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Author Topic:   Evolution Requires Reduction in Genetic Diversity
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 18 of 1034 (691699)
02-24-2013 1:18 PM
Reply to: Message 13 by Faith
02-24-2013 3:18 AM


Ring Species -- Greenish Warbler -- and Genetic Diversity
What you haven't yet grasped is that SELECTION always inevitably reduces genetic diversity. That is the substance of my argument very oversimplified. You can have mutations galore within a population but once you have selection of whatever mix of mutations -- or alleles however formed -- selection reduces genetic diversity in the new population. Selection brings a certain allele mix to expression in the phenotype BY ELIMINATING COMPETING ALLELES from the gene pool. Yes it will take some time to work through this argument.
Of course selection reduces the variations in a breeding population, because it winnows out the variations that are least advantageous. But evolution is a two-step process:
If you keep one foot planted and only move the other foot you don't get very far. Move both feet and you can walk from the east coast to the west coast - even if one foot is placed randomly and the other is always directed in a westerly direction.
Think of it this way:
  1. increase variation by mutation/s
  2. decrease variation by selection
  3. repeat
Step randomly, step west, step randomly, step west ...
As an example, let's take the Greenish Warbler in Siberia:
Greenish warblers
quote:
The greenish warbler ring species
Greenish warblers (Phylloscopus trochiloides) inhabit forests across much of northern and central Asia. In central Siberia, two distinct forms of greenish warbler coexist without interbreeding, and therefore these forms can be considered distinct species. The two forms are connected by a long chain of populations encircling the Tibetan Plateau to the south, and traits change gradually through this ring of populations. There is no place where there is an obvious species boundary along the southern side of the ring. Hence the two distinct 'species' in Siberia are apparently connected by gene flow. By studying geographic variation in the ring of populations, we can study how speciation has occurred. This unusual situation has been termed a 'circular overlap' or 'ring species'. There are very few known examples of ring species.
Plumage Patterns
West Siberian greenish warblers (P. t. viridanus) and east Siberian greenish warblers (P. t. plumbeitarsus) differ subtly in their plumage patterns, most notably in their wing bars, which are used in communication. While viridanus has a single wing bar, plumbeitarsus has two. Around the southern side of the ring, plumage patterns change gradually.
Genetics and history
Genetic data show a pattern very similar to the pattern of variation in plumage and songs. The two northern forms viridanus and plumbeitarsus are highly distinct genetically, but there is a gradient in genetic characteristics through the southern ring of populations. All of these patterns are consistent with the hypothesis, first proposed by Ticehurst (1938), that greenish warblers were once confined to the southern portion of their range and then expanded northward along two pathways, evolving differences as they moved north. When the two expanding fronts met in central Siberia, they were different enough that they do not interbreed.
As one subpopulation went west it accumulated mutations to the genes for plumage, size and mating songs, mutations that changed their original alleles to different ones. At each stage they had the same number of alleles, just a different mix from the original population.
As the other subpopulation went east is accumulated different mutations to the genes for plumage, size and mating songs, mutations that changed their original alleles to different ones. At each stage they had the same number of alleles, just a different mix from the original population, and a different mix from the other subpopulation.
P. t. trochiloides branches into P. t. ludlowii going west and P. t. obscuratis going east. Three subpopulations with different sets of alleles.
The process continues as P. t. ludlowii branches into P. t. nitidus going further west and P. t. viridanus going north, while P. t. obscuratis branches into P. t. plumbeitarsus and ending up with five subpopulations with different sets of alleles.
With the evolutionary two-step, the variations seen are fully explained.
Evolution Requires Reduction in Genetic Diversity
By selection/drift ... and
Evolution Requires Increases in Genetic Diversity
By mutations.
Enjoy.

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This message is a reply to:
 Message 13 by Faith, posted 02-24-2013 3:18 AM Faith has replied

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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 91 of 1034 (691867)
02-25-2013 9:19 PM
Reply to: Message 41 by Dr Adequate
02-25-2013 11:42 AM


Re: Walking Requires Staying In The Same Place
As walkists admit (such as the notoriously pro-walkist Wikipedia): "In humans and other bipeds, walking is generally distinguished from running in that only one foot at a time leaves contact with the ground and there is a period of double-support."
This means that walking requires leaving the right foot fixed in one place. Because I am not very bright, I shall now insist that this means that walking requires the right foot must be fixed in one place all the time. This means that someone walking cannot move from the spot, but can only turn around in circles.
Actually the right foot can only move in random directions, so it always ends up back where it started.
On this principle, I shall assert that micro-walking (for example to the shops and back) is perfectly possible, even though this flatly contradicts what I've just said. I'm not big on logical consistency. However, macro-walking, for example hiking the Appalachian trail, is clearly impossible, because you could not do that by merely revolving on the spot, which as I've explained is all a person can ever do when walking.
Yes the random motion of the right foot means that you can sometimes get to the shops in town, but that you cannot cover the Appalachian Trail where you will likely go over a cliff. This demonstrates that random foot motion overall is deleterious.
Enjoy

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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 320 of 1034 (725807)
05-01-2014 10:43 PM
Reply to: Message 1 by Faith
02-22-2013 6:14 PM


Dr A to Faith
See Message 267, Message 272, Message 282, Message 287 of this thread.
Edited by RAZD, : correct link
Edited by RAZD, : ...

