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Author Topic:   What is the mechanism that prevents microevolution to become macroevolution?
Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 136 of 301 (346385)
09-04-2006 9:11 AM
Reply to: Message 122 by Faith
09-02-2006 11:00 PM


Re: allozymes and other stuff
Why is showing divergence of relevance to our discussion?
Because they are discussing divergeance in genotype. We're not talking here about phenotypical differences - they're using 16s and mtDNA sequence differences between the populations to show that genetically these populations are diverging. Some of them, indeed, as in the second article I linked to, are very different from each other. Not just 'cause one population has different stripe patterns, or whatever.
Why is showing greater genetic divergence across greater distance of relevance to our discussion?
Well, for one thing, the greater the geographic distance between the populations, the less gene flow there is - which calls into question your contention that the differences seen are due only to recombination or some kind of skewed frequency distribution. In addition, the most distant populations (from each other) contain novel alleles not found in the populations closer to each other, which leads to the question: "Where did these sequences come from?".
PLEASE point to where you or this abstract have shown how genetic diversity is increased.
How about the very first line of the abstract?:
quote:
The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations.
AND...
We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was resampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern).
The full article goes on to discuss - in some detail - the reasoning behind this. Since the full article isn't on-line (unless you have a subscription), you can see a similar set of research in the PNAS article I provided (which is available free). I can also provide other, similar, references if it makes you feel any better. The point is molecular/genetic level studies of diverging populations (incipient speciation) show genotype differences that simply cannot be accounted for by changes in frequency distribution of pre-existing alleles. These are not hypothetical examples, but examinations of real-world populations.
The mere existence of one identifiable mutation would not prove that increased genetic diversity caused the divergence, and nothing you have said shows that reduced genetic diversity which produces new phenotypes is not the explanation.
You stated things along these lines several times, so I'll ask you again: how does "reduced genetic diversity" create "new phenotypes"? This contention is so completely counterintuitive that I'm half convinced I'm missing something in what you're trying to say.
The abstract is too technical for me to read.
So, actually reading the research is probably out of the question? But you won't take my word for what the articles say when I try and use simpler terms to explain it? That being the case, I ask you again "Where do we go from here?"

This message is a reply to:
 Message 122 by Faith, posted 09-02-2006 11:00 PM Faith has replied

Replies to this message:
 Message 142 by Faith, posted 09-04-2006 2:29 PM Quetzal has not replied
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Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 137 of 301 (346389)
09-04-2006 9:40 AM
Reply to: Message 121 by Faith
09-02-2006 10:15 PM


Re: On predictions and tests.
OK, I guess I missed that. Perhaps he is right, perhaps whole genes are lost, at least in some speciation events.
If you think he's right, perhaps you can pick up his dropped gauntlet and provide one, single, solitary real-world example where this has occurred?
I'd love to but it's very hard in the same way it is hard for scientists to come up with examples of all the bazillion mutations they assume to be the driving force of evoluation, and even harder of course for us nonscientists because we have to depend on your data, and without the technical knowledge, galling though that is to all concerned. I hope you will forgive us but this is simply the reality of the EvC debate unless more scientifically knowledgeable creationists come along.
If this is the case, perhaps it would be better for you to hold off on critiquing research you seem to be admitting you don't understand? Or even forebearing to argue against the conclusions of the folks who are actually researching the subject - at least until the putative "scientifically knowledgeable creationist" appears?
You've put your finger on one of the most frustrating parts of the EvC debate. Someone who admits they don't understand the science and can't be bothered to learn it feels free to utterly dismiss its findings, and in the same breath refuses to accept someone else's simplified explanation. Very strange, and something I've never understood. Perhaps you can explain why this makes sense to you.
It's all theory at this point.
Perhaps, but if so it's "theory" (in the common-usage sense) based on absolutely nothing except imagination.
However, as I recall, you gave no examples of increasing genetic diversity at all, of phenotypic divergence but not increasing genetic diversity. You merely asserted that it was there, the same way you asserted that mutations were behind phenotypic divergence, without proving it.
No, I provided a simplified explanation of what the article contained, as you requested. The specific molecular data that led the researchers to their conclusions is contained in the article. This is kind of a corollary to the problem I mentioned above. It's perhaps a failing on my part that I can't see how to communicate the conclusions in terms you'll accept without providing the technical details you have stated repeatedly you don't understand. When you accuse me of failing to provide the technical details, in spite of the fact that they are contained in the reference, but when any kind of technical detail is provided you state you don't understand them, I'm afraid we have a terminal case of (as so eloquently expressed in the movie "Cool Hand Luke"), "a failure to communicate".
I'm open to suggestions.
See? As if "increasing divergence" is some kind of evidence against me, although this is exactly what I'm saying is to be expected from my own scenario. Your evidence simply does not prove your explanation of this divergence in terms of increasing genetic diversity.
The studies aren't dealing with phenotype - they deal with the molecular and genetic data (i.e., genotype). When I speak of diversity, I'm talking genetic diversity based on molecular data - not phenotype.
If now you are changing the subject to decrease in genome size, how easy would it be to identify the death of a gene?
I'm not the one making the claim. Ask MJ - it's his assertion. You tell me...

