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Author Topic:   Evolution Requires Reduction in Genetic Diversity
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Message 3 of 1034 (691635)
02-23-2013 9:51 AM
Reply to: Message 1 by Faith
02-22-2013 6:14 PM


As you say, it is unwieldy. Would it be possible to compose a shorter opening post that is original (rather than cut-n-pastes) and doesn't contain lines like, "So there's your substance and now you can bring on your stupid answers as usual. Ho hum."
The part of your argument that I think is understood is that since sub-subspecies such as Herefords (of cattle) and chihuahuas (of wolves) have reduced genetic diversity, and since new species begin from isolated populations consisting of a subspecies or sub-subspecies, that therefore speciation can only occur from a reduction of genetic diversity. I don't think many would have a problem with a discussion based upon this style of speciation. It's fairly representative and it's unarguably true since by definition a subset is always an incomplete representation of the full set.
The part that isn't clear is your view of the role of mutations. You appear to be arguing that if mutations really had the effect that evolution claims then species would be inconstant and perpetually changing, which is precisely what evolution does claim based upon the available evidence. I think discussion would center around this and not around the initial reduction in genetic diversity that can be associated with speciation.
If the above is a sufficiently accurate representation of your views then I can just promote this now and you wouldn't have to attempt a rewrite of the opening post. I'll be checking back in in a few hours.

--Percy
EvC Forum Director

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Message 5 of 1034 (691638)
02-23-2013 1:37 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Evolution Requires Reduction in Genetic Diversity thread in the Proposed New Topics forum.

  
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Message 136 of 1034 (691977)
02-26-2013 6:54 PM


Moderator On Duty
Regretfully I am recusing myself from discussion in this thread and taking on a moderator role beginning tomorrow morning. Please keep your focus on the topic.

--Percy
EvC Forum Director

  
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Message 387 of 1034 (757698)
05-12-2015 9:11 AM
Reply to: Message 384 by Denisova
05-11-2015 1:33 PM


Re: No 'new functions'
Denisova writes:
I DO hope you know that bacteria don't reproduce sexually.
True in a strict sense, but they do engage in sex, the technical term is conjugation.
But sexual reproduction DOES NOT change alleles.
It depends upon how you define sexual reproduction. If it's defined as extending from the production of gametes through fertilization then since a mutation could occur during that process it must therefore be acknowledged that sexual reproduction can change alleles.

--Percy
EvC Forum Director

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Message 388 of 1034 (757699)
05-12-2015 9:23 AM
Reply to: Message 385 by Faith
05-11-2015 7:16 PM


Re: No 'new functions'
Faith writes:
Sorry, I don't accept anything about bacterial genetics (your E. coli example) as applying in this discussion. You have to use examples from sexually reproducing creatures.
Participants don't get to dictate the parameters of discussion. Please explain why you don't believe bacterial genetics are relevant to this discussion.
I believe junk DNA is genes that died over the millennia as a result of the Fall, most as a result of the Flood which was a very severe bottleneck. If about 95% of the genome is junk DNA today, a rough guess would be that maybe about .0003% was junk DNA at the time of the Flood.
...
The only thing I suggest is that genes died as a result of all those people and animals dying in the Flood, whose traits were lost to the species and therefore the alleles for those traits, so the genes just died and remain in the genome as corpses.
Please concentrate defense of your position on scientific evidence. The Bible is an excellent source of ideas and inspiration, but not of scientific evidence. If you believe that for the most part junk DNA is once-active DNA that has been disabled (and certainly some of it is) then you must support that idea with facts.
Edited by Admin, : Grammar.

--Percy
EvC Forum Director

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Message 404 of 1034 (757765)
05-13-2015 6:48 AM
Reply to: Message 395 by Tanypteryx
05-12-2015 9:39 PM


Re: genetic diversity
Tanypteryx writes:
And you have been wrong a bazillion times. This is completely assbackwards. When you are getting new traits you are adding diversity.
Here you seem to be saying that new traits can only emerge from added diversity, but then you go on to say something more inclusive:
The processes of evolution absolutely do not require a reduction of diversity.
This seems to allow that new traits can also emerge from reduced diversity, so I'm not sure what your position is, and Faith may not be either.
It might be helpful, since this thread just recently resumed active discussion, if Faith could provide a clear statement of her position. My understanding of Faith's position is that because breeders bring out new traits by reducing genetic diversity that speciation must bring out new traits through the same process. If I have this right then what's missing is a description of what speciation has that breeding doesn't, since breeding doesn't result in speciation.
What's also missing is an explanation of the underlying genetics, since the genome differences between even the most different of breeds of the same species (e.g., dog and wolf) aren't in degree or character anything like the genome differences between even very closely related species (e.g., red squirrel and grey squirrel).
Edited by Admin, : Fix quote attribution.

