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Author Topic:   Introduction to Genetics
Faith 
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Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 139 of 236 (719608)
02-15-2014 7:46 PM
Reply to: Message 138 by RAZD
02-15-2014 6:41 PM


Predictability of Genetic Variability
As whole genomes become sequenced and the variations of individuals mapped against a "species standard" genome, there is no way that this variability will NOT be mapped.
As it stands with the current state of genomes there are no locations holding hidden variations sufficient to result in anything more than variation level change that would be expected via evolution views of mutations moving a section of DNA from one location to another -- not enough to change a domestic cat into a tiger or vice-versa ... which of course would be within what is expected of the evolutionary model.
Should we expect anything more from the creationist model?
The best way to see a trend in the amount of genetic variability would be by comparing genomes from a series of population splits into daughter populations where you know the number of founding individuals and what sort of phenotypic changes came to characterize each population over some known number of generations. I've come to think of the percentage of heterozygosity as the main indicator, and I've thought this could be tested by looking for the percentage of heterozygosity in a series of ring species in the wild, but probably the best test would be in the laboratory where you could control for all the variables.
Basically what you are saying is that each speciation results in a genetic bottleneck for the subspecies. And that this would be a permanent condition for the subspecies.
Not a bottleneck because that involves a very drastic reduction in numbers for the founding of a new population, and I'm thinking of a more normal-sized founding population. But I AM saying that the trend to [ABE: REDUCED/ABE] genetic variability should be the case in all such population splits anyway, and yes, that it would be a permanent condition for the subspecies barring a reintroduction of gene flow.
And thus we can test for whether
a. subpopulations after a speciation event have less variation than the parent population, l...
No RAZD, not "less VARIATION," but less GENETIC VARIABILITY. There is a big difference. You may be getting much greater variation in the phenotypes, in fact you should, but the genetic variability should also be getting reduced in the process.
b. the genetic variability stays at a low level after a speciation event.
OK. You are of course counting on mutations, which of course you expect to be viable mutations that make real alleles and occur in the germ cells so they can be passed on. But if such mutations did enter into the picture it should have the same effect as the reintroduction of gene flow from any source: that is, it would change the new subspecies' phenotypic character into something else. It would in effect be a new "speciation" or subspeciation. But I don't think you'd find any genuine increase in the genetic variability anyway, so OK, yes, that would be a test.
Would you agree that if the initial cause of reproductive isolation was physical isolation -- say the parent population occupies a peninsula and an earthquake or hurricane causes part of the peninsula to become an island, with a gap that this population cannot cross -- that the population on the remaining peninsula and on the island have the same amount of variation\variability?
I'm not sure why HOW the formation of a daughter population should change things. Migration of the new population to a new geographic area would accomplish the same thing, assuming reproductive isolation as well. In any case it depends on the numbers involved. If the number of individuals on the new island is appreciably smaller than the number in the parent population [ABE: actually the population left on the peninsula which may or may not reflect the genetic situation of the original parent population /ABE] it should show a reduction in genetic variabilithy, but not right away. At first if you checked individual genomes they'd have the same genetic variability of course. It would take a few generations for the different gene frequencies in the two populations to show up in the development first of many different phenotypes and then a recognizable new phenotypic character for the population as a whole, and that's when I'd expect a reduction in genetic variability to start to become measurable.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
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 141 of 236 (719700)
02-16-2014 6:04 PM
Reply to: Message 140 by herebedragons
02-16-2014 4:58 PM


