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Author Topic:   The End of Evolution By Means of Natural Selection
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 217 of 851 (554266)
04-07-2010 2:50 AM
Reply to: Message 216 by Faith
04-07-2010 1:28 AM


Re: In Faith's defense...
Faith writes:
...creationists who see the entire geological column as the result of the Flood wouldn't expect to find a rabbit anywhere except in the upper strata with the other land animals.
Or maybe rabbits would be at the bottom because they got trampled by the bigger animals in the stampede to high ground.
That makes just as much sense as what you're saying.

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 216 by Faith, posted 04-07-2010 1:28 AM Faith has not replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


(2)
Message 252 of 851 (554941)
04-10-2010 10:51 PM
Reply to: Message 250 by Faith
04-10-2010 9:18 PM


Re: ring species genotypes are different
Faith writes:
Wherever there is a real allele it's been there from the beginning. Mutations only make disease and junk, that's my conclusion.
Let me see if I understand what you're saying here. Let's start with the issue of alleles.
From Wikipedia:
quote:
Alleles are now understood to be alternative DNA sequences at the same physical locus, which may or may not result in different phenotypic traits.
Here's your argument, as I understand it.
1. Every species has been Created with a set number of alleles for each of its genes. No more can ever be created than are already there.
2. Apparent speciation events occur when a daughter population splits off from its parent and, for whatever reason, starts to express traits that have been dormant in the parent. The alleles for that trait were there all along, but had not yet been expressed.
3. The daughter population will have fewer alleles for some genes than the parent does. One of the reasons that these apparently new traits were not expressed in the parent population was because they were being "crowded out", so to speak, by other alleles. With fewer alleles in the daughter population, these other, heretofore unseen traits will now have a chance to be expressed.
4. Thus what looks like greater diversity in the new population is actually a reduction in diversity, since nothing really new has been expressed in the new daughter population, and the daughter population has fewer alleles for some genes than the parent does.
5. Mutations are the result of genetic damage. Mutations cannot create new alleles. It can only damage them, creating disease or other disability. There is no such thing as a beneficial mutation.
6. Thus many of the fundamental principles of the Theory of Evolution are incorrect. Mutation cannot be a source of new variation. Natural selection will therefore only decrease, rather than increase, genetic variation.
So far as I can tell, this is the substance of your argument. Before I go on, would you let me know if I'm not representing it correctly?

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 250 by Faith, posted 04-10-2010 9:18 PM Faith has replied

Replies to this message:
 Message 253 by Faith, posted 04-10-2010 11:16 PM ZenMonkey has not replied
 Message 263 by Faith, posted 04-11-2010 2:35 PM ZenMonkey has replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 265 of 851 (555018)
04-11-2010 5:06 PM
Reply to: Message 263 by Faith
04-11-2010 2:35 PM