This message is a reply to:
 Message 121 by Faith, posted 09-02-2006 10:15 PM Faith has replied

Replies to this message:
 Message 139 by Faith, posted 09-04-2006 12:14 PM Quetzal has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 138 of 301 (346428)
09-04-2006 12:07 PM
Reply to: Message 135 by qed
09-04-2006 8:54 AM


Re: Sciencey stuff not a reply
Some of these definitions are pretty wide of the mark.
Specifically...
Allele: A chunk of dna responsible for ....
An allele is has 2 slightly different forms dependent on whether one is thinking of classical or molecular genetics.
A classical mendelian allele is simply one form of a mendelian gene. Alleles are alternative forms of specific genes and may be dominant or recessive in terms of the phenotypic traits they produce.
A moelcular allele is usually a genetic polymorphism where there are extant sequences in a population where the genetic sequence is different, often only in a single nucleotide. These need not neccessarily be in a classical molecular biology gene, i.e. in a region coding for production of a protein.
Divergence: The gradual seperation of a species into two non-interbreeding species.
Divergence has a lot of different usages and what you describe particularly is more appropriately described as incipient speciation or simply speciation. Divergence usually simply describes any differences in genetic or morphological traits between and group of organisms.
Devolution (Evo): A subset of evolution defined by semantics.
I have never actually come across anyone in evolutionary biology using the terms 'Devolution' or 'De-evolution'. By specifically searching for the term on pubmed I can still only find about 10 references and only a handfull use the term in a way which your definition would fit.
Junk DNA: Ok popular science has hijacked this term leading to a heap of confusion, when Eukaryote non-sex cellular dna is replicated the last chunk of the chromosome is not copied, theres a bunch of useless
DNA tagged onto the end and this gets slowly lopped off with each new
generation of cellular division.
You seem to be saying that Junk DNA is simply telomeric DNA. In fact the usage of 'junk' that you dismiss, for non-coding DNA with either no function or an as yet unknown function, is common in the scientific literature.
I think what you are trying to do is worthwhile but as far as clearing up the communication difficulties goes I fear you are more likely to exacerbate them with these particular definitions.
TTFN,
WK

This message is a reply to:
 Message 135 by qed, posted 09-04-2006 8:54 AM qed has replied

Replies to this message:
 Message 140 by qed, posted 09-04-2006 12:53 PM Wounded King has not replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 139 of 301 (346431)
09-04-2006 12:14 PM
Reply to: Message 137 by Quetzal
09-04-2006 9:40 AM


Re: On predictions and tests.
If now you are changing the subject to decrease in genome size, how easy would it be to identify the death of a gene?
I'm not the one making the claim. Ask MJ - it's his assertion. You tell me...
Actually, I doubt he made the assertion that every speciation involves the loss of a gene or genes, which was your claim in your Message 108. Kindly reference this.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 137 by Quetzal, posted 09-04-2006 9:40 AM Quetzal has replied

Replies to this message:
 Message 141 by Quetzal, posted 09-04-2006 1:09 PM Faith has replied

qed
Inactive Member


Message 140 of 301 (346443)
09-04-2006 12:53 PM
Reply to: Message 138 by Wounded King
09-04-2006 12:07 PM


Re: Sciencey stuff not a reply
Cheers for that, you're quite right. Though some of the definitions "divergence" in particular were aimed at following the precedent set in this thread.
"Devolution" is a Creationist conception, you'll struggle to find it in any reputable journal. I ventured a guess based on Sciam's "Answers to Creationist nonsense" article. The main point is that Neodarwinism does not judge one form of creature to be better than another thus "Devolution" is meaningless.
The "Junk DNA" rant was pulled straight from the ramblings of my Genetics lecturer, i don't have the time or energy to track down a nickname but i don't think it matters so long as telomeres and introns are not confused as they seem to have been earlier in this thread.
How about 'TOE TAGs' for a new pet name?
Edited by qed, : No reason given.

