the operations that select and reduce and isolate bring about.

You can get variation without speciation with or without mutations, in populations that aren't changing much, but then you aren't getting the kind of evolution that could ever make a new species out of an old one; but if you have speciation which is essential to species-to-species or macroevolution then ironically evolution comes to a halt at that point. {ABE: I realize I have to add that while speciation is defined by the point at which interbreeding stops, in some cases where that occurs the new population(s) or species may still have quite a bit of variability left, so that evolution doesn't necessary stop there as I have been claiming -- I keep thinking too much of speciation at the end of a long train of population splits such as in ring species, but that isn't always the situation. It's still true that there is a trend of reduced genetic diversity with every population split or genetic drift and so on and you aren't ever going to get macroevolution from this process.}

Adding mutations at that point you have a new species also stops {ABE: Interferes with or prevents resumed} evolution. You'll get new traits, you'll get variation, but you won't get speciation so you won't get macroevolution. You have to have the selecting and isolating to get speciation and macroevolution and yet those processes ultimately prevent macroevolution from ever occurring.

If the creation event happened in the distant past, then it seems likely that most species that ever existed have all become extinct, and that many surviving species were once more diverse thAn they are today.

Yes. (corrected your "then" to a "than," pet peeve of mine)

Also, it assumes that all the forms of life that we do observe were created in essentially the same form in which we see them today.

No. It implies (not assumes) not extremely different but appreciably different life forms from which all we see today evolved, simply playing out their gene pools. There most likely has been an enormous variety in each species of which we still see quite a bit but nothing like there must have been in the past. At least sabre-tooths and house tabbies all together in the cat species for instance, giant forms and miniature forms and so on. All from the same built-in gene pool.

No significant change can have taken place, as the number of alleles for any given trait were all established from the beginning.

Oh but there had to have been an incredible wealth of genetic possibilities at the beginning that is not seen at all today, that produced incredible varieties over the millennia. Just take a look at the fossil record -- quite a collection of creative variations and adaptations of formerly thriving creatures, some of which we no longer see at all, but some obviously the ancestors of ours.

When I read that the bacterial genome is "packed" compared to that of most (all?) other species, because it has either little or no junk DNA (can't seem to find that clearly stated) I take that as a model for the original packed genome of every species, all sorts of great genetic possibilities we no longer see in the world for any of the higher animals, and the amount of junk DNA as a record of how much variation and adaptation has been lost in each.

This also leads me to conclude that you believe that the Earth as we see today is in essentially the same condition as when it too was first created.

Why? I don't get where you get these ideas out of my theory. In this case it may not be possible to read backward to the Creation, I'm not sure, so I do bring in my YEC assumptions:

Which are quite the opposite to what you expect. Starting with the Fall which introduced death which didn't previously exist and is what now determines that there is going to be an eventual end to all these genetic processes which otherwise would not have been the case. Without death there would have been a thousand times more marvelous variations of every species that live forever.

Also the Flood which broke up, sorted out and stratified the entire Earth -- which previously probably had a fairly uniform land mass like the other planets, and the Flood was accompanied or followed by by volcanic action and tectonic action and most likely meteoric showers as well, some or all of which may have contributed to the massive death in the Flood. And of course the Flood was a huge huge bottleneck that cut off enormous varieties of life from our modern world. Testimony to unimaginable diversity in living things before the Flood. Big changes. Nothing the same. The earth is a wrecked planet compared to what it was at the Creation.

Had there been any significant environmental changes in the past then that would likely have resulted in natural selection pressures that would have eliminated far more species than we see today, as there would be no way for new species to emerge in response to those changes.

Well, you have to assume an enormously large genetic capacity the farther back you go, to explain what we still see of the varieties still possible.

But again, new species (variations that can no longer interbreed) emerge ONLY in response to the selecting-isolating processes. That's my argument. You get new species ALONG WITH inability to further vary or speciate. Speciation is the result of these selecting processes.

Am I still correct in my understanding of your views?

Farther and farther from them.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : green edits


This message is a reply to:
 Message 64 by ZenMonkey, posted 04-12-2010 5:40 PM ZenMonkey has responded

Replies to this message:
 Message 67 by ZenMonkey, posted 04-13-2010 12:29 AM Faith has responded
 Message 75 by ZenMonkey, posted 04-17-2010 5:20 PM Faith has responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 68 of 87 (555308)
04-13-2010 3:59 AM
Reply to: Message 66 by Blue Jay
04-12-2010 11:25 PM


Re: Passing the Torch: Yeah but Faith still gets her say.
Well, if Bluejay is going to post on this thread, although it's called a Summary, I'm going to answer it even if it involves me in two conversations. That's better than twenty anyway. I should have realized that I'd regard it as controversial.

I entered this discussion trying to probe various points of Faith’s argument, looking for where miscommunication and misunderstanding came in. It didn’t take long before we were talking only about mutation: it's quite obvious to everybody that this is where Faith takes exception to the evolution paradigm.

Yes, but as far as the case I'm trying to make goes, that didn't have to come up; as far as the way the debate went, it was of course inevitable that it came up. I started out quite willing to make my case with mutations in the mix, I was simply assuming mutations, but when post after post nobody was getting what I was trying to say and kept insisting that mutations refuted my argument, finally I gave in to the pressure to take the side trip into mutations, very reluctantly.

In the discussion about mutations I was confronted with a fact I'd put on the back burner while pursuing my argument: that the evidence for mutations is so scanty and yet evolutionists talk about them as if they were fact, and I realized how many times I've been bamboozled by that claim into simply assuming that mutations happen -- despite past experience with just how scanty the evidence actually is.

And that got me outraged on behalf of all who try to understand the problems in this debate or just understand what is claimed by evolution, and I realized that this claim IS fraud, IS deceit. And that became the focus of my side of the discussion at that point --for better or worse and probably worse as it put off even further getting into the meat of my main argument. Which I still claim SHOULD be arguable with or without mutations.

However, we talked about mutation from two angles: (1) whether or not mutations can actually produce new alleles and (2) whether or not the production of new alleles by mutation would make a difference in Faith’s scenario anyway.

I attempted to explain the difference between the genotype and the phenotype of a mutation, and Faith claimed to understand this. In her defense, I think she did know the difference, but just hadn’t spent enough time considering it to realize that her arguments were failing to distinguish them.

This is simply mystifying. I've been making CONSTANT use of the distinction from the first time I put together this argument -- it's of the ESSENCE of the argument. All this can show is that I'm still not getting it across, but the idea that I don't know the difference in ANY sense is evidence of some real miscommunication. But I see you say I don't know the difference with respect to mutations -- as opposed to what?