--Percy
EvC Forum Director

This message is a reply to:
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Message 407 of 1034 (757774)
05-13-2015 12:01 PM
Reply to: Message 405 by Faith
05-13-2015 11:32 AM


Re: genetic diversity
Hi Faith,
The attribution was wrong, must have been thinking "Faith" while I was supposed to be typing "Tanypteryx", who replied in Message 406 and apparently wasn't confused by the mistake.

--Percy
EvC Forum Director

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Message 409 of 1034 (757780)
05-13-2015 12:57 PM
Reply to: Message 408 by Faith
05-13-2015 12:08 PM


Re: genetic diversity
Faith writes:
Apparently breeding can result in speciation.
No one doubts this, especially given the necessarily multi-faceted definition of species. While breeding *can* result in speciation, it almost never does, even though each and every mating pair is specifically selected rather than the much more random selection of mating pairs in nature.
As Tanypteryx reminds us, and as Darwin made clear in Origins, domestic breeding provides a clear example of the power of selection. What it doesn't provide is an effective method of creating new species.

--Percy
EvC Forum Director

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Message 432 of 1034 (757876)
05-15-2015 7:33 AM
Reply to: Message 423 by Denisova
05-14-2015 3:39 PM


Re: genetic diversity
Denisova writes:
That picture shows, all to see before our own eyes, that genetic diversity has INCREASED. Because:
1. ONCE you only had one phenotype, O. orientalis
2. NOW we have MANY phenotypes
3. more phenotype variation means more genetic diversity.
If you're measuring species genetic diversity by the variety of genes and the variety of alleles for each gene across a species, I don't think #3 is correct. If you're using some other measure of genetic diversity then it would be helpful if that were made clear.

--Percy
EvC Forum Director

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Message 433 of 1034 (757877)
05-15-2015 7:55 AM
Reply to: Message 425 by Faith
05-14-2015 3:55 PM


Re: genetic diversity
Faith writes:
And as I also keep arguing, even if mutation really did accomplish this [increase in genetic diversity], any subpopulation that develops new traits or phenotypes can only do it with the reduction of genetic variability in its own collective genome.
This point would seem central to your position. It seems to be saying that new traits or phenotypes can be produced by novel combinations of existing alleles, but not of mutated alleles. It would be helpful if you could make clear how this could be.
Unfortunately the ToE got itself all wrapped up in the wrong assumption that the formation of subspecies is accompanied by greater genetic diversity, which is basically what everyone here is arguing.
If I could more accurately summarize the position of the other side, they do not believe that speciation is dependent upon either an increase or decrease genetic diversity. They believe speciation can be accompanied by either. Certainly the "speciation via isolated subpopulation" scenario that is most often discussed because of its simplicity often begins with a reduction in genetic diversity, but not necessarily so, and it isn't the only scenario leading to speciation.

--Percy
EvC Forum Director

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Message 434 of 1034 (757878)
05-15-2015 8:08 AM
Reply to: Message 427 by jar
05-14-2015 5:24 PM


Re: genetic diversity
jar writes:
The fact is that you position has been proven to be as wrong as your assertion of the "Fall" and that one of the "Biblical Floods" ever happened.
Just as you deny what the Bible actually says you continue to deny what even reality says.
But fortunately your fantasies have nothing to do with reality and nonsense like the "Fall" or some imagined "Biblical Flood" have no place in science or a discussion about reality or biology.
Since your post is the first to mention the Bible that I've read today I'll take this opportunity to let the thread know that I'm going to be asking everyone in the discussion to avoid touching on Biblical topics. I'll also be asking everyone to avoid supposition and support positions with facts.