Re: Factual versus interpretive tendentious terminology
I don't think you mean to suggest that all members of the dog "kind" are all just subspecies, do you?
Yes, of course. There's the Kind and then there are subspecies or variations on the Kind.
I understand better what your objections are and will try to do my best to accommodate them.
Thank you.
What you are actually disagreeing with is the mechanisms that lead to that event, not the event itself
I certainly don't see how this is true. Population splits are the best example of how new subspecies are formed, and I make a lot of my case about how this leads to decreased genetic variability from this example, so the idea I'm objecting to the mechanisms makes no sense.
Your proposed mechanism for speciation is geographic isolation with a reduction in genetic diversity. It is this reduction in genetic diversity that causes the two populations to be identified and separate species or subspecies. This is not what mainstream thinking proposes.
No, it's my own theory which I think pretty clearly parallels a lot of creationist thinking, though the usual way it's thought about is that there is not an increase in "information." At some point I realized that phenotypic change by population splits actually requires a decrease in genetic variability in the new population as compared with the former population, and I know this isn't going to be apparent right away. The difference in gene/allele frequencies ought to be apparent pretty soon though. The new gene frequencies, more of some alleles, fewer of others, should produce new phenotypes in individuals in the new population within a few generations. This doesn't look like a decrease in genetic variability because you are also getting a higher percentage of some alleles along with a lower percentage of others. And in fact in the first daughter population all the alleles of the former MAY be present so you DON'T have a decrease. But you are NEVER going to have an increase unless there is resumed gene flow, and that of course destroys the whole example of population splits.
But if just one allele didn't make it into the new population that's a decrease, and that's very likely to happen with population splits. Again, it's never going to work the other way, you'll never have an increase because you are simply taking a portion of the existing alleles into the new population. So, never an increase, possibly no decrease, but nevertheless very likely a decrease, a loss of alleles. That's the trend.
And if the daughter population splits again then you are VERY likely to have a decrease in genetic variability, and this is what I think happens in ring species. And no this is not mainstream thinking at all. I think by the time a species has evolved around a ring the last population should have much less genetic variability than the first, and this should demonstrate the principle I keep arguing here: that such a decrease in genetic variability is inevitable in the processes of evolution that produce new phenotypes or varieties or races or breeds. And since that is the case, you have the processes of evolution working against the assumptions of the ToE, which needs more rather than less variability to be true.
The only answer to this is mutations, because they appear to provide an increase in genetic variability. IF they made viable alleles this would be true, but that's the same as reintroducing gene flow which would change the character of the population, so the species in a ring species, say, wouldn't remain that particular species. I just don't think that happens or could happen. But this IS the only objection there is to the scenario I keep laying out so eventually it will have to be better answered than I've done so far.
I AM objecting to the idea that what they lead to is a new "species" rather than just another subspecies. I see no justification for that term since the mechanisms are not different.
We will have to discuss speciation more in depth later on, you do have a different idea of how speciation works (ie. the mechanism).
In a sense there's no reason not to use "species" because it merely implies a new variety or race, but within the ToE it implies validation of the ToE itself so I think it helps to try to make a distinction.
I still don't see that I have a different idea of how speciation works, however, I'm simply insisting on calling it a subspecies so as to avoid the implication that the Kind can evolve or vary in any way outside the Kind.

This message is a reply to:
 Message 140 by herebedragons, posted 02-16-2014 4:58 PM herebedragons has replied

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


Message 147 of 236 (719777)
02-18-2014 1:28 AM
Reply to: Message 146 by AZPaul3
02-17-2014 9:54 PM


Re: An Interesting Graphic
I am unable to read that page. It's hard on my eyes from the whiteness and the print is too small. I could probably make it readable but I'd have to have a good reason for doing that, if you could explain that to me. Thanks.
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 155 of 236 (719830)
02-18-2014 2:47 PM
Reply to: Message 151 by Taq
02-18-2014 11:04 AM


Re: Paradigm clash
Reality shows that genomes can be different without causing harm.
Odd you would think I or anyone thought otherwise.

This message is a reply to:
 Message 151 by Taq, posted 02-18-2014 11:04 AM Taq has replied

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


Message 158 of 236 (719861)
02-18-2014 7:37 PM
Reply to: Message 156 by Taq
02-18-2014 4:48 PM


Re: Paradigm clash
Genomes ARE different from kind to kind, and also through the processes that bring about subspecies.. Don't see what that has to do with mutations being destructive.
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 160 of 236 (719869)
02-18-2014 10:13 PM
Reply to: Message 159 by Taq
02-18-2014 9:48 PM


Re: Paradigm clash
But I'm not claiming that changing a genome is even what happens when mutations change genes. It's still the same genome, but with unhealthy elements, such as junk DNA which is probably mostly the result of mutations, just as human beings are human beings even if suffering from genetic disease. There IS in a sense many ways a genome changes that have nothing to do with mutations, most of it having to do with normal routes to the formation of new species/subspecies/races.
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 162 of 236 (719884)
02-19-2014 12:55 AM
Reply to: Message 161 by Taq
02-18-2014 10:47 PM


Re: Paradigm clash
I don't mean that junk DNA is unhealthy in the sense that it causes disease, it is unhealthy in the sense that it represents a weakened genetic situation, being a lot of dead or half dead or nonfunctioning DNA that in former times was most likely protective of health in all kinds of ways. The junk DNA would not be selected against because it doesn't DO anything, it just occupies space in the genome like a cemetery.