She repeatedly asked me to provide evidence of a beneficial mutation having occurred, but I initially resisted, because I thought it was more important to get her to accept the general concept of mutations being different from phenotypes before I got into discussing the data. In retrospect, I’m not sure I agree with my reasoning there.

Oh brother. If this is what you were doing no wonder we were not getting anywhere.

But really I was more insisting that there IS no evidence of mutations that make real living normal useful alleles, than I was demanding that you produce some.

I decided to first focus on the second angle: whether or not the existence of beneficial mutations would make a difference for Faith’s model.

Considering that nobody, including you, ever really got what my model is about, the idea of figuring out whether mutations would make a difference or not is premature to say the least.

The combination of the paper about the human mutation rate and the data about the elephant seal populations was enough to show that: If each human has an average of 0.6 new alleles due to mutation, then the current population of elephant seals (100,000) should harbor somewhere in the neighborhood of 60,000 alleles that did not exist before the bottleneck (this math assumes that all seals living today are first-generation descendants of seals that survived the bottleneck, so it does not take into account all the seals that had lived and died between the bottleneck and now). From the standpoint of the population, that is a lot of new material to work with.

That's fine, but since my model had not yet even been described in a way I could accept, that wasn't any point that I could start applying such information to it.

Since Faith continued to push for evidence of beneficial mutations, I presented her with a couple of papers showing the emergence of antimicrobial resistance in bacteria by random mutation. These were studies that really couldn’t be argued with: they started with a known allele, found variation in the population for the trait controlled by the gene, showed that the variation had was associated with genotypic variation, and demonstrated that the mutant allele outperformed the original allele. I was then able to compare it with other mutations that had happened the same way, but had had negative effects on the phenotype, and thereby, to finally show that a “diseased” phenotype is not necessarily tied to a “diseased” process.

it is possible that at that point of the discussion there were so many loose ends left behind in my mind, and your argument so unrelated to anything that I thought important, that I didn't give it the attention it deserves. But I'm not sure about that at all. In any case I can't take bacteria as models for universal genetic rules as you all do.

When you go to bacteria for your argument it feels like some sort of trick, especially when the focus to that point had been on genetic diseases in human beings. Oh I know perfectly well that genes should behave the same no matter what creature's genome they're in, but bacteria are really different from higher organisms and especially in their genome which apparently has lots more possibilities than the genomes of most other living creatures, so extrapolating from bacteria to humans really should not be admissible in my opinion. If there is no evidence of mutations making ordinary alleles for higher animals -- in any numbers that could suggest it's a habit of mutations to do so at least -- then that lack of evidence is important and gives support to MY side of the argument.

Faith acknowledged that this was evidence of a mutation that was beneficial for the bacterium. This is the power of empirical evidence at work. This evidence actually caused Faith to make a re-evaluation of her argument.

The most positive thing in this statement is the recognition that poor mentally deficient Faith can understand empirical evidence when she sees it.

But it did not cause me to reevaluate my argument. I wanted to acknowledge you'd made your case although it didn't carry any weight with me at that point, and I realized that was bad timing for you since you'd had to work hard to assemble your evidence and I did feel bad about that. But it didn't cause me to reevaluate my argument because I suspect the validity of bacteria as examples anyway, and that suspicion had consolidated at that point, due to the basic genomic differences between them and most other living things. But ALSO I was still reacting to my recognition of the duplicity of science in claiming mutations are fact on the basis of nothing but assumption -- and bacteria. All that had just come out in our discussion and I was in the middle of a general disgust against science at that point.

So I offered you cookies, knowing none of it was your fault and that I'd unfortunately interfered with your hard work.

Unfortunately, she ultimately decided that the “beneficial” mutation was to be interpreted from an anthropocentric point of view.

NO. I decided that bacteria cannot serve as evidence for what happens in higher forms of life BECAUSE THEY ARE DIFFERENT GENETICALLY. That is NOT an "anthropocentric" point of view.

She did not learn from her mistake of conflating the consequences of something with the nature of its cause,

I made no such mistake. Leaving bacteria aside, in sexually reproducing creatures mutations are mistakes in the DNA duplication process -- you want to assume this is just normal and it produced all the known alleles and goes on producing them (athough we'd have a terrific glut of them at this point if that were true as we have plenty in most cases already and the effort of mutations can only be redundant) and I merely insist on the RECOGNIZED fact that it's a MISTAKE, and that in biological terms is a DISEASE PROCESS. And the actual EVIDENCE in hand is that mutations have produced thousands of genetic diseases in humans, which certainly is a result consistent with a process that is a known mistake, and otherwise seems to mostly replace functioning alleles with nonfunctioning or noncoding or at least inscrutable lengths of nucleotides, gobbledygook, which sure sounds like another case of a disease process at the genetic level no matter what scientists say to try to make out it's all normal biology, normal genetics. I make no mistake myself in arguing that there is a correspondence between the two levels, I'm actively claiming the scientist's attempt to turn a mutational sow's ear into an allelic silk purse is some sort of delusion they indulge themselves in.

and has instead settled on a decision of pretty much the same fallacious logical formula. If anything, I have at least shown that this is no longer a safe assumption. Yet, Faith still wants it to be the null hypothesis, the one that we take as true when the evidence can be viewed as consistent with multiple explanations.

Sorry, I stopped following you here.

This is not how logic or science works: we take the safe routes, the paths of least resistance.

This is to deny the heavy bias that leads to hallucinating mutations in variations without evidence for them, to assuming open-ended variations without the ability to prove it, to insisting that mutations are a normal process just because the theory requires it although the facts of how they are formed belie it.

This means our null hypothesis is always that what we have demonstrated in one organism applies equally well to any other organism, unless there is good reason to suspect that it doesn’t apply outside of the demonstration organism. “Bacteria are very different from higher organisms,” does not constitute a “good reason.” Nor does the relative amount of “junk DNA.” Yet, these are the only reasons that Faith could come up with for why we should work under the assumption that the data found in bacteria do not apply to “higher organisms.”

Yeah, poor old mentally deficient Faith.

My assessment is that Faith needs to confront the math: because she has acknowledged that beneficial mutations can happen (even though she has decided that the word should be redefined to only refer to benefits to “higher organisms”), she can only challenge the idea by arguing that they are too infrequent to be of consequence to genetic diversity. She needs to show that there is no situation under which the rate of allele addition by mutation can outpace the rate of natural selection.