--Percy
EvC Forum Director

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Message 435 of 1034 (757879)
05-15-2015 8:25 AM
Reply to: Message 428 by Faith
05-14-2015 7:44 PM


Re: genetic diversity -- rest of Denisova
Faith writes:
Although your 5% and in fact your whole previous paragraph are a total confusion, at least this one ends up correctly representing my view that most of the initial genome is now junk DNA, thanks predominantly to the Flood bottleneck. NOT MUTATIONS.
...
They should have had functioning appendix and gall bladder among other things, both of which aren't very useful to us any more. I think along these lines because of the hundreds of years people lived up until the Flood.
...
abe: Didn't say that right. Meant people who died in the Flood
I'm asking all participants to avoid references to Biblical topics in this thread.
Edited by Admin, : Remove the phrase "or in any science thread" because it turned out to be more broadly interpreted than intended.

--Percy
EvC Forum Director

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Message 465 of 1034 (757967)
05-17-2015 2:25 PM


Moderator Introduced Definitions
To move discussion forward I'd like to introduce simple definitions for species and genetic diversity. People are free to use other definitions, certainly species has no one definition, but they should clearly define the definition they are using. But I think these definitions should serve very well most of the time.
  • Species: A group of individuals capable of breeding with one another to produce fertile offspring. Obviously this definition doesn't apply everywhere, most obviously to asexual species, but it is by far the definition people most often have in mind when discussing evolution.
    In particular this should resolve a recent issue where Faith wanted to claim that two individuals could be of the same species yet not be able to interbreed, see Message 441 and Message 443, particularly this sentence in the latter:
    Faith writes:
    Yes I do want to claim that two populations that can't interbreed are the same species.
    Redefining words that already have a clear definition is a sure road to confusion, something this moderator will work hard to avoid. True, the definition of species is long and nuanced and full of qualifications, but not for populations of sexual species. Faith's attempted redefinition of species for sexual populations is hereby disallowed.
  • Genetic Diversity: I'm open to discussion about this, but unless there are some objections and/or better ideas I'd like to propose the following definition for general usage. For a population, genetic diversity is the number of loci (a locus is a particular gene at a particular location on a particular chromosome) and the number of alleles for each loci across all individuals of that population. For example, if across all individuals there are 38,500 different genes (even if not all individuals have all genes), then that's the number of genes in the population. If that number should rise to 38,501 then that would represent an increase in genetic diversity. Or if across all individuals there are a total of 1,500,000 different alleles across all genes (though of course no individual would have all the alleles), then that's the number of alleles in the population. If that number should rise by one to 1,500,001 then that would represent an increase in genetic diversity.

--Percy
EvC Forum Director

Replies to this message:
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Message 476 of 1034 (757993)
05-18-2015 7:04 AM
Reply to: Message 467 by Faith
05-17-2015 5:35 PM


