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Author Topic:   Natural Limitation to Evolutionary Processes (2/14/05)
Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 1 of 299 (185074)
02-14-2005 9:48 AM


When I posted here briefly a few years ago we creationists seemed to have the main problem of not being able to show the clear end point we claim must exist for the processes of evolution. Evolutionists claim these processes are open ended, creationists claim they are limited to the Kind or Species itself, these "processes of evolution" including natural selection, migration, genetic drift and mutation with some subcategories such as bottleneck and founder effect.
I was playing with the idea that the fact that some examples of speciation (such as the cheetah) demonstrate a severely limited genetic variability suggests that evolution reaches a built-in ending point. Since then I haven't thought about these questions much but when they came up again recently in another forum I became even more convinced that this is the case.
Originally that discussion came up around the PBS series on Evolution in the Fall of 2001. I just reviewed it. http://EvC Forum: Review: PBS's Evolution -->EvC Forum: Review: PBS's Evolution I got a couple of nice responses from Mark24 to my contribution but since I never came back I didn't know they were there until now. I hope I will answer them in this.
In that discussion I complained about the PBS program's defining as evolution what a creationist would regard as simple variation within a species, which in the two cases given were brought about by natural selection. 1) Genetically variable bacteria are attacked by an antibiotic which kills off all but one gene type which is resistant to it. This type then proliferates and becomes a new headache for the human race who have been trying to get rid of the whole species for some time now. What happens? The program calls this an example of evolution. What it is, and Mark24 acknowledged this, is merely natural selection working in pre-existing genetic types. 2) A type of newt is threatened by a snake in a certain locale and as the snake wipes out much of the population of the newt the newt develops a poison that kills the snake or causes it to avoid the poisonous newts. This was also called evolution in the PBS series but again all it is is the natural selection of a more adaptable type of newt by the predator snake. In turn the snake had to evolve immunity to the poison. All this is not evolution, merely natural selection from among given genetic possibilities. The genetic capacity for a poison type was already present in the species, but natural selection brought it out in response to environmental threat.
Now, in every case of natural selection the genetic variability of the species is reduced. The new adapted population has less capacity to change. In some cases there may still be quite a bit of variability left, but it is nevertheless less than the previous population's ability to adapt, and if the process continues to yet another adaptation in this poisonous newt its ability to change or "evolve" will be reduced even further. Ultimately it is conceivable that a branch of the newt population could become like the cheetah with such fixed alleles that no change in any direction is possible. The same can be said of the bacteria population. It may have reached the limit of its adaptability.
It seems to me that this can be said about all the "processes of evolution," with the exception of migration into a population and mutation. Migration out of a population leaves both the remaining populations genetically reduced. This is what happened with Darwin's Galapagos turtles. They are both likely to develop traits peculiar to themselves from their reduced allotment of alleles, and unless the process continues may remain able to crossbreed, but the point is that the process of migration reduces the variability of the group, or to put it another way, reduces the frequencies of alleles in the population.
The same with genetic drift, bottleneck and founder's effect, in fact in this case the effect is particularly dramatic. In migration a population splits into two or more, but both populations may live on, as in the case of the Galapagos turtles. In genetic drift some portion of the population dies and the resultant loss of genetic variability in the surviving portion cannot be reclaimed by remixing as could conceivably occur in migration. In bottleneck and founder effect the population reduction is even more drastic. The new populations develop new traits but their genetic adaptability has been sharply reduced.
Now all these processes are called evolution and are said to lead to speciation. In fact the Hardy-Weinberg principle was formulated to explain why the processes of reduced genetic diversity don't occur faster. Populations may remain relatively static, NOT evolving. When any of the "processes of evolution" occur they are no longer in "Hardy-Weinberg equilibrium" but are "evolving."
However, all these "processes of evolution" lead to reduced genetic variability. In fact, I believe this is a rule: the processes of speciation ALWAYS result in reduced genetic variability, at the extremes to the point of absolute inability to vary in any direction at all. This effect is acknowledged in many things I've read on the subject, because the extremes often lead to concern about extinctions, but its theoretical implications seem to have been overlooked: How can evolution proceed via processes that inevitably lead to the inability to evolve?
I left out two of the processes of evolution, migration into the population and mutation. Migration into the population from a previously split-off group does increase genetic variability and thus the overall health of the group, but I don't see how you can get conditions for evolution out of this situation. If anything the population tends to homogenize over time and remain relatively stable. But THEN if any of the OTHER processes occur, killing off a portion of the group either by natural selection or genetic drift, or separating the group into smaller groups again, the same processes of "evolution" and "speciation" will occur as above -- and always with reduced genetic variability at each change.
As for mutation, Mark24 suggested that mutation increases evolution potential, balancing out the effect of the loss of genetic variability through these processes, and claimed that mutation occurs at an amazingly rapid rate. I need to look into that, but for the moment I would just consider the possibility that beneficial mutations are occurring in all populations. What happens then? Either the population absorbs the new characteristics, homogenizes and remains relatively stable over time as in the case of immigration of new genetic material, or it is subjected to "processes of evolution" that reduce its genetic variability as in all the above cases.
I suppose you could postulate that enormous numbers of mutations over time could transform a species into another species without any of the other "processes of evolution" occurring, but this isn't how the theory goes: all the emphasis is on the processes that reduce variability as THE processes by which evolution, that is, speciation, occurs.
I believe that these facts show that evolution simply does not occur past certain given limits that are built into the genome of the species, and that this constitutes the "barrier" to further evolution into new species that creationists have believed must be there. It seems that every process that produces change, evolution, speciation, while doing so also produces less and less ability to change or evolve or speciate, and there's no way you can get evolution past the far fringes of a given species out of such processes.
According to creationism, there is abundant variability and adaptability built into each species that gradually plays out over time. This is not evolution. It is often called "microevolution" but since that term implies a "macroevolution" I tend to avoid it. But that is what it refers to, intraspecies variability which can be quite enormous. Unfortunately in our fallen world these processes lead to death and ultimately even species extinction, the opposite of open-ended evolution. In the original world of Eden they would simply go on to produce wonderful varieties.
This message has been edited by Faith, 02-14-2005 09:58 AM
Edited by Faith, : To add date of thread to title
Edited by Faith, : No reason given.
Edited by Faith, : Changed the title back; the creationist angle is clear in the posts.