The very fact that you use the term "rate" means you don't get what I'm trying to prove. But anyway. Sure, I'll do my best with all the mutations you can throw at me.

Yet, convincing her that this is the case has been the entire thrust of the three threads she has participated in on this subject: I sincerely hope that ZenMonkey is able to accomplish what the rest of us have not been able to do.

Trying to convince me that mutations refute my argument HAS been the thrust of all this effort here, despite the fact that NOBODY has ever really grasped the argument.

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 66 by Blue Jay, posted 04-12-2010 11:25 PM Blue Jay has not yet responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 69 of 87 (555410)
04-13-2010 1:24 PM
Reply to: Message 67 by ZenMonkey
04-13-2010 12:29 AM


Re: Picking up from the other thread.
Hello Zen,
I was rereading my post to you this morning and had to put in some changes in the yellow section, some of which I did in orange to make it easier for you to find.
Faith

This message is a reply to:
 Message 67 by ZenMonkey, posted 04-13-2010 12:29 AM ZenMonkey has not yet responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 70 of 87 (555437)
04-13-2010 3:29 PM


deleted
deleted Side Trip on Mutations.
I realized this would only clutter up the thread.
But I've saved it for later.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 71 of 87 (555496)
04-14-2010 1:04 AM


I really don't see how you can get breeds, varieties, species, new traits, new phenotypes, unless a population undergoes reduction of diversity.

You all assume it's possible.

Zen Monkey, could you spell out exactly how this could happen? Add in your mutations at whatever point you like and take it from there. How do you get a dog breed by making sure lots of genetic diversity is in the mix? I mean LOTS. I mean by not protecting the animal from breeding with whatever it likes so diversity will increase. Same as no natural selection or genetic drift or migration happening in nature. Isn't that what mutations would do?

Then if selection DOES occur it will just reduce them as I'm claiming in order to produce the specific breed. In the end you HAVE to have reduced diversity or you don't get a new breed/species/variety/phenotype/ set of traits.

I know you're going to say you have BOTH mutations and selection, but please, YOU do the math and explain it to me how it is possible to get new breeds or varieties without genetic depletion. Please.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 72 of 87 (555690)
04-15-2010 1:01 AM



Zen Monkey:
Assuming you are still planning on coming back -- with of course THE definitive argument against mine -- while I'm waiting I occasionally reread things and this time ended up adding some edits in green. Mostly just being repetitive I'm afraid but letting you know in case it matters.
Faith

By the way, thought I'd add that I appreciate the way you've approached this so far, with all the questions to try to clarify what I'm saying. And it did bring out places where you did get a different idea than I intended so it's been fruitful.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


Replies to this message:
 Message 73 by Admin, posted 04-15-2010 9:04 AM Faith has not yet responded
 Message 74 by ZenMonkey, posted 04-16-2010 3:20 PM Faith has not yet responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 76 of 87 (556190)
04-18-2010 12:09 AM
Reply to: Message 75 by ZenMonkey
04-17-2010 5:20 PM


Re: Picking up from the other thread.
quote:
--------------------------------------------------------------------------------
Populations do not gain new alleles from the random sampling of alleles passed to the next generation, but the sampling can cause an existing allele to disappear. Because random sampling can remove but not replace an allele, and because random declines or increases in allele frequency will influence the expected allele distributions for the next following generation, genetic drift drives a population towards genetic uniformity over time. When an allele reaches a frequency of 1 (100%) it is said to be "fixed" in the population and when an allele reaches a frequency of 0 (0%) it is lost. Once an allele becomes fixed, genetic drift comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time

You don't give the source of this quote but I've run across many such descriptions in my ponderings about this subject. I didn't just make up my model out of the blue. I did read up on a lot of material. I even thought I would be quoting from a lot of it but it turns out to be hard to locate when I need it and in the heat of the conflict here that hasn't been happening.

So up to this point it appears that you agree in large part with modern biology: genetic drift will deplete alleles randomly and natural selection will deplete or promote alleles in response to environmental pressures. The effect of natural selection will obviously be more noticable for alleles related to traits that confer reproductive advantage. Neutral traits will be more affected by drift, unless certain alleles for genes that code for neutral traits are linked somehow to other genes that are not neutral.

OK.

The answer to my question of whether an allele that has been reduced but not eliminated will regain its former frequency in a population turns out to be no. The distribution of alleles in one generation is only dependent on distirbution in the prior generation, all else being equal. So if we lose a lot of black rabbits and a lot of the relatively dominant B alleles from our population, it's more likely than not that the B allele is not going to make a comeback. There are only so many times that a given carrier for that particular allele can produce offspring, after all, so even if B is highly dominant with regard to the alleles for other fur colors, it can only get out into the gene pool a limited number of times. Again, I note that in this case we're focusing on neutral traits only. I believe that we both agree that an allele for a trait that does confer a reproductive advantage has a much greater chance of regaining its status in a population after some stochastic event reduces its numbers at some point.

Definitely. And my focus is on the processes that bring about reproductive advantage and create new reproducing populations.

We also agree that under your model, once a given allele has disappeared, there is no mechanism by which to restore it. If you get rid of the B allele for black fur, then there is no way to have any more black rabbits.

Agreed.

My second question over at the other thread had to do with recessive genes. I asked:

ZenMonkey writes:
Given all of the above, it is also inevitable that the Tan allele would have to manifest itself from time to time in every generation, even if it were recessive to all the others? Is there any way that we can have this Tan allele hiding in the gene pool but never actaully producing any tan rabbits?

My answer is yes, if it's so rare that it hardly ever pairs with another tan allele but predominantly occurs in heterozygous combinations. It won't appear because all the other alleles are dominant to it. Of course it COULD appear rarely nevertheless.

This didn't get discussed as much though nwr said this at Message 387:

nwr writes:
If the population size is very small, that could happen. With any significant population size, the probability is so low that you would not expect it. If it was observed that the recessive trait never appeared, that would probably be taken as evidence that it is fatal.

I have always assumed this to be true; no allele can be so recessive that it never manifests at all. Sooner or later you have to have two parents both contribute the recessive allele. If they didn't, if an allele were both relatively recessive and also rare, I deem it highly likely that drift would remove it eventually if it were neutral.

OK

On the other hand, if it did affect reproductive success, then natural selection would keep it from being rare if the related trait was beneficial or eliminate it if the trait was disadventagous. Do you want to contest this, or can we both accept that there are no hidden alleles, only relatively rare and relatively common ones?

I don't want to contest what you actually wrote, no, but what I always meant about suppressed alleles was that they were rare and rarely expressed.