Re: No 'new functions'
Faith writes:
Although I think I have a fair grasp of how genetics works at the genome level, and that much understanding IS necessary to the argument, if someone starts putting up charts from the genetics laboratory it's just a snow job designed to avoid addressing MY points.
The Lenski E. coli example addresses your main point (that evolution is driven by reductions in genetic diversity) more directly than any other.
The kind of evidence that matters in this discussion is on the level of claims to known mutations in whatever species we are talking about, their KNOWN functions, what they are KNOWN to code for and the KNOWN results of such mutations in KNOWN cases, plus proof of changes in genetic diversity from subpopulation to subpopulation of an actual living species and so on.
The E. coli example satisfies these criteria by providing "KNOWN" facts better than any other raised in this thread.
Here I get a lot of assertions of increased genetic diversity without a shred of evidence, and Denisova in particular asserts it more on the basis of the ToE's assuming it than any actual known facts.
Regarding E. coli, your statement that it is "without a shred of evidence" is hard to credit. Again, that example has more "actual known facts" than any other mentioned here. It is Denisova's responsibility to bring those facts out, and if he hasn't or if the facts don't support his premise then you should challenge him about it.
E. coli may demonstrate some interesting genetic information, but only about E. coli and not about my argument.
You seem to be committing a significant fallacy. How is the example of E. coli gaining genetic diversity not relevant to your claim that genetic diversity can only decrease? More generally, how is it that the E. coli example is irrelevant because it is only about E. coli, but your sheep example *is* relevant even though it is only about sheep?
I'm ruling that the Lenski E. coli experiments are directly related to the topic and cannot be dismissed.
Please concentrate defense of your position on scientific evidence. The Bible is an excellent source of ideas and inspiration, but not of scientific evidence. If you believe that for the most part junk DNA is once-active DNA that has been disabled (and certainly some of it is) then you must support that idea with facts.
That's really quite a handicap you are imposing on me here.
Not at all - I'm just stating a fundamental requirement of science: evidence. What you've provided so far is a hypothesis. It's based upon the Bible, but for EvC Forum that's fine. What you must do next is provide evidence for your hypothesis. Let me be specific:
I believe junk DNA is genes that died over the millennia as a result of the Fall,...
...
The only thing I suggest is that genes died as a result of all those people and animals dying in the Flood,...
Your hypothesis contains an apparent contradiction, since first you state that genes dying are a long term result of the Fall, but then you state it was a result of the Flood. But my main concern is that you understand that your main responsibility is providing evidence for your hypothesis. For example, people will reasonably expect that evidence will be forthcoming for genes dying around 6500 years ago (the Fall) and 4700 years ago (the Flood). And they'll expect that evidence will be forthcoming for how a mass die-off by drowning can affect genomes. All I meant in my message is that you must understand that issuing hypotheses is accompanied by an obligation to support those hypotheses with facts. A statement that they're consistent with what is already known is not evidence, plus in this case that must remain an open question (at a minimum) since the evidence from ancient DNA contradicts your claims.
Edited by Admin, : Typo.
Edited by Admin, : Grammar.

--Percy
EvC Forum Director

This message is a reply to:
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Replies to this message:
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Message 477 of 1034 (757995)
05-18-2015 7:36 AM
Reply to: Message 469 by herebedragons
05-17-2015 6:35 PM


Re: Moderator Introduced Definitions
herebedragons writes:
I would say this is ultimately what genetic diversity is, however, for all practical purposes it is impossible (at this time) to quantify this extent of genetic diversity.
Yes, of course. My examples using specific values for the number of genes and alleles were intended to make clear just what an increase or decrease in genetic diversity is. However difficult actual quantification might be in the real world, it can be an aid to hypothetical thinking to consider specific values.
Let me state it another way. If a population's genome should acquire an additional gene, that's an increase in genetic diversity. Or if it should lose an existing gene then that's a decrease in genetic diversity. And if a gene of that population's genome should acquire an additional allele then that's an increase in genetic diversity. Or if it should lose an existing allele (meaning no individual of the population possesses that allele) then that's a decrease in genetic diversity.
More important to diversity is what proportion of the loci are polymorphic and what fraction of the individuals are heterozygotic at a given loci. Not only are these the measures that are important to conservation, they are more readily measured.
Sure, but wouldn't that definition be more appropriate to a different discussion? People are trying to help Faith understand that genetic diversity can increase through mutation. Mutation can add and subtract both genes and alleles, and when that happens across a population it is obvious that genetic diversity increases or decreases.
Now of course mutation directly affects proportions of polymorphism and heterozygosity, but it seems more difficult to talk about genetic diversity in those terms. For example, varying heterozygosity of a specific loci helps measure the genetic diversity of a population. Fundamentally the type of genetic diversity this is measuring is how much variation there is across individuals in a population.
But I think what we're really interested in this discussion is the fundamental genetic diversity of a species. We don't really care to what degree a specific allele is distributed across a population. If that allele becomes more common or less common in the population it has absolutely nothing to do with mutation. All we care about is that that allele exists and continues to exist. Only if it should cease to exist in that population would it be a change in genetic diversity that this discussion would care about. And of course if that allele should experience a mutation then its gene now has one additional allele that it didn't possess before, and that means the population's fundamental genetic diversity has increased, which this discussion would also care very much about.
Perhaps that I'm finding myself forced to modify the term "genetic diversity" by adding the modifier "fundamental" up front means that what's really important to this discussion is not genetic diversity but something different though similar.
Edited by Admin, : Wordsmithing in 2nd para.

--Percy
EvC Forum Director

This message is a reply to:
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