Replies to this message:
 Message 3 by PaulK, posted 02-14-2005 10:31 AM Faith has replied
 Message 4 by Wounded King, posted 02-14-2005 12:36 PM Faith has replied

AdminNosy
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Message 2 of 299 (185078)
02-14-2005 10:14 AM


Thread moved here from the Proposed New Topics forum.

PaulK
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Joined: 01-10-2003
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Message 3 of 299 (185084)
02-14-2005 10:31 AM
Reply to: Message 1 by Faith
02-14-2005 9:48 AM


quote:
As for mutation, Mark24 suggested that mutation increases evolution potential, balancing out the effect of the loss of genetic variability through these processes, and claimed that mutation occurs at an amazingly rapid rate. I need to look into that, but for the moment I would just consider the possibility that beneficial mutations are occurring in all populations. What happens then? Either the population absorbs the new characteristics, homogenizes and remains relatively stable over time as in the case of immigration of new genetic material, or it is subjected to "processes of evolution" that reduce its genetic variability as in all the above cases.
I think you need to check your reasoning on this point.
If you accept for the sake of argument that new variation is entering the population through mutation then what happens depends on the rate at which new variations appear against the rate at which variation is lost through selection. Only if the rate at which variation is lost is greater than the rate at which new variation enters the population will there be a net decrease in variation.

This message is a reply to:
 Message 1 by Faith, posted 02-14-2005 9:48 AM Faith has replied

Replies to this message:
 Message 5 by Faith, posted 02-14-2005 5:37 PM PaulK has replied

Wounded King
Member (Idle past 110 days)
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 4 of 299 (185121)
02-14-2005 12:36 PM
Reply to: Message 1 by Faith
02-14-2005 9:48 AM


1) Genetically variable bacteria are attacked by an antibiotic which kills off all but one gene type which is resistant to it. This type then proliferates and becomes a new headache for the human race who have been trying to get rid of the whole species for some time now. What happens? The program calls this an example of evolution. What it is, and Mark24 acknowledged this, is merely natural selection working in pre-existing genetic types.
This may well be the case in the wild but it is possible to perform similar selection for antibiotic resistance artificially on a population grown from a single bacterium which is known not to have antibiotic resistance. Fora an example see...
Evolution of drug resistance in experimental populations of Candida albicans.Cowen LE, Sanglard D, Calabrese D, Sirjusingh C, Anderson JB, Kohn LM.
J Bacteriol. 2000 Mar;182(6):1515-22.
Adaptation to inhibitory concentrations of the antifungal agent fluconazole was monitored in replicated experimental populations founded from a single, drug-sensitive cell of the yeast Candida albicans and reared over 330 generations. The concentration of fluconazole was maintained at twice the MIC in six populations; no fluconazole was added to another six populations. All six replicate populations grown with fluconazole adapted to the presence of drug as indicated by an increase in MIC; none of the six populations grown without fluconazole showed any change in MIC. In all populations evolved with drug, increased fluconazole resistance was accompanied by increased resistance to ketoconazole and itraconazole; these populations contained ergosterol in their cell membranes and were amphotericin sensitive. The increase in fluconazole MIC in the six populations evolved with drug followed different trajectories, and these populations achieved different levels of resistance, with distinct overexpression patterns of four genes involved in azole resistance: the ATP-binding cassette transporter genes, CDR1 and CDR2; the gene encoding the target enzyme of the azoles in the ergosterol biosynthetic pathway, ERG11; and the major facilitator gene, MDR1. Selective sweeps in these populations were accompanied by additional genomic changes with no known relationship to drug resistance: loss of heterozygosity in two of the five marker genes assayed and alterations in DNA fingerprints and electrophoretic karyotypes. These results show that chance, in the form of mutations that confer an adaptive advantage, is a determinant in the evolution of azole drug resistance in experimental populations of C. albicans.
It also depends upon what definition of evolution you are working under, if you are simply thinking in terms of changes in allelic frequency then selection on 'pre-existent'variation is a perfectly legitimate example of evolution. You are obviously thinking of evolution as something generating novelty, but even with that point of view the experimental evidence shows that antibiotic resistance can arise as a novel mutation in a non-resistant population.
What is very important is not to make the mistaken assumption that this is neccessarily being put forward as a response to the antibiotic. Even in the experiment I referenced the antibiotic is added after the single progenitor has expanded over many generations, to introduce variation to the population, before the antibiotic is introduced. Depending on the type of antibiotic it is certainly not impossible for resistance to arise de-novo in the presence of the antibiotic, but such a demonstration is not required to show evolution in action.
The genetic capacity for a poison type was already present in the species, but natural selection brought it out in response to environmental threat.
This is a tricksy statement, from an evolutionary perspective simply using DNA as its genetic material is sufficient to produce the 'genetic capacity' for poison no matter what the species.
TTFN,
WK

