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Author Topic:   The End of Evolution By Means of Natural Selection
RAZD
Member (Idle past 296 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 376 of 851 (556041)
04-16-2010 8:18 PM
Reply to: Message 374 by Faith
04-16-2010 7:58 PM


Re: dominance vs hidden alleles
Hi Faith,

However, I've worked it through and I see that you are all right, the dominants will not change their proportion barring reproductive advantage, they will retain the same proportion through all generations, ...

Hold that thought and savor it. Dominance of a neutral allele is unrelated to it's selection (because it is neutral).

Perhaps then we can relate this to your concept of hidden alleles that emerge in small populations ... presumably because other alleles that have kept it hidden are lost.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 374 by Faith, posted 04-16-2010 7:58 PM Faith has responded

Replies to this message:
 Message 378 by Faith, posted 04-16-2010 8:24 PM RAZD has responded

  
Faith 
Suspended Member (Idle past 336 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 377 of 851 (556042)
04-16-2010 8:20 PM
Reply to: Message 375 by nwr
04-16-2010 8:10 PM


Re: dominance
There can still be less blacks than the other colors.

I don't see how if black is dominant to all the others, brown is dominant to grey and grey is dominant to tan. If there is no reproductive advantage operating at all then they should sort themselves into a descending order of proportions from black to tan more or less as Zen Monkey laid it out.

But of course,

"due to the dominance, the proportion of blacks in the population will be greater than the proportion of black alleles in the gene pool"
as you said.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 375 by nwr, posted 04-16-2010 8:10 PM nwr has responded

Replies to this message:
 Message 379 by nwr, posted 04-16-2010 8:27 PM Faith has responded
 Message 385 by Dr Adequate, posted 04-16-2010 11:37 PM Faith has not yet responded

  
Faith 
Suspended Member (Idle past 336 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 378 of 851 (556043)
04-16-2010 8:24 PM
Reply to: Message 376 by RAZD
04-16-2010 8:18 PM


Re: dominance vs hidden alleles
Hold that thought and savor it. Dominance of a neutral allele is unrelated to it's selection (because it is neutral).

I don't believe I've made that mistake. RAZD.

Perhaps then we can relate this to your concept of hidden alleles that emerge in small populations ... presumably because other alleles that have kept it hidden are lost.

I described such a situation a few posts above, which I just sharpened up by edit based on this discussion -- bottom of Message 366.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 376 by RAZD, posted 04-16-2010 8:18 PM RAZD has responded

Replies to this message:
 Message 384 by RAZD, posted 04-16-2010 10:56 PM Faith has responded

  
nwr
Member
Posts: 5714
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 6.2


Message 379 of 851 (556044)
04-16-2010 8:27 PM
Reply to: Message 377 by Faith
04-16-2010 8:20 PM


Re: dominance
Faith writes:
I don't see how if black is dominant to all the others, brown is dominant to grey and grey is dominant to tan.

The black allele might be very rare. If only 1% of the alleles in the gene pool are for black, then you get about 1.75% of the population with a black trait.

This message is a reply to:
 Message 377 by Faith, posted 04-16-2010 8:20 PM Faith has responded

Replies to this message:
 Message 380 by Faith, posted 04-16-2010 8:34 PM nwr has acknowledged this reply

  
Faith 
Suspended Member (Idle past 336 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 380 of 851 (556045)
04-16-2010 8:34 PM
Reply to: Message 379 by nwr
04-16-2010 8:27 PM


Re: dominance
Well, yes, of course, and I've been working with that kind of example myself in my argument, but in this case I was trying to stick with a "perfectly" proportioned population because I thought that was what Zen Monkey was doing.

This message is a reply to:
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Blue Jay
Member (Idle past 1589 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 381 of 851 (556049)
04-16-2010 10:13 PM
Reply to: Message 359 by Wounded King
04-14-2010 3:59 AM


Re: Beneficial and deleterious mutations
Hi, Wounded King.

Wounded King writes:

Well it hasn't happened over the previous five years, so I shouldn't hold my breath if I were you. Nothing has helped, including dozens of people explaining the overwhelming importance of the environmental context of a mutation for it to be judged beneficial in words of one syllable to her.

Well, she did acknowledge that at least one of the mutations I presented did have a beneficial effect on the bacterium's phenotype. Of course, she found another philosophical viewpoint to preserve her original argument (at least in semantic form), which is a product of a larger issue than her denial of beneficial mutations.

I realize that I made no ground in convincing her of the importance and logical power of scientific theories. Like so many creationists, she has concluded that the "ideal" version of science is a simple fact-gathering enterprise with no thinking involved beyond the planning needed to design experiments for the collection of data.

