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Author Topic:   Reduction of Alleles by Natural Selection (Faith and ZenMonkey Only)
Blue Jay
Member (Idle past 141 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 61 of 87 (555125)
04-12-2010 9:13 AM
Reply to: Message 60 by Admin
04-11-2010 6:10 AM


Re: The Road from Here
Hi, Admin.

Obviously, I've completed my part of this debate, but it feels like it just ended without any real closure.

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

Ultimately, the thread's fate should be Faith's choice, since I won't be participating anymore, either way.


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

Darwin loves you.


This message is a reply to:
 Message 60 by Admin, posted 04-11-2010 6:10 AM Admin has acknowledged this reply

Replies to this message:
 Message 62 by ZenMonkey, posted 04-12-2010 4:23 PM Blue Jay has not yet responded

  
ZenMonkey
Member (Idle past 1954 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


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


Re: The Road from Here
Bluejay writes:

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

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


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

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


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

  
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 63 of 87 (555208)
04-12-2010 4:34 PM


I'd like to see Bluejay's summary and ZenMonkey's opening post before I decide what I want to do.
    
ZenMonkey
Member (Idle past 1954 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


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


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

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

Faith writes:

ZenMonkey writes:

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

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

I should be more precise here. If an allele for a particular trait is actually elimnated, then under your model it would necessarily never reappear in a given population. Whether by natural selection, genetic drift, of some other cause, once the last black fur allele is gone, then there will never be another black rabbit. If that's the case, then it should also be very likely if not certain that alleles for certain traits have already gone extinct for any number of populations, and we might never know about it. For example, there could very well have been a population of red-furred rabbits at one time, but that allele has now gone extinct. (Of course, I'm referring to rabbits having red fur in the same way that other creatures have red hair, not fire engine red.)

Faith writes:

ZenMonkey writes:

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

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

So we should agree if fur color is a neutral trait that confers no reproductive advantage, then if some accident reduces the frequency of a given allele at some point, but doesn't eliminate it, then it's highly probable that eventually the allele will reestablish itself in the population and regain its former standing, so to speak. This assumes that the event that reduced the allele was only a one-time effect and not a continuous pressure. Otherwise we have a case of natural selection over-riding dominance in establishing the frequency of an allele. But so long as an allele still exists, and so long as it remains neutral and not subject to natural selection pressures, then the dominance relationships of the various alleles should be the prime determinant of how often the traits they produce will appear in the population.

Faith writes:

ZenMonkey writes:

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

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

So just to be clear, if your model says that genetic diversity will always decline and never increase, then we should see a consistant decline not only in traits but also in species. There can't be any new species, only changes brought about by the elimination of alleles and shifts in their frequency in various populations. Or do you believe that by eliminating certain traits you can create a daughter population that can no longer breed with its parent? How much change do you think the elimination of traits can bring about?

It appears that you agree with at least some of the Theory of Evolution, that the frequency of alleles in population does change over time and that natural selection as well as genetic drift and other causes, are what change that frequency. Where you appear to disagree is that alleles can be changed in such a way that new, viable alleles and new traits can ever be produced.

Your position also assumes the standard conditions of Young Earth Creationism. For one, the creation event must have been relatively recent for there still to be so many species of plants and animals to still be around. If the creation event happened in the distant past, then it seems likely that most species that ever existed have all become extinct, and that many surviving species were once more diverse then they are today. Also, it assumes that all the forms of life that we do observe were created in essentially the same form in which we see them today. No significant change can have taken place, as the the number of alleles for any given trait were all established from the beginning. This also leads me to conclude that you believe that the Earth as we see today is in essentially the same condition as when it too was first created. Had there been any significant environmental changes in the past then that would likely have resulted in natural selection pressures that would have eliminated far more species than we see today, as there would be no way for new species to emerge in response to those changes.

Am I still correct in my understanding of your views?


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

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


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

  
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 65 of 87 (555249)
04-12-2010 7:45 PM
Reply to: Message 64 by ZenMonkey
04-12-2010 5:40 PM


Re: Picking up from the other thread.
There are a couple of points in this last exchange that I'd like to clarify, and then we can push on.

...I should be more precise here. If an allele for a particular trait is actually elimnated, then under your model it would necessarily never reappear in a given population. Whether by natural selection, genetic drift, of some other cause, once the last black fur allele is gone, then there will never be another black rabbit.

Yes.

If that's the case, then it should also be very likely if not certain that alleles for certain traits have already gone extinct for any number of populations, and we might never know about it. For example, there could very well have been a population of red-furred rabbits at one time, but that allele has now gone extinct. (Of course, I'm referring to rabbits having red fur in the same way that other creatures have red hair, not fire engine red.)