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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 338 of 1034 (726292)
05-07-2014 9:34 PM
Reply to: Message 334 by Faith
05-07-2014 8:25 PM


And what would convince you Faith?
Sorry, you aren't persuading ME.
And what would convince you Faith?
For instance ...
(was subtitle): Re: and I still say (macro) evolution is impossible
Macroevolution is speciation and the formation of nested hierarchies.
This has been observed.
This means that your saying that "(macro) evolution is impossible" cannot be true.
... These require limiting the numbers of individuals, you aren't going to get breeds or species unless you do that ...
Black pocket mice. Twice.
Again your claim cannot be true.
Enjoy.

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This message is a reply to:
 Message 334 by Faith, posted 05-07-2014 8:25 PM Faith has replied

Replies to this message:
 Message 351 by Faith, posted 05-08-2014 5:59 AM RAZD has replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 354 of 1034 (726316)
05-08-2014 8:51 AM
Reply to: Message 351 by Faith
05-08-2014 5:59 AM


Re: And what would convince you Faith?
Message 347: The "tiny populations" in my scenarios are not all that tiny, they are simply populations that are SMALLER THAN THE PARENT POPULATION when they split off,l not necessarily "tiny.
You do realize that any division of a population makes smaller populations than the parent population?
... These require limiting the numbers of individuals, you aren't going to get breeds or species unless you do that ...
Black pocket mice. Twice.
A few black mice within the white mouse population get selected, there's your smaller number of individuals. They take up residence on the lava and are able to survive and reproduce on the lava so their population grows while any white mice that are with them die off and their alleles with them; and now you have a new subspecies of black mice.
The black mice evolved within the parent population before it split off into a smaller population -- exactly the opposite of your argument. So they invalidate your claim that "... These require limiting the numbers of individuals, you aren't going to get breeds or species unless you do that ..." rather than support it.
Because of those mutations, deleterious in the parent population's sandy ecology, they were able to take advantage of the opportunity provided by the lava beds, a different ecology, where the mutation was advantageous. The parent population continued to inhabit the sandy ecology, in the same numbers as before, maintaining all the tan mice alleles, a population that did not have any black mice alleles. Remember this happened twice and with different mutations causing the black mice in two different areas separated by a large deleterious (to black mice) sandy ecology.
Macroevolution is speciation and the formation of nested hierarchies.
This has been observed.
Nested hierarchies beyond the known genetically related groups are pure mental constructs, ...
No Faith, I mean in the world today: speciation and the formation of nested hierarchies has been observed -- your "known genetically related groups." This is what is defined in evolutionary biology as macroevolution.
So you agree that "known genetically related groups" form nested hierarchies of species. And I am pointing out that this is defined as macroevolution.
Now if you are using a different definition of macroevolution then you are confusing yourself again by misuse of words.
... mental constructs, fantasies, arrangements on the basis of subjectively assessed morphologies. No, they have not been "observed" merely imagined.
And yet, curiously, different people get the same results. And the results from morphological analysis and genetic analysis agree. Why does this happen if it is subjective Faith?
Since genetic diversity is reduced by the processes of evolution, the selection and isolation of traits, you cannot get evolution beyond the Species or Kind.
Speciation has occurred so either "evolution beyond the Species" has occurred or your statement is meaningless or poorly worded. Again I recommend you use the word "clade" rather than species.
Descendants of any species will always be a member of the same clade/s that includes the parent species. The black mice are in the same clade as the tan mice.
So each clade should have a clear and unambiguous beginning?
An imaginative construct says my evidence from observable living things can't be true, eh? I've even many times given a laboratory test for it. If I were in a position to set it up I'd have done it some time ago.
Why don't you lay out your purported laboratory experiment rather than make mysterious allusions to it.
And I note that you did not answer the question: what would convince you Faith?
Enjoy.

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This message is a reply to:
 Message 351 by Faith, posted 05-08-2014 5:59 AM Faith has replied

Replies to this message:
 Message 359 by Faith, posted 05-08-2014 9:29 AM RAZD has replied
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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 363 of 1034 (726350)
05-08-2014 12:07 PM
Reply to: Message 359 by Faith
05-08-2014 9:29 AM