As long as she holds to this opinion and refuses to accept that theories are not endpoints--but also sources---of knowledge, getting her to acknowledge one or two of our factoids is a only pyrrhic victory.

I think you're right: her issues are deeper than just this specific argument.


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

Darwin loves you.


This message is a reply to:
 Message 359 by Wounded King, posted 04-14-2010 3:59 AM Wounded King has not yet responded

  
ZenMonkey
Member (Idle past 3402 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 382 of 851 (556050)
04-16-2010 10:25 PM
Reply to: Message 362 by nwr
04-16-2010 4:25 PM


Re: Restoration of diminished alleles.
nwr writes:

With no reproductive advantage, the relative proportion of each gene in the next generation will be almost identical to the relative proportion in the current generation.

The black gene remains dominant in the genetic sense, that possession of that gene results in the black trait. However, the proportion of black creatures will forever remain insignificantly small unless there is some statistical freak event that causes a major change in the relative gene frequencies.

That makes sense to me. The frequency of the Black allele in one generation, no matter how dominant, would stay the same in the next generation because there are only so many rabbits to go around. If only one rabbit has it, whether heterozygote or homozygote, then he or she is still only going to be able to pass it on once in any single given mating.

Thanks.


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:
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ZenMonkey
Member (Idle past 3402 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 383 of 851 (556051)
04-16-2010 10:26 PM
Reply to: Message 363 by CosmicChimp
04-16-2010 4:49 PM


Re: Restoration of diminished alleles.
CosmicChimp writes:

Random mating is assumed to be occurring in such ideal situations.

That was my assumption, trying to be as simple as possible while still being reality-based.


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 363 by CosmicChimp, posted 04-16-2010 4:49 PM CosmicChimp has acknowledged this reply

  
RAZD
Member (Idle past 296 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 384 of 851 (556053)
04-16-2010 10:56 PM
Reply to: Message 378 by Faith
04-16-2010 8:24 PM


Re: dominance vs hidden alleles
Hi Faith

Perhaps then we can relate this to your concept of hidden alleles that emerge in small populations ... presumably because other alleles that have kept it hidden are lost.

I described such a situation a few posts above, which I just sharpened up by edit based on this discussion -- bottom of Message 366.

ABE: After the rest of the discussion here I realize the black won't come to dominate without reproductive advantage of some sort (and in fact that was my very first response to Zen Monkey on the other thread when he raised this question), but it is true that all the other colors will now show up in the new population that were suppressed by the dominant black in the parent population (by drift of course in that situation).

Except that your supposed hidden alleles were never seen in previous populations, and this does not fit with the patterns above.

Message 361: Here's how I work out all the possible combinations of four alleles.

Black + Black = Black
Black + Brown = Black
Black + Grey = Black
Black + Tan = Black

Brown + Black = Black
Brown + Brown = Brown
Brown + Grey = Brown
Brown + Tan = Brown

Grey + Black = Black
Grey + Brown = Brown
Grey + Grey = Grey
Grey + Tan = Grey

Tan + Black = Black
Tan + Brown = Brown
Tan + Grey = Grey
Tan + Tan = Tan

So all the possible pairings give us 7 Black rabbits, 5 Brown rabbits, 3 Grey rabbits, and 1 Tan rabbit.

In every 16 rabbits (if the alleles are evenly spread).

43.75% Black (with 7 carriers)
31.25% Brown (with 7 carriers)
18.75% Gray (with 7 carriers)
06.25% Tan (with 7 carriers)

If we assume that 50% of the Black alleles are knocked out of the population by some stochastic event, then there are twice as many of the other alleles than the black alleles (to keep the math relatively simple), and then we get:



BlackBrownBrownGrayGrayTanTan
BlackBlack
Black
Black
Brown
Black
Brown
Black
Gray
Black
Gray
Black
Tan
Black
Tan
BrownBrown
Black
Brown
Brown
Brown
Brown
Brown
Gray
Brown
Gray
Brown
Tan
Brown
Tan
BrownBrown
Black
Brown
Brown
Brown
Brown
Brown
Gray
Brown
Gray
Brown
Tan
Brown
Tan
GrayGray
Black
Gray
Brown
Gray
Brown
Gray
Gray
Gray
Gray
Gray
Tan
Gray
Tan
GrayGray
Black
Gray
Brown
Gray
Brown
Gray
Gray
Gray
Gray
Gray
Tan
Gray
Tan
TanTan
Black
Tan
Brown
Tan
Brown
Tan
Gray
Tan
Gray
Tan
Tan
Tan
Tan
TanTan
Black
Tan
Brown
Tan
Brown
Tan
Gray
Tan
Gray
Tan
Tan
Tan
Tan

So all the possible pairings give us 13 Black rabbits, 20 Brown rabbits, 12 Grey rabbits, and 4 Tan rabbits in every 49 rabbits (if the alleles are evenly spread).