This message is a reply to:
 Message 138 by Wounded King, posted 09-04-2006 12:07 PM Wounded King has not replied

Quetzal
Member (Idle past 5871 days)
Posts: 3228
Joined: 01-09-2002


Message 141 of 301 (346445)
09-04-2006 1:09 PM
Reply to: Message 139 by Faith
09-04-2006 12:14 PM


Re: On predictions and tests.
Actually, I doubt he made the assertion that every speciation involves the loss of a gene or genes, which was your claim in your Message 108. Kindly reference this.
Gimme a break, Faith. Unlike you and I, who have been talking about alleles in a population (although we disagree what that means), your hero specifically discussed speciation in the context of losing genes. See his msg 34. In that message he specifically tries to use the example of a population "containing 30,000 genes" which "loses" 10 genes. The whole paragraph there is pretty ridiculous anyway since a) we don't talk about X number of genes in a population - only in an organism - we talk about numbers of alleles; and b) you personally have about 30,000 genes in your own body, which renders his entire point pretty ludicrous.
I don't make stuff up, Faith. You of all people should know this by now. I would really appreciate it if you'd quit accusing me of it. Your error here was in trying to defend MJ's indefensible point - which actually detracts from what you're trying to argue. You don't NEED him - you are capable of making your own arguments quite well. Don't fall for the "any port in a storm" - especially since that port isn't very good.
Added by edit: I can't believe that's the only point in that entire post you chose to respond to.
Edited by Quetzal, : No reason given.

This message is a reply to:
 Message 139 by Faith, posted 09-04-2006 12:14 PM Faith has replied

Replies to this message:
 Message 143 by Faith, posted 09-04-2006 2:30 PM Quetzal has not replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 142 of 301 (346461)
09-04-2006 2:29 PM
Reply to: Message 136 by Quetzal
09-04-2006 9:11 AM