Yes, quite possible. I almost made this point myself in answer to your remark about purple fur. Yes, there could be other fur colors and patterns that no longer appear in any population of rabbits anywhere.

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.

This assumes that the event that reduced the allele was only a one-time effect and not a continuous pressure. Otherwise we have a case of natural selection over-riding dominance in establishing the frequency of an allele.

OK, you apparently have in mind a dominant, the dominant black fur then. OK, if it's a one-time event that reduced it and it's dominant, eventually it would come back but it could be a VERY long time, longer than most of my scenarios allow for. {abe} Seems most likely to me that whatever selection pressure reduced it wouldn't let up. But the main thing to say here is that there are many ways variability can be increased, such as by populations rejoining, gene flow resuming, and previously reduced alleles being restored over time as in this example -- and of course also if mutations do anything remotely like you all believe they do -- but when all that is going on you aren't getting the phenotypic definition that is along the way to speciation, which is the necessary stepping stone to macroevolution, which therefore is prevented from happening.

But so long as an allele still exists, and so long as it remains neutral and not subject to natural selection pressures, then the dominance relationships of the various alleles should be the prime determinant of how often the traits they produce will appear in the population.

If no selection pressure, yes.

So just to be clear, if your model says that genetic diversity will always decline and never increase, then we should see a consistant decline not only in traits but also in species. There can't be any new species, only changes brought about by the elimination of alleles and shifts in their frequency in various populations.

Not at all. The opposite. This is the WAY you get new species is my claim.

It is the processes that reduce genetic diversity that bring out new traits, which is the essence of evolution after all, and there is no reason except accidental factors (size of population, environmental benevolence) that these processes must stop until the genetic diversity is depleted to such an extent that further evolution is at an end. At that point most likely you will have speciation. Any population that reaches that extremity will probably be a species, but the trend alll along has been in that direction. It's not too often reached, fortunately, though some populations do fine in that condition (the seals) and there will most likely be plenty of other lines of the same organism it's closely related to that aren't close to speciation, but that is the direction that selection, drift, migration, and so on ALWAYS take populations according to my understanding.

Or do you believe that by eliminating certain traits you can create a daughter population that can no longer breed with its parent? How much change do you think the elimination of traits can bring about?

All the change needed for speciation , speciation based on genetic mismatch anyway, yes, but only from a population that is already genetically depleted, very likely the end population in a ring series as I have been presenting it, for instance. Otherwise you get populations with new variations and SOME reduced genetic diversity but not necessarily extreme.

The argument is that there is a continual trend in this direction in all populations, though very slow in any that remain numerous AND various, even apparently not operating at all in some of those cases, and only seen at the extremes after many selecting, reducing or isolating events OR a one-time major event like a bottleneck or founder effect.

It appears that you agree with at least some of the Theory of Evolution, that the frequency of alleles in population does change over time and that natural selection as well as genetic drift and other causes, are what change that frequency.

Of course. Evolutionists do valid science most of the time and are able to describe phenomena in a way one can work with, WHEN they aren't just assuming stuff like mutations that they can't prove. There is no problem with the mechanisms of change, it's the assumed and unproven claim of OPEN-ENDED change that is false.

Where you appear to disagree is that alleles can be changed in such a way that new, viable alleles and new traits can ever be produced.

Yes. Feel a need to qualify this a bit now just for a reminder that while I'm now convinced that if you ever get an occasional "beneficial" -- I prefer "normal" or "functioning" -- allele from mutation, it's only a chemical fluke, I started out accepting the creation of new alleles through mutation and I'm willing to go back to that position. It really doesn't matter at all what the source of variation is, the processes of reduction and selection that are necessary to forming new varieties, and speciation itself, will eliminate most of it. Because getting whole new breeds and populations with a particular character depends on this process of reduction.

Your position also assumes the standard conditions of Young Earth Creationism.

Actually I don't start from that assumption. I think it is important to emphasize this. I do not argue FROM myYEC position at all on this topic although many insist on assuming I do. The argument about reducing diversity to get new traits could come from any position at all.

I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path. ALL evolving paths would ultimately lead to that end, but they aren't all doing it at the same rate. It DOES of course seem like it would fit into a YEC framework better than any other.

For one, the creation event must have been relatively recent for there still to be so many species of plants and animals to still be around.

It would seem so, but as I said, although it appears to be most compatible with YEC dating, the argument doesn't derive from a particular notion of the age of the earth, it stands on its own. If you have a built-in cache of alleles that doesn't change, then it is all running out to speciation where it must stop. It's not derived from theory or belief, it's completely empirical and ought to be testable somehow or other.

I still claim that if you add in mutations you'll end up at the same point anyway, just delayed and by a more complicated route full of starts and stops, because you simply do not GET speciation without the reduction in genetic diversity that the operations that select and reduce and isolate bring about.