26.5% Black (with 13 carriers)
40.8% Brown (with 24 carriers)
24.5% Gray (with 24 carriers)
08.2% Tan (with 24 carriers)

Not really a significant change in proportions for an impact of 50% of the Black alleles being removed. The population as a whole will still be predominantly Black, Brown and Gray in appearance, while the rare Tan rabbit goes from 6% to 8%.

The allele that benefits (increases in appearance of the phenotype) the most from this change is the Brown one, the second most dominant allele in the original population, as essentially Black and Brown exchange places.

Somehow I don't think this validates your claim.

Enjoy

Edited by RAZD, : added end

Edited by RAZD, : added carriers


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 378 by Faith, posted 04-16-2010 8:24 PM Faith has responded

Replies to this message:
 Message 388 by Faith, posted 04-17-2010 1:07 AM RAZD has responded

  
Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 385 of 851 (556057)
04-16-2010 11:37 PM
Reply to: Message 377 by Faith
04-16-2010 8:20 PM


Let's Try This Again
I don't see how if black is dominant to all the others, brown is dominant to grey and grey is dominant to tan.

No, of course you don't see that. This is because you have never studied genetics even so far as to understand even the words that you are using.

I may have said this before. And I am going to say it again.

You are hopelessly ignorant about genetics, so what you need to do now is to get a basic textbook about genetics so that you at least know the meaning of the vocabulary that you are using.

For pity's sake, Faith.


This message is a reply to:
 Message 377 by Faith, posted 04-16-2010 8:20 PM Faith has not yet responded

  
ZenMonkey
Member (Idle past 3402 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 386 of 851 (556061)
04-16-2010 11:57 PM
Reply to: Message 365 by Dr Adequate
04-16-2010 5:23 PM


Re: No, You Lose
Dr Adequate writes:

You haven't done the math, and you are misunderstanding the word "dominant".

Faith is, of course, talking complete rubbish. But unfortunately, so are you.

Well, it's never my intention to talk complete rubbish, but it does happen from time to time.

As PaulK points out above, I was, however much I tried not to, confusing the allele with the trait. I believe that given the somewhat artificial constraints of the problem - no mutation, a single trait being determined by a single gene, random mating, and a trait with no reproductive advantage or disadvantage - that this should end up being mostly about math. Thus I turn to you, Dr.

The pairings that I did were inadequate, as I now see. If I start with a standard Mendelian square, this is more like it. I think.

Here's what happens when I do the math by brute force. I'll start out as simply as I can: just two alleles with Black (B) dominant and Brown (r) recessive to respect to each other. If a homozygous (BB) black rabbit mates with a homozygous brown (rr) rabbit, then I believe we have 100% probability of black offspring, as all four possibile outcomes will be heterozygous Br, and thus an even distribution of alleles. Breed any two of those heterozygous Br rabbits, and we have a 75% possibility of a black pup and 25% possibility of a brown one: BB, Br, rB, rr. If I then look at all the possible combinations of any two of that generation of rabbits mating at random, we'll have 16 potential pairings, which can happen in six different ways. (For the sake of my own sanity, I'm going to represent both Br and rB as Br.)

1. BB + BB = BB, BB, BB, BB
2. BB + Br = BB, BB, Br, Br
3. Br + Br = BB, Br, Br, and rr
4. BB + rr = Br, Br, Br, Br
5. Br + rr = Br,, Br, rr, rr
6. rr + rr = rr, rr, rr, rr

Out of the 16 possible pairings, I see that combination 1 can happen only once, combination 2 can happen four times, combination 3 can happen four times, combination 4 can happen two times, combination 5 can happen four times, and combination 6 can happen only once. So out of the sixteen possible pairings, we'll have 64 possible outcomes:

BB x 16 (25%), Br x 32 (50%), and rr x 16 (25%)

So it looks like once again we'll have 75% probibility of black offspring and 25% probibility of brown offspring.

I hope that I'm still doing ok.

So the question comes down to this. Given a situation in which we don't allow our rabbits to breed exponentially, however much they might want to, but stay at a simple replacement rate of one pair producing two offspring per generation, will this ratio of distribution of alleles and traits remain constant from generation to generation? (I assume that a steady replacement rate would represent a static environment and a stable population.) I get completely lost in trying to work with more than two alleles - dealing with two for just three generations was hard enough. But can I assume that the same concept of a consistant probability for the distribution of alleles across the generations would hold?

