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Author Topic:   The End of Evolution By Means of Natural Selection
nwr
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Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 350 of 851 (555473)
04-13-2010 7:47 PM
Reply to: Message 349 by Wounded King
04-13-2010 7:25 PM


Re: Beneficial and deleterious mutations
Wounded King writes:
Seriously NWR, if you are claiming that Faith's lack of understanding is due to evil neo-darwinists using the term 'Beneficial mutation' then you left reality at a severe tangent some time in the past.
Of course I am not saying that. I am well aware that her creationist commitments are the major source of the problem. However, in this particular thread which has been discussing mutations, it has been a significant factor.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 356 of 851 (555499)
04-14-2010 1:37 AM


This is really a comment for Faith in Message 71 of thread Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only).
Faith writes:
I really don't see how you can get breeds, varieties, species, new traits, new phenotypes, unless a population undergoes reduction of diversity.
I think I understand what you are getting at.
Let's imagine a very early mammal. And perhaps there were 10 alleles for a particular gene. Note that my hypothetical example is very unrealistic.
Suppose those are allele 1, allele 2, ..., allele 10.
Allele 1 produces some doglike traits.
Allele 2 produces some catlike traits.
Allele 3 produces some mouselike traits.
Allele 4 produces some monkeylike traits.
etc.
You are saying that in order to get a dog, you have to lose allele 2, allele 3, allele 4, etc. And you see that as a loss of diversity.
However, what can happen is that, with new mutations, these are replaced by allele 1.1, allele 1.2, allele 1.3, etc which are variations of doglike traits. So there can be still just as much diversity as measured in the number of alternative alleles, but the new diversity is more narrowly spread and all within the doglike range.
Edited by nwr, : Add message reference for the other thread.

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 362 of 851 (555994)
04-16-2010 4:25 PM
Reply to: Message 361 by ZenMonkey
04-16-2010 4:09 PM


Re: Restoration of diminished alleles.
I disagree with your math.
ZenMonkey writes:
Again, in this model we have complete dominance, a single gene coding for a single trait, and a trait that is neutral in character, giving no reproductive advantage.
That's the key here.
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.

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Replies to this message:
 Message 363 by CosmicChimp, posted 04-16-2010 4:49 PM nwr has seen this message but not replied
 Message 366 by Faith, posted 04-16-2010 5:44 PM nwr has replied
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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 372 of 851 (556030)
04-16-2010 6:56 PM
Reply to: Message 366 by Faith
04-16-2010 5:44 PM


Re: dominance
Faith writes:
Surely genetic dominance does confer some population dominance too.
That depends on what you mean by "population dominance".
If 1% of the alleles present at that location are black (taken as a percentage over the entire population), then 1.75% of the population will have a black trait. That comes from the counting of instances shown by ZenMonkey, and assumes random distribution of pairings. Nevertheless, in the next generation the proportion of black genes will remain at 1%, again assuming random pairings. In practice there can be some drift, but it will be small unless there is a reproductive advantage for one of the alleles.
Faith writes:
Next generation all the heterozygous B's also pass on their blackness, ...
Actually, no, they don't. If two heterozygous Bs mate, then 1/4 of their offspring will have no B allele. That's the expected statistical outcome, though a particular mating pair might happen to have a different distribution.
Faith writes:
It would be quite a project to work it all through with the hierarchy of dominance specified, but since black is dominant over all the others it seems pretty clear that eventually black should come to dominate the whole population, all other things being equal.
You only have to count the alleles present in the next generation. For a particular mating pair, each of their two alleles has a 50% probability of being used in a particular reproductive event. List out the possibilities, much as ZenMonkey did, and then count. You will see that the proportion in the next generation is the same as in the current generation. The only way that changes, is if there is a selective advantage so that combinations don't all have the same probability of surviving into the next generation.

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 Message 366 by Faith, posted 04-16-2010 5:44 PM Faith has replied

Replies to this message:
 Message 374 by Faith, posted 04-16-2010 7:58 PM nwr has replied

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 375 of 851 (556040)
04-16-2010 8:10 PM
Reply to: Message 374 by Faith
04-16-2010 7:58 PM


Re: dominance
Faith writes:
That is "some population dominance," as I said also -- meaning there will always be more black rabbits than the other three colors, and more browns than greys and tans, and more greys than tans, barring any kind of selecting factor -- but they will not increase in proportion.
That's almost right.
There can still be less blacks than the other colors. But, due to the dominance, the proportion of blacks in the population will be greater than the proportion of black alleles in the gene pool.

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 Message 374 by Faith, posted 04-16-2010 7:58 PM Faith has replied

Replies to this message:
 Message 377 by Faith, posted 04-16-2010 8:20 PM nwr has replied

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


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.