You can get variation without speciation with or without mutations, in populations that aren't changing much, but then you aren't getting the kind of evolution that could ever make a new species out of an old one; but if you have speciation which is essential to species-to-species or macroevolution then ironically evolution comes to a halt at that point. {ABE: I realize I have to add that while speciation is defined by the point at which interbreeding stops, in some cases where that occurs the new population(s) or species may still have quite a bit of variability left, so that evolution doesn't necessary stop there as I have been claiming -- I keep thinking too much of speciation at the end of a long train of population splits such as in ring species, but that isn't always the situation. It's still true that there is a trend of reduced genetic diversity with every population split or genetic drift and so on and you aren't ever going to get macroevolution from this process.}

Adding mutations at that point you have a new species also stops {ABE: Interferes with or prevents resumed} evolution. You'll get new traits, you'll get variation, but you won't get speciation so you won't get macroevolution. You have to have the selecting and isolating to get speciation and macroevolution and yet those processes ultimately prevent macroevolution from ever occurring.

If the creation event happened in the distant past, then it seems likely that most species that ever existed have all become extinct, and that many surviving species were once more diverse thAn they are today.

Yes. (corrected your "then" to a "than," pet peeve of mine)

Also, it assumes that all the forms of life that we do observe were created in essentially the same form in which we see them today.

No. It implies (not assumes) not extremely different but appreciably different life forms from which all we see today evolved, simply playing out their gene pools. There most likely has been an enormous variety in each species of which we still see quite a bit but nothing like there must have been in the past. At least sabre-tooths and house tabbies all together in the cat species for instance, giant forms and miniature forms and so on. All from the same built-in gene pool.

No significant change can have taken place, as the number of alleles for any given trait were all established from the beginning.

Oh but there had to have been an incredible wealth of genetic possibilities at the beginning that is not seen at all today, that produced incredible varieties over the millennia. Just take a look at the fossil record -- quite a collection of creative variations and adaptations of formerly thriving creatures, some of which we no longer see at all, but some obviously the ancestors of ours.

When I read that the bacterial genome is "packed" compared to that of most (all?) other species, because it has either little or no junk DNA (can't seem to find that clearly stated) I take that as a model for the original packed genome of every species, all sorts of great genetic possibilities we no longer see in the world for any of the higher animals, and the amount of junk DNA as a record of how much variation and adaptation has been lost in each.

This also leads me to conclude that you believe that the Earth as we see today is in essentially the same condition as when it too was first created.

Why? I don't get where you get these ideas out of my theory. In this case it may not be possible to read backward to the Creation, I'm not sure, so I do bring in my YEC assumptions:

Which are quite the opposite to what you expect. Starting with the Fall which introduced death which didn't previously exist and is what now determines that there is going to be an eventual end to all these genetic processes which otherwise would not have been the case. Without death there would have been a thousand times more marvelous variations of every species that live forever.

Also the Flood which broke up, sorted out and stratified the entire Earth -- which previously probably had a fairly uniform land mass like the other planets, and the Flood was accompanied or followed by by volcanic action and tectonic action and most likely meteoric showers as well, some or all of which may have contributed to the massive death in the Flood. And of course the Flood was a huge huge bottleneck that cut off enormous varieties of life from our modern world. Testimony to unimaginable diversity in living things before the Flood. Big changes. Nothing the same. The earth is a wrecked planet compared to what it was at the Creation.

Had there been any significant environmental changes in the past then that would likely have resulted in natural selection pressures that would have eliminated far more species than we see today, as there would be no way for new species to emerge in response to those changes.

Well, you have to assume an enormously large genetic capacity the farther back you go, to explain what we still see of the varieties still possible.

But again, new species (variations that can no longer interbreed) emerge ONLY in response to the selecting-isolating processes. That's my argument. You get new species ALONG WITH inability to further vary or speciate. Speciation is the result of these selecting processes.

Am I still correct in my understanding of your views?

Farther and farther from them.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : green edits


This message is a reply to:
 Message 64 by ZenMonkey, posted 04-12-2010 5:40 PM ZenMonkey has responded

Replies to this message:
 Message 67 by ZenMonkey, posted 04-13-2010 12:29 AM Faith has responded
 Message 75 by ZenMonkey, posted 04-17-2010 5:20 PM Faith has responded

    
Blue Jay
Member (Idle past 141 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 66 of 87 (555278)
04-12-2010 11:25 PM


Passing the Torch: End of the Bluejay Era
I've written up a brief synopsis of my arguments on this thread, as well as my assessment of Faith's arguments and where the debate sits at my departure. As always, I appear to have written too much, but I hope at least some people take the time to read it.