It seems obvious to me that diploid organisms, by definition, carry only two alleles for each gene and no more, and donate one and only one to any individual offspring it produces. There is no other place for an allele to hide. And yet you say this (emphasis mine):

Faith writes:
I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path.

I'd like to understand your reasoning here. Let's go back to the rabbits, but before we do, I want to ask you about another aspect of your model.

ABE: Please note that here Zen Monkey has changed the subject, saying he'll get back to this quote of mine he just posted above. His merely raising a query about what I meant there inspired Percy to give him a POTM for proving me wrong about my supposedly claiming it's possible for individual traits to never ever be expressed, which is not what I was saying. I have answered this in Message 80 -- Faith.

I can't find where you've stated this explicitly, but your model implies both a fixed pool of alleles and fixed genes for every species. That is to say, there is a single "correct" arrangement of genes for every species - one for frogs, one for rabbits, one for humans, and so on - and that deviation from that genome does not produce new species but only genetic disease. In other words, alleles are the possible varieties for each gene, but that the genome for any given speicies is invariant.

You may be right that my model implies all this, and it sounds right, but since I've never worked it out on that level I'm a bit wary of agreeing too readily.

If you go by the crude model of DNA as a recipe, certain alleles allow you to substitue one similar ingredient for another - cashews for peanuts, for example - but that you can't just eliminate nuts from the recipe and still claim that you have the same recipe and thus the same critter. Your model seems to require a unique genome for each species, which can't be altered in any meaningful way, with alleles producing a set number of variations for the genes in each genome. Please let me know if this doesn't follow from your model.

I believe it does but again it's not something I've worked through myself. I may not be completely ready to abandon the possibility of genetic changes over generations in other words. But tentatively, OK, it sounds right enough.

Now back to the rabbits.

It seems to me that if you start with a single pair, you can have at most a total of four alleles for any given gene.

True.

Let's try a heterozygous black rabbit carrying a relatively recessive Brown (r) allele with its relatively dominant Black (B) one, thus: Br. Give it a grey rabbit that also has the relatively recessive Tan (t) alllele along with its relatively dominant Grey one (G), thus: Gt. If we mate Br with Gt, we have four possible outcome for each offspring for that mating: Bg, Bt, Gr, and Rt.

It helps me to keep these in descending order of dominance {ABE: as ZM defined it in Message 361}, so I get Bg, Bt, Rg and Rt. Two blacks and two browns.

Thus the odds are 50% that a mating will produce a black rabbit, at 25% chance that you get a grey, and a 25% chance that you'll have a brown rabbit.

Isn't it 50% black and 50% brown because brown is dominant to grey and grey to tan?

Though your odds are 50/50 that any given offspring will carry the recessive Tan allele, you won't see any tan rabbits from this particular mating.

Although I think you got the first set of combinations wrong, this is nevertheless the result either way. Yes, 50/50 unexpressed recessive tan.

However, if you have two rabbits from this mating (or another pair with the same genetic complement, makes no difference) who have the recessive T allele, you get something like this: Br, Bt, Rt, and Tt.

Got to work it through myself: BT + RT = BR, BT, TR, TT. OK we agree.

Now all of a sudden you have a 25% chance of producing a tan rabbit, and the T allele also has a 75% chance of being transmitted, increasing the odds even more for its survival and manifestation.

OK

And, I also note that there is no way under your model for you to ever see a white rabbit in any subsequent generation.

Not given the restricted range of colors as you've defined them. But albinism I suppose must always be a possibility.

There is no place for the W allele to be transmitted. The T allele is effectively hidden for now, but W is nowhere to be found and will not, under your model, ever show itself. Do you agree with this as well?

ZM, it's only true for the specific definition you've given of the range of colors possible, which I've been accepting as hypothetical. Yes, out of that defined range W is not going to appear except as the genetic disease albinism. But in reality white may be one of the built-in alleles, of the result of a combination of genes that affect the trait.

Obviously, if this pair didn't happen to produce any Bt or Rt offspring, or if such offspring never managed to reproduce, then you're gotten rid of all possible tan rabbits as well, am I right?

IF there was only one pair with this combination AND they didn't produce any recessive T's, OR there were only four offspring with the classical Mendelian spread we've been considering here and they didn't reproduce at all, yes, no more tan rabbits in the population. End of the Tan Dynasty. Kaput.

After all, it's impossible for every offspring of every organism to live long enough to reproduce. Some must live long enough to do so if the species is to keep from going extinct, but not all of them. The point is one that you've made yourself many times, I think: in a situation in which no new viable alleles can arise, genetic diversity will only decrease and never increase.

I'm glad we agree about this.

I believe that you've also come to the position that even in a model in which a mutation can produce something viable - a new W allele that can produce a white rabbit, for example - that the number of such mutations will never be significant enough for white rabbits to gain a place in the general population.

Unless it's selected and my whole emphasis is on the selecting processes which include all that isolate a small gene pool.

Or are you simply going to stick with the idea that there is no mutation that can change the G allele into a W or something similar, and that mutations are only agents of genetic damage. This would be in agreement with the similar idea that no mutation can affect a genome in such a way that you can turn one species into another, equally viable species.

I'm back to accepting mutations for the purpose of argument.

Oh, and I have one more question, just to be clear about another aspect of your model. Should any given rabbit, no matter what particular alleles it happens to have, be able to mate with any other rabbit?

I think that at the extremes of genetic depletion you should find rabbits that can't interbreed with others of ancestral populations.

Its genome should be the same, after all, and the alleles should only be responsible for variation among various traits. It believe that it's still true that any given dog can mate with any other dog, no matter how different they look. Agreed, you may have to use artificial insemination to breed dogs that are radically different in size, but otherwise, there is no barrier that I know of that would make dog varieties actually different species, unable to interbreed.

This is true, and rabbits may be like dogs in this respect. But there are many species where genetic depletion would become too severe for interbreeding. Think about my favorite example, the cheetah. It has many fixed loci. I don't know for sure but it probably has all the same genes as any other cat population but it can't interbreed with any of the others and this seems to have everything to do with those fixed loci. At such an extreme of genetic depletion it seems most likely you'd always get inability to interbreed based on the genetic situation alone.

But also keep in mind that although I refer to speciation as the end result of the processes I'm describing, it doesn't necessarily always have to occur for the point to be made. The point is based on the fact of genetic depletion that allows new breeds or varieties to be developed, and this is the case wherever you have such new varieties or breeds whether they ever go to speciation or not. It may be that dogs and cats and rabbits can never really evolve in this sense because they never reach a point where interbreeding has become impossible and their traits are permanently fixed.