Re: And what would convince you Faith?
If the black mice occurred within the white population they were still a smaller population there, and no doubt prey while they were there.
So you just can't admit that your claim " ... These require limiting the numbers of individuals, you aren't going to get breeds or species unless you do that ... " is falsified by the black mice evolving their traits within the parent population -- without limited numbers of individuals in the parent population causing their new traits.
... breeds or species ...
A better term is variety. The black mice are a new variety that evolved from the tan mice.
Definitional arguments are just game-playing.
Curiously I prefer to think that using agreed on terms for agreed on meanings enhances communication and clarifies thought. In that light I also think that using terms as they are used in science to debate science is one way to ensure you are actually debating the science rather than just playing word games.
You have noticed speciation and nested hierarchies but you have not noticed them beyond the Kind, that part is all imagination.
Perhaps another foray into cladistics can clarify the discussion:
Clade - Wikipedia
quote:
A clade (from Ancient Greek κλάδος, klados, "branch") or monophylum (see monophyletic) is a group consisting of an ancestor and all its descendants, a single "branch" on the "tree of life".[1] The ancestor may be an individual, a population or even a species (extinct or extant). Many familiar groups, rodents and insects for example, are clades; others, like lizards and monkeys, are not (lizards excludes snakes, monkeys excludes apes and humans).
Cladogram (family tree) of a biological group. The red and blue boxes at right and left represent clades (i.e., complete branches). The green box in the middle is not a clade, but rather represents an evolutionary grade, an incomplete group, because the blue clade at left is descended from it, but is excluded.
And as new species continue to arise from existing species, cladistics is more flexible in categorizing the new diversity of life than traditional taxonomy.
As can readily be seen from this diagram is that this is precisely (imho) how "kinds" would descend from a parent original kind. The question between creationism and evolution then becomes what and how many original kinds were involved.
Blue plus green is a clade and so is blue\green plus red. A clade located within a larger clade is said to be nested within that clade: the red clade is nested within the blue\green\red clade. The blue clade is nested within the blue\green clade.
A clade with nested clades is also called a nested hierarchy.
So is Red a kind and Blue/Green another kind or are all three one kind?
A difference in degree ... or difference in kind? How can you tell where the clades began?
And I note that you still did not answer the question: what would convince you Faith?
Enjoy

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This message is a reply to:
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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 413 of 1034 (757796)
05-14-2015 10:02 AM
Reply to: Message 408 by Faith
05-13-2015 12:08 PM


response moved here
Hi Faith, hope you are feeling better. I've been in bed with a sever cold\flue\allergy (not sure which, but headaches and coughing, so I'm just catching up on these threads).
Apparently breeding can result in speciation. At least there is one known instance, according to Wikipedia on Speciation:
There are many instances of speciation known about, but that is not one of the traits that are normally considered desirable during breeding (because you may want\need to use hybridization).
I'm moving my comments from Message 204 on the If evolution is true, where did flying creatures come from? thread here as they are more pertinent to this topic:
HI Faith,
I have to stop here in your voluminous post.
Yes, we both tend to get verbose. If you like we can break it up into multiple posts if length becomes a problem in covering the topics.
Selection certainly applies here as Darwin himself was doing the selecting, at times rather drastically isolating a trait of his choosing and breeding to enhance that trait until the bird was dominated by it to the exclusion of other characteristics. If there was some reason in nature for the development of the same trait you would see Natural Selection at work to the same end.
Agreed, but I would also note that the result of natural selection are individuals within a species that are adapted to survive and breed in their ecology, while human selection is for traits that appeal to humans, whether they have any survival or reproductive value, and for that reason a lot of domesticated breeds of pigeon, horses, sows, pigs, dogs and cats have traits that would be disadvantageous in the wild or even lethal without human medical interference. Different purpose → different effect.
His insight was that the selection process occurred naturally, where animals that survived and bred passed their genes (that enabled them to survive and be selected by mates for breeding) to the next generation.
Yes, this was his insight but he didn't have the knowledge that would tell him that the changes that occur through selection, natural or artificial, are limited by the fact that selection eliminates alleles in the process of developing new phenotypes. Eventually the new breed or type may be quite strikingly different from others of its kind but it will of necessity have much less genetic ability for any further evolution. ...
You've been told and shown and shown and told that this is not true, this belief of yours that no new alleles are produced. There are some examples in other replies to you.
Curiously I think Zatara had a good new example in Message 61:
Anyone who has raised identical twins has observed the dramatic effects of mutation in just one generation. Their twins may have started out with identical DNA, having come from the same zygote; however, in just nine months in utero the mutations have yielded differences noticeable to all but a casual observer.
Their DNA came from the same original single celled zygote, but during fetal development the process of cell division and duplication and selection for which aspects of their DNA is expressed becomes different as different mutations are incorporated into the development of the individual fetuses -- where did those differences come from if not mutation Faith?

