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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 1 of 87 (553158)
04-01-2010 4:59 PM


GREAT DEBATE: FAITH AND BLUEJAY ONLY!

I would like to continue the discussion Faith began in The End of Evolution By Means of Natural Selection in the Great Debate forum, if she is interested in continuing it.

I値l focus my comments on this portion of her OP there:

Faith writes:

But whether we are talking only about a change in a single trait or in many traits at once, the trend is ALWAYS toward genetic depletion. You can add as many new alleles as you think mutation can come up with at any point in this progression, but when these selection and isolating processes go to work on them the very same thing happens. You may get a new trait but you'll always get it at the expense of all the other genetic possibilities, and when this occurs with many traits you eventually get speciation, fixed loci, and such limited ability for further variation evolution is for all intents and purposes at an end.

This topic has caused a lot of frustration (primarily for Faith herself), so I値l try to tread softly and take it easy. I値l provide a basic comment on each sentence from the above quotation: these will serve as prompts that can be used by Faith to start her side of the discussion however she chooses.

Faith, please let me know what I may have misunderstood from your statements, and help me find if and where I'm off base on any or your points.

Faith writes:

But whether we are talking only about a change in a single trait or in many traits at once, the trend is ALWAYS toward genetic depletion.

I can only address this statement by appealing to mutation, which is known to happen at extremely higher rates than natural selection happens. If mutation is disallowed, then this statement may very well be quite true.

However, if mutation is allowed, then it becomes a question of comparing the rate of selection-mediated diversity loss to the rate of mutation-mediated diversity gain.

Do you agree with that?

-----

Faith writes:

You can add as many new alleles as you think mutation can come up with at any point in this progression, but when these selection and isolating processes go to work on them the very same thing happens.

For this one, we need to consider a timeline of events, including the following events:

  1. Onset of selection pressure
  2. Emergence of new alleles
  3. Extermination of alleles selected against

And, the following considerations:

  1. Other concurrent selection pressures
  2. Genetic linkage between different alleles
  3. Magnitude of each selection pressure

If we choose to pursue this complex model, I think we値l quickly find that decreasing genetic diversity is not so inevitable as you have argued. I'll hold off on the specifics until you're ready to discuss it.

-----

Faith writes:

You may get a new trait but you'll always get it at the expense of all the other genetic possibilities, and when this occurs with many traits you eventually get speciation, fixed loci, and such limited ability for further variation evolution is for all intents and purposes at an end.

I explained a bit about genetic fixation in a few other places. Fixation is what you池e talking about: the elimination of all alleles for a certain gene except for one.

I do not think that fixation is inevitable, and I知 certain will never occur at all positions in the genomes of all individuals within a single population.

Selection pressures simply cannot be orchestrated such that any single organism can contain all the 澱est alleles for all genes: so, naturally, we should expect that no single combination of alleles will be absolutely superior to all other possibilities in a population.

As an example, let me present Uta stansburiana, the 途ock-paper-scissors lizard I referred to earlier in your thread. This is an (admittedly unusual) example of a population that has reached a relatively stable balance between different genotypes. This sort of 澱alancing act is what is going on in nearly all populations, all the time: the equilibrium oscillates between different character states, occasionally leading to the complete extinction of a certain trait, but also often leading to a complete rebound of a rare allele.

-----

I look forward to your responses, and I hope I won稚 upset you and frustrate you too much in our discussion.

Edited by Bluejay, : Some reformatting, "do you agree with that?" and "I'll hold off on the specifics until..."

Edited by Bluejay, : Alter title in accordance with Faith's wishes.

Edited by Bluejay, : No reason given.

Edited by Admin, : Change title now that ZenMonkey is taking over for Bluejay.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


Replies to this message:
 Message 3 by Faith, posted 04-02-2010 7:58 AM Blue Jay has responded
 Message 5 by Faith, posted 04-03-2010 6:07 PM Blue Jay has responded
 Message 15 by Faith, posted 04-04-2010 1:07 AM Blue Jay has not yet responded
 Message 16 by Faith, posted 04-04-2010 2:40 AM Blue Jay has responded

  
AdminSlev
Member (Idle past 2080 days)
Posts: 113
Joined: 03-28-2010


Message 2 of 87 (553180)
04-01-2010 7:10 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Reduction of Traits by Natural Selection (Faith and Bluejay Only) thread in the Proposed New Topics forum.
  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 3 of 87 (553238)
04-02-2010 7:58 AM
Reply to: Message 1 by Blue Jay
04-01-2010 4:59 PM


Thank you for starting the thread. I think I'll let things simmer down before I come back to it.