I entered this discussion trying to probe various points of Faith’s argument, looking for where miscommunication and misunderstanding came in. It didn’t take long before we were talking only about mutation: it's quite obvious to everybody that this is where Faith takes exception to the evolution paradigm.

However, we talked about mutation from two angles: (1) whether or not mutations can actually produce new alleles and (2) whether or not the production of new alleles by mutation would make a difference in Faith’s scenario anyway.

I attempted to explain the difference between the genotype and the phenotype of a mutation, and Faith claimed to understand this. In her defense, I think she did know the difference, but just hadn’t spent enough time considering it to realize that her arguments were failing to distinguish them. She repeatedly asked me to provide evidence of a beneficial mutation having occurred, but I initially resisted, because I thought it was more important to get her to accept the general concept of mutations being different from phenotypes before I got into discussing the data. In retrospect, I’m not sure I agree with my reasoning there.

I decided to first focus on the second angle: whether or not the existence of beneficial mutations would make a difference for Faith’s model. The combination of the paper about the human mutation rate and the data about the elephant seal populations was enough to show that: If each human has an average of 0.6 new alleles due to mutation, then the current population of elephant seals (100,000) should harbor somewhere in the neighborhood of 60,000 alleles that did not exist before the bottleneck (this math assumes that all seals living today are first-generation descendants of seals that survived the bottleneck, so it does not take into account all the seals that had lived and died between the bottleneck and now). From the standpoint of the population, that is a lot of new material to work with.

Since Faith continued to push for evidence of beneficial mutations, I presented her with a couple of papers showing the emergence of antimicrobial resistance in bacteria by random mutation. These were studies that really couldn’t be argued with: they started with a known allele, found variation in the population for the trait controlled by the gene, showed that the variation had was associated with genotypic variation, and demonstrated that the mutant allele outperformed the original allele. I was then able to compare it with other mutations that had happened the same way, but had had negative effects on the phenotype, and thereby, to finally show that a “diseased” phenotype is not necessarily tied to a “diseased” process.

Faith acknowledged that this was evidence of a mutation that was beneficial for the bacterium. This is the power of empirical evidence at work. This evidence actually caused Faith to make a re-evaluation of her argument. Unfortunately, she ultimately decided that the “beneficial” mutation was to be interpreted from an anthropocentric point of view.

She did not learn from her mistake of conflating the consequences of something with the nature of its cause, and has instead settled on a decision of pretty much the same fallacious logical formula. If anything, I have at least shown that this is no longer a safe assumption. Yet, Faith still wants it to be the null hypothesis, the one that we take as true when the evidence can be viewed as consistent with multiple explanations.

This is not how logic or science works: we take the safe routes, the paths of least resistance. This means our null hypothesis is always that what we have demonstrated in one organism applies equally well to any other organism, unless there is good reason to suspect that it doesn’t apply outside of the demonstration organism. “Bacteria are very different from higher organisms,” does not constitute a “good reason.” Nor does the relative amount of “junk DNA.” Yet, these are the only reasons that Faith could come up with for why we should work under the assumption that the data found in bacteria do not apply to “higher organisms.”

My assessment is that Faith needs to confront the math: because she has acknowledged that beneficial mutations can happen (even though she has decided that the word should be redefined to only refer to benefits to “higher organisms”), she can only challenge the idea by arguing that they are too infrequent to be of consequence to genetic diversity. She needs to show that there is no situation under which the rate of allele addition by mutation can outpace the rate of natural selection. Yet, convincing her that this is the case has been the entire thrust of the three threads she has participated in on this subject: I sincerely hope that ZenMonkey is able to accomplish what the rest of us have not been able to do.


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

Darwin loves you.


Replies to this message:
 Message 68 by Faith, posted 04-13-2010 3:59 AM Blue Jay has not yet responded

  
ZenMonkey
Member (Idle past 1954 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


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


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


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

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


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

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

  
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 68 of 87 (555308)
04-13-2010 3:59 AM
Reply to: Message 66 by Blue Jay
04-12-2010 11:25 PM


Re: Passing the Torch: Yeah but Faith still gets her say.
Well, if Bluejay is going to post on this thread, although it's called a Summary, I'm going to answer it even if it involves me in two conversations. That's better than twenty anyway. I should have realized that I'd regard it as controversial.

I entered this discussion trying to probe various points of Faith’s argument, looking for where miscommunication and misunderstanding came in. It didn’t take long before we were talking only about mutation: it's quite obvious to everybody that this is where Faith takes exception to the evolution paradigm.

Yes, but as far as the case I'm trying to make goes, that didn't have to come up; as far as the way the debate went, it was of course inevitable that it came up. I started out quite willing to make my case with mutations in the mix, I was simply assuming mutations, but when post after post nobody was getting what I was trying to say and kept insisting that mutations refuted my argument, finally I gave in to the pressure to take the side trip into mutations, very reluctantly.