Dominant and recessive and so forth.
Hi Faith,
No, those points didn't come from a website, creationist or otherwise. I just wanted, as Percy suggested, to be sure that I understood your position correctly. I'm glad that you agree that it's substantially correct.
Let's walk through a simple but realistic hypothetical model to see how your proposal plays out. How about rabbits?
Faith writes:
it's possible that there was once some sort of chemical event that produced viable alleles -- from a built-in potential set of possibilities, however -- that has since been lost to the vast majority of living things.
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. If that is so, then for rabbits, we can take any given gene locus, say the one that codes for fur color, and determine that there are only a limited, defined number of alleles for that gene. There will be alleles for brown fur, black fur, grey fur, and so on, but no alleles that would produce green fur or purple fur. (This is highly simplified, since many genes can contribute to any given observable trait. Nevertheless, I believe that there are also plenty of traits that are determined by a single gene. And even if traits are complex enough that there are always more than just one gene involved in shaping them - say for example, a whole suite of genes involved in determining body size - that doesn't substantially change things. We can still realistically focus on the contribution of a single gene to that suite.)
Back to the rabbits. Rabbits are diploid, just like most living things that we're familiar with. Under normal circumstances, each parent will contribute one allele for any given gene. Alleles are considered dominant or recessive based on how they manifest in the phenotype, that is, what the organism looks like.
Faith writes:
Yes, and "crowded out" I suppose probably has something to do with dominant and recessive versions.
This is not really correct. Dominance describes the relationship between two alleles for a single gene.
quote:
It is critical to understand that dominance is a genotypic relationship between alleles, as manifested in the phenotype. It is unrelated to the nature of the phenotype itself, e.g., whether it is regarded as ‘normal or abnormal,’ ‘standard or nonstandard,’ ‘healthy or diseased,’ ‘stronger or weaker,’ or ‘more or less’ extreme.
For our rabbits, each parent would contribute one allele for fur color to its offspring. So if grey fur (G) were dominant with respect to black fur (B), then the possible combinations are:
GG: a rabbit with grey fur
GB: a rabbit with grey fur
BG: a rabbit with grey fur
BB: a rabbit with black fur
Again, this has nothing to do with how desirable it is to have grey fur or black fur. This is simply how genetics plays out. (We're still dealing with a simple system of complete dominance, but the principle remains the same for more complex situations.)
Here it should be obvious that the possibilities are limited. Under ordinary circumstances, an organism will at most have two alleles for any given gene, and no more. There is no place for additional alleles to hide. There may be an allele that is recessive to all the others, and so can be passed to generation to generation but only manifesting in the rare circumstances in which both parents pass on the recessive version. Nevertheless, if it exists at all, it will have to appear from time to time, however infrequently. In other words, if there is an allele for tan fur that is recessive to all the others, it will still manifest when two parents, say a BT father (who would be black) and a GT mother (who would be grey), produce a TT offspring (who would be tan).
One more time. If an allele is "normal" it will always appear in a breeding population from time to time, even if it doesn't do so very often.
Faith writes:
I try to avoid using the term "speciation" unless inability to interbreed has resulted from the population split, but just in the loose sense of a population having developed a new phenotype after such a split, it's true enough.
So under your model, if a population splits off, whether by isolation or natural selection or some other mechanism, in such a way that certain alleles are lost, the frequency with which a given allele may manifest might change, but no new alleles will be created. 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).
All other things being equal, if fur color doesn't contribute in any meaningful way to a rabbit's' ability to produce more rabbits, then the frequency of a given allele in a population should be determined by whether it is dominant or recessive to the other alleles for that gene. However, if fur color does matter, then the frequency of alleles will be affected by the environment. So even if the allele for tan fur is recessive to all the others, if having tan fur starts to provide a reproductive advantage, then its presence in a population will increase and you'll start seeing more tan rabbits than before. Remember, dominance is only a relationship between alleles. It has nothing to do with whether or not it codes for a "desirable" trait or is a "strong" or "weak" allele. If tan fur is an advantage, then you will inevitably see more tan rabbits than black rabbits, since tan rabbits will reproduce more often.
That's Natural Selection. In this regard, your model appears to be in agreement with the standard biological model. 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.
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.
I'll pause here once again to see if I'm misrepresenting your position in any way, or if you disagree with any new material that I've presented.

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 263 by Faith, posted 04-11-2010 2:35 PM Faith has replied

Replies to this message:
 Message 267 by Faith, posted 04-11-2010 5:51 PM ZenMonkey has not replied
 Message 271 by Faith, posted 04-12-2010 12:23 AM ZenMonkey has not replied
 Message 281 by Admin, posted 04-12-2010 7:48 AM ZenMonkey has replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 312 of 851 (555135)
04-12-2010 11:05 AM
Reply to: Message 281 by Admin
04-12-2010 7:48 AM


Re: Dominant and recessive and so forth.
Admin writes:
Would you like to continue the discussion with Faith in a one-on-one over at Reduction of Alleles by Natural Selection (Faith and Bluejay Only)?
If Faith is interested, I would like to finish walking through the thought experiment that I've begun with her here, and it would be less noisy if we did so over on the other thread. I don't know nearly as much biology as Bluejay does, however, so I might need correction and back-up from time to time. (Heck, lyx2no has to fix my math most of the time even if I'm just figuring volume or area.) If folks are willing to use this thread to thwack me if I go astray over on the other one, then I'm game.