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 Message 1 by Faith, posted 02-14-2005 9:48 AM Faith has replied

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Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 5 of 299 (185242)
02-14-2005 5:37 PM
Reply to: Message 3 by PaulK
02-14-2005 10:31 AM


Considering rapid rate of mutation
quote:
As for mutation, Mark24 suggested that mutation increases evolution potential, balancing out the effect of the loss of genetic variability through these processes, and claimed that mutation occurs at an amazingly rapid rate. I need to look into that, but for the moment I would just consider the possibility that beneficial mutations are occurring in all populations. What happens then? Either the population absorbs the new characteristics, homogenizes and remains relatively stable over time as in the case of immigration of new genetic material, or it is subjected to "processes of evolution" that reduce its genetic variability as in all the above cases.
quote:
I think you need to check your reasoning on this point.
If you accept for the sake of argument that new variation is entering the population through mutation then what happens depends on the rate at which new variations appear against the rate at which variation is lost through selection. Only if the rate at which variation is lost is greater than the rate at which new variation enters the population will there be a net decrease in variation.
First, are you accepting the rest of what I said, that is, that except for mutation and immigration all the "evolutionary processes" produce decreased variability, or less ability to change, which would seem highly incompatible with the theory of evolution?
As for a very high rate of beneficial variations changing the picture here, assuming that such occur for the sake of argument as you propose, which I believe is highly doubtful, even if huge quantities of new adaptive alleles were to enter the population [at least as problematic a possibility as the idea of God's intervention I would think], natural selection and the other evolutionary processes are going inexorably to operate in the direction of decreasing variability among them. There would be more adaptability possible but with each new selection of a survival-enhancing or adapted trait comes decreased variability. Even if the process continues, and more variability enters into each new reduced population it is still subject to the same processes of reduction of variability -- and if that were in reality the case and an abundance of adaptive possibilities were constantly occurring in all populations then why would anybody worry about extinctions? So given the scenario you propose I think the usual process of reduced variability will produce adaptive or neutral changes in the phenotype as usual, but it will simply take longer to play itself out than if a given complement of alleles belongs to the Species at the outset, which is the creationist view. In other words it doesn't ultimately matter whether you have twenty adaptive possibilities in a population or 20,000, as the processes of evolution are going to relentlessly reduce their variability over time in either case.
Of course you may also imagine that among all these beneficial mutations are changes in the direction of something outside the characteristics of the Species if you are going to get "macroevolution" out of this formula, BUT at any point that you have a new population that has been created by all the processes that inexorably reduce variability you nevertheless have created a situation that has less ability to evolve beyond itself and again is self-limiting at SOME point WAY before any further evolution could possibly occur. Also this doesn't fit the time frame evolution posits, as macroevolution changes would have to be considered to be going on within populations at all times rather than accumulated in slow increments over unimaginable aeons of time.
This message has been edited by Faith, 02-14-2005 17:38 AM
This message has been edited by Faith, 02-14-2005 17:49 AM

This message is a reply to:
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Replies to this message:
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 Message 143 by Archer Opteryx, posted 08-16-2006 6:10 AM Faith has replied

Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 6 of 299 (185336)
02-14-2005 9:28 PM
Reply to: Message 4 by Wounded King
02-14-2005 12:36 PM