Why is showing divergence of relevance to our discussion?
Because they are discussing divergeance in genotype. We're not talking here about phenotypical differences - they're using 16s and mtDNA sequence differences between the populations to show that genetically these populations are diverging. Some of them, indeed, as in the second article I linked to, are very different from each other. Not just 'cause one population has different stripe patterns, or whatever.
The divergence of genotypes is the same as the divergence of phenotypes as far as what I'm saying goes. I expect both to diverge. I expect speciation or incipient speciation to be occurring in the two subspecies at the far ends of the territory. I've been saying this in the last few pages. I have been arguing that this divergence of phenotypes AND genotypes is the result of the differing frequencies of alleles between the two populations, and most likely the loss of some alleles as well in one or both populations which is what "reduced genetic diversity" means.
In other words, divergence of both phenotype and genotype is no refutation of anything I've said but a confirmation of it. And since this appears to be the whole supposed refutation offered by that article, it fails; in fact it confirms my view and not yours.
Why is showing greater genetic divergence across greater distance of relevance to our discussion?
Well, for one thing, the greater the geographic distance between the populations, the less gene flow there is - which calls into question your contention that the differences seen are due only to recombination or some kind of skewed frequency distribution.
This does NOT refute what I'm saying, but the opposite, it confirms it, as I've already said. I have repeatedly said that I EXPECT greater divergence with greater distance, and that gene flow would INTERFERE with speciation --- the reduction or absence of gene flow ENHANCES the speciation processes. It appears that you haven't even made the slightest effort to follow the argument. You are describing this article as proving exactly what I've been saying, yet you are claiming it refutes me.
I suppose it is that you have such a totally evolution-focused bias that you can't hear this thing I'm saying no matter how many times I say it.
In addition, the most distant populations (from each other) contain novel alleles not found in the populations closer to each other, which leads to the question: "Where did these sequences come from?".
There is no reason whatever to assume that these alleles are novel in the sense of brand new. My argument has been from the beginning that when you have a strong shift in allelic frequencies, which in ring species is very likely to include the loss of some alleles, you get VERY new allelic combinations, new genotypes, new phenotypes. The novel alleles are not novel in the sense of brand new to the species, they were simply suppressed or latent or of very low frequency in the original combined population, and may very well now be completely absent except in the population where they are noted -- why? Because they were low frequency to begin with. Merely sampling a few individuals would likely miss their existence too if they continue to exist in low frequency.
PLEASE point to where you or this abstract have shown how genetic diversity is increased.
How about the very first line of the abstract?:
quote:
The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations.
So what you mean by "increased genetic diversity" is merely mutations.
But absolutely nothing in anything you have said about what the article is about demonstrates that mutations have any part whatever in any of it.
The mere fact of divergence or incipient speciation, and the presence of some supposedly novel alleles, seems to be enough to prove in your mind that mutation must have a part, but this is merely assumed. Nothing has been said to demonstrate that this is the case.
What is actually described of the circumstances fit MY scenario -- the divergence of phenotypes and genotypes, the lack of gene flow, the appearance of previously suppressed alleles, all that proves what I have been saying from the beginning. It is all thoroughly explained by allelic shuffling and reduction of genetic diversity (loss of alleles).
Mutation has no necessary role in any of this, and there is not one iota of evidence that it actually does in this case, in anything you've said or the article has said.
It seems to be the case that mutation is merely assumed to have a role because you aren't grasping the fact that it is not necessary, that when there is reduced gene flow and clear divergence between the populations, or incipient speciation, changed allele frequencies including previously suppressed alleles now being expressed, and lost alleles (or loss of genetic diversity), explain it perfectly.
Since you aren't grasping that, or refuse to believe it, being evolution-focused, you stick mutation in there to explain it. But you must SHOW that mutation has contributed to this at all instead of assuming it. You haven't done this, nor has the article. The fact is mutation isn't involved, you and the article are simply projecting it into the scene by assumption.
AND...
quote:
We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was resampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern).
All of which is apparently focused on proving that divergence and even incipient speciation has occurred, which is far from disputed by me.
The full article goes on to discuss - in some detail - the reasoning behind this. Since the full article isn't on-line (unless you have a subscription), you can see a similar set of research in the PNAS article I provided (which is available free). I can also provide other, similar, references if it makes you feel any better. The point is molecular/genetic level studies of diverging populations (incipient speciation) show genotype differences that simply cannot be accounted for by changes in frequency distribution of pre-existing alleles. These are not hypothetical examples, but examinations of real-world populations.
But none of what you've said actually demonstrates that the genotype differences can't be accounted for as I've claimed, you have merely asserted it. All completely hollow claims. The entire scenario is easily explained by allelic shuffling. I can't even understand why you doubt this. There is nothing in the scenario itself to suggest it can't occur as I've described.
You, and the article, are simply *asserting* that alleles are novel without proving they are novel (just because they didn't turn up in a sampling of the population left behind?), and merely *asserting* that mutation is bringing about the genotypic diversity instead of proving it, and so on. Again, you seem to think that the mere facts of divergence and reduced gene flow are evidence enough, although they are evidence for what I'm saying instead.
AGAIN, despite your offering of evidence, there is no ACTUAL evidence for your position in any of this, because everything you have actually provided supports MY position instead.
The mere existence of one identifiable mutation would not prove that increased genetic diversity caused the divergence, and nothing you have said shows that reduced genetic diversity which produces new phenotypes is not the explanation.
You stated things along these lines several times, so I'll ask you again: how does "reduced genetic diversity" create "new phenotypes"? This contention is so completely counterintuitive that I'm half convinced I'm missing something in what you're trying to say.
Thank you for asking, I appreciate it very much, and you ARE missing what I'm trying to say despite my many repetitions of it.
So let me try it again to say it clearly, God willing:
What I'm claiming is that a reduction in genetic diversity (loss of alleles) is the OVERALL trend over time in all the processes that lead to speciation. These are the same processes that bring about change in allele frequencies, only from time to time the change is a reflection of alleles having been lost altogether. This is clearly the case in bottleneck which is why the cheetah keeps coming up -- a dramatic unusual extreme case of speciation that involves great loss of genetic diversity that I bring up to illustrate the principle. I also bring up domestic breeding of animals such as dogs, because it is also demonstrable there that a loss of alleles brings about a new breed, and that no amount of inbreeding of that type would turn up a whole raft of alleles that other dog breeds possess. The absence of these alleles is part of the definition of the breed, a part of the process of developing a new phenotype, genotype, organismal type etc.
Many events that bring about a new phenotype are merely the shuffling of alleles rather than outright loss of diversity through loss of alleles, but the ONLY cases where an increase in numbers of kinds of alleles occurs is hybridization. Gene drift may increase the frequency of some and reduce the frequency of others, but an actual increase in alleles only happens with hybridization or the recombination of previously isolated populations. Since hybidization is the ONLY situation in which an increase in genetic diversity occurs, and you think an increase is necessary to speciation, then hybridization should be where you would look for evolution to occur. But it isn't where you look. You look where there is no increase or even a decrease, but without recognizing this decrease as intrinsice to the processes of speciation.
In none of these processes except hybridization does the production of a new phenotype involve an increase in genetic diversity (increase in kinds of alleles). Population splits either do not reduce genetic diversity, simply changing frequencies, or they DO reduce genetic diversity through loss of alleles, which must happen quite frequently when populations split off in a series of splits as in the example of ring species, so that the farthest apart populations would have alleles that the other doesn't have at all or has at very low frequencies.
The point is that since increase in diversity is of absolutely no use in speciation (unless you want to count hybridization as THE track to evolution), but decrease allows formerly suppressed alleles to produce new phenotypes, the overall trend of speciation processes is reduction of genetic diversity.
These are all the normal processes that bring about speciation. Nothing new is needed. There are plenty of alleles for all kinds of variations of most species. But out at the extremes of speciation there will be fewer alleles per locus, and this also no doubt accounts for the inability to interbreed with other populations of the same species.
Again these are the NORMAL proceses of speciation.
Now you want to introduce mutation into a process that doesn't need it for starters. You think genetic diversity must increase for speciation to occur, the opposite is counterintuitive as you say. I suppose it is. You have to get rid of alleles for others to form new phenotypes, that's all. Otherwise a population will stay pretty much the same or slowly change through gene drift as frequencies change due to internal influences. Change in phenotype/genotype requires a new allelic collection that reduces or gets rid of the old in order to allow the expression of something new and different.
ENTER MUTATION. But where does it enter into this scenario? It appears that evolution merely assumes it, because it assumes that all alleles were once brought about by mutation. It is not needed for speciation. Certainly it occurs, perhaps now and then it is selected, I wouldn't deny that, I just haven't seen that it actually contributes anything necessary or important to speciation, which follows from allelic shuffling quite well.
I hope that's clear for the umpteenth time.
The abstract is too technical for me to read.
So, actually reading the research is probably out of the question?
I'd have to look up a dozen words, have to study to understand their whole context of usage in science, so yes, it is probably out of the question.
But you won't take my word for what the articles say when I try and use simpler terms to explain it? That being the case, I ask you again "Where do we go from here?"
I did take your word for it. I took what you said about it completely straight, and I answered, more than once by now, that it is not proving what you think it proves.