The title doesn't express what I believe, though. I don't believe that TRAITS are reduced; in fact they're increased in the scenario I have in mind. The way I picture it, it's ALLELES that are decreased AS new traits emerge. {ABE 4/10 -- What I mean is that EXPRESSED traits increase; obviously genes and traits correspond in numbers, but the point is that new traits EMERGE, get EXPRESSED when the gene frequencies change, and specifically when you lose alleles for old traits}

ABE: Percy objected to this idea on the original thread and I answered him there but I'll bring it over here where you can answer what i said. I'm still not going to get to your post for a while.

It's what I've been trying to argue all along, Percy. When is it that a trait attributed to a new "mutation" shows up in a domestic breed? Isn't it when the breed is already highly inbred, which allows new (or formerly suppressed) alleles to get expressed? (Many of these new traits are unhealthy as breeders know and have to take into account in choosing mates for their breeds, but sometimes it's a new desirable trait or "mutation") All along I've pointed to domestic breeding as an example of this process where you get new breeds by eliminating the alleles for competing traits. If those alleles remain the selected traits can't get expressed -- or more accurately, there isn't any selection happening, new traits aren't emerging if the competing alleles remain. Selection OF a trait means you are isolating it from competing types and their alleles. I've simply extended this principle to natural selection and the related processes of genetic drift and bottleneck and migration which also isolate a population so that new traits can emerge -- as competing alleles are reduced or eliminated.

What I'm so arrogantly and cheekily doing is arguing against the common evolutionist assumption that change simply builds on change in a linear or additive fashion.

I'm SURE I'm not getting this said clearly. I'm sure I'm leaving out some essential part of the description and that without it the scientists here can't follow me. But it's not mutations.

ABE: Of course traits are the expression of alleles so you do remove traits when you remove alleles. So don't think I don't recognize that. I'm talking about what gets EXPRESSED. NEW traits means traits that are getting newly expressed, that change the look of a population. In order for them to come to characterize the population alleles for other traits at the same gene have to go.

OK I won't say it again now, but I hope it's clearer.

Edited by Faith, : add quote

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 1 by Blue Jay, posted 04-01-2010 4:59 PM Blue Jay has responded

Replies to this message:
 Message 4 by Blue Jay, posted 04-02-2010 1:36 PM Faith has responded

    
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 4 of 87 (553281)
04-02-2010 1:36 PM
Reply to: Message 3 by Faith
04-02-2010 7:58 AM


Hi, Faith.

I've altered the title in accordance with your preferences. I agree: let痴 take our time on this, and make sure we池e communicating effectively.

In that spirit, I wanted to ask for a bit of elaboration/clarification:

Faith writes:

I don't believe that TRAITS are reduced; in fact they're increased in the scenario I have in mind. The way I picture it, it's ALLELES that are decreased AS new traits emerge.

How do you envision new traits emerging? Not by mutation, I gather?

Having traits and alleles show different diversity patterns seems contradictory to me. Granted, there isn稚 a one-to-one correlation between allelic diversity (you can have some traits that emerge without new alleles emerging, and you can have new alleles emerge without producing any new traits), but I would think that there should be a general trend of correlation between allelic and trait diversity, given that all traits ultimately trace back to alleles.

I知 also uncertain as to how trait diversity is increasing in your scenario.

I would appreciate any explanation or clarification on this point. Take whatever time you need or want to do so.

-----

In the meantime, perhaps a bit of terminology would be beneficial, just to make sure we池e both clear on what we池e talking about:

gene: a region of the genome that encodes a certain product
allele: one of several sequence variants of a gene

character: a physical attribute of an organism
trait: one of several variants of a character

genotype: a suite of alleles in a single organism
phenotype: a suite of traits in a single organism

Also, are you familiar with the mechanisms of mutation and evolutionary genetics (e.g., crossing over, independent assortment, point mutations, insertions/deletions, etc.)? We might not need to talk about these, but, just in case...