Novel mutations?
quote:
1) Genetically variable bacteria are attacked by an antibiotic which kills off all but one gene type which is resistant to it. This type then proliferates and becomes a new headache for the human race who have been trying to get rid of the whole species for some time now. What happens? The program calls this an example of evolution. What it is, and Mark24 acknowledged this, is merely natural selection working in pre-existing genetic types.
This may well be the case in the wild but it is possible to perform similar selection for antibiotic resistance artificially on a population grown from a single bacterium which is known not to have antibiotic resistance. Fora an example see...
What you are doing is changing the subject. I presented the scenario of the "evolution" of a bacteria population in answer to the PBS "Evolution" program's claim that it represents evolution by mutation. The answer is no, it is merely natural selection from pre-existing genetic possibilities, "classical natural selection" as Mark24 put it three years ago. In fact the diagram given in the program even showed the existence of the adaptive type in the starting population, which was the only type left after the antibiotic killed off the rest. Yet they called this evolution, meaning mutation. It is not mutation. The same was said about the "evolution" of the newt, but again the potential for a poisonous kind was already in the population, merely selected by the snake. I find this confusion in many discussions of evolution. I have to assume the program had scientific consultants so how explain this kind of elementary confusion?
As for your example of resistance to an antibiotic in a population grown from a single bacterium, I see no reason to suppose this was the result of any novel processes, but of changes that naturally occur, just as in the above examples, having to do with genetic variability built into a single bacterium, however that happens. Your point that "the antibiotic is added after the single progenitor has expanded over many generations, to introduce variation to the population before the antibiotic is introduced" shows the expectation of variation under such circumstances. Assuming such variations are beneficial or at least not lethal implies this is not mutation, but business as usual for bacterial genes. Novel beneficial mutation would imply something nearly mystical, like the introduction of changes by a beneficent power from outside wouldn't it? But I would assume that what is going on simply follows the pattern of what bacteria were patterned to do. Besides the pre-antibiotic variation that was established, the fact that four separate genes were ultimately affected in the acquisition of resistance to the antibiotic also suggests quite a bit of variability built into the original code.
(By the way I'm not a scientist and it would help if you would keep the scientific jargon to a minimum. I don't know what MIC means, or the labels of the different kinds of genes, but I think I've grasped the general point in any case).
quote:
It also depends upon what definition of evolution you are working under, if you are simply thinking in terms of changes in allelic frequency then selection on 'pre-existent'variation is a perfectly legitimate example of evolution. You are obviously thinking of evolution as something generating novelty, but even with that point of view the experimental evidence shows that antibiotic resistance can arise as a novel mutation in a non-resistant population.
I'm using the definition of evolution you can find at most biology websites and at Talkorigins.com, "Changes in gene (allele) frequencies in a population over time." In fact I have been using this definition in a sense as an argument against the idea of novel mutations as having much if anything to do with evolution, as PBS misrepresented the situation. There are multiple allelic possibilities for many genes in many species, which provide for perfectly normal variation in the species without introducing anything novel. They obey Mendel's laws. I've discovered that you can get the most lucid understanding of these processes from animal breeders rather than scientists. They seem to know how many different genes are involved in the production of different colors and patterns of coats in dog breeds for instance, and how these can combine to produce desired results in offspring. This is all genetic business as usual, involving no novel mutations. Novel mutations would be unpredictable in any case, but the business of breeders is prediction.
quote:
What is very important is not to make the mistaken assumption that this is neccessarily being put forward as a response to the antibiotic. Even in the experiment I referenced the antibiotic is added after the single progenitor has expanded over many generations, to introduce variation to the population, before the antibiotic is introduced. Depending on the type of antibiotic it is certainly not impossible for resistance to arise de-novo in the presence of the antibiotic, but such a demonstration is not required to show evolution in action.
I would suggest that "for resistance to arise de-novo in the presence of the antibiotic" definitely flirts with mystical processes outside the normal workings of nature. If one could count on such happy interventions in any species whatever we could stop worrying about death and extinctions altogether it seems to me.
quote:
The genetic capacity for a poison type was already present in the species, but natural selection brought it out in response to environmental threat.
This is a tricksy statement, from an evolutionary perspective simply using DNA as its genetic material is sufficient to produce the 'genetic capacity' for poison no matter what the species.
Again, the PBS program (probably a NOVA but I don't remember) presented the situation as if the adaptation were the result of novel mutation, while I see no reason to assume that it's any more than a genetic potential for a poisonous type being allowed to be expressed phenotypically when great numbers of the population have been killed.
I don't know what you mean about DNA's own ability to produce poison, but this implies a completely other scenario than either PBS's or mine which I'd need you to explain. In any case, the poison type didn't occur in the population until it had been drastically reduced by natural selection, and apparently it is not a novel mutation but a built-in factor in any case.
To get back to my own topic however, when you say that "if you are simply thinking in terms of changes in allelic frequency then selection on 'pre-existent' variation is a perfectly legitimate example of evolution" I agree as far as "microevolution" is concerned, as I go on to point out that all the "processes of evolution" that bring about these changes in fact lead to reduced genetic variability which is inconsistent with the idea of "macroevolution" over time.
I wasn't "obviously thinking of evolution as something generating novelty" except to answer the implications in some statements that that is what some believe evolution is. In any case, as I answered Paulk, even on the remote possibility that such mutations do occur in great frequencies, the populations they occur in are nevertheless subject to the same "evolutionary processes" which inevitably lead only to decreased evolutionary potential, which defeats the whole theory of evolution. IMHO of course.