Greenish warblers again

... When a trait is selected its genotype is also selected, and alleles for other expressions of the same trait are soon eliminated from the population of birds from which the trait is being bred. If the selection continues generation after generation a point may be reached where ONLY the alleles for the chosen trait are present, all others having been left behind in the original population. if this goes on long enough in nature it is easy enough to see how a subpopulation could develop inability to interbreed with other populations of the same Species, from sheer genetic mismatch ...
Curiously we can actually examine this claim in more detail with the Asian greenish warblers (Phylloscopus trochiloides):: different traits in each subpopulation, traits that govern plumage variations and mating and call song variations:
quote:
Genetic data show a pattern very similar to the pattern of variation in plumage and songs. The two northern forms viridanus and plumbeitarsus are highly distinct genetically, but there is a gradient in genetic characteristics through the southern ring of populations. All of these patterns are consistent with the hypothesis, first proposed by Ticehurst (1938), that greenish warblers were once confined to the southern portion of their range and then expanded northward along two pathways, evolving differences as they moved north. When the two expanding fronts met in central Siberia, they were different enough that they do not interbreed.
Note that it is hypothesized that the original parent population that these varietals all descended from was "once confined to the southern portion of their range" ... SO: if your hypothesis were true (that varietals only arise by the loss of alleles in the descendant populations) that they would KNOW that one population was the source of the others as it would still have ALL the alleles of ALL the varietals.
Sadly (for you), the genetic evidence tells us that no one population has more alleles than the others, to say nothing of combining all of them: there isn't one population that has all the alleles of all the variants.
Further note that none of the populations are completely isolated from the others, that there are small overlapping zones between them:
So there isn't complete genetic isolation and gene flow is possible from one end to the other. This gene flow is limited by the distance the individual birds will travel from where there were born to where they nest and mate and rear young during their lives, so gene flow from one end to the other could take several generations.
Now I would expect a corollary of your hypothesis (that divergence from a parent population results in loss of alleles) to be that when the populations converge in an overlap zone and interbreed that the alleles would be recombined in the hybrid zones and tend to restore the number of alleles from the original parent population in the hybrid population.
Your problem is that there are four such zones -- (1st) between viridanus and ludlowi, (2nd) between ludlowi and trochiloides, (3rd) between trochiloides and obscuratus and (4th) between obscuratus and plumbeitarsus. Which of these is your parent population with the more complete set of alleles?
Additionally, with gene flow from each of these hybrid zones to each neighboring varietal zone, we would expect (from your hypothesis) that the intermediate varietals would be hybrids between each of their end (hybrid) zones, ie that ludlowi would be a hybrid between the 1st and 2nd zones, that trochiloides would be a hybrid between the 2nd and 3rd zones, and that obscuratus would be a hybrid between the 3rd and 4th zones, and continuing this reasoning we should see trochiloides as a hybrid between ludlowi and obscuratus, that even if trochiloides was not the original parent population posited in your hypothesis that it should, via convergence of the populations, have characteristics more like this posited parent population that the other varietals.
That we do NOT see the hybridizing restoring the full allele distribution to one of these populations means one of two things:
  1. that the posited parent population with a full mix of alleles available is not as robust and able to survive and breed as the daughter populations each with less alleles than this (which doesn't fit with your hypothesis)... or
  2. that this posited parent population with a full mix of alleles never existed, and the varietals are due to mutations along the way as they spread out, variations that spread back and forth with gene flow without being combined into one master population that would have all the alleles.
Can you explain how this evidence does not invalidate your hypothesis?
Evolution with mutations and natural selection explains these population variations without the problems your hypothesis has.

Pelycodus again

Now I want you to look at the bottom line in this graph, below where it says P.ralstoni:
Under the "P" there is a thicker line, and this designates where more of the population is found, with the thinner lines to each side designating the variation in the population to each extreme right and left. You will note that these thicker lines stagger back and forth a fair bit as you go up in the diagram to younger populations.
If I draw a vertical line from the right end of the bottom population (below "P.ralstoni) ...
  1. as I ascend to younger populations where do the new traits to the right of this line come from?
  2. when I get to P.trigonodus the whole population is to the right of P.ralstoni: where do the traits of that population come from?
Remember that the overlaps from level to level, showing more than 50% of these populations have identical traits, is an indication that they represent the same species/clade breeding population changing over time and adapting to the ecology.
Next, If I draw a vertical line from the right end of P.trigonodus I can repeat my questions:
  1. as I ascend to younger populations where do the new traits to the right of this new line come from?
  2. when I get to the group just below "N.venticolis" that whole population is to the right of P.trigonodus: where do the traits of that population come from?
This latter group is now twice removed from the base population that we started with: how do you explain their traits with your hypothesis?
Further, if I now draw a vertical line from the left end of P.jarrovii down, then according to your hypothesis that alleles are lost, then ALL the alleles expressed in the base population to the left of this line are now apparently lost in this descendant population, but extending that line up we see traits similar to the original traits returning to the point where N.nunienus seems to recapture most the original traits.
Note that the traits involved here are size related traits (size of bones, teeth, body mass, etc), and other traits (coloration, vocalization, etc) are not included so that younger populations would still not appear like the base population even though they now share size related traits.
How can you explain this with your hypothesis? Can you explain how this evidence does not invalidate your hypothesis?
Note that if you posit that traits can become hidden and then re-expressed later when conditions suit (as you have posited hidden traits that become expressed, as I expect you to claim for traits to the right of my lines - and as you have claimed for the foxes - that this invalidates your claim that the traits are lost and thus results in a death spiral of lost traits).
Evolution with mutations and natural selection easily explains these population variations without the multiple contradiction problems your hypothesis has.

Foxes again

You say nothing about artificially induced mutations here, and there is absolutely no need for them. This change was possible because the genetic material for the chosen traits was already present in the fox genome and could be selected over several generations. This is how all breeds of animals were originally developed, by selection of the traits desired by the breeder, selection meaning basically reproductive isolation of the individuals with those traits. ...
Not quite correct Faith -- the ONLY trait selected was tameness, and this was done specifically to make the foxes easier to handle on the fox farms where they are raised for their desired black lush fur. That white spots developed is contrary to what the desired result was.
The reason is that tameness is related to adrenalin levels and adrenalin is a hormone that affects fetal development paths, including fur color, ear and tail characteristics. This is about mutations that occur during fetal development because of the different hormonal environment for the fetus. Mutations that affect the timing of development.