-----

I look forward to this: it痴 going to be fun. Except, now it seems that we're going to have an audience with commentary privileges. I hope I don't get camera-shy.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 3 by Faith, posted 04-02-2010 7:58 AM Faith has responded

Replies to this message:
 Message 8 by Faith, posted 04-03-2010 11:08 PM Blue Jay has responded

  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 5 of 87 (553515)
04-03-2010 6:07 PM
Reply to: Message 1 by Blue Jay
04-01-2010 4:59 PM


graphic attempts
As long as you are polite there shouldn't be a problem and so far so good, I appreciate it.

I can only address this statement by appealing to mutation, which is known to happen at extremely higher rates than natural selection happens. If mutation is disallowed, then this statement may very well be quite true.

However, if mutation is allowed, then it becomes a question of comparing the rate of selection-mediated diversity loss to the rate of mutation-mediated diversity gain.

Do you agree with that?

No I don't. This is what everybody keeps saying and while I have the picture in my mind of how you're all wrong I haven't been able to get it said in a satisfactory way. I also keep trying to come up with graphic ways of expressing it but that's also very difficult because you have to distinguish between the population itself as individuals making up the population, the different traits scattered among them, and the genes and alleles for those traits, AND whatever mutations have to be added into the mix. So I haven't been able to come up with a proper representation of what I have in mind. I can only throw out a very crude image, and here are a couple:

This one is just a more elaborate version of the one I posted earlier on the other thread, meant to represent the alleles for one gene in one population represented by 100 individuals -- far more alleles than one would normally expect to find I understand but I wanted to represent them in terms of great genetic diversity in order to make the point. According to evolutionists these would have originally been mutations and some of them may be new mutations. The point of the graphic is to show what happens over succeeding generations if one of them is strongly selected over all the others:

from great diversity to little via selection

Seems to me that if selection is working in a population it will gradually or rapidly displace alleles no matter how many you start with or how rapidly mutation introduces new ones (though the chances of getting more than one mutation at one locus isn't very high I would suppose even over many generations -- but even if you did the same process I'm trying to lay out should apply).

The other attempt at a graphic representation is meant to show what happens when a small portion of a population is isolated from the parent population as when it migrates away. ANYTHING that isolates a portion of the population fits for this example though. Then I also include a second migration and this time try to show how a mutation that appeared just before the migration is included and happens to spread in the new population, whether by genetic drift or natural selection or whatever.

Again I overdo the representation of great genetic diversity, so that I can show what happens when a small portion of that diversity is isolated and you end up with maybe a big population but always with less genetic diversity even if a mutation is included.

reproductive isolation

I guess I could do one and add more mutations in the first migrated population to show that if selection and isolation keep happening they too will get reduced to some pared down proportion.

In each new population you are getting a new phenotype though, which is also schematically indicated in the graphics, which is what evolution tends to focus on to the exclusion of the reduction of genetic diversity that brings it about.

I've left the rest of your post for my next one.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 1 by Blue Jay, posted 04-01-2010 4:59 PM Blue Jay has responded

Replies to this message:
 Message 6 by Blue Jay, posted 04-03-2010 7:26 PM Faith has responded

    
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 6 of 87 (553526)
04-03-2010 7:26 PM
Reply to: Message 5 by Faith
04-03-2010 6:07 PM


Re: graphic attempts
Hi, Faith.

Faith writes:

Bluejay writes:

However, if mutation is allowed, then it becomes a question of comparing the rate of selection-mediated diversity loss to the rate of mutation-mediated diversity gain.

Do you agree with that?

No I don't. This is what everybody keeps saying and while I have the picture in my mind of how you're all wrong I haven't been able to get it said in a satisfactory way.

I think you池e expressing yourself just fine: it痴 perfectly coherent and it痴 a great basic explanation of the process of natural selection.