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 Message 377 by Faith, posted 04-16-2010 8:20 PM Faith has replied

Replies to this message:
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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


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.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 394 of 851 (556092)
04-17-2010 8:07 AM
Reply to: Message 391 by Faith
04-17-2010 2:04 AM


Re: dominance vs hidden alleles
Faith writes:
Mutation is assumed in a couple of instances but mostly it's a complicated discussion of how you get different traits from combinations of dominants and recessives.
The fact that mutation is only mentioned a few times does not show that there were not other mutations. The breeders would be mainly concerned with mutations with visible traits that might be attractive to bird owners. They would not notice mutations that did not cause visible changes.
Faith writes:
Without grasping all the particulars, I'd say this suggests that in the wild if birds migrate away from a parent population to set up new populations you could easily get many new types of bird populations just from the built-in alleles.
Yes, but they wouldn't be considered a separate species unless there were further divergence from the original group. Maybe a mutation allows them to feed on a tougher seed than before, and because that tougher seed is abundant in the new environment you get strong selection pressure to favor the new mutation.

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 Message 391 by Faith, posted 04-17-2010 2:04 AM Faith has replied

Replies to this message:
 Message 397 by Faith, posted 04-17-2010 1:19 PM nwr has replied
 Message 400 by Faith, posted 04-17-2010 2:14 PM nwr has replied

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 402 of 851 (556129)
04-17-2010 2:30 PM
Reply to: Message 397 by Faith
04-17-2010 1:19 PM


Re: dominance vs hidden alleles
Faith writes:
Seems to me 1) this process produces some very striking divergence and 2) descriptions of new species don't make them sound like much more than the same species with some striking new characteristics.
There is a big difference between natural selection and artificial selection.
With artificial selection, the breeders are usually attempting to emphasize the differences, and to make them more pronounced. This leads to creatures with widely different traits but only small genetic differences.
With natural selection, the tendency is for the unusual traits to be blended back into the population. So you mostly only see noticeably different characteristics when there are rather larger genetic differences.
Faith writes:
OK, you want to insist on mutations, though the descriptions could just as well apply to new combinations of built-in alleles as to mutations so I see no need for mutations -- AND the mutations are as usual assumed and not known for a fact to be the source of any given novelty -- but for my purposes I don't really think it matters because the processes that select and isolate and reduce genetic diversity will operate on both just the same.
These days they are doing quite a bit of DNA sequencing, and measuring the genetic differences between species. If somebody were to discover two separate species where the only genetic differences were that one of the species had lost some of the alleles of the other, that would likely make big news. Possibly it would also lead to reconsideration of whether those are really parts of the same species.
I am not a biologist (I'm a mathematician and computer scientist). But it sure seems to me that the experimental evidence is indicating that there are mutations involved in the formation of species. That said, the species classification is a bit arbitrary and sometime revised on new information.
Faith writes:
Again, it is apparent that whenever mutations are invoked it is an assumption that usually isn't proved. A new trait emerges, it's called a mutation, it's assumed. Sometimes the gene can be pinpointed and the change accounted for as a mutation, but the theory that all alleles come from such changes isn't proved by that, still merely assumed.
It isn't just assumed. Sure, sometime new species are defined without checking the DNA. However, when checks are later made, they seem to show that there were indeed mutations. Presumably biologists have a pretty good eye for recognizing this, though sometime classifications are changed.
Keep in mind that it isn't that there is a new mutation, and a new species springs up. It's more likely that a new mutation just adds to the genetic diversity of the existing population. Then some other event, perhaps a new predator or a new food source, changes the selection pressures and that divides the population into separate sub-populations which then drift apart. These subpopulations then pick up more genetic diversity with further mutations. It isn't just selection, and it isn't just mutation that gives rise to new species. It is both acting in conjunction with one another.
Faith writes:
If mutations happen to be occurring more frequently now than in the past, and they are accidents or mistakes that sometimes produce something neutral that can be regarded as desirable, such as by breeders, but couldn't have produced all alleles, how could this be known?
I disagree with the frequent description of mutations as mistakes or accidents or copying errors. It seems to me that they should be considered part of how biology works. If somebody were designing a biological system (as a theistic evolutionist might believe), that designer would probably want to design a system that produced random mutations. The "designed" mutation rate would need to be low - too high a rate would cause problems. But it would need to be high enough that there is variety around to allow some of the population to be able to resist unpredicted new diseases or environmental changes or predators.
Faith writes:
But I didn't want to stay in the conversation about mutations right now. Even if they do occur and account for the material for variation (really, I nearly choke saying that because I'm so convinced it doesn't happen except possibly very rarely) but even if they do, the processes of selection and isolation that bring out new characteristics for new populations still reduce the genetic diversity in producing these new varieties no matter what its original source.
I don't think there is actually much disagreement with that. Most would agree that selection and isolation can lead to a change in phenotype and a reduction in diversity. Where we disagree with the thesis of your OP, is that we see the diversity being replenished over time, as new mutations accumulate.