and Bacteria again

Bacteria don't function genetically or reproductively the way sexually reproducing animals do ...
Actually the point of bacteria is that cell division and multiplication during fetal development is the same process that bacteria use to reproduce. Thus bacteria developing new traits and fetal development changing to develop new traits (the fox fur, ears and tail traits) are the same process - adaptation to a different chemical environment with new mutations.

denial is not evidence

... and I refuse to accept such "evidence." But of course that's the best you can do to answer my obvious points, isn't it?
Curiously I think I (and others) have done more than answer your "obvious points" and raised (again) legitimate points that you have yet to answer. Sadly I expect your "answer" to be more denial rather than confronting the evidence.
There is a lot more evidence that supports evolution, evidence of mutation providing new alleles, evidence of selection and drift causing an accumulation of new traits in species over time.
There is no evidence that traits are only lost and never gained, but there is evidence of traits being gained.
Enjoy
Thought I'd be able to post today but my eyes are hurting, so I have to put it off again.
sad to hear, I have another friend with macular degeneration, it sucks.
Enjoy
Edited by RAZD, : ..
Edited by RAZD, : sp

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This message is a reply to:
 Message 408 by Faith, posted 05-13-2015 12:08 PM Faith has replied

Replies to this message:
 Message 445 by Faith, posted 05-16-2015 1:44 AM RAZD has replied
 Message 450 by Faith, posted 05-16-2015 12:11 PM RAZD has replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 414 of 1034 (757797)
05-14-2015 10:28 AM
Reply to: Message 410 by Dr Adequate
05-13-2015 6:48 PM


Re: genetic diversity
can I say "Baaa humbug" ???
One of the reasons that (I think) there is less speciation in domestic breeds versus wild variants is that breeders frequently cross-breed to (a) cure genetic diseases and (b) generate new variants, so they end up breeding for continued ability to interbreed between varieties.
Now if Faith's hypothesis were correct, it seems to me that a corollary would be that hybridizing between variations should be able to recover (or tend to recover) the original base genetics, ie you should be able to combine the genomes of O. aries to get O. orientalis ... and do it without losing traits ...
Enjoy

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RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 436 of 1034 (757887)
05-15-2015 1:45 PM
Reply to: Message 431 by Denisova
05-15-2015 5:23 AM


Re: genetic diversity -- new alleles = mutation
Denisova writes:
2. So, plain observation learns that alleles must have been added since the days of Adam and Eve. The mere fact that some traits are related to more than one gene does not change anything to this simple observation.
I agree, but it does depend on the quality of the extra "alleles" as Isaid.
Alleles being added means a gain in genetic diversity.
There's no way around this.
More to the point alleles being added mean mutation that increased genetic diversity.
Enjoy

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This message is a reply to:
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 Message 439 by Faith, posted 05-15-2015 6:28 PM RAZD has seen this message but not replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 437 of 1034 (757895)
05-15-2015 5:07 PM
Reply to: Message 422 by Faith
05-14-2015 2:42 PM


dating methods and consilience of evidence
Your dating methods are highly suspect, and you really haven't "shown" me evidence. ...
You continue to say this even though you haven't addressed the consilience of evidence in Age Correlations and An Old Earth, Version 2 No 1. When I bring up this evidence in other threads you say you can't explain it.
... Go out and collect some ring species and read the DNA of the populations at different points around the ring. That's where I think the evidence should be. Chipmunks around the Sierra, salamanders in northern California, seagulls around the northern Atlantic, etc.
And this has been done, as I noted in Message 413:
Curiously we can actually examine this claim in more detail with the Asian greenish warblers (Phylloscopus trochiloides):: different traits in each subpopulation, traits that govern plumage variations and mating and call song variations:
quote:
Genetic data show a pattern very similar to the pattern of variation in plumage and songs. The two northern forms viridanus and plumbeitarsus are highly distinct genetically, but there is a gradient in genetic characteristics through the southern ring of populations. All of these patterns are consistent with the hypothesis, first proposed by Ticehurst (1938), that greenish warblers were once confined to the southern portion of their range and then expanded northward along two pathways, evolving differences as they moved north. When the two expanding fronts met in central Siberia, they were different enough that they do not interbreed.
Note that it is hypothesized that the original parent population that these varietals all descended from was "once confined to the southern portion of their range" ... SO: if your hypothesis were true (that varietals only arise by the loss of alleles in the descendant populations) that they would KNOW that one population was the source of the others as it would still have ALL the alleles of ALL the varietals.
Sadly (for you), the genetic evidence tells us that no one population has more alleles than the others, to say nothing of combining all of them: there isn't one population that has all the alleles of all the variants.
Message 420
Now if Faith's hypothesis were correct, it seems to me that a corollary would be that hybridizing between variations should be able to recover (or tend to recover) the original base genetics, ie you should be able to combine the genomes of O. aries to get O. orientalis ... and do it without losing traits ...
I think that would depend on how far the processes of evolution have gone, because after a time of inbreeding of a new subpopulation its genome would have changed, developing its own gene frequencies, losing alleles that don't get passed on, increasing others and so on, so that even if hybridization is still possible it probably won't recover the original genetic situation exactly. But quite a bit should be recovered nevertheless. If not, it will develop a new breed anyway.
This is an ongoing process in the greenish warblers, genetic isolation has not occurred at this point and each population still interbreeds with the neighboring population in the hybrid zones. We do not see one population with more alleles than the others.
We do not see the pattern of genetic loss that your hypothesis claims.
Enjoy.