My only point of confusion is why you think this process will inevitably lead to complete allele depletion. I think that痴 going to be too big a question to try to tackle in one step, so let me ask a simpler question (and a follow up):

Do you agree that, if mutation is allowed, then new mutations can, at least in principle, produce new alleles?

If so, doesn稚 basic reasoning tell us that the change in diversity can be determined by comparing the number of new alleles produced by mutations to the number of old alleles exterminated by natural selection?

-----

Keep in mind, we池e still just considering one gene here. I don稚 want to get into a multiple-gene scenario until we致e cleared up how to measure changes in diversity for one gene.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 5 by Faith, posted 04-03-2010 6:07 PM Faith has responded

Replies to this message:
 Message 7 by Faith, posted 04-03-2010 8:51 PM Blue Jay has responded

  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 7 of 87 (553546)
04-03-2010 8:51 PM
Reply to: Message 6 by Blue Jay
04-03-2010 7:26 PM


Re: graphic attempts
I think you池e expressing yourself just fine: it痴 perfectly coherent and it痴 a great basic explanation of the process of natural selection.

Well, thank you, but it hits me as odd then that you didn't get it well enough to give the right title to the thread (actually I prefer reduction of genetic diversity myself) and Percy didn't get it well enough to respond to my first post and though others keep saying they get it, in fact insist on it quite noisily, I know they don't. It's very hard to take seriously any objections until I know what I'm trying to say is understood. THEN I could take the objections more seriously.

Sorry if I sound snappish here as it suddenly sounds to me. But it does seem that if I were getting it across you would have had a title that reflected it.

My only point of confusion is why you think this process will inevitably lead to complete allele depletion.

ABE: It doesn't necessarily even if you get speciation, I've tried to stick to saying genetic REDUCTION. Some cases of speciation do appear to involve depletion such that there's no place to go genetically from where they are. But I'm convinced that ALL cases of speciation (or true breeding in domestic contexts) MUST involve genetic REDUCTION to a recognizable extent -- well, it just seems obvious to me: If you have a well established breed, and it has, oh, golden fur with special brown markings you simply do not want an allele for black fur and blurry markings in the population. Right? What you call fixed is what you want, and you want it for all traits that characterize your breed if you can get them without bringing genetic problems along with them and that includes all the characteristics, the whole body type and all the rest. And what IS that but severely reduced genetic diversity??????

But why to genetic reduction or depletion? Because if you really do get what my graphic is saying and you agree with it, it ought to be clear that what this process does on the small scale of one gene under selection pressure it will also do over time with other genes, and if the trait for each holds it can only be because there are no competing alleles. You aren't going to get a fixed trait let alone speciation if there are.

Somebody pointed out a while back that I'm focused more on speciation than anything else and that's correct. I don't see how you can have evolution in any sense that supposedly leads to species evolving into other species without many speciation events along the way myself.

Perhaps this is what you need to explain to me.

Of course it doesn't appear that natural selection ever really goes to speciation -- or rarely anyway; that seems to depend on reduction of population numbers through migration or other such effect. Such a reduction in population could occur of course under really extreme natural selection in which a predator wipes out a large number.

Under the condition of isolation of a small portion of a population it can't be only one gene that is affected by the reduction in numbers, many genes must also have fewer alleles available in the new population just because there are fewer members to start with -- that way you're going to get a lot of change in the population in just a few generations it seems to me, change from what the species looked like in the parent population. Just from population reduction and reproductive isolation, not even natural selection. No longer the same markings on the salamander population in the ring series but a whole new characteristic set of markings for the new population and no doubt other changes not quite so obvious. All thanks to reduced genetic diversity.

I know you all think I'm an ignoramus, thanks a lot, but I see no other way you get phenotypic change that actually comes to characterize a population, or gets as far as speciation, without eliminating alleles.

And for this not to be recognized in domestic breeding boggles MY mind.

I think that痴 going to be too big a question to try to tackle in one step, so let me ask a simpler question (and a follow up):

Do you agree that, if mutation is allowed, then new mutations can, at least in principle, produce new alleles?

I've been accepting it for the sake of discussion all along. Think I even stated it in the previous post.

