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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 62 of 87 (555205)
04-12-2010 4:23 PM
Reply to: Message 61 by Blue Jay
04-12-2010 9:13 AM


Re: The Road from Here
Bluejay writes:

So, if the thread is going to be closed, I would like to post a summation message before it closes. If someone else is going to pick up where I left off, a summation may not be necessary.

After all the hard work that you put into this thread, Bluejay, I think that you really ought to write a summary of what you accomplished. Faith and I are going to continue the conversation, albeit in a different direction, so I'll leave it up to you to decide to do so now or to save your summation until she and I have finished as well.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 61 by Blue Jay, posted 04-12-2010 9:13 AM Blue Jay has not yet responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 64 of 87 (555220)
04-12-2010 5:40 PM


Picking up from the other thread.
Rather than do a substantial recap, I'll refer anyone's who's interested back to Message 271 in the The End of Evolution By Means of Natural Selection thread, which is Faith's last reply to me.

So far I'm still working through Faith's position. There are a couple of points in this last exchange that I'd like to clarify, and then we can push on.

Faith writes:

ZenMonkey writes:

Thus if we have a population of rabbits in which the allele for black fur has been lost, we may see a lot more tan rabbits than formerly, but we still won't suddenly start seeing red rabbits if there were no red rabbits before. What looks like an apparent increase in diversity (more tan rabbits) is an actual loss of diversity (no more black rabbits).

Or just fewer if the black fur frequency has been simply very reduced. Yes.

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. 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.)

Faith writes:

ZenMonkey writes:

Alleles that produce traits that confer a reproductive advantage will become more prevalent, and alleles that produce traits that are disadvantageous will become less prevalent or even vanish.

Yes. But I hardly ever talk about natural selection alone; I usually include the random ways changes can occur, genetic drift and migration and geographic isolation and so on.

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. 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. 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.

Faith writes:

ZenMonkey writes:

If your model is correct, and there is no mechanism for producing new alleles, then you are right - genetic diversity can only decline and never increase. There is no source for new alleles to emerge, only for existing ones to either thrive or fail.

If that is really the case then all that's left IS to show that mutations don't occur (although I still think that even if mutations do occur at anything like the rate expected by evolutionists, the processes that reduce will even cut them down in the end). So somebody has to do some research to determine if any of the assumed mutations ever produce a viable allele.

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. 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?

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. 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.

Your position also assumes the standard conditions of Young Earth Creationism. 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. 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 then they are today. 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 significant change can have taken place, as the the number of alleles for any given trait were all established from the beginning. 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. 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.

Am I still correct in my understanding of your views?


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


Replies to this message:
 Message 65 by Faith, posted 04-12-2010 7:45 PM ZenMonkey has responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 67 of 87 (555288)
04-13-2010 12:29 AM
Reply to: Message 65 by Faith
04-12-2010 7:45 PM


Re: Picking up from the other thread.
Thanks, Faith. You've given me a lot to work with here and I will take some time to digest it properly.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 65 by Faith, posted 04-12-2010 7:45 PM Faith has responded

Replies to this message:
 Message 69 by Faith, posted 04-13-2010 1:24 PM ZenMonkey has not yet responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 74 of 87 (555972)
04-16-2010 3:20 PM
Reply to: Message 72 by Faith
04-15-2010 1:01 AM


Absent but not inattentive.
My apologies for being away from this thread. Real life intrudes from time to time. But I've been contemplating your model and have some more questions which I hope I can get to sooner rather than later.

In the meantime, I've got a math question relevant to this discussion that I'm tossing out to the general public over on the The End of Evolution By Means of Natural Selection thread. It's not of huge consequence, but it is something that I'd like clarified.

Also, don't be expecting me to come up with THE definitive argument quite yet. My primary task here is still making sure I understand your position clearly.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 72 by Faith, posted 04-15-2010 1:01 AM Faith has not yet responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


(2)
Message 75 of 87 (556152)
04-17-2010 5:20 PM
Reply to: Message 65 by Faith
04-12-2010 7:45 PM


Re: Picking up from the other thread.
Hi Faith. Thanks for your patience.

Let's pick up with a quick look at a side issue that I took over to the The End of Evolution By Means of Natural Selection thread. At Message 361 I enlisted what turned out to be some much-needed assistance in clarifying the issues in the following exchange you and I had here:

Faith writes:

ZenMonkey writes:

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.