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Replies to this message:
 Message 7 by crashfrog, posted 02-14-2005 9:33 PM Faith has replied
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crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 7 of 299 (185337)
02-14-2005 9:33 PM
Reply to: Message 6 by Faith
02-14-2005 9:28 PM


The answer is no, it is merely natural selection from pre-existing genetic possibilities,
But they design the experiment so that the population is decended, clonally, from one individual - what's called a "monoculture." Since bacteria are haploid, we know that one individual can have at most one allele for every gene.
So if genetic variants are being selected for or against in the mature population, we know that those variants arose through mutation. So we know that mutation is occuring. Selection among mutated variants is, of course, evolution. Your analysis is quite inaccurate.
Besides the pre-antibiotic variation that was established, the fact that four separate genes were ultimately affected in the acquisition of resistance to the antibiotic also suggests quite a bit of variability built into the original code.
Yes. And that variability is expressed through the occurance of mutations.

This message is a reply to:
 Message 6 by Faith, posted 02-14-2005 9:28 PM Faith has replied

Replies to this message:
 Message 10 by Faith, posted 02-14-2005 9:53 PM crashfrog has replied

pink sasquatch
Member (Idle past 6100 days)
Posts: 1567
Joined: 06-10-2004


Message 8 of 299 (185340)
02-14-2005 9:35 PM
Reply to: Message 5 by Faith
02-14-2005 5:37 PM


adaptation does not reduce variability
Hi Faith,
Even if the process continues, and more variability enters into each new reduced population it is still subject to the same processes of reduction of variability...
And it is still subject to the same processes of increases in variability. These rates of variability accumulation are traits like any other, and are selected for like any other trait. That is, if an organism reduces its rate of genetic variability accumulation, (as in the development of "perfect" DNA replicating mechanisms), it may be selected against in times of habitat change, while others of the species with "imperfect" replication may fare better.
...and if that were in reality the case and an abundance of adaptive possibilities were constantly occurring in all populations then why would anybody worry about extinctions?
There will always be instances where available genetic variation is not enough to prevent extinction in response to habitat change. This is not a problem for evolution, though, as you seem to suggest. Natural selection works by causing the death of unfit organisms - sometimes this happens at the species level.
As for a very high rate of beneficial variations changing the picture here, assuming that such occur for the sake of argument as you propose,...
Just to be clear here, PaulK said nothing about beneficial variation in his post, he only wrote of increases and decreases in variation. Every new non-lethal variation has the potential to be beneficial, but that is up to selective forces.
In other words it doesn't ultimately matter whether you have twenty adaptive possibilities in a population or 20,000, as the processes of evolution are going to relentlessly reduce their variability over time in either case.
Individuals with those twenty "adaptive possibilities" will be more successful in the population, because they will have increased fitness. Importantly, this does NOT mean that the other 19,980 organisms in the population are going to immediately die off, causing a drastic reduction in variability. Rather, all of the organisms will continue to try to pass on their genes. The ones with the adaptations will be more successful, and will interbreed with other population members without the adaptations. Variability is NOT lost when a beneficial mutation is selected for in a large population; rather that mutation increases throughout the population, why the diversity of the rest of the genome remains intact.
As an example, a mutation appears in a frog that allows it greater fly-catching success. Since this frog is more fit than the rest of the population, he will sire more offspring than other frogs, causing the fly-catching-mutation to spread through the population the frog lives in. However, the spread of the fly-catching-mutation has no effect on the genetic variation contributing to other traits, like predator evasion or the immune system. The genetic variability remains intact.
Does that make sense?

This message is a reply to:
 Message 5 by Faith, posted 02-14-2005 5:37 PM Faith has not replied

pink sasquatch
Member (Idle past 6100 days)
Posts: 1567
Joined: 06-10-2004


Message 9 of 299 (185343)
02-14-2005 9:52 PM
Reply to: Message 6 by Faith
02-14-2005 9:28 PM


Novel mutations? YES!!!
I've discovered that you can get the most lucid understanding of these processes from animal breeders rather than scientists.
Did you know Darwin thought the same thing?
They seem to know how many different genes are involved in the production of different colors and patterns of coats in dog breeds for instance, and how these can combine to produce desired results in offspring. This is all genetic business as usual, involving no novel mutations. Novel mutations would be unpredictable in any case, but the business of breeders is prediction.
But novel mutations do occur in animal husbandry, and breeders select for these mutations despite the fact that they are unpredictable. There's a lot of money and fame to be earned in the world of animals breeding if you are the only person with a particular allele.
Check out the Nearly Hairless Club, devoted to hairless guinea pigs, whose hairlessness comes from a mutation that only recently appeared (in I think the last decade or so). Prior to that, the hairless "Baldwin" allele did not exist in any guinea pig population, anywhere. Baldwins have now achieved some measure of popularity, and thus the mutation has been selected for.
Are you really arguing that adaptive mutations never occur? If you are interested, there is the thread Beneficial Mutations which you may find interesting.