If so, doesn稚 basic reasoning tell us that the change in diversity can be determined by comparing the number of new alleles produced by mutations to the number of old alleles exterminated by natural selection?

But natural selection also exterminates any NEW alleles that occur for genes that are undergoing selection for some other allele. And anything that cuts a population down to smaller numbers is also going to eliminate a lot of those new mutations, leave them back in the old population.* Then the new population may hypothetically acquire some new mutations too and they will either be selected out or work their way through the population, and then such as in the case of a ring series of populations a new small migration will occur and lots of the mutations will again be left behind. Yes you'll be getting interesting new phenotypes as this occurs, but you're not ever going to get an increase in genetic diversity ALONG WITH the kinds of changes that bring out such new phenotypes or lead to speciation because they depend on reduced genetic diversity.

*Meanwhile back in the old population you may still have opportunities for further variation and selection and even possibly multiple directions for new lines out to speciation if you've still got plenty of genetic diversity there. Where the reduction in diversity comes in is where you are getting new phenotypes, new populations characterized by new phenotypes that is, and ultimately what is called speciation, which I believe has to be a dead end genetically speaking.

Keep in mind, we池e still just considering one gene here. I don稚 want to get into a multiple-gene scenario until we致e cleared up how to measure changes in diversity for one gene.

OK, well I got ahead of you then.

Edited by Faith, : No reason given.

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This message is a reply to:
 Message 6 by Blue Jay, posted 04-03-2010 7:26 PM Blue Jay has responded

Replies to this message:
 Message 9 by Blue Jay, posted 04-03-2010 11:18 PM Faith has responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 8 of 87 (553563)
04-03-2010 11:08 PM
Reply to: Message 4 by Blue Jay
04-02-2010 1:36 PM


finishing your earlier post
How do you envision new traits emerging? Not by mutation, I gather?

By the coming to the fore of previously unexpressed alleles, probably mostly recessive ones in some cases (these technical things I'd like to know more about), by new combinations of alleles getting an opportunity to be expressed and that sort of thing. I don't deny that there may be some mutations but I really haven't seen any evidence for them -- the whole idea that mutations are the source of alleles is strictly an assumption based on evolutionary theory, as Dr. A put it on another thread recently, and the actual evidence of what happens to the DNA to form what is called a mutation doesn't look very hopeful for anything evolution would need for all the claims made for it. But again, I'm not going to deny mutations, I don't know how much mutation may be involved. But I do generally focus on the reservoir of already-existing alleles as the source of the changes I have in mind. However, that's not a crucial thing either -- the source COULD be mutations and it seems to me no great difference in the scenerio I have in mind is made by that. It still takes selection and isolation to carve out a new phenotype from whatever the source material is. And every time I think through the processes involved I end up convinced that there IS an end to these processes of reduction that are the crucial element in defining a species. Even if every gene had new mutations and a new species was formed only from those new mutations, forming it would require at least the reduction of, and if you want your new species solidly fixed in its characteristics, then the actual loss of, all other alleles for all those genes.

I do think of the cheetah as a species created by one of the normal means by which species are brought about, though Wounded King slapped me around quite a bit for the thought.

Having traits and alleles show different diversity patterns seems contradictory to me.

Well, of course you always have an allele for a trait, roughly speaking anyway, but for a given trait to be expressed over time and become characteristic of a population requires that all the others not be expressed, and ultimately lost altogether from the population if the trait is to become fixed. That way while you are getting a new trait or phenotype you are also losing alleles in order to get it fixed.

Granted, there isn稚 a one-to-one correlation between allelic diversity (you can have some traits that emerge without new alleles emerging, and you can have new alleles emerge without producing any new traits), but I would think that there should be a general trend of correlation between allelic and trait diversity, given that all traits ultimately trace back to alleles.

Yes, well I see my language can be confusing as certainly there should be an allele for a trait as I say above. But then in that same paragraph I'm trying to explain how the new trait comes to fixation when the genetic diversity is reduced. Perhaps there is a better way of saying it.

I知 also uncertain as to how trait diversity is increasing in your scenario.