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RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 422 by Faith, posted 05-14-2015 2:42 PM Faith has not replied

Replies to this message:
 Message 446 by Tangle, posted 05-16-2015 3:35 AM RAZD has replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 455 of 1034 (757944)
05-16-2015 5:57 PM
Reply to: Message 446 by Tangle
05-16-2015 3:35 AM


Re: dating methods and consilience of evidence
The modern idea of ring species is that they don't exist. In fact some people said that many years ago when I was learning about evolution but now there's genetic evidence that shows that they all seem to have had a geographic isolation event at some or at several points in their evolution. See
https://whyevolutionistrue.wordpress.com/...-no-ring-species
It's still proof of evolution, just not the neat story we'd like it to be. Shame, I was very fond of the gull ring.
So it seems there was some geological isolation and then the groups rediscovered each other in the hybrid zones. Not as neat as before, but still not a total loss, imho, as they still show genetic variation around the ring and they still show how speciation can occur -- the major driver being species divergence between daughter populations.
Also I am not surprised that they found hybrids of the two nothern variants, as it was pretty evident to me that the barrier was sexual selection and not genetic incompatibility. Brings to mind an old study that showed the longer a male went without breeding the more he tried to mate with things that looked less and less like their ideal mate (done with stickleback minnows).
As far as I can see the only real difference is that divergence around the ring is clumpy rather than smooth, and I don't really understand why smooth would be expected: genetic change is essentially clumpy -- you don't really get a mixing of parental genes but a mosaic of genes and how they are expressed. After all that's why Mendelian genetics works.
Enjoy

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This message is a reply to:
 Message 446 by Tangle, posted 05-16-2015 3:35 AM Tangle has not replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 458 of 1034 (757950)
05-16-2015 9:34 PM
Reply to: Message 445 by Faith
05-16-2015 1:44 AM


continuing in bits
I'm going to have to do that but I'll also not answer other posts while I'm working on yours so maybe I can get through it all.
My attention span is ~10 minutes at this point, what with coughing, headaches, congestion and the effects of the medications ...
... The whiteness of the chart hurts my eyes so I don't want to spend more time on it but I spent enough to know I'm not getting what I'm supposed to get out of it. ...
I'll try to make a more viewable version when I get to it below (or in following posts).
I am also going to try to be brief and hit the important points.
When it comes to human selection or natural selection ...
... since despite the different purpose the methods are the same.
Agreed: variation and selection and isolation of populations to maintain those variations.
I know you believe this but nothing has yet really challenged the point I keep trying to make.
And our time is best spent on zeroing in on where your argument differs from evolutionary models.
For the evolutionary model variation develops from mutations in the species, and this occurs whether we are talking about the whole species or isolated populations. Whether or not isolated populations start with the same number of alleles, or not, depends on the size of the population.
For your model - as I understand it - variation occurs through either removal of some alleles from the population or by mutations that deteriorate the alleles, and this occurs whether we are talking about whole species or isolated populations, however you also argue that when a population divides that one or the other or both will not have a full set of alleles, but a subset of them ... and thus less genetic variation.
First of all I have never heard of the parents of twins having this sort of experience before this. And it doesn't fit with what is said about mutations not making a noticeable difference for many generations, besides all the negatives that far outnumber anything positive that they ever produce. Mutations occur, yes, but not useful mutations except very very rarely, and not even mutations that actually code for something recognizable either. This is what I've gleaned from various discussions of mutations, not something I made up.
Generally speaking this is true (except that a large number are neutral and can become beneficial later.
However, all the identical twins I know do have some variations in appearance, and also in behavior\temperment. These differences must arise from development variations as they started with identical genes from a single zygote. This development is controlled by the DNA interaction with hormones\chemicals during development.
There are many examples of developmental mutations causing single generation variations -- from missing or additional fingers or toes to siamese twins to fatally deformed fetuses. There are genes called HOX genes that control the development of the fetus and any alteration to those genes will show immediate results. This is part of evo-devo evolution.
The upshot is that there are several mechanisms that result in variations available for selection, some that are not deleterious nor necessarily beneficial, just different.
Nor are these differences necessarily advantageous or deleterious (depending on how extreme they are).
Nor do they necessarily challenge your hypothesis -- it is just evidence that mutations happen.
I have to stop now
Enjoy

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RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 445 by Faith, posted 05-16-2015 1:44 AM Faith has not replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 466 of 1034 (757969)
05-17-2015 2:47 PM
Reply to: Message 450 by Faith
05-16-2015 12:11 PM