In the discussion about mutations I was confronted with a fact I'd put on the back burner while pursuing my argument: that the evidence for mutations is so scanty and yet evolutionists talk about them as if they were fact, and I realized how many times I've been bamboozled by that claim into simply assuming that mutations happen -- despite past experience with just how scanty the evidence actually is.

And that got me outraged on behalf of all who try to understand the problems in this debate or just understand what is claimed by evolution, and I realized that this claim IS fraud, IS deceit. And that became the focus of my side of the discussion at that point --for better or worse and probably worse as it put off even further getting into the meat of my main argument. Which I still claim SHOULD be arguable with or without mutations.

However, we talked about mutation from two angles: (1) whether or not mutations can actually produce new alleles and (2) whether or not the production of new alleles by mutation would make a difference in Faith’s scenario anyway.

I attempted to explain the difference between the genotype and the phenotype of a mutation, and Faith claimed to understand this. In her defense, I think she did know the difference, but just hadn’t spent enough time considering it to realize that her arguments were failing to distinguish them.

This is simply mystifying. I've been making CONSTANT use of the distinction from the first time I put together this argument -- it's of the ESSENCE of the argument. All this can show is that I'm still not getting it across, but the idea that I don't know the difference in ANY sense is evidence of some real miscommunication. But I see you say I don't know the difference with respect to mutations -- as opposed to what?

She repeatedly asked me to provide evidence of a beneficial mutation having occurred, but I initially resisted, because I thought it was more important to get her to accept the general concept of mutations being different from phenotypes before I got into discussing the data. In retrospect, I’m not sure I agree with my reasoning there.

Oh brother. If this is what you were doing no wonder we were not getting anywhere.

But really I was more insisting that there IS no evidence of mutations that make real living normal useful alleles, than I was demanding that you produce some.

I decided to first focus on the second angle: whether or not the existence of beneficial mutations would make a difference for Faith’s model.

Considering that nobody, including you, ever really got what my model is about, the idea of figuring out whether mutations would make a difference or not is premature to say the least.

The combination of the paper about the human mutation rate and the data about the elephant seal populations was enough to show that: If each human has an average of 0.6 new alleles due to mutation, then the current population of elephant seals (100,000) should harbor somewhere in the neighborhood of 60,000 alleles that did not exist before the bottleneck (this math assumes that all seals living today are first-generation descendants of seals that survived the bottleneck, so it does not take into account all the seals that had lived and died between the bottleneck and now). From the standpoint of the population, that is a lot of new material to work with.

That's fine, but since my model had not yet even been described in a way I could accept, that wasn't any point that I could start applying such information to it.

Since Faith continued to push for evidence of beneficial mutations, I presented her with a couple of papers showing the emergence of antimicrobial resistance in bacteria by random mutation. These were studies that really couldn’t be argued with: they started with a known allele, found variation in the population for the trait controlled by the gene, showed that the variation had was associated with genotypic variation, and demonstrated that the mutant allele outperformed the original allele. I was then able to compare it with other mutations that had happened the same way, but had had negative effects on the phenotype, and thereby, to finally show that a “diseased” phenotype is not necessarily tied to a “diseased” process.

it is possible that at that point of the discussion there were so many loose ends left behind in my mind, and your argument so unrelated to anything that I thought important, that I didn't give it the attention it deserves. But I'm not sure about that at all. In any case I can't take bacteria as models for universal genetic rules as you all do.

When you go to bacteria for your argument it feels like some sort of trick, especially when the focus to that point had been on genetic diseases in human beings. Oh I know perfectly well that genes should behave the same no matter what creature's genome they're in, but bacteria are really different from higher organisms and especially in their genome which apparently has lots more possibilities than the genomes of most other living creatures, so extrapolating from bacteria to humans really should not be admissible in my opinion. If there is no evidence of mutations making ordinary alleles for higher animals -- in any numbers that could suggest it's a habit of mutations to do so at least -- then that lack of evidence is important and gives support to MY side of the argument.

Faith acknowledged that this was evidence of a mutation that was beneficial for the bacterium. This is the power of empirical evidence at work. This evidence actually caused Faith to make a re-evaluation of her argument.

The most positive thing in this statement is the recognition that poor mentally deficient Faith can understand empirical evidence when she sees it.

But it did not cause me to reevaluate my argument. I wanted to acknowledge you'd made your case although it didn't carry any weight with me at that point, and I realized that was bad timing for you since you'd had to work hard to assemble your evidence and I did feel bad about that. But it didn't cause me to reevaluate my argument because I suspect the validity of bacteria as examples anyway, and that suspicion had consolidated at that point, due to the basic genomic differences between them and most other living things. But ALSO I was still reacting to my recognition of the duplicity of science in claiming mutations are fact on the basis of nothing but assumption -- and bacteria. All that had just come out in our discussion and I was in the middle of a general disgust against science at that point.