The way the salamanders in the ring species get new traits from population to population. They all look different. Each population has its own characteristic phenotype. It's not exactly trait diversity that is increasing in a certain sense, it's that new traits that weren't getting expressed in the previous population are having an opportunity to get expressed in this new population, because the reduced numbers in the migration are mixing the genes in new proportions to allow this. New phenotypes do develop from bottlenecks. They also develop from less drastic population reductions. These are the extremes where genetic reduction on out to genetic depletion is easily demonstrated, but they should also indicate that there is a trend from earlier stages of the emergence of new traits from new gene frequencies through the progressive reduction of alleles if you are ever going to have a new species.

I would appreciate any explanation or clarification on this point. Take whatever time you need or want to do so.

Sorry I didn't get back to this sooner.

In the meantime, perhaps a bit of terminology would be beneficial, just to make sure we池e both clear on what we池e talking about:

gene: a region of the genome that encodes a certain product
allele: one of several sequence variants of a gene

Yes. I have a lot of questions about how the function of a gene which is made up of thousands of separate chemical codes can even be identified at all if you can get into that. Though it may not be terrificially relevant here.

character: a physical attribute of an organism
trait: one of several variants of a character

OK, though I tend to use them synonymously so you might have to clarify further if I create confusion by my use of them.

genotype: a suite of alleles in a single organism
phenotype: a suite of traits in a single organism

OK, but I also use phenotype as a trait which is the expression of a single allele and I'm sure I've seen it used that way. I use it when I'm afraid "trait" will be too ambiguous.

Also, are you familiar with the mechanisms of mutation and evolutionary genetics (e.g., crossing over, independent assortment, point mutations, insertions/deletions, etc.)? We might not need to talk about these, but, just in case...

Read up on mutations from time to time and have some notion how they are formed during the process of replication, but no, I don't feel I'm really up on how all this happens.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 4 by Blue Jay, posted 04-02-2010 1:36 PM Blue Jay has responded

Replies to this message:
 Message 13 by Blue Jay, posted 04-03-2010 11:57 PM Faith has responded

    
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 9 of 87 (553564)
04-03-2010 11:18 PM
Reply to: Message 7 by Faith
04-03-2010 8:51 PM


Re: graphic attempts
Hi, Faith.

Let me clear up a couple managerial type things here. I値l post a response to the 杜eaty portions of your post in a second reply to follow shortly after this one.

Faith writes:

But it does seem that if I were getting it across you would have had a title that reflected it.

I humored you on the title.

selection doesn稚 work on alleles, it works on traits. If an organism has camouflaged coloration, natural selection doesn稚 care if its genotype is Aa or AA. So, the only thing natural selection can actually reduce directly is traits. Because alleles are the cause of these traits, natural selection working on these traits will necessarily impact the alleles, too.

There really wasn稚 anything wrong with the title I proposed: it said exactly what I wanted it to say. I changed it because I wanted to avoid this little discussion until the Great Debate had been agreed upon and established.

On a somewhat related note, I also apologize for not having posted a message at your topic informing you of this debate (that痴 standard etiquette). I wanted to wait until was promoted, but, by then, Percy had already posted the note.

-----

Faith writes:

Bluejay writes:

My only point of confusion is why you think this process will inevitably lead to complete allele depletion.

It doesn't necessarily even if you get speciation, I've tried to stick to saying genetic REDUCTION.

A thread with two wordsmiths can be extremely trying on everybody痴 patience. This is me talking from personal experience.

I had originally written 兎xtinction, and then thought better of it and switched it to 電epletion, which is a slightly softer word that still conveys a similar idea. Unfortunately, I forgot to edit out 田omplete. I guess 途eduction could be seen as slightly softer than 電epletion, but I don稚 see a meaningful distinction to be made there, and my usage of 電epletion wasn稚 intended as anything different from your usage of 途eduction.

Let痴 just agree not to get too picky about semantics outside of the usage of well-established terminology (trait, allele, gene, etc.): I think we値l both be happier that way.

-----

Faith writes:

Bluejay writes:

Keep in mind, we池e still just considering one gene here. I don稚 want to get into a multiple-gene scenario until we致e cleared up how to measure changes in diversity for one gene.

OK, well I got ahead of you then.