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Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 10 of 299 (185346)
02-14-2005 9:53 PM
Reply to: Message 7 by crashfrog
02-14-2005 9:33 PM


quote:
The answer is no, it is merely natural selection from pre-existing genetic possibilities,
But they design the experiment so that the population is decended, clonally, from one individual - what's called a "monoculture." Since bacteria are haploid, we know that one individual can have at most one allele for every gene.
So if genetic variants are being selected for or against in the mature population, we know that those variants arose through mutation. So we know that mutation is occuring. Selection among mutated variants is, of course, evolution. Your analysis is quite inaccurate.
Besides the pre-antibiotic variation that was established, the fact that four separate genes were ultimately affected in the acquisition of resistance to the antibiotic also suggests quite a bit of variability built into the original code.
Yes. And that variability is expressed through the occurance of mutations.
I get your point but it sounds awfully mystical that mutations simply show up out of the blue in order to provide resistance to the antibiotic. I don't understand the processes involved in single-cell reproduction but this kind of explanation just doesn't fit with scientific assumptions. Whatever it is that leads to resistance, or in fact to variation in the population at all from a single individual HAS to be pre-programmed, has to follow a Law of some sort, or we're out in la-la land. Perhaps this situation has to do with the definition of "mutation" -- I've certainly discovered that that is one malleable term. What about the fact that MOST mutations are acknowledged to be not beneficial in any way at all? How does resistance to the antibiotic develop in this population before something lethal to its existence develops given that mutations of all kinds are supposedly occurring apace?
In any case, I don't want to lose sight of my original observation which I see the next poster is going to address: the very processes that select the adaptive trait involve the reduction of genetic variability in the population, which is inconsistent with the overall theory of evolution. That is, no matter how the new strain of bacteria arrived, increasing variability temporarily, its selection involves a reduction in variability, and even if the increase in variability is enormous, the processes that select from it spell an end to the variability eventually. OR -- following out the assumption of exuberant mutations in all populations, how come the cheetah can't evolve further? It would seem to follow from such ideas that it could.

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crashfrog
Member (Idle past 1544 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 11 of 299 (185415)
02-15-2005 12:52 AM
Reply to: Message 10 by Faith
02-14-2005 9:53 PM


I get your point but it sounds awfully mystical that mutations simply show up out of the blue in order to provide resistance to the antibiotic.
No, they show up at random. The mutation is there before the antibiotic is introduced; it waxes and wanes in the population at random because there's no selection pressure on it yet. That's not the only mutation that is occuring, of course. All kinds of mutations are happening.
Absolutely nobody is proposing that the mutations show up on demand. That's Lamarkianism, not evolution.
How does resistance to the antibiotic develop in this population before something lethal to its existence develops given that mutations of all kinds are supposedly occurring apace?
At random, via mutation. Along with countless other traits.
Whatever it is that leads to resistance, or in fact to variation in the population at all from a single individual HAS to be pre-programmed
If it's random, how can it be pre-programmed? You can't program randomness, by definition. Even computers can't be programmed to be random - they have to look up numbers from a pre-generated random table.
The mutation for the antibiotic resistance is random; we know this because when we measure it in a population without antibiotic, the number of individuals with the gene increases and decreases at random. You can see this trend illustrated here:
Are Mutations Harmful?
The graph on this page is exactly what we would expect to see in a situation of random mutation.
Perhaps this situation has to do with the definition of "mutation" -- I've certainly discovered that that is one malleable term.
Not really. I think what's happening is that you see it applied to a number of different situations but you fail to understand how all the different situations are really the same. Mutation is simply when an organism has genetic sequences that it did not inheret from its parent(s).
the very processes that select the adaptive trait involve the reduction of genetic variability in the population, which is inconsistent with the overall theory of evolution.
It isn't inconsistent, though. But I like the way you're thinking about it. Evolution is like a dynamic balance between expanding variation via mutation and contracting variation via selection. The variation expands at random; the variation contracts in a way that is anything but random. The result are organisms adapted to their environment.
That is, no matter how the new strain of bacteria arrived, increasing variability temporarily, its selection involves a reduction in variability
Yes. But the reduction in variability is non-random; its a selection. The less fit variants are removed, and so the average fitness of the population increases. Variation expands from the center, but contracts from the bottom. That translates into an upward movement in regards to fitness.

This message is a reply to:
 Message 10 by Faith, posted 02-14-2005 9:53 PM Faith has not replied

PaulK
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Posts: 17838
Joined: 01-10-2003
Member Rating: 4.1


Message 12 of 299 (185422)
02-15-2005 2:31 AM
Reply to: Message 5 by Faith
02-14-2005 5:37 PM


Re: Considering rapid rate of mutation
No, I don't agree with everything you said - I CERTAINLY don't agree that genetic drift reduces variation (quite the opposite). Nor do I agree that the cheetah represents a normal outcome (the cheetah suffered a SEVERE genetic bottleneck - a population reduction so bad that extinction would be the normal outcome plus lesser bottlenecks trhough more recent hunting). I focussed on the one point I did since it was crucial to your argument and needed to be rethought.
Let us also be clear that I am not necessarily proposing a high rate of beneficial mutations. The rate of mutation requied only needs to be igh enough to maintain variation and neutral mutations will do - so long as they have a phenotypic effect. In neutral mutations that remain neutral or neutral mutations that become deleterious - or even mildly deleterious mutations will do, since their removal still accounts for part of the loss.
The real problem here however is that you are not addressing my point. Your whole argument depends on the assumption that the rate at which variation is lost must exceed th rate at which variation is introduced by mutation. You've offered no reason to beleive that the former rate is very high (although you claim that it is) or that the rates cannot balance. So I ask you again to reconsider your claim - and if you cannot support it accept that your argument lacks a foundation.