So I offered you cookies, knowing none of it was your fault and that I'd unfortunately interfered with your hard work.

Unfortunately, she ultimately decided that the “beneficial” mutation was to be interpreted from an anthropocentric point of view.

NO. I decided that bacteria cannot serve as evidence for what happens in higher forms of life BECAUSE THEY ARE DIFFERENT GENETICALLY. That is NOT an "anthropocentric" point of view.

She did not learn from her mistake of conflating the consequences of something with the nature of its cause,

I made no such mistake. Leaving bacteria aside, in sexually reproducing creatures mutations are mistakes in the DNA duplication process -- you want to assume this is just normal and it produced all the known alleles and goes on producing them (athough we'd have a terrific glut of them at this point if that were true as we have plenty in most cases already and the effort of mutations can only be redundant) and I merely insist on the RECOGNIZED fact that it's a MISTAKE, and that in biological terms is a DISEASE PROCESS. And the actual EVIDENCE in hand is that mutations have produced thousands of genetic diseases in humans, which certainly is a result consistent with a process that is a known mistake, and otherwise seems to mostly replace functioning alleles with nonfunctioning or noncoding or at least inscrutable lengths of nucleotides, gobbledygook, which sure sounds like another case of a disease process at the genetic level no matter what scientists say to try to make out it's all normal biology, normal genetics. I make no mistake myself in arguing that there is a correspondence between the two levels, I'm actively claiming the scientist's attempt to turn a mutational sow's ear into an allelic silk purse is some sort of delusion they indulge themselves in.

and has instead settled on a decision of pretty much the same fallacious logical formula. If anything, I have at least shown that this is no longer a safe assumption. Yet, Faith still wants it to be the null hypothesis, the one that we take as true when the evidence can be viewed as consistent with multiple explanations.

Sorry, I stopped following you here.

This is not how logic or science works: we take the safe routes, the paths of least resistance.

This is to deny the heavy bias that leads to hallucinating mutations in variations without evidence for them, to assuming open-ended variations without the ability to prove it, to insisting that mutations are a normal process just because the theory requires it although the facts of how they are formed belie it.

This means our null hypothesis is always that what we have demonstrated in one organism applies equally well to any other organism, unless there is good reason to suspect that it doesn’t apply outside of the demonstration organism. “Bacteria are very different from higher organisms,” does not constitute a “good reason.” Nor does the relative amount of “junk DNA.” Yet, these are the only reasons that Faith could come up with for why we should work under the assumption that the data found in bacteria do not apply to “higher organisms.”

Yeah, poor old mentally deficient Faith.

My assessment is that Faith needs to confront the math: because she has acknowledged that beneficial mutations can happen (even though she has decided that the word should be redefined to only refer to benefits to “higher organisms”), she can only challenge the idea by arguing that they are too infrequent to be of consequence to genetic diversity. She needs to show that there is no situation under which the rate of allele addition by mutation can outpace the rate of natural selection.

The very fact that you use the term "rate" means you don't get what I'm trying to prove. But anyway. Sure, I'll do my best with all the mutations you can throw at me.

Yet, convincing her that this is the case has been the entire thrust of the three threads she has participated in on this subject: I sincerely hope that ZenMonkey is able to accomplish what the rest of us have not been able to do.

Trying to convince me that mutations refute my argument HAS been the thrust of all this effort here, despite the fact that NOBODY has ever really grasped the argument.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


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Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 69 of 87 (555410)
04-13-2010 1:24 PM
Reply to: Message 67 by ZenMonkey
04-13-2010 12:29 AM


Re: Picking up from the other thread.
Hello Zen,
I was rereading my post to you this morning and had to put in some changes in the yellow section, some of which I did in orange to make it easier for you to find.
Faith
This message is a reply to:
 Message 67 by ZenMonkey, posted 04-13-2010 12:29 AM ZenMonkey has not yet responded

    
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
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Message 70 of 87 (555437)
04-13-2010 3:29 PM


deleted
deleted Side Trip on Mutations.
I realized this would only clutter up the thread.
But I've saved it for later.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


    
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 71 of 87 (555496)
04-14-2010 1:04 AM


I really don't see how you can get breeds, varieties, species, new traits, new phenotypes, unless a population undergoes reduction of diversity.

You all assume it's possible.

Zen Monkey, could you spell out exactly how this could happen? Add in your mutations at whatever point you like and take it from there. How do you get a dog breed by making sure lots of genetic diversity is in the mix? I mean LOTS. I mean by not protecting the animal from breeding with whatever it likes so diversity will increase. Same as no natural selection or genetic drift or migration happening in nature. Isn't that what mutations would do?