Well, no you didn稚: I was only referring to my own post. I値l remember never to use the royal 努e outside of my kingdom again.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 7 by Faith, posted 04-03-2010 8:51 PM Faith has responded

Replies to this message:
 Message 10 by Faith, posted 04-03-2010 11:23 PM Blue Jay has responded

  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 10 of 87 (553565)
04-03-2010 11:23 PM
Reply to: Message 9 by Blue Jay
04-03-2010 11:18 PM


Re: graphic attempts
Just saw this, have a quickdraw response:

selection doesn稚 work on alleles, it works on traits

Many discussions of evolution claim so, but Dawkins insists it works on genes and goes to some lengths to explain this. Seems to me it's six of one and half a dozen of the other.

ABE: You want to make a distinction between dominance and recessiveness, OK, I do keep this in mind wherever it seems relevant.

Um, how does your "humoring" me on the title explain your using a title that doesn't reflect what I am trying to say?

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 9 by Blue Jay, posted 04-03-2010 11:18 PM Blue Jay has responded

Replies to this message:
 Message 19 by Blue Jay, posted 04-04-2010 12:02 PM Faith has responded

    
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 11 of 87 (553566)
04-03-2010 11:27 PM


Hi, Faith.

You may be going too fast for me now!

My next response may be somewhat less soon than I anticipated. I should be able to get it out tonight sometime.

Thanks.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


Replies to this message:
 Message 12 by Faith, posted 04-03-2010 11:33 PM Blue Jay has not yet responded

  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 12 of 87 (553567)
04-03-2010 11:33 PM
Reply to: Message 11 by Blue Jay
04-03-2010 11:27 PM


OK, I just happened to be hanging out here but I have to leave now anyway.
This message is a reply to:
 Message 11 by Blue Jay, posted 04-03-2010 11:27 PM Blue Jay has not yet responded

    
Blue Jay
Member (Idle past 137 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 13 of 87 (553571)
04-03-2010 11:57 PM
Reply to: Message 8 by Faith
04-03-2010 11:08 PM


The crux
Hi, Faith.

I was going to make a detailed, step-by-step response to all of your points, but I think it would be more effective to focus on just the elephant in the room, now that I am aware that it's there.

Faith writes:

[New traits emerge by] the coming to the fore of previously unexpressed alleles, probably mostly recessive ones in some cases (these technical things I'd like to know more about), by new combinations of alleles getting an opportunity to be expressed and that sort of thing.

This contradicts the main point of your argument, and is really the crux of the argument I致e been trying to bring against you.

You have been arguing that natural selection should eliminate most of the genetic diversity in a population. You have a parent population with all kinds of allelic diversity in a model where allelic diversity is inexorably reducing over time. So, why shouldn稚 this process also be working in the parent population? What is different about the parent population that allows it to maintain high levels of genetic diversity?

Edited by Bluejay, : No reason given.


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 8 by Faith, posted 04-03-2010 11:08 PM Faith has responded

Replies to this message:
 Message 14 by Faith, posted 04-04-2010 12:29 AM Blue Jay has responded

  
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 14 of 87 (553578)
04-04-2010 12:29 AM
Reply to: Message 13 by Blue Jay
04-03-2010 11:57 PM


Re: The crux
You have been arguing that natural selection should eliminate most of the genetic diversity in a population. You have a parent population with all kinds of allelic diversity in a model where allelic diversity is inexorably reducing over time. So, why shouldn稚 this process also be working in the parent population? What is different about the parent population that allows it to maintain high levels of genetic diversity?

Its size. Its much greater numbers.

Of course if it isn't that large then it too may very well show the same processes in operation as any population that has been cut off from it. In fact you could hypothetically have half a dozen or more populations splitting up from an original large population and all going in different directions. The size of each population should determine how rapidly and conspicuously the selection processes operate in it. The smaller the population the more dramatic the phenotypic changes and the greater the reduction or depletion of genetic diversity.

In a very large well mixed population very little evolution happens as I understand it.

(But I've also said it may be that natural selection isn't nearly as effective at making all these changes as simple population reduction and isolation itself, however that comes about.)