This message is a reply to:
 Message 136 by Quetzal, posted 09-04-2006 9:11 AM Quetzal has not replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 143 of 301 (346462)
09-04-2006 2:30 PM
Reply to: Message 141 by Quetzal
09-04-2006 1:09 PM


Re: On predictions and tests.
I'm not accusing you of making stuff up, merely misreading.
In Message 34 he is talking about a loss of alleles of ten genes, not a loss of genes:
MJF writes:
Let's suppose we have a species that possesses 30,000 genes. Two populations form from this species that become geographically isolated. Originally, there's a lot of genetic redundancy (or overlap). So let's suppose that of the original 30,000 genes, all the alleles are present for 29,990 genes. But for a small number of genes (10 in this case) there is geographic isolation, no overlap between populations. This occurs purely by chance, remember. So, is there a reduction of genetic diversity? Not really, the sum population still possesses the full diversity of alleles among its 30,000 genes. However there has been a reduction of genetic diversity as seen in each population.
I'm a bit unclear about what he is saying about what is isolated from what, but it's not at all unclear that he's not talking about a loss of ten genes but a loss of alleles for those ten genes.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 141 by Quetzal, posted 09-04-2006 1:09 PM Quetzal has not replied

Philip
Member (Idle past 4722 days)
Posts: 656
From: Albertville, AL, USA
Joined: 03-10-2002


Message 144 of 301 (346468)
09-04-2006 2:45 PM
Reply to: Message 123 by EZscience
09-03-2006 8:09 AM


Re: Mutation Fallacies in Macro-ToE
Your mistaken inference is that mutations are not occurring simply because so many loci are fixed for a single allele. There (they) likely are occuring, but rates are very low because effective population size is very low, or the sequences of the alleles in question are highly conserved.
If WK, Quetzel, you, or anyone would mechanistically explain a single beneficial mutation pressure as a valid mechanism for speciation, I request you explain where on a gene this is viable:
1) Mutation in 'plasmids', 'mutable areas?', "hot spots?" (Then you'd agree beneficial mutation is just a misnomer for 'inherent adaptability')
2) Mutation in highly conserved sequences of the genotype? (I trust your answer is "no" to 'hopeful monsters')
3) Then, raw beneficial mutations are *really occurring* somewhere between these 2 extremes of (1) 'mutable areas' (biological misnomers) and (2) 'highly-conserved areas' of the gene(s) (impossible mutations)?
Thus, do you percieve *mutable-highly-conserved-genes* (#3 above) as an acceptable oxymoron, as part of an honest hypothesis, or as part of a valid mechanism for beneficial mutation(s)?
(Note: please continue to focus on valid mutational pressures only)

DISCLAIMER: No representation is made that the quality of scientific and metaphysical statements written is greater than the quality of those statements written by anyone else.

This message is a reply to:
 Message 123 by EZscience, posted 09-03-2006 8:09 AM EZscience has replied

Replies to this message:
 Message 156 by EZscience, posted 09-05-2006 7:01 AM Philip has replied

Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 145 of 301 (346554)
09-04-2006 9:02 PM
Reply to: Message 88 by RAZD
09-01-2006 9:30 PM