This message is a reply to:
 Message 397 by Faith, posted 04-17-2010 1:19 PM Faith has replied

Replies to this message:
 Message 405 by Faith, posted 04-17-2010 4:35 PM nwr has replied

  
nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 403 of 851 (556130)
04-17-2010 2:42 PM
Reply to: Message 400 by Faith
04-17-2010 2:14 PM


Re: back to dog breeds
Faith writes:
There's enormous divergence between dog breeds and yet dogs have such high genetic variability that they never come to form separate species so that the breeds always have to be carefully managed by their breeders to prevent contaminating their select gene pools. Hard to find more divergence than between say a greyhound and a Pekinese, or a Great Dane and a chihuahua and so on.
If you want to say mutations account for these differences I'm only going to say as usual that in most cases you don't know that for a fact and merely assume it, but I'm also not going to object beyond that.
This has a lot to do with the differences between the artificial selection of the breeder, and natural selection that occurs in nature.
Artificial selection is usually done to emphasize differences in exhibited traits. Thus you can have relatively large differences in characteristics, with only a small amount of genetic difference involved. With natural selection, those kinds of differences in traits tend to blend back into the population and don't make as obvious a difference in the population as a whole. So, by the time you see large differences in traits between natural populations, the genetic differences between those populations are likely to be considerably greater than the genetic differences involved in domestic breeding.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 407 of 851 (556160)
04-17-2010 6:54 PM
Reply to: Message 405 by Faith
04-17-2010 4:35 PM


Re: Not a mere race between selection and mutation
I'll try to keep this short.
Faith writes:
Yes, that is the main argument here, which I keep trying to answer by saying that it doesn't matter what the source of the variation is. That is, when a new trait undergoes selection and isolation in order to become a characteristic of a new population, the variability is lost, and MUST be lost or the new characteristic will not emerge. It will be blended back instead and lost in the larger population as you mention above. But when selection and isolation occur, that is the usual road to speciation, which is even confirmed by that diagram from Wikipedia I posted earlier:
File:Speciation modes.svg - Wikipedia
If you add mutations at that point you will only lose your new variety or species as it all blends back together again, same as in your own example above when a new trait emerges in a large population without being selected, or when a bred dog accidentally mates with a mutt.
I am chiefly commenting on the "If you add mutations at that point ..." part.
If you add new mutations that generate the alleles that were eliminated, then indeed that would lose the new species if those alleles were not heavily selected against. However, the new mutations can be for different genes, and provide additional variation that is consistent with continuing to be part of the new species.

This message is a reply to:
 Message 405 by Faith, posted 04-17-2010 4:35 PM Faith has replied

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 468 of 851 (556717)
04-20-2010 9:37 PM
Reply to: Message 466 by Dr Adequate
04-20-2010 9:10 PM


Re: Explanation And Apology
Dr Adequate writes:
I was trying to make a point (which I thought was funny) about the use of Wikipedia as a gold standard.
Yes, I also thought that was funny. I guess my irony detector was functioning properly.
I wasn't sure whether you had done the editing, or had noticed that it had been edited. Not that it much mattered which.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 747 of 851 (559049)
05-06-2010 10:19 AM
Reply to: Message 746 by Admin
05-06-2010 9:41 AM


Re: Status Report
No, I am not volunteering.
It is unrealistic for evolutionists to expect Faith to agree with them. And it is unrealistic for Faith to expect evolutionists to agree with her. On the other hand, it is quite reasonable for evolutionists to express their position, and to expect Faith to acknowledge their position while still refusing to agree with it. And it is reasonable for Faith to express her view, and to expect evolutionists to acknowledge her view while still disagreeing with it.
In my opinion, the thread started out within the reasonable zone, and continued there for a while. Then it left the reasonable zone, and went into the zone of unrealistic expectations, and that is when it began to deteriorate.
I think people on both sides need to recognize when they have reached that position, and be prepared at that point to "agree to disagree" instead of continuing a debate which has deteriorated to the point where it makes no sense to continue.
My suggestion to Faith, is that she make a final summary statement in the thread. Some evolutionists have already made final statements. When there has been sufficient time for final summary statements, the thread could be closed.

This message is a reply to:
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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 749 of 851 (559058)
05-06-2010 10:58 AM
Reply to: Message 748 by Percy
05-06-2010 10:50 AM


Re: Status Report
Faith's beliefs are very dear to her. What you describe, is her protecting those beliefs against contrary evidence. Doing what one must do to protect what one holds valuable does not seem at all irrational to me.
Sure, from our perspective it, and in terms of our beliefs and values, it would be irrational for us to act in that way. However, rationality is an inherently relative notion, so we should not be judging her rationality relative to our point of view.

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