I'm trying to keep the focus on the most usual understanding of evolution -- change in gene frequencies that brings about new variations or species, while pointing out that this must involve reduction in genetic diversity -- which I've never seen mentioned in the same context though it may be mentioned as a problem in other contexts.

I've made up for my absence with a rather long post, so take your time replying to it. I appreciate the chance to explore how your model works.

OK. I do keep being surprised at how hard it is to get this across since I'm so familiar with it and find it so compatible with what I've read in biology and genetics and so on ( not that I've read a GREAT deal, since I'm no scientist, but a few books, plenty of online stuff, not enough to make Dr. A happy but not too shoddy). I suppose the problem simply is the habit of assuming that variation adds to variation in a neverending series so that the possibility that such variation actually requires genetic reduction is too much of a contradiction to digest. But I do believe it is the reality of the situation that is simply usually overlooked.

So take all the time you need to get it figured out.

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Edited by Faith, : to add orange edit

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Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 80 of 87 (556266)
04-18-2010 5:02 PM
Reply to: Message 75 by ZenMonkey
04-17-2010 5:20 PM


Correcting a misunderstanding
Since Percy in Message 2 on the POTM thread April, 2010, Posts of the Month claims you pulled some sort of coup with this comment, which because of how it was arranged in the post -- Message 75 -- I never got to answer -- you said you'd get back to it but I don't see where you did -- I'm going to comment on it separately here:

I have always assumed this to be true; no allele can be so recessive that it never manifests at all. Sooner or later you have to have two parents both contribute the recessive allele. If they didn't, if an allele were both relatively recessive and also rare, I deem it highly likely that drift would remove it eventually if it were neutral. On the other hand, if it did affect reproductive success, then natural selection would keep it from being rare if the related trait was beneficial or eliminate it if the trait was disadventagous. Do you want to contest this, or can we both accept that there are no hidden alleles, only relatively rare and relatively common ones? It seems obvious to me that diploid organisms, by definition, carry only two alleles for each gene and no more, and donate one and only one to any individual offspring it produces. There is no other place for an allele to hide. And yet you say this (emphasis mine):

Faith writes:
I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path.

Percy seems to think you proved me wrong by arguing that there's no such thing as an unexpressed allele / trait. But that completely misses my point.

Percy says: ZenMonkey has neatly picked up on a key issue with Faith's speciation views that I think has gone unnoticed so far and that looks promising for clarifying the problems to Faith. Here he describes why it's unlikely for an allele to never be expressed:

What I said, again:

a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool

In this remark I was not talking about individual alleles.

I was talking about an array of possible variations (or better, varieties) or even species that could be made from the given complement of built-in alleles. I was talking about whole new varieties, the many many possible combinations of different traits potential in the built-in complement of genes and their alleles (back to the Creation) that could make up whole new varieties or species, not individual traits.

(ABE: "COMBINATION" is the key concept here -- although I also believe that I tacitly included in this particular comment a notion that many alleles from many species must have been completely eliminated over the centuries and millennia by now, so that what we have now is a very small complement of the original endowment. That loss also figures into the overall loss of possible combinations that could form varieties we'll never see.)

Because new varieties are the result of selection or isolation of a portion of a gene pool, there will ALWAYS be a vast majority of possible combinations from that built-in cache of genetic possibilities that simply never happen, that won't be combined and isolated together so that they never come to be new variations at all ever.

Zen Monkey apparently also misread my statement in the same way (as Percy did) in the first place, which he took out of context thinking it meant something else, and I never had the opportunity to answer it because of his saying he would get back to it.

Please consider it answered.

{ ABE: The misunderstanding may be due to my using the term "variation" when "variety" would have been more accurate.

I also suspect that if Zen Monkey had raised the issue again I would have been able to answer it and resolved the misunderstanding. }

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This message is a reply to:
 Message 75 by ZenMonkey, posted 04-17-2010 5:20 PM ZenMonkey has responded

Replies to this message:
 Message 82 by ZenMonkey, posted 04-18-2010 6:59 PM Faith has responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 81 of 87 (556277)
04-18-2010 6:52 PM


Oy
Now I'm being accused of "moving goal posts" and lacking integrity by Cosmic Chimp Message 4 on the POTM thread where he agrees with Percy about Zen Monkey's supposedly catching me in an error, which I've tried to correct above.

I badly need a break.

See you all eventually.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
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Joined: 10-06-2001


Message 85 of 87 (556301)
04-18-2010 10:01 PM
Reply to: Message 82 by ZenMonkey
04-18-2010 6:59 PM


Re: Correcting a misunderstanding
That piece of a post of mine that seems to have caused so much confusion came from Message 65 and was in the context of answering a question about YEC views -- a topic which came out of the blue from my perspective. In any case, it was NOT the context of talking about the fate of individual alleles.

ZM said:

Your position also assumes the standard conditions of Young Earth Creationism.

And I answered:

Actually I don't start from that assumption. I think it is important to emphasize this. I do not argue FROM my YEC position at all on this topic although many insist on assuming I do. The argument about reducing diversity to get new traits could come from any position at all.

I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path. ALL evolving paths would ultimately lead to that end, but they aren't all doing it at the same rate. It DOES of course seem like it would fit into a YEC framework better than any other.

I simply made a side comment about the complete overview, which I did probably make because the subject of YEC views had been brought up -- of how there are so many varieties potential in the whole species allotment of alleles that never get expressed, which does derive from my YEC position -- "available in all species" I said, and then went on to say in THAT context "most of which never get expressed in this world."

I was not talking about whether or not a given allele can be expressed in a given population, I was not talking about "hidden" alleles at all.

I did start out saying I was sticking to the argument but then I threw that side comment in and I guess that's what is so confusing, but it is not about the specific gene pool of a given population and not about the fate of a given allele in that population, it's about an overview of entire species: The many varieties potential in them, which are made up of combinations of a variety of alleles, can't all be expressed because selection brings about only particular genetic paths of variation, not all the possible ones. Not alleles, whole varieties.

I'm sorry for the confusion but I'm not moving any goal posts or changing any rules. It was a side comment and should be treated as such -- or made a separate topic.

I really seriously do need a break. I hope to be back to deal with the other posts eventually.


This message is a reply to:
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Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 86 of 87 (556428)
04-19-2010 8:08 PM
Reply to: Message 79 by ZenMonkey
04-18-2010 3:23 PM


Re: Picking up from the other thread.
You don't give the source of this quote but I've run across many such descriptions in my ponderings about this subject.