Re: are bottlenecks tied to speciation?
What I'm saying is that a bottleneck is simply an extreme version of a number of the selecting and population-splitting processes that cause new traits to appear in the phenotype
The question is whether it must always result in this. I don't think so.
Considering how many alleles must be no longer available, forcing the few that got bottlenecked to define the new organism / phenotype /genotype, I hardly see how it could avoid bringing about new traits.
Speciation may cause a bottleneck, if it is of the founding population variety and the population is small.
Well, I suppose it's possible that the bottleneck simply might select out the very alleles that are already most expressed in the population and there would be little phenotypic change. I can't think of another way this might happen.
It may make no selection of alleles at all. Think of a population of 10,000 individuals and 1 in 10 survive a random catastrophe by luck not genetics\selection -- they just happened to be in the right place.
I used "selection" in the informal sense of "random selection" -- I guess that can be confusing. I didn't mean anything like the alleles were chosen, only that they did just *happen* to get bottlenecked. But there certainly is a different collection of alleles from the original population since many must have had to be left behind.
The distribution of alleles in both populations is the same, both in kinds of alleles involved and in their relative number -- say a bell curve distribution -- so that the shape of the distribution is the same, just the total population is reduced. The result is the same degree of diversity (the same bell curve) just fewer individuals.
The species will still have the same distribution of alleles.
Well, but the whole point of the bottleneck (and founder effect) example is that it is not at all likely that you would get anything like the same distribution as was in the original population, because the new population is so much smaller. Two alleles per gene might be the total available in such a case, whereas there might have been even a dozen or more for the same genes in the original population. So unless the original population was already very allele-poor you are not going to get anything like the same diversity, you are going to get something dramatically different from the original after a few generations of inbreeding in the new population with the very few allelic possibilities.
Yes, drift is the situation of no population split which we've been acknowledging may change the phenotype without reduction in diversity. It's the natural playing out of changing allelic frequencies in the population that brings this about in this case.
Speciation without bottleneck, bottleneck without speciation, therefore not necessarily related. It's like a grid:
----------------------------------
| no-speciation | speciation |
| bottleneck | bottleneck |
----------------------------------
| no-speciation | speciation |
| no-bottleneck | no-bottleneck |
----------------------------------
Any population can fall into any one of those four quadrants at different times.
There are other factors involve that make a strict relationship problematical, imh(ysa)o.
Well, I'm trying to avoid being all that strict, I'm trying to argue a TREND here, a trend TOWARD speciation that involves overall reduction of genetic diversity, normally over many generations, not a clearcut formula for instant speciation. The usefulness of the bottleneck and founder effect examples is that they cut to the chase -- they are examples of a drastic reduction in genetic diversity while at the same time they should be expected to demonstrate the formation of a new phenotype or even speciation as a result of this reduction.
Only mutation. Nothing else.
No, mutation has no bearing on whether population fall into one quadrant or another -- there are other factors that affect which quadrant they are in that can override any relation between speciation and bottlenecks. The only way that a strict relationship could exist is if two corners of the grid could not be populated with different species at different times.
I don't know why you are focused on a "strict relationship" since I've been trying to say that this is trend, not a strict anything. Overall you get a reduction in genetic diversity along with the development of new phenotypes. But there are situations where such a reduction doesn't happen of course, such as gene drift within a population or a population split in which both are quite numerous, or any form of selection that simply reduces the frequency of alleles in a population without eliminating them. To get the genetic reduction I'm talking about alleles are totally eliminated, they no longer figure in genotypes for their traits so new traits from other alleles take their place and gradually shape the new phenotype.
Again, the bottleneck simply demonstrates this process of reduction of alleles at an extreme. Most situations simply shuffle alleles rather than eliminating them altogether.
But in neither case is there an increase in alleles. All these processes that lead toward speciation either shuffle or reduce alleles. The only situation in which there is an increase in alleles is hybridization but this does not introduce anything new, it simply recombines formerly separated alleles.
My remark about mutation was that mutation is absolutely the only thing that could possibly ADD alleles. All the processes of speciation otherwise over time involve reduction of alleles.
But there is definitely a loss of diversity IN the subpopulations and this is what we are talking about. If they can't interbreed then they can't recombine their alleles so the diversity they share between them is meaningless.
It does NOT reduce the diversity in the total population of life on the planet, and it allows the now separated populations to expand their population diversity with subsequent mutation, thus ending up with more diversity than the total population of life on the planet started with: that is the issue.
I haven't claimed that genetic diversity is reduced for anything but the population being discussed, in which it brings about new phenotypes and even speciation.
The idea that mutation now takes over and produces new alleles is pure fantasy, an assumption dropped into the story without any warrant whatever. For starters, mutation is not needed for speciation, since the shuffling of preexisting alleles alone can bring it about, most especially the expression of formerly suppressed alleles when others are lost to the population -- this is all it takes to form new species or variations out of the existing collection of allelic possibilities. Mutation is absolutely NOT needed. Again, while mutations do occur, and are occasionally selected, it has not been shown that they contribute anything beyond negligible (or destructive) to the formation of new species.
{EDIT: EXCEPT OF COURSE IN BACTERIA. And here's an answer to that one, Crash, if you're paying attention. You are dealing with ONE cell there. You get a mutation that allows that cell to survive a threat and multiply. But multicelled creatures do not get mutations in all their reproductive cells all that predictably, do they? They don't get mutations at anything like a rate that would contribute useful traits, and as you have said many times MOST of such mutations are either supposedly useless or a bad thing.}
So there does seem to be this idea that speciation CAUSES bottlenecks.
That is the other problem with the supposed relationship - in some cases {A} can happen before {B} and in some cases {B} can happen before {A}. That makes it hard to show that {A} causes {B} eh?
Sorry I am not following you. Bottlenecks MAY cause a new species, but I don't see how species cause bottlenecks, they may simply exemplify them.
some speciations cause bottlenecks in daughter populations
some speciations don't cause bottlenecks in daughter populations
some bottlenecks cause speciation
some bottlenecks don't cause speciation
Conclusion: bottlenecks and speciation are not necessarily related events.
Um, I hope the above has clarified what I was saying since none of this represents it.
{Edit: First, I haven't said that bottlenecks are CAUSED BY speciation at all, this is your own thing completely. And second, I'm sure bottlenecks don't always cause speciation, but it would be very unusual if they didn't bring about new phenotypes in the new population with its drastically reduced genetic diversity (numbers of alleles available per gene.)
Edited by Faith, : No reason given.
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 146 of 301 (346571)
09-04-2006 11:37 PM
Reply to: Message 6 by Archer Opteryx
08-26-2006 11:54 AM