Your response was to this statement by me:

New traits emerge by the coming to the fore of previously unexpressed alleles, probably mostly recessive ones in some cases (these technical things I'd like to know more about), by new combinations of alleles getting an opportunity to be expressed and that sort of thing.

This contradicts the main point of your argument, and is really the crux of the argument I致e been trying to bring against you.

Of course I don't see any contradiction here. I'm still describing the same situation of a relatively small population which is allowing the expression of previously unexpressed alleles and new combinations. Its smaller size is bringing all this out by mixing a smaller collection of traits and their alleles, since others were left behind. The smaller the population the more dramatic and faster the effects; if the population is pretty good sized they will still operate but not as fast or dramatically.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 13 by Blue Jay, posted 04-03-2010 11:57 PM Blue Jay has responded

Replies to this message:
 Message 18 by Blue Jay, posted 04-04-2010 11:44 AM Faith has not yet responded

    
Faith
Member
Posts: 25264
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 15 of 87 (553581)
04-04-2010 1:07 AM
Reply to: Message 1 by Blue Jay
04-01-2010 4:59 PM


rest of post #1
For this one, we need to consider a timeline of events, including the following events:

1.Onset of selection pressure

2.Emergence of new alleles

3.Extermination of alleles selected against

And, the following considerations:

1.Other concurrent selection pressures

2.Genetic linkage between different alleles

3.Magnitude of each selection pressure

If we choose to pursue this complex model, I think we値l quickly find that decreasing genetic diversity is not so inevitable as you have argued. I'll hold off on the specifics until you're ready to discuss it.

OK, may the timing be right. Sounds interesting.

Faith writes:
You may get a new trait but you'll always get it at the expense of all the other genetic possibilities, and when this occurs with many traits you eventually get speciation, fixed loci, and such limited ability for further variation evolution is for all intents and purposes at an end.

I explained a bit about genetic fixation in a few other places. Fixation is what you池e talking about: the elimination of all alleles for a certain gene except for one.

Yes, I think that's at least the end point of what I'm talking about and I've taken your point and have been using it.

I do not think that fixation is inevitable, and I知 certain will never occur at all positions in the genomes of all individuals within a single population.

Well, my context is what happens in speciation and along the path to it, not in all other conditions of life organisms may be found in, and there may be plenty of variation where the processes I'm describing are not happening. This series of events maybe doesn't even happen frequently, I don't really know, but it seems to me it MUST happen if you're ever going to get new variations that lead to speciation.

If no change in happening in a population I wouldn't expect even much in the way of a loss of genetic diversity to be apparent, if any.

But someone has suggested that speciation may not be all that important to evolution. So again it would be good if you could explain how that might be. I can't think of any other way you could get the kinds of changes the ToE predicts over time.

Selection pressures simply cannot be orchestrated such that any single organism can contain all the 澱est alleles for all genes: so, naturally, we should expect that no single combination of alleles will be absolutely superior to all other possibilities in a population.

I don't see the relevance of this but I'll read on. I really don't take natural selection as seriously as the theory would have me do, because it seems to me that the simple division of a population that brings about a smaller population as in a migration of a small portion to a geographically isolated area, has much more effect in changing the character of a species and is much more likely to lead to ultimate speciation than natural selection is, and I gather from my reading that some population geneticists see it this way also. I don't tend to think in terms of better or worse alleles either, except for harmful mutations, it seems to me it's all simply interesting and creative possibilities for variation, and that natural selection only really operates when there is genuine pressure. How often that occurs I don't know, do scientists?

As an example, let me present Uta stansburiana, the 途ock-paper-scissors lizard I referred to earlier in your thread. This is an (admittedly unusual) example of a population that has reached a relatively stable balance between different genotypes. This sort of 澱alancing act is what is going on in nearly all populations, all the time: the equilibrium oscillates between different character states, occasionally leading to the complete extinction of a certain trait, but also often leading to a complete rebound of a rare allele.

Yes, I can see that that could describe a very common situation in populations, but then I'd point out that this isn't evolution or change toward speciation, which is the process in which the reduction of genetic diversity occurs that I'm talking about, as it produces new phenotypes, sometimes some rather dramatic new types.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
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