Sorry. That bit about loss of alleles due to drift came from the Wikipedia article on genetic drift that I had just referred to (and which I wish I had read much earlier in the game).

Sounded familiar. I've read through many evolution-related wikipedia article many times by now, not that I always remember what they say.

I don't want to contest what you actually wrote, no, but what I always meant about suppressed alleles was that they were rare and rarely expressed.

This is an important point. Do you now agree that there can't be any genuinely hidden alleles and that any viable allele, no matter how rare or recessive, will have to be expressed from time to time in any population?

I never really doubted it, ZM. This is just something I offer as a possible explanation for how some dramatic changes can come about through isolation of a small part of a population from a larger population. There are many ways the genetic situation can contribute to this, not just one you happen to pick such as this one. But when I do give such examples I do also think them through. The idea in this case is what I described on the other thread a couple hours ago or so. A recessive allele could become rare enough by its homozygous phenotype's being selected against that further pairings would be rare enough to almost never happen. And since they're selected against they wouldn't last long anyway. In this way a trait COULD become so rare as to be "hidden" (though did I actually use that word? I thought I used the term "suppressed" for this phenomenon. Anyway).

THEN from a large population (say 1000 for a round number) with very few of these recessive alleles (say ten) I picture an emigration occurring of oh say 100 individuals which just happens to include 5 of those "hidden" alleles, to a new region where they become geographically isolated, and I figure that within a few generations that allele is going to get expressed, maybe even right away. AND of course I suppose that in this new area it's not selected against for some reason. And IF by chance it might even be selected FOR then it could come to dominate the appearance of the new population in not too many generations, demonstrating a very simple if not terribly likely way there can be dramatic change between parent and daughter populations. It's basically the same principle at work in all cases I have in mind, a change in gene frequencies, that makes the change, but extreme examples can make it clearer. It's just one of many scenarios that could occur in my model. I'm not stuck on it particularly, it IS extreme obviously, but it DOES work nevertheless.

In other words, that if our rabbits still had the allele for reddish fur, we would have to end up seeing some reddish rabbits sooner or later, even if infrequently.

yes.

I thought that your point was that isolation allowed previously rare alleles to become more prevalent and more expressed,

If you mean by "prevalent" of higher proportion in a new population, yes, it can allow this, and therefore yes they'll be more expressed. Because of the increase in their frequency in the new population They come to contribute their traits in much higher proportion than in the parent population, and when all the different genes for different traits that have also undergone change in frequencies through this emigration are figured into the overall picture you get quite a bit of phenotypic change in a relatively short time -- just from isolation of a smaller population from a larger. If you add selection and/or drift the change will only increase.

The rarity of the allele, again, is only for purposes of example of the principle. This is going to happen with any allele whose frequency increases in the new population though usually not to as dramatic an extent.

giving the appearance of greater variety but actually indicating decreased diversity. But there's a significant difference between infrequently expressed and never seen.

Yes, but I don't know why you are making so much of that as it is just one example out of many that could be used. If "infrequently expressed" means "doesn't appear for twenty generations" that's ALMOST "never seen."

I've always assumed that it's something along these lines that explains how once in a great great while they get a true "red heifer" in Israel.

http://en.wikipedia.org/wiki/Red_Heifer

The existence of a red heifer that conforms with all of the rigid requirements imposed by halakha is a biological anomaly. The animal must be entirely of one color, and there are a series of tests listed by the rabbis to ensure this, for instance, the hair of the cow must be absolutely straight (to ensure that the cow had not previously been yoked, as this is a disqualifier). According to Jewish tradition, only nine Red Heifers were actually slaughtered in the period extending from Moses to the destruction of the Second Temple. Mishnah Parah recounts eight, stating that Moses prepared the first, Ezra the second, Simon the Just and Yochanan the High Priest prepared two each, and Eliechonnai ben Hakkot and Hanameel the Egyptian prepared one each. (Mishna Parah 3:5)

The absolute rarity of the animal , combined with the mystical ritual in which it is used, have given the Red Heifer special status in Jewish tradition. ... efforts have been made in modern times by Jews wanting to rebuild the Temple to locate a red heifer and recreate the ritual. However, multiple candidates have been disqualified, as late as 2002.

That is, this rare animal shows up at very long intervals, so there must be something going on in the genetic situation that suppresses the necessary genetic combination for long periods and then gets rearranged in a way that permits it to get expressed. (It doesn't seem like mutation would account for this because the same mutation would have to occur each time.)

Of course they're awfully picky too as only a couple of brown hairs disqualify it. But even close candidates appear to be a rare occurrence.

... your model implies both a fixed pool of alleles and fixed genes for every species. That is to say, there is a single "correct" arrangement of genes for every species - one for frogs, one for rabbits, one for humans, and so on - and that deviation from that genome does not produce new species but only genetic disease. In other words, alleles are the possible varieties for each gene, but that the genome for any given speicies is invariant.

You may be right that my model implies all this..

This is also pretty important, so we should explore this aspect of your model further once you've had some time to work through it.

This is getting far away from anything I consider to be important in this discussion. Working back to the Creation wouldn't be an easy thing to do. I can only make half-educated guesses about how all this started out. The important thing ought to be simply establishing whether what I'm describing in the present actually occurs or not.

Like I said, it certainly seems to be strongly implied. If at some unspecified creation event every species was given its full set of alleles, it stands to reason that its genome must also necessarily have been clearly defined at that time.

It figures but it's impossible to imagine all the possible functions God could have given the genetic system. Even some form of mutations COULD be involved. Obviously, if you take my model back to the ark you have to posit enormously larger genetic potential in each of the eight people and all the animals than exists today, because all the human "races" and all the land animal varieties we now have had to have come off the ark. How this might have been done I don't know. I postulate a more "packed" genome. BUT I also try to avoid getting into this because while it's an interesting side trip it's not in any way essential to my argument. Figuring out how the three couples, the sons of Noah and their wives, managed to repopulate the earth from just their own genetic potentials is an interesting thing to ponder nevertheless. The genetic picture HAD to be very different in some crucial ways from how it works today. But that's definitely a side trip, not part of this argument that I can see.

(Can we assume that in these creation event, the creator made enough individuals from each species to carry all of the alleles for its particular genome?

Well, certainly not human beings, who were only two. All humanity was in their genomes. How I don't know. Just that they had to have all the alleles within their own genomes (many many more genes for the same trait for one thing perhaps, polyploidy for another perhaps,) etc. -- OR the genetic system to make them via chemical changes like mutations, not by mistake but some kind of law, not like we see today.