Re: what is the mechanism inhibiting change?
Rereading this thread, realized I could answer some contentions a little more clearly perhaps:
Research has proven genetic changes due to mutation. Research has proven that some genetic mutations enable an organism's survival in its environment. Research has shown that subsequent generations exhibit further genetic changes. There is no reason to doubt that changes accrue over time.
Creationists deny that small genetic changes can accrue over time.
This is false. We are constantly affirming that genetic changes accumulate, creating new varieties or breeds as a regular thing, even to the point of speciation. What we deny is that this goes beyond the Kind and that it involves mutations. All it takes is the playing out of the given complement of allelic possibilities, as I spend this entire thread, and a few other threads, explaining.
Creationists are obligated to show what would prevent this, if they wish their ideas to be treated seriously as science.
We have no interest in demonstrating that small genetic changes don't accrue over time; we affirm that they do. We merely deny that they accrue beyond the Kind, and in this thread I'm arguing where the barrier to further evolution / divergence /variation /speciation beyond the Kind is to be found.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 147 of 301 (346586)
09-05-2006 1:41 AM
Reply to: Message 136 by Quetzal
09-04-2006 9:11 AM


Endangered species = reduced alleles
It isn't hard to find discussions of these common phenomena in relation to conservation programs with endangered species, that is, the reduction in genetic diversity through population isolation. What they usually leave out of the discussion is that these processes are related to speciation, certainly at least the development of new genotypes and phenotypes, or divergence of populations phenotypically one from another, which is a step on the way to speciation.
As the article you linked is concerned to prove, the geographically isolated populations of Ensatina can probably be termed incipient species or possibly even species due to their lack of contact with one another or lack of gene flow between them. This means that each is inbreeding with its own different frequencies of alleles and possibly even an absence of some that the other population retains. This gets called incipient speciation in that article. Perhaps Ensatina is not yet on the verge of extinction, but a few more splits off the existing populations, leaving more alleles behind, and it could very well go in that direction.
Anyway, what I've been talking about all along is this common pattern which leads to the endangerment of species (in the very process of differentiating them). Here's one discussion of this pattern.
Page not found – Essig Museum of Entomology
Population Genetics and Endangered Species
In applying the principles of population genetics to the field of endangered species conservation, biologists are interested primarily in genetic variation, in particular its distribution and maintenance. In general genetic diversity is considered to be a good thing, and the more the better. In terms of population structure, multiple large populations of a species which are in some way in contact with each other provide a good situation for maintaining variation.However, in the case of endangered species, we are generally faced with the opposite situation: a small number of populations which are isolated from one another, each containing a small number of individuals.
...Connectedness is generally measured by examining the frequencies of different alleles, or forms of a specific gene, at several different genes. If the frequencies differ significantly between two areas, it is likely that there is some restriction in gene flow between them.
Which is what the article about Ensatina identifies.
If it appears that there is no difference in frequencies from one area to another, it may be supposed that there is some genetic connection preventing differentiation (other interpretations are, of course, possible). The interpretation of genetic connectedness is difficult as its significance is situation dependent. Strong interpopulational connectedness (presumably through frequent migration) will be good for promoting the maintenance of overall genetic diversity; rare alleles are less likely to disappear in a larger population.
Isolation, which leads to formation of new phenotypes or incipient speciation, not mentioned here but think about it, is BAD for genetic diversity which bodes ill for the prospects of the species in a fallen world.
And if mutation were anywhere near the power claimed for it, so many species would not be on the verge of extinction as a result of becoming isolated and changing in the ways that may be called incipient speciation or outright speciation.
Edited by Faith, : No reason given.
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 148 of 301 (346590)
09-05-2006 2:11 AM
Reply to: Message 147 by Faith
09-05-2006 1:41 AM