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 Message 5 by Faith, posted 02-14-2005 5:37 PM Faith has replied

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 Message 13 by Faith, posted 02-15-2005 8:39 AM PaulK has replied

Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 13 of 299 (185466)
02-15-2005 8:39 AM
Reply to: Message 12 by PaulK
02-15-2005 2:31 AM


Re: Considering rapid rate of mutation
quote:
No, I don't agree with everything you said - I CERTAINLY don't agree that genetic drift reduces variation (quite the opposite).
Sorry, this is absolutely known. ALL the processes that select out a portion of a population as a rule reduce the total allelic potential so that a reduced allelic potential, meaning reduced genetic variability, defines the smaller populations. Genetic drift is only one of the processes that does this, and it does it through the death of a part of a population which makes the reduction irreparable. Depending on the extent of the process the reduction may not be particularly noticeable, but the process nevertheless tends in the direction of reduction of allelic frequencies and therefore of genetic variability. NO WAY is it "quite the opposite" as you claim.
quote:
Nor do I agree that the cheetah represents a normal outcome (the cheetah suffered a SEVERE genetic bottleneck - a population reduction so bad that extinction would be the normal outcome plus lesser bottlenecks trhough more recent hunting).
I didn't say it was a normal outcome, I emphasized that it is at an extreme. Bottleneck is simply an extreme version of genetic drift. Nevertheless the cheetah is the normal expectable result of selection to that extreme. Selection processes always reduce allelic frequencies in a population, and at the extremes reduce them extremely.
The point is that this extreme is one very possible -- though extreme it is not an anomaly -- outcome of processes described as "processes of evolution" that lead to "speciation." This is correct, these processes DO lead to "speciation" -- this is how new types emerge in a population, by isolation of a portion of a population which reduces the allelic frequencies so that new allelic combinations come to the fore as old ones are eliminated or suppressed. The cheetah is one example of speciation at an extreme. The fact that its extreme loss of genetic variability makes it particularly vulnerable to extinction is crucial to my point -- this extreme end product of the very processes that lead to speciation and are called "processes of evolution" in fact demonstrates the opposite effect -- not evolution but potential extinction, not higher genetic potentials but lower. This demonstrates that there is a built-in limit to the processes of evolution, and that limit may be defined as the Species itself beyond which evolution is impossible.
That is, a Species starts out with a very great built-in potential for variation. (This variability is scattered throughout whole populations although I believe an assumption consistent with creationist theory is that at one time individual members of Species contained within themselves much more potential for variation, probably in the form of more gene loci for given traits -- the loss of such previous genetic richness could account for "junk DNA" which could simply reflect the death of previous genetic potentials in the genome, lost through many processes of selection).
The processes of variation (called "speciation" by evolutionists) proceed by selecting out portions of the built-in potential for expression in the phenotype. The process ALWAYS involves reduction of the frequency of alleles and of genetic variability because for new traits to come to the fore new allelic combinations are required and you don't get these unless other allelic expressions are somehow suppressed -- or unfortunately in some cases actually killed. This process of "speciation" works beautifully within the creationist model of variation limited to a Species, but it contradicts the evolutionist model of open-ended change.
quote:
I focussed on the one point I did since it was crucial to your argument and needed to be rethought.
Let us also be clear that I am not necessarily proposing a high rate of beneficial mutations. The rate of mutation requied only needs to be igh enough to maintain variation and neutral mutations will do - so long as they have a phenotypic effect. In neutral mutations that remain neutral or neutral mutations that become deleterious - or even mildly deleterious mutations will do, since their removal still accounts for part of the loss.
I may not be following you at this point, but my observation is that the processes that SELECT the variations REDUCE genetic variability and that this is the overall tendency in ALL processes of speciation or "evolution." I believe that much of what is called "mutation" is in fact merely pre-existing allelic potentials that come to the fore as combinations typical of the parent population are eliminated from the new population. That was clearly the case in the PBS example of the bacteria and the newt and I find the term used carelessly in similar contexts -- no new material is being added, it's that previously suppressed potentials are getting expressed. The resistant form of the bacteria were already present in the original population but did not express in the phenotype until the majority of that population was eliminated. Same with the poisonous newt.
quote:
The real problem here however is that you are not addressing my point. Your whole argument depends on the assumption that the rate at which variation is lost must exceed th rate at which variation is introduced by mutation.
I believe in actual reality this is simply factual. If variability were being introduced at any observable rate whatever, there would never be a genetically stable population. In any relatively stable population you simply do not see an increase in variability which is what would seem to be implied by your statement. Shouldn't observable changes just be occurring from generation to generation if phenotypically expressable mutations did in fact occur at any noticeable rate? They simply do not. (They do not in populations that reproduce sexually, at least. Your example of the bacterium introduces an element that is outside the context here, but does suggest a capacity for variation that is contained within the bacterium itself. Sexually reproducing populations (deer, bears, raccoons, kangaroos, marmots, mice) do not demonstrate this abundance of increasing variability which I would think should be expected according to your claim). (The only remotely similar process would be immigration in which new genetic potentials are added and through generations produce new phenotypes, even a totally new character to the whole population -- but this is nothing more than the REintroduction of allelic potentials, not anything truly new.)
But very observable changes DO occur through the processes of selection which are what bring about new varieties, or "speciation" by concentrating certain allelic potentials at the expense of others in an overall reduction of genetic variability. This IS the process by which new "species" or types come about, in a word REDUCTION. This part of evolutionary theory is abolutely correct.
quote:
You've offered no reason to beleive that the former rate is very high (although you claim that it is) or that the rates cannot balance. So I ask you again to reconsider your claim - and if you cannot support it accept that your argument lacks a foundation.
I believe you are probably using the term "mutation" to describe what are really pre-existing potentials in a gene pool. The whole idea of an increase in variability is a fiction and the only source of such a misimpression that I can see is the misnaming of normal variations as mutations.
This message has been edited by Faith, 02-15-2005 08:42 AM
This message has been edited by Faith, 02-15-2005 08:53 AM