Then if selection DOES occur it will just reduce them as I'm claiming in order to produce the specific breed. In the end you HAVE to have reduced diversity or you don't get a new breed/species/variety/phenotype/ set of traits.

I know you're going to say you have BOTH mutations and selection, but please, YOU do the math and explain it to me how it is possible to get new breeds or varieties without genetic depletion. Please.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


    
Faith
Member
Posts: 25319
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 72 of 87 (555690)
04-15-2010 1:01 AM



Zen Monkey:
Assuming you are still planning on coming back -- with of course THE definitive argument against mine -- while I'm waiting I occasionally reread things and this time ended up adding some edits in green. Mostly just being repetitive I'm afraid but letting you know in case it matters.
Faith

By the way, thought I'd add that I appreciate the way you've approached this so far, with all the questions to try to clarify what I'm saying. And it did bring out places where you did get a different idea than I intended so it's been fruitful.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


Replies to this message:
 Message 73 by Admin, posted 04-15-2010 9:04 AM Faith has not yet responded
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Admin
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Message 73 of 87 (555750)
04-15-2010 9:04 AM
Reply to: Message 72 by Faith
04-15-2010 1:01 AM


Well, this isn't fair. ZenMonkey can take as much time as he likes, but it isn't fair to you that you have no posting permissions over in Biological Evolution while awaiting a response here, so I'm going to restore them for now.


--Percy
EvC Forum Director

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ZenMonkey
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Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


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


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

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

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


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

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


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

  
ZenMonkey
Member (Idle past 1954 days)
Posts: 428
From: Portland, OR USA
Joined: 09-25-2009


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


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

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

Faith writes:

ZenMonkey writes:

So we should agree if fur color is a neutral trait that confers no reproductive advantage, then if some accident reduces the frequency of a given allele at some point, but doesn't eliminate it, then it's highly probable that eventually the allele will reestablish itself in the population and regain its former standing, so to speak.

I don't see why this is "highly probable." It COULD regain its former standing, but it doesn't seem to me to be "probable" that it would come back to that extent from its highly reduced position. I would think something would have to favor it, some sort of selection for that to happen -- yes, reproductive advantage of some sort.

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

quote:
Populations do not gain new alleles from the random sampling of alleles passed to the next generation, but the sampling can cause an existing allele to disappear. Because random sampling can remove but not replace an allele, and because random declines or increases in allele frequency will influence the expected allele distributions for the next following generation, genetic drift drives a population towards genetic uniformity over time. When an allele reaches a frequency of 1 (100%) it is said to be "fixed" in the population and when an allele reaches a frequency of 0 (0%) it is lost. Once an allele becomes fixed, genetic drift comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time

So up to this point it appears that you agree in large part with modern biology: genetic drift will deplete alleles randomly and natural selection will deplete or promote alleles in response to environmental pressures. The effect of natural selection will obviously be more noticable for alleles related to traits that confer reproductive advantage. Neutral traits will be more affected by drift, unless certain alleles for genes that code for neutral traits are linked somehow to other genes that are not neutral.

The answer to my question of whether an allele that has been reduced but not eliminated will regain its former frequency in a population turns out to be no. The distribution of alleles in one generation is only dependent on distirbution in the prior generation, all else being equal. So if we lose a lot of black rabbits and a lot of the relatively dominant B alleles from our population, it's more likely than not that the B allele is not going to make a comeback. There are only so many times that a given carrier for that particular allele can produce offspring, after all, so even if B is highly dominant with regard to the alleles for other fur colors, it can only get out into the gene pool a limited number of times. Again, I note that in this case we're focusing on neutral traits only. I believe that we both agree that an allele for a trait that does confer a reproductive advantage has a much greater chance of regaining its status in a population after some stochastic event reduces its numbers at some point.

We also agree that under your model, once a given allele has disappeared, there is no mechanism by which to restore it. If you get rid of the B allele for black fur, then there is no way to have any more black rabbits.

My second question over at the other thread had to do with recessive genes. I asked:

ZenMonkey writes:

Given all of the above, it is also inevitable that the Tan allele would have to manifest itself from time to time in every generation, even if it were recessive to all the others? Is there any way that we can have this Tan allele hiding in the gene pool but never actaully producing any tan rabbits?

This didn't get discussed as much though nwr said this at Message 387:

nwr writes:

If the population size is very small, that could happen. With any significant population size, the probability is so low that you would not expect it. If it was observed that the recessive trait never appeared, that would probably be taken as evidence that it is fatal.