Had I done my homework and read up on genetic drift and fixation, I would have been able to answer my own question.

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

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.

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.

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.

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?

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. 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.

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.

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. 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.

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. 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. 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.

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. 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. 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.

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

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? 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 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. 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.

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? 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.

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.

Edited by ZenMonkey, : No reason given.

Edited by ZenMonkey, : Repairing faulty sentence structure.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 65 by Faith, posted 04-12-2010 7:45 PM Faith has responded

Replies to this message:
 Message 76 by Faith, posted 04-18-2010 12:09 AM ZenMonkey has responded
 Message 80 by Faith, posted 04-18-2010 5:02 PM ZenMonkey has responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 78 of 87 (556238)
04-18-2010 11:16 AM
Reply to: Message 77 by Admin
04-18-2010 8:41 AM


Re: Picking up from the other thread.
Admin writes:

ZenMonkey didn't completely describe the dominance hierarchy, but it can be implied from the outcome he described. Here's his full dominance hierarchy:

Black > Grey > Brown > Tan

Actually, Faith is right. In the rabbit scenario we've been using since Message 361 in the The End of Evolution By Means of Natural Selection thread, the hierarchy has been:

quote:
...the allele for black fur is dominant to all the others, that for brown fur is dominant to grey but recessive to black, and that tan is recessive to all the others...

To be fair, had this not already been the agreed-upon order, you're right; the hierarchy could easily been seen from the results and would have been just as you said.

My mistake.

Edited by ZenMonkey, : Spelling, dammit.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 77 by Admin, posted 04-18-2010 8:41 AM Admin has acknowledged this reply

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


(1)
Message 79 of 87 (556256)
04-18-2010 3:23 PM
Reply to: Message 76 by Faith
04-18-2010 12:09 AM


Re: Picking up from the other thread.
Hi Faith. A briefer post this time, just to clear up some things before we move on.

Faith writes:

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).

Faith writes:

ZenMonkey writes:

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.

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? 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. I thought that your point was that isolation allowed previously rare alleles to become more prevalent and more expressed, giving the appearance of greater variety but actually indicating decreased diversity. But there's a significant difference between infrequently expressed and never seen.

Faith writes:

ZenMonkey writes:

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.

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. 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. (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? 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.) 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. 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.

Faith writes:

It helps me to keep these in descending order of dominance, so I get Bg, Bt, Rg and Rt. Two blacks and two browns.

You're right, as I noted above. This is consistent with the allele dominance relationships that we've been using so far. My apologies for slipping up. And as you note, the end result comes out the same.

Faith writes:

ZenMonkey writes:

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.

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:

Faith writes:

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.

Yes.

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. 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.

Faith writes:

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.

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

On to the elusive W allele. I probably should have picked a different color so as not to confuse the issue with albinism, but we'll let that stand.

Faith writes:

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.

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

This is also important. I guess that there are really two things to figure out here.

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?

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. 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. 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?

Faith writes:

ZenMonkey writes:

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.

I don't understand why this would be so. 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. 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? 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?

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? 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. 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?

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.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 76 by Faith, posted 04-18-2010 12:09 AM Faith has responded

Replies to this message:
 Message 86 by Faith, posted 04-19-2010 8:08 PM ZenMonkey has not yet responded

  
ZenMonkey
Member (Idle past 3205 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


(1)
Message 82 of 87 (556280)
04-18-2010 6:59 PM
Reply to: Message 80 by Faith
04-18-2010 5:02 PM


Re: Correcting a misunderstanding
Now I'm afraid that your clarification has made things more confusing for me.

My understanding is that an allele is:

quote:
...one of a series of different forms of a genetic locus.

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.) 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 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.

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.

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

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.

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.

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.

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

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? Are you implying that each individual somehow carries with it all possible alleles for every gene locus in its genome? Where else do genes exist, except in the individual organisms that carry them?

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. 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.

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. 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.


I have no time for lies and fantasy, and neither should you. Enjoy or die.
-John Lydon

What's the difference between a conspiracy theorist and a new puppy? The puppy eventually grows up and quits whining.
-Steven Dutch


This message is a reply to:
 Message 80 by Faith, posted 04-18-2010 5:02 PM Faith has responded

Replies to this message:
 Message 85 by Faith, posted 04-18-2010 10:01 PM ZenMonkey has not yet responded
 Message 87 by Faith, posted 04-20-2010 1:01 AM ZenMonkey has not yet responded

  
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