The Bible doesn't say how many of the other animals were originally created. God commands the waters to bring forth sea life "abundantly." Whether that means many at one time, or in twos or whatever number applies to a particular species, that then propagated abundantly from the same kind of genomic situation as the humans isn't said.

But this is all irrelevant to my argument.

In other words, if you have 8 alleles for a particular gene locus, then there must have been at least four individuals of this species of animal made at the time of creation.)

Not necessarily, but it's possible, maybe even more. All the indications are that the whole world was very different then, so also the genetic situation.

But again I insist, this is all irrelevant to my argument.

Up until now you've asserted that genetic changes at the level of allele alteration are generally harmful and a sign of damage, so then it does seem reasonable that larger changes that affect the entire genome are even more likely to be harmful.

I've said the preponderance of the EVIDENCE is that the VAST majority of mutations are harmful in one way or another.

Larger changes that affect the entire genome? You are going to have to be a lot clearer about what you have in mind here. If you're talking about differences back around the Creation I assume it was all perfect in those days and only gradually deteriorated down the millennia after the Fall, and then rather drastically changed after the Flood.

Again, this is all utterly irrelevant to my argument.

Also, the notion of genetic stability is also strongly implied in any creation model. One can of course differ about what is specifically meant by the term "kind", which is the most common term used when discussing this sort of immutability, and I would really rather not open up that whole discussion. But I'm interested to see what you think about this aspect of your model.

Genetic stability? The Biblical picture is of all Creation being made perfect and then as a result of the Fall gradually deteriorating as death and disease and damage to the planet itself entered.

But I figure we could know more about the former times if we at least had it right about what's really going on today for a solid basis for extrapolating backwards.

It was my understanding that your model clearly posits a limited number of alleles for any given gene, established at creation. We had this exchange over at Message 271 on the The End of Evolution By Means of Natural Selection thread:

But what we have today is NOTHING like what we had back at the Creation. Generations have died that weren't originally meant to die. Alleles have died too, even genes (that's basically what junk DNA is, dead genes). There was ORIGINALLY a given cache of alleles, I have no way of knowing how many or how they were originally packed into the genomes of our first parents or anything like that, or if perhaps they were potential in a chemical changing system as I suggested, of which perhaps current mutations are the expression of what the Fall did to it. This is a WILD guess, I have NO way of knowing.

NONE of this has anything to do with my argument!

ZenMonkey writes:
So regardless of whether or not this event took place at Creation or at some later date, the end result is that there will only ever be a set, defined number of alleles for any given gene in any given population.

No, by now there appear to be many different ways this has worked out. Some genes in some species have lots of alleles scattered through the population, some have fewer, some have many genes for a particular trait, some only one, there's no predictable pattern any more that I can see.

Now admittedly this is mostly me talking here and not you. Nevertheless, you seem to have been clear all along that the number of alleles in a given population can only decline and never increase, thus leading to the inevitable reduction in genetic diversity. The limited set of four alleles for rabbit fur color was meant to be a faithful representation of this aspect of your model.

Yes, that works out fine for today's situation. Of course there may be more genes that affect the fur, but I guess that's another subject.

Since the limited allele set is the central feature of your entire model on which all else depends, I assume that you still think this.

"The limited allele set is the central feature of my model?"

It is? No, I don't think so. Even on my own YEC beliefs it's not. But I've also said I accept mutations for the sake of argument. That's hardly making a limited allele set the central feature.

If the term "central feature" applies at all, it would be how the selection processes work, what they do to whatever alleles there happen to be.

Perhaps it will clarify if I say that I suppose there could have been a time a few millennia ago when the genes of every creature were not only more numerous for each trait but had a hundred alleles for each. Perhaps an exaggeration, but many more anyway. In such a circumstance the same selection and isolation effects would also be operating to reduce the genetic diversity and bring out new varieties but with such an enormous diversity to begin with you could get many more varieties or species according to the interbreeding criterion than we do today. Even with a bottleneck there would still be more diversity for a given species to continue to vary from than there is today.

ZenMonkey writes:
I believe that you've also come to the position that even in a model in which a mutation can produce something viable - a new W allele that can produce a white rabbit, for example - that the number of such mutations will never be significant enough for white rabbits to gain a place in the general population.

I'm not aware of coming to that position. I figure if I'm going to accept mutations as the source of alleles for the sake of discussion then I also accept that they'll behave like any other allele.

First, can your model support the possibility that some rearranging of the G allele can result in a brand new, perfectly viable W allele? This goes against the thrust of your argument, but on the other hand you seem to be accepting it, at least provisionally. What do you really think?

I don't even know what it means. Show me how you think this works and I'll tell you if it fits my model or not.

Second, it seems that in accepting the possibility of new alleles, you're putting these new alleles on the same footing as the "suppressed" alleles of your model, insofar you've asserted here that they would probably get swallowed up in a large population, but would have a chance to emerge in a smaller, isolated population if they were selected for.

That was simply logically noting that one single allele in a sea of alleles doesn't really have much chance unless some fluke puts it in a smaller population. Many here have already said as much about mutations that occur and then disappear.

In fact, I believe that you've asserted that in such smaller populations, what some folks call mutations are actually only heretofore unseen or "suppressed" alleles, and that there's no way to tell the difference.

OK.

If that's true, then isn't the reverse also true? If you can't tell the difference, then couldn't what you're calling suppressed alleles actually be new ones?

Yes, that's why I have to accept mutations for the sake of argument. If I could prove they aren't mutations but pre-existing alleles I wouldn't have to do that.

Oh, and I have one more question, just to be clear about another aspect of your model. Should any given rabbit, no matter what particular alleles it happens to have, be able to mate with any other rabbit?

Not sure about a particular allele situation, but in terms of a whole population that has undergone inbreeding of a subset of alleles with a new gene frequency, I believe the population geneticists have said this discrepancy in the mix of the same alleles alone prevents interbreeding. See that Wikipedia article on Speciation and its diagram which I've posted many times on the other thread and maybe here too.

I think that at the extremes of genetic depletion you should find rabbits that can't interbreed with others of ancestral populations.

I don't understand why this would be so.I If there are no new alleles, and more importantly, no changes to the genome, then even at the end of genetic depletion, as you describe it, the members of an isolated population will still have the same genetic makeup as the larger originating population, albeit with less variety.

I don't know why exactly either except that a new reduced mix of alleles inbred over many generations can differ enough from other populations for interbreeding to be a problem, especially if there are fixed loci I gather. The population geneticists appear to be saying this.