I have always assumed this to be true; no allele can be so recessive that it never manifests at all. Sooner or later you have to have two parents both contribute the recessive allele. If they didn't, if an allele were both relatively recessive and also rare, I deem it highly likely that drift would remove it eventually if it were neutral. On the other hand, if it did affect reproductive success, then natural selection would keep it from being rare if the related trait was beneficial or eliminate it if the trait was disadventagous. Do you want to contest this, or can we both accept that there are no hidden alleles, only relatively rare and relatively common ones? It seems obvious to me that diploid organisms, by definition, carry only two alleles for each gene and no more, and donate one and only one to any individual offspring it produces. There is no other place for an allele to hide. And yet you say this (emphasis mine):

Faith writes:

I start with the argument itself, the idea that you have a built-in complement of alleles, age unspecified, that are available in all species for making a huge array of interesting variations, most of which never get expressed in this world, and do it simply by isolating portions of the gene pool, which is what ultimately brings about "speciation" and the inability to vary further along a particular genetic path.

I'd like to understand your reasoning here. Let's go back to the rabbits, but before we do, I want to ask you about another aspect of your model.

I can't find where you've stated this explicitly, but your model implies both a fixed pool of alleles and fixed genes for every species. That is to say, there is a single "correct" arrangement of genes for every species - one for frogs, one for rabbits, one for humans, and so on - and that deviation from that genome does not produce new species but only genetic disease. In other words, alleles are the possible varieties for each gene, but that the genome for any given speicies is invariant. If you go by the crude model of DNA as a recipe, certain alleles allow you to substitue one similar ingredient for another - cashews for peanuts, for example - but that you can't just eliminate nuts from the recipe and still claim that you have the same recipe and thus the same critter. Your model seems to require a unique genome for each species, which can't be altered in any meaningful way, with alleles producing a set number of variations for the genes in each genome. Please let me know if this doesn't follow from your model.

Now back to the rabbits.

It seems to me that if you start with a single pair, you can have at most a total of four alleles for any given gene. Let's try a heterozygous black rabbit carrying a relatively recessive Brown (r) allele with its relatively dominant Black (B) one, thus: Br. Give it a grey rabbit that also has the relatively recessive Tan (t) alllele along with its relatively dominant Grey one (G), thus: Gt. If we mate Br with Gt, we have four possible outcome for each offspring for that mating: Bg, Bt, Gr, and Rt. Thus the odds are 50% that a mating will produce a black rabbit, at 25% chance that you get a grey, and a 25% chance that you'll have a brown rabbit.

Though your odds are 50/50 that any given offspring will carry the recessive Tan allele, you won't see any tan rabbits from this particular mating. However, if you have two rabbits from this mating (or another pair with the same genetic complement, makes no difference) who have the recessive T allele, you get something like this: Br, Bt, Rt, and Tt. Now all of a sudden you have a 25% chance of producing a tan rabbit, and the T allele also has a 75% chance of being transmitted, increasing the odds even more for its survival and manifestation.

And, I also note that there is no way under your model for you to ever see a white rabbit in any subsequent generation. There is no place for the W allele to be transmitted. The T allele is effectively hidden for now, but W is nowhere to be found and will not, under your model, ever show itself. Do you agree with this as well?

Obviously, if this pair didn't happen to produce any Bt or Rt offspring, or if such offspring never managed to reproduce, then you're gotten rid of all possible tan rabbits as well, am I right? After all, it's impossible for every offspring of every organism to live long enough to reproduce. Some must live long enough to do so if the species is to keep from going extinct, but not all of them. The point is one that you've made yourself many times, I think: in a situation in which no new viable alleles can arise, genetic diversity will only decrease and never increase. I believe that you've also come to the position that even in a model in which a mutation can produce something viable - a new W allele that can produce a white rabbit, for example - that the number of such mutations will never be significant enough for white rabbits to gain a place in the general population. Or are you simply going to stick with the idea that there is no mutation that can change the G allele into a W or something similar, and that mutations are only agents of genetic damage. This would be in agreement with the similar idea that no mutation can affect a genome in such a way that you can turn one species into another, equally viable species.

Oh, and I have one more question, just to be clear about another aspect of your model. Should any given rabbit, no matter what particular alleles it happens to have, be able to mate with any other rabbit? Its genome should be the same, after all, and the alleles should only be responsible for variation among various traits. It believe that it's still true that any given dog can mate with any other dog, no matter how different they look. Agreed, you may have to use artificial insemination to breed dogs that are radically different in size, but otherwise, there is no barrier that I know of that would make dog varieties actually different species, unable to interbreed.

I've made up for my absence with a rather long post, so take your time replying to it. I appreciate the chance to explore how your model works.

Edited by ZenMonkey, : No reason given.

Edited by ZenMonkey, : Repairing faulty sentence structure.


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

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


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

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

  
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