Re: response moved here: RAZD pt 3 Pelycodus
I'm feeling a bit better today, the allergies seem to have let up.
This is part of your discussion of the chart about Pelycodus. I get that going up the chart is going from older to newer specimens but I need more of an explanation of the whole chart. The names and numbers on the left margin refer to what? locations of some fossils I assume, and their ages or numbers or what? And what do the numbers along the bottom indicate: millions of years?
Yes, the vertical scale is age -- relative age from layering and the law of superposition. The words are the geological names of the layer formations, and yes the fossils are of course embedded in those layers
The horizontal scale is size (and traits related to size, like weight). Thus we have a genetic trait that is expressed in the phenotypes within the population -- the line shows the variation within each population and the thicker sections are to denote the majority of the distribution (which is not always the center of the whole distribution).
Let me see if I can reproduce it within the limits of text the graphic data from Message 413
          --------o--------   3             2        ----------o----------
N.nunienus 3 2 N.venticolis
--===3-- 2 ---===========-
-=3==---- 2 =
-3--====--- 2
3 ----===-----2--- =
---3-====--------2-
-3---=====-----2
3 ---===2==== =
3 ----------2---------------------------*
3 -------====2==---
3--=======----2
3------------=2=----------
3 P.jarrovii
------3=========----2--------
--===-- 3 2
---=====3====---------2-----
==3== 2
3 === 2
-----==3=----- 2
1 ----===3==-----------2
1 p.trigonodus
1 ------=====--3--------
1 ------===----3--
1 ==== 3
1 ----====--3------
1 === 3
1 ---=======3==--------
--1---======---- 3
1-----========-3-------------
1 --==-- 3
------1---====-------3----
1 ----=======--3----------
1 -----=====---3------------
--------=1=====---------3
----=1===---- 3
---------1====------ 3
1======- 3
P.ralstoni 3
--------===----1 3
Please recognize that this is an approximation of the graph, but that the relative lengths and positions are as accurate as I can make them. I hope this is easier on your eyes.
Now I'll repeat what I said in Message 413 about the graph:
Under the "P" there is a thicker line, and this designates where more of the population is found, with the thinner lines to each side designating the variation in the population to each extreme right and left. You will note that these thicker lines stagger back and forth a fair bit as you go up in the diagram to younger populations.
If I draw a vertical line from the right end of the bottom population (below "P.ralstoni) ...
  1. as I ascend to younger populations where do the new traits to the right of this line come from?
  2. when I get to P.trigonodus the whole population is to the right of P.ralstoni: where do the traits of that population come from?
Remember that the overlaps from level to level, showing more than 50% of these populations have identical traits, is an indication that they represent the same species/clade breeding population changing over time and adapting to the ecology.
Next, If I draw a vertical line from the right end of P.trigonodus I can repeat my questions:
  1. as I ascend to younger populations where do the new traits to the right of this new line come from?
  2. when I get to the group just below "N.venticolis" that whole population is to the right of P.trigonodus: where do the traits of that population come from?
This latter group is now twice removed from the base population that we started with: how do you explain their traits with your hypothesis?
Further, if I now draw a vertical line from the left end of P.jarrovii down, then according to your hypothesis that alleles are lost, then ALL the alleles expressed in the base population to the left of this line are now apparently lost in this descendant population, but extending that line up we see traits similar to the original traits returning to the point where N.nunienus seems to recapture most the original traits.
Note that the traits involved here are size related traits (size of bones, teeth, body mass, etc), and other traits (coloration, vocalization, etc) are not included so that younger populations would still not appear like the base population even though they now share size related traits.
How can you explain this with your hypothesis? Can you explain how this evidence does not invalidate your hypothesis?
Note that if you posit that traits can become hidden and then re-expressed later when conditions suit (as you have posited hidden traits that become expressed, as I expect you to claim for traits to the right of my lines - and as you have claimed for the foxes - that this invalidates your claim that the traits are lost and thus results in a death spiral of lost traits).
Evolution with mutations and natural selection easily explains these population variations without the multiple contradiction problems your hypothesis has.
Note that I have inserted the numbers for the lines: "1" for the line described in (a), "2" for the line described in (c) and "3" for the line described in the 2nd paragraph after (d), so you can see where they fit on the data.
Of additional interest is that the red line with an * and no thick section is about where the division of the parent population into two sub-groups begins, with large variants to the right and small variants to the left, which then becomes a gap in the data that shows absence of interbreeding between these daughter populations.
If we only looked at the data from the red line up, then your argument that the traits are split between the populations with each daughter population losing traits the other population has could be applied.
However when we look at the longer history we see that traits that should have been lost from P.rastoni in the P.jarrovii population reappear.
Either traits are not lost but go from hidden to expressed and from expressed to hidden ... or new traits evolve.
I await your explanation.
Enjoy
ps -- that text diagram will not copy well for reasons beyond my control

we are limited in our ability to understand
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RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 450 by Faith, posted 05-16-2015 12:11 PM Faith has replied

Replies to this message:
 Message 468 by Faith, posted 05-17-2015 5:42 PM RAZD has replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 470 of 1034 (757975)
05-17-2015 6:52 PM
Reply to: Message 468 by Faith
05-17-2015 5:42 PM