This message is a reply to:
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PaulK
Member
Posts: 17838
Joined: 01-10-2003
Member Rating: 4.1


Message 14 of 299 (185469)
02-15-2005 8:52 AM
Reply to: Message 13 by Faith
02-15-2005 8:39 AM


Re: Considering rapid rate of mutation
Genetic drift is NOT a selective process. So what is "absolutely known" about selective processes simply does not apply.
And you're simply wrong that genetic bottlenecks represent a form of selection. A bottleneck is caused by a redution in the population to a low number - whether it is selective or not. The YEC view of Noah's Flood represents a massive bottleneck for all affected species.
And it is absolutely daft to insist that species start out with a huge amount of potential for variation. More likely they start out with comparatively little variation and variation accumulates as the population expands.
And this is also badly wrong:
quote:
If variability were being introduced at any observable rate whatever, there would never be a genetically stable population
This essentially denies that genetic drift happens at all ! Alternatively you could consider the alternative that stabilising selection generally removes new variations INSTEAD of existing variability.
BTW perhaps you would like to clarify what you mean by "pre-existing potentials". It appears to refer to the variations already present - which would be a clear misrepresentation of my point since I expressly refer to mutation as adding new variations.

This message is a reply to:
 Message 13 by Faith, posted 02-15-2005 8:39 AM Faith has replied

Replies to this message:
 Message 15 by Faith, posted 02-15-2005 9:09 AM PaulK has not replied

Faith 
Suspended Member (Idle past 1521 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 15 of 299 (185473)
02-15-2005 9:09 AM
Reply to: Message 14 by PaulK
02-15-2005 8:52 AM


Re: Considering rapid rate of mutation
quote:
Genetic drift is NOT a selective process. So what is "absolutely known" about selective processes simply does not apply.
Funny it's categorized on so many biology sites as a "process of evolution" then. I myself am pointing out that all those processes (with the exception of immigration and mutation) are processes of selection. For heaven's sake it's obvious. It selected out the cheetah. It selected out the northern elephant seals. All a bottleneck is is an extreme form of genetic drift. I've found THAT on umpteen biology websites too.
quote:
And you're simply wrong that genetic bottlenecks represent a form of selection. A bottleneck is caused by a redution in the population to a low number - whether it is selective or not. The YEC view of Noah's Flood represents a massive bottleneck for all affected species.
That is true, and it most certainly IS a form of selection. What on earth can you be thinking? Noah and his family were selected out of all human types to propagate and only their genetic potentials were preserved out of the entire previous human population. Their genetic potentials were obviously severely reduced from the previous. Darwin's Galapagos turtles were selected by isolation from the parent population on the mainland. Whatever isolates a portion of the gene pool is selection. What on earth is your definition of "selection" anyway?
quote:
And it is absolutely daft to insist that species start out with a huge amount of potential for variation. More likely they start out with comparatively little variation and variation accumulates as the population expands.
You have the evolutionist assumption. I am trying to introduce the creationist assumption. Your assumption is not borne out by the facts. Increasing variation is a fiction. All new types are formed from a reduction in genetic potentials.
quote:
And this is also badly wrong:
If variability were being introduced at any observable rate whatever, there would never be a genetically stable population.
This essentially denies that genetic drift happens at all !
Excuse me??? It sounds like YOU are denying that a genetically stable population happens at all!!
quote:
Alternatively you could consider the alternative that stabilising selection generally removes new variations INSTEAD of existing variability.
BTW perhaps you would like to clarify what you mean by "pre-existing potentials". It appears to refer to the variations already present - which would be a clear misrepresentation of my point since I expressly refer to mutation as adding new variations.
I'm DISAGREEING with your view not representing it. What you call mutation I believe is really the expression of pre-existing allelic potentials, as exemplified in the discussion of the PBS example of the bacteria and the newt.
I think my conversation with you has ended as you seem to be making no effort whatever to follow what I'm saying.

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Replies to this message:
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