Say you've got a population in which our recessive T allele became for some reason the sole survivor, with all the other varieties the victims of drift. (Or selection, if fur color somehow did start conferring a reproductive advantage.) At this extreme of genetic depletion, you'd have a population of nothing but tan rabbits, which would look significantly different from the parent population. But why should a TT rabbit from this population - all else being equal - be any different from a TT rabbit from the parent population?

I would suppose it has to do with the overall mix of alleles for many traits that has developed over generations of inbreeding, not any particular allele like T. I don't know how it works either -- and I expected all YOU guys to know how it works! Because so much of what I've read appears to be saying this. But you don't get a new population of tan rabbits without also changing the gene frequencies of all the other traits just because of the effect of the reduced numbers in the migration from which they all inbred, so that's where I assume the telling difference occurs.

If in the original population there was nothing keeping a TT from mating productively with a Bg, for example, why should it be any different if that TT came from a population in which there was nothing else?

See above.

Faith writes: But there are many species where genetic depletion would become too severe for interbreeding. Think about my favorite example, the cheetah. It has many fixed loci. I don't know for sure but it probably has all the same genes as any other cat population but it can't interbreed with any of the others and this seems to have everything to do with those fixed loci. At such an extreme of genetic depletion it seems most likely you'd always get inability to interbreed based on the genetic situation alone.

But cheetahs can still always mate with other cheetahs, yes?

Of course. They're nearly clones of one another!

We don't expect all members of the cat family to be able to interbreed with each other. They are different species, after all, with unique genomes.

Exactly.

If cheetahs couldn't breed with lions before they got squeezed through their bottleneck, why should we be surprised that they can't breed with them now?

I'm not surprised.

Looks like I've ended up with another long post. Thanks for helping me work though this. Please let me know if there's anything I'm misunderstanding or that I've skipped over in your replies. There's also still a lot of your model still to discuss, so I apologize if the pace has been slow.

OK, but I believe you are going off track now. More off track than on anyway.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 79 by ZenMonkey, posted 04-18-2010 3:23 PM ZenMonkey has not yet responded

  
Faith 
Suspended Member (Idle past 144 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 87 of 87 (556465)
04-20-2010 1:01 AM
Reply to: Message 82 by ZenMonkey
04-18-2010 6:59 PM


Re: Correcting a misunderstanding
My understanding is that an allele is:
quote:
--------------------------------------------------------------------------------
...one of a series of different forms of a genetic locus.
--------------------------------------------------------------------------------

Check.

We were using a very simple but still realistic example in which I was positing a single gene locus for rabbits that was the sole determinant of fur color. (More realistic models would reflect more complex relationships among genes and how they affect traits, but I think that we agreed that the simpler version would still serve to illustrate the basic idea.)

Check.

I further posited that there were - as I thought would be required by your model - a total of four alleles for this locus: Black, Brown, Grey, and Tan. (The exact number is arbitrary, but the important thing is that the number of alleles be defined and limited.)

I don't get what "required by my model" has to do with it, since it's just a standard type of example, but

check.

I believe that you agreed to the following with regards to this model:

1. Fur color for each individual is determined by the dominant allele at that gene locus.

Check.

2. Each rabbit would carry two of these alleles, whether two different ones or two of the same allele, and pass on one of them to each of its offspring.

Check.

3. Once an allele was eliminated from the population, there was no mechanism by which it could return.

Check.

Your position on the next two points still seems a little unclear, but my impression was that you agreed to them as well.

4. There is no mechanism by which to create new alleles that were not already present at the unspecified creation event. Just as you can't restore an extinct allele, neither can you create a new one.

Check.

5. There is no other way for alleles to be transmitted from generation to generation except by being passed along in their proper place in the gene locus, one from each parent. In other words, a Bt rabbit can't also have the Grey allele hidden somewhere in its DNA that it could also pass on to its offspring.

Check.

Lastly, I thought that you also agreed to the following:

6. No allele, no matter how rare or recessive, could avoid being expressed in a population from time to time. So even if our T allele was expressed rather infrequently, due to it being recessive to the others, nevertheless, if it existed at all, there were always going to be tan rabbits in the population, however few they might be.

Except for long periods, even many generations, as in the case I described above when it never appears at all,
Check.

Could you please clarify where I've misunderstood you in any of the above?

Check.

Faith writes:
I was talking about an array of possible variations (or better, varieties) or even species that could be made from the given complement of built-in alleles. I was talking about whole new varieties, the many many possible combinations of different traits potential in the built-in complement of genes and their alleles (back to the Creation) that could make up whole new varieties or species, not individual traits.

This confuses me as well. What built-in alleles are you talking about, other than the two for each gene locus carried by every individual?

The total of ALL the alleles possessed by a species at a given time or ever possessed by it back to the Creation. That just happened to be what I was saying in that particular quote that became such a problem. A different subject. It was an aside.

Are you implying that each individual somehow carries with it all possible alleles for every gene locus in its genome?

No. I'm talking about the total population in that particular quote.

Where else do genes exist, except in the individual organisms that carry them?

Is it not logically possible to refer to the total collection of alleles and/or genes in a particular species or population as a "given complement"? Sorry that wasn't clear but I would think it would be clear by now.

Also, what do you mean by a gene pool? I get the impression that you're describing some universal DNA resevoir, which can somehow be drawn upon to create untold numbers of different species in endless combination.

I may be a bit sloppy about this, I'm not sure without a specific reference, but I suppose I assume context explains it and perhaps it doesn't. Sometimes I might be referring to the gene pool shared by a particular population, say the daughter population's own gene pool, other times I might be talking about the entire gene pool for the species. A dog breed has its own particular gene pool, but there is also the gene pool shared by all dogs. I'm sorry if I haven't been clear about the context.

But again, DNA only exists in the individual organism and nowhere else. If in our example the T allele in rabbits goes extinct, then it matters not that there is a similar locus on hamsters that has a similar allele that codes for tan hamsters. Varieties are limited by the finite number of alleles in a given population.

Yes. Sorry, I really don't understand why you are having a problem except that perhaps I haven't been clear enough in specifying the particular context in which I'm using a term.

I suspect that you'll be able to clear up much of my confusion when you reply to my last post in more detail, especially where it touches on the immutability of the genome.

I hope I did.

Perhaps I'm being hasty in commenting here before you've had the chance to go over that post. I'll wait to see what you have to say before I go on.

OK.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 82 by ZenMonkey, posted 04-18-2010 6:59 PM ZenMonkey has not yet responded

  
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