Re: Endangered species = reduced alleles
Here's the problem I'm talking about in the context of domestic breeding. From the very first sentence it ought to be clear that the very processes of developing a new breed or species lead to reduction in genetic diversity. Speciation=reduction in genetic diversity. BUT this is bad for the species' survival prospects so they are trying to encourage breeders to avoid this usual speciation process:
Too many breeders follow the "breeding for extinction" paradigm. Start with too few founders, close the registry to new imports, inbreed and breed your preeminent males as many times as possible. It is a guaranteed recipe for degrading the gene pool. Breeders will visit the Diversity web site, read some of the information, and come away still believing that what I propose will lead to deterioration of their line, often insisting that the best and most successful breeders don't breed this way. They don't see the relevance of the strategies for saving endangered species or populations, and maintain that the factors taken into consideration for the Mexican or Ethiopian wolf don't apply to Canis familiaris.
http://www.lhasa-apso.org/health/wolves.htm
It's rather odd that this common fact that reduced genetic diversity is associated with the development of new species is not easily recognized among evolutionists. They put all their hopes on this phantasm called mutation, yet have never shown that mutation occurs in any degree or quality that could overcome the effects of the inevitable downside of speciation -- the trend to extinction. Mutation occurs, it sometimes gets selected, and all their focus goes there.
Meanwhile, species speciate further and further and get closer and closer to extinction, and conservationists have to deal with the nitty gritty reality that speciation is NOT a healthy development. The implication from this fact that there's no way that evolution could ever be built on such a reality seems never to enter any evolutionist's mind. They just claim that it's all saved by .... The Mighty Mutation, this fantasy that can't be demonstrated to do anything like what is claimed for it.
Meanwhile, again, conservationists are working to UNDO the effects of speciation, because, well, it just plain doesn't go in the direction of evolution, it goes in the direction of extinction. Imagine that.
Because loss of genetic diversity in endangered species is often associated with inbreeding and a reduction in reproductive fitness (Reed and Frankham 2001), efforts to increase the genetic diversity of the endangered Korean goral should be considered as a high priority for conservation of this species.
Cross-Species Amplification of Bovidae Microsatellites and Low Diversity of the Endangered Korean Goral | Journal of Heredity | Oxford Academic
The fact is that all living things were given a genetic package back at the Creation and it has simply been playing out ever since, losing much of its contents over the centuries and millennia, but still capable of a lot of variation. Only now more and more species are getting out to the speciation limits of their Kind where extinction threatens.
Edited by Faith, : No reason given.

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PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.3


Message 149 of 301 (346591)
09-05-2006 2:28 AM
Reply to: Message 147 by Faith
09-05-2006 1:41 AM


Re: Endangered species = reduced alleles
I don't see how this is supposed to help your argument in any of the points under dispute. The fact that the bottleneck in itself has not instantly converted the isolated populations into new species in itself for instance suggests that there is something more to speciation than a bottleneck. (As should be obvious - if there were no new alleles every individual in the "new" species would have been possible in the original species)
quote:
And if mutation were anywhere near the power claimed for it, so many species would not be on the verge of extinction as a result of becoming isolated and changing in the ways that may be called incipient speciation or outright speciation.
But this is BEYOND the power attributed to mutation. Mutation is not credited with the power to automatically rescue populations from the immediate consequences of a depleted gene-pool. It takes time (the cheetahs are still recovering, slowly, for instance).
The simple fact is that neither extinction nor salvation through mutation are inevitable in such a situation. Small isolated populations just have a harder time surviving.

This message is a reply to:
 Message 147 by Faith, posted 09-05-2006 1:41 AM Faith has replied

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RickJB
Member (Idle past 4990 days)
Posts: 917
From: London, UK
Joined: 04-14-2006


Message 150 of 301 (346600)
09-05-2006 3:42 AM
Reply to: Message 146 by Faith
09-04-2006 11:37 PM


Re: what is the mechanism inhibiting change?
Faith writes:
What we deny is that this goes beyond the Kind and that it involves mutations.
This is a good thread, Faith. However:-
1. You have yet to define "kind" in any meaningful way.
2. You have yet to show any evidence contrary to what others have told you about mutations other than your own opinion.
I find it inriguing how far you are prepared to accept evolution in the hope of finding some sort of limit to it. You might want to be careful though, you might suddenly realise you've crossed the point of no return....
Edited by RickJB, : No reason given.
Edited by RickJB, : No reason given.

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