Re: RAZD pt 3 Pelycodus
Drat, RAZD, I know you went to a lot of trouble reconstructing that chart for me and I thank you for that, but I still look at it and your descriptions and feel I don't have any idea what point you are trying to make. ...
So let's try to break it down verbally.
The bottom horizontal line represents a population (Pelycodus ralstoni) with variations in the size of individuals in the population, and the predominant size is represented by the thicker section of the line.
Other lines represent populations of the same species at later times, as they are embedded in layers above the bottom layer, the higher they are the younger they are.
The ages are relativistic based on the geological layers and the law of superposition.
Each of the fossil lines overlap the lines of the layer below and the layer above and thus they show continuity of the species from one line to the next.
The variable in question is size. What we see is that size in each population differs in distribution from one layer to the next, and this would be due to the alleles that govern body size.
There is an overall general trend from the original smaller fossils to larger fossils as you rise from the bottom layer to Pelycodus trigonodus, about half-way up the chart, and at this point all the fossils at this level are larger than all the fossils of the bottom original population layer. This is shown by the vertical line marked by the 1's in the diagram.
This trend continues through Pelycodus jarrovii, about 3/4ths up the chart and up to the red line. At this point the population divides, with one population continuing the trend to larger fossils up to the top of the chart with N.venticolis.
The vertical line marked with the 2's shows that these top larger fossils are all larger than the Pelycodus trigonodus population, which are all larger than the original population at the bottom. None of the Pelycodus trigonodus population are the same size as either the top or the bottom, so the size of the fossils in N.venticolis are twice removed from the size of the original population.
But the population at the red line splits and forms two populations with different sizes:
  • the ones to the right keep the larger fossils size and the trend to larger fossils in higher\newer layers
  • the other population takes the small size from the red line and reverses the trend, and instead trends to smaller fossil sizes in the higher\newer layers.
Line 3 is a vertical line from the left end of Pelycodus jarrovii, and following it down we see that all the original base population were smaller than the smallest fossil at the Pelycodus jarrovii level -- so all of those alleles should be lost to the species at this point according to your hypothesis.
But as we follow the line up we see the second population trending smaller crosses this line and continues to get smaller up to N.nunienus, when all of the fossils are to the left of line 3 ... when alleles for these sizes should not be available anymore, having been lost. In fact ~half of N.nunienus are the same size as Pelycodus ralstoni.
Here it is again:
          --------o--------   3             2        ----------o----------
N.nunienus 3 2 N.venticolis
--===3-- 2 ---===========-
-=3==---- 2 =
-3--====--- 2
3 ----===-----2--- =
---3-====--------2-
-3---=====-----2
3 ---===2==== =
3 ----------2---------------------------
3 -------====2==---
3--=======----2
3------------=2=----------
3 P.jarrovii
------3=========----2--------
--===-- 3 2
---=====3====---------2-----
==3== 2
3 === 2
-----==3=----- 2
1 ----===3==-----------2
1 p.trigonodus
1 ------=====--3--------
1 ------===----3--
1 ==== 3
1 ----====--3------
1 === 3
1 ---=======3==--------
--1---======---- 3
1-----========-3-------------
1 --==-- 3
------1---====-------3----
1 ----=======--3----------
1 -----=====---3------------
--------=1=====---------3
----=1===---- 3
---------1====------ 3
1======- 3
P.ralstoni 3
--------===----1 3
In evolutionary terms it makes sense for the two lineages to diverge in size as that means they forage for food in different locations rather than compete for the same resources.
Because evolution theory does not depend on a finite supply of alleles there is no conflict with variation back and forth in size from small to large and then to small again.
Because your hypothesis does depend on a finite supply of alleles there is a conflict when one set (ie - for small size) is lost. You can invent new alleles for the larger fossils from your hidden allele magic black box, but not for a return to small size alleles, because you have been adamant that they are lost as the population diverges from the parent population.
Enjoy

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RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 468 by Faith, posted 05-17-2015 5:42 PM Faith has replied

Replies to this message:
 Message 478 by Faith, posted 05-18-2015 2:12 PM RAZD has replied

  
RAZD
Member (Idle past 1517 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 545 of 1034 (758233)
05-22-2015 1:13 PM
Reply to: Message 529 by Denisova
05-21-2015 11:41 AM


walkingsticks and wings
Interesting article!
Another one dealing with lost traits is (from Message 18 on the Silly Design Institute: Let's discuss BOTH sides of the Design Controversy... thread):
See Figure 1 from Nature 421, 264 - 267 (16 January 2003); doi:10.1038/nature01313 (reproduced below)
Walkingstick insects originally started out as winged insects (blue at start and top row). That diversified.
And some lost wings (red). And diversified.
And some regained wings (blue again). And diversified.
And one lost wings again (Lapaphus parakensis, below, red again).

And this doesn't even address the ones where one sex (usually male) has wings and the other sex doesn't (the red includes these, so it is hard to determine from this graphic how many times the female sex gained and lost wings independent of the winged males).
From a Design standpoint, this is not intelligent design, it is either "Make up your #*! mind" design, or it is classic "Now you see it now you don't" silliness.
That thread is mostly to address ID arguments about "both sides" ... and the cases where males are winged and females not usually have large females for lots of eggs.
It should be evident that the DNA sequences for the wings are not lost, but turned on and off by control sequences that are modified one way or the other. The genetics must be truly fascinating on these guys.
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 529 by Denisova, posted 05-21-2015 11:41 AM Denisova has replied

Replies to this message:
 Message 546 by Denisova, posted 05-22-2015 3:58 PM RAZD has replied

  
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