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 281 by Admin, posted 04-12-2010 7:48 AM Admin has replied

Replies to this message:
 Message 318 by Faith, posted 04-12-2010 2:22 PM ZenMonkey has not replied
 Message 320 by Admin, posted 04-12-2010 2:44 PM ZenMonkey has not replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 361 of 851 (555988)
04-16-2010 4:09 PM


Restoration of diminished alleles.
Faith and I had the following exchange in Message 65 of the Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only) thread.
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.
As I understand it so far, in Faith's model every species has a set number of alleles for any given gene locus, and thus a finite set of possible traits arrising from those alleles. In the simple example I've been using I posit a situation in which a single gene controls fur color in rabbits, with a pool of alleles coding for black fur, grey fur, etc. It seems logical to me that if fur color is a genuinely neutral trait giving no reproductive advantage, then the prevelance of any given fur color in a population will be primarily determined by the dominance relationships among the various alleles. In other words, if 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, then under normal, essentially static conditions there should be relatively more black rabbits than all the others, more browns than greys, and that tan rabbits will be the rarest. That's what the standard Mendelian d/r chart leads me to think anyway. 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. I believe that this would be the general statistical distribution of fur color in any group of rabbits with these four alleles. 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.
My assertion is this: if some accident temporarily reduced the numbers of a certain allele - say that there was a volcanic erruption that just happened to bury almost but not quite all of the black rabbits - then eventually that allele would re-establish itself in the general population in the same relative position it had before. To me, this simply follows out from the math, that with nothing else to stop it, the Black allele would simply by virtue of its being dominant to all the others, have to regain its position after a sufficient number of generations, even if you started with just one surviving black rabbit.
Given the limits I've described, am I right, or am I missing something here?
It now occurrs to me that a second, perhaps even more vital question arrises from this situation. 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?
For the sake of the argument, please stick with the given limits and don't drag in partial dominance, mutation, natural selection with regard to this trait, or other concepts that lie outside the realm of this hypothetical. I really believe that this should work out just by virtue of the math, but I'd like to be sure.

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 362 by nwr, posted 04-16-2010 4:25 PM ZenMonkey has replied
 Message 364 by PaulK, posted 04-16-2010 5:11 PM ZenMonkey has not replied
 Message 365 by Dr Adequate, posted 04-16-2010 5:23 PM ZenMonkey has replied
 Message 371 by Faith, posted 04-16-2010 6:18 PM ZenMonkey has not replied

  
ZenMonkey
Member (Idle past 4770 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:
 Message 362 by nwr, posted 04-16-2010 4:25 PM nwr has seen this message but not replied

  
ZenMonkey
Member (Idle past 4770 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 seen this message but not replied

  
ZenMonkey
Member (Idle past 4770 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 replied

Replies to this message:
 Message 387 by nwr, posted 04-17-2010 12:27 AM ZenMonkey has not replied
 Message 389 by Dr Adequate, posted 04-17-2010 1:21 AM ZenMonkey has not replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 484 of 851 (556834)
04-21-2010 9:48 AM
Reply to: Message 481 by Percy
04-21-2010 8:59 AM


Re: Mutations Revisited 2
Percy writes:
How many closely related species are different in only their allele frequencies? Squirrels? Finches? Cats? Any species at all?
I'd be highly interested in this as well. The ability of speciation arising simply out of allele differences is a part of the train of thought I'm following on the other thread. Probably not the most important part, but one I'd like to be clear on.
And if anyone sees me making any egregious errors in my train of thought over there, please let me know.
Edited by ZenMonkey, : Clarity.

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 481 by Percy, posted 04-21-2010 8:59 AM Percy has seen this message but not replied

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 759 of 851 (559807)
05-11-2010 6:13 PM


Not a summation either.
I am also, in a strange, perverse way, going to regret seeing this thread close. I feel even more remorseful that Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only) will have to close, too. If nothing else, it showed me how really ignorant I was about genetics myself. What I was attempting to to was to go step-by-step with Faith through her argument to see how it held up just in terms of its own logic. How well that was going to work will now never be known. It does look as if this thread went on to cover a lot of the ground that I suspected I was going to get to as well.
My thanks to Bluejay for sustaining that debate as long as he did. I was not worthy to follow him.

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

  
ZenMonkey
Member (Idle past 4770 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


Message 760 of 851 (559810)
05-11-2010 6:17 PM
Reply to: Message 758 by Percy
05-11-2010 5:51 PM


Re: Not really a summation
I'm pretty sure that that's what Faith was going to have to fall back on: some magical form of universal polyploidy that was present at the Creation Event and has now utterly vanished (exept maybe in bacteria, with their "packed genome").
Edited by ZenMonkey, : Clarity.

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 758 by Percy, posted 05-11-2010 5:51 PM Percy has seen this message but not replied

  
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