I brought this question over here since it's actually somewhat peripheral to my train of thought over on the Great Debate thread, but I wanted to clear it up for myself. Obviously I did indeed need quite a bit of clearing up.

Also, I think that my second question is the more interesting one. Is it possible, in the above scenario, for a recessive allele to remain unexpressed as a trait entirely, or is the probability for that too slim?


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 365 by Dr Adequate, posted 04-16-2010 5:23 PM Dr Adequate has responded

Replies to this message:
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nwr
Member
Posts: 5714
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 6.2


Message 387 of 851 (556064)
04-17-2010 12:27 AM
Reply to: Message 386 by ZenMonkey
04-16-2010 11:57 PM


Re: No, You Lose
ZenMonkey writes:
Given a situation in which we don't allow our rabbits to breed exponentially, however much they might want to, but stay at a simple replacement rate of one pair producing two offspring per generation, will this ratio of distribution of alleles and traits remain constant from generation to generation?

The ratio will drift a little due to randomness. If there is a selective advantage for some combinations, then it will change more than just random drift.

ZenMonkey writes:
But can I assume that the same concept of a consistant probability for the distribution of alleles across the generations would hold?

Yes, still the same with multiple generations. The ratio remains nearly constant, except for a little drift due to randomness.

ZenMonkey writes:
Is it possible, in the above scenario, for a recessive allele to remain unexpressed as a trait entirely, or is the probability for that too slim?

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.

This message is a reply to:
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Faith 
Suspended Member (Idle past 336 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 388 of 851 (556070)
04-17-2010 1:07 AM
Reply to: Message 384 by RAZD
04-16-2010 10:56 PM


Re: dominance vs hidden alleles
ABE: After the rest of the discussion here I realize the black won't come to dominate without reproductive advantage of some sort (and in fact that was my very first response to Zen Monkey on the other thread when he raised this question), but it is true that all the other colors will now show up in the new population that were suppressed by the dominant black in the parent population (by drift of course in that situation).

Except that your supposed hidden alleles were never seen in previous populations, and this does not fit with the patterns above.

RAZD, you seem to be making up my side of the argument for me.

I've given many different examples over the thread. The example I was giving above, using Zen Monkey's hierarchy of fur colors, was of a population in which black had come to so completely dominate through drift or some kind of selection process that the expression of a homozygous recessive just about never happened because it would be that rare in a very large population of predominantly BBs for the pairings to occur -- and the BBs are so prevalent BECAUSE black has been severely selected. The others might of course still occur. But the point is that in a migration to start a smaller daughter population it could happen that you'd get enough of the heterozygous blacks to increase their frequencies relative to the BBs and that would allow the other colors to be expressed far more than in the parent population. It's a really simple example, simply another example how it IS the change in gene frequencies alone that changes the phenotype for the new population without any addition of mutations.

Whatever happened to the definition of evolution as change in gene frequencies anyway? This supposedly describes what happens through selection or drift or migration -- you shouldn't need mutations to get a new character to a new population.

{ABE: My argument, just for a reminder, is that it is the SELECTION processes -- including drift and migration and so on -- that change the frequencies, and dominant and recessive alleles come into play as a way of explaining how under selection some traits could completely disappear from a population or at least become extremely rare and then start showing up in greater numbers in a daughter population.

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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Replies to this message:
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 Message 391 by Faith, posted 04-17-2010 2:04 AM Faith has not yet responded
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Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 389 of 851 (556071)
04-17-2010 1:21 AM
Reply to: Message 386 by ZenMonkey
04-16-2010 11:57 PM


Re: No, You Lose
But can I assume that the same concept of a consistant probability for the distribution of alleles across the generations would hold?

Only if the population is infinitely large.

If it isn't, and if no new mutations occur, then given enough time one of the variant alleles must become fixed in the population. And the question of which allele is "dominant" has nothing to do with which one will become fixed.

If new mutations do arise, which they will, then the question becomes moot.


This message is a reply to:
 Message 386 by ZenMonkey, posted 04-16-2010 11:57 PM ZenMonkey has not yet responded

  
Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 390 of 851 (556072)
04-17-2010 1:25 AM
Reply to: Message 388 by Faith
04-17-2010 1:07 AM


Re: dominance vs hidden alleles
Whatever happened to the definition of evolution as change in gene frequencies anyway?

What "happened" to it? It's still there (pace your slight misstatement) and one day we hope that you'll understand it.

Again I would urge you to get your hands on some basic text about genetics and read it.


This message is a reply to:
 Message 388 by Faith, posted 04-17-2010 1:07 AM Faith has not yet responded

  
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