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 Message 161 by Taq, posted 02-18-2014 10:47 PM Taq has replied

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


Message 164 of 236 (719887)
02-19-2014 1:04 AM
Reply to: Message 161 by Taq
02-18-2014 10:47 PM


Re: Paradigm clash
In reality, mutations change genomes. Are we talking about reality or not?
They don't change genomes in the absurd sense you were implying.
Junk DNA is not unhealthy, first of all. If it was, it would be selected against. It isn't.
Mutations that cause genetic diseases are selected against. This is why genetic diseases like hemophilia are not spreading through the population at rates consistent with drift.
However, there is an amazingly long list of genetic diseases and they do take their toll. The fact that such diseases are selected against is itself a toll on the human race for that matter, being the cause of death.
We also observe that each person is born with around 30 to 50 substitution mutations. Each person is not born with 30 to 50 genetic diseases. Obviously, the vast bulk of mutations are not deleterious. That is what reality shows us.
I'm aware that most mutations are "neutral" in that they don't do anything observable at all. However, since I regard them as a disease process in themselves, a destructive process, a mistake in the system, it seems likely that that so many of them lurking in each person's body represents some degree of compromise of the system's healthy function that isn't observable, but could accumulate over generations until it is observable.
Edited by Faith, : No reason given.
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 165 of 236 (719888)
02-19-2014 1:07 AM
Reply to: Message 163 by Taq
02-19-2014 1:01 AM


Re: Paradigm clash
The evidence is really mostly in what I hear from you all, about the LACK of evidence for beneficial mutations, plus the long long list of known genetic diseases. In reality YOU don't have any evidence for your belief that mutations are the source of normal alleles.
ABE: The claims otherwise are just a statement of my model, which is based on the expectation that life is deteriorating rather than evolving.
Edited by Faith, : No reason given.
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 168 of 236 (719891)
02-19-2014 1:10 AM
Reply to: Message 166 by Taq
02-19-2014 1:08 AM


Re: Paradigm clash
I meant your original absurd statement of what you thought I was saying, which unfortunately I've now forgotten, something about animal DNA, sorry, forgot.

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


Message 169 of 236 (719892)
02-19-2014 1:10 AM
Reply to: Message 167 by Taq
02-19-2014 1:09 AM


Re: Paradigm clash
Shown me? Where?

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


Message 170 of 236 (719893)
02-19-2014 1:13 AM
Reply to: Message 167 by Taq
02-19-2014 1:09 AM


Re: Paradigm clash
I am showing you that evidence. Among the 40 million mutations that separate humans and chimps are beneficial mutations that are responsible for the beneficial adaptations seen in both species. They are right there.
I believe you are simply CALLING normal functioning alleles "mutations." You are not giving evidence that that is actually what they are, this supposedl reality you keep claiming it is. It's just the usual word game, the definitional "evidence" of the ToE which isn't evidence at all.
Edited by Faith, : No reason given.
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 171 of 236 (719897)
02-19-2014 6:33 AM
Reply to: Message 142 by herebedragons
02-17-2014 9:53 AM


Re: Factual versus interpretive tendentious terminology
Yes, of course. There's the Kind and then there are subspecies or variations on the Kind.
I realize this is your premise, but it is going to cause a lot of confusion to rewrite taxonomic classifications.
Well I don't kid myself that anybody is going to accept my view of things to the point that there would be any need to rewrite anything. That would only happen if this creationist view were recognized as true. How soon you think that's going to come about?
It doesn't make sense to call the red fox, domestic dog, and crab-eating fox subspecies of the original created kind (we can call it Canidae originalis ). [ABE]or to have subspecies of subspecies[/ABE] Classifications are for human convenience to facilitate discussion. Grouping organisms into classifications help us better understand what we are talking about.
I don't know what all is part of a Kind though. I don't see any need to rename anything until that is known.
If you agree that there was an original "ark kind" which then split into two daughter populations, which split again into four daughter populations, etc ... , you will be able to develop a branching cladogram that will look something like this: [chart]You may disagree with the arrangement, but you agree with the basic premise; that the members of the dog kind originated from a common ancestral group, Canidae originalis. Maybe you could propose a very general idea of how you think a tree would look like in you scenario. For example, I would think that the domestic dog would need to branch off very, very early since they have been part of recorded history for many, many years and have undergone heavy breeding. (also keep in mind that the tree shown doesn't include extinct species that are included in Canidae). Then we can apply some tests to your hypothesis to see how well the data supports it.
This just doesn't reflect the way I think about any of this so I don't know what tests could possibly apply. I wouldn't make charts because I don't know what all is in any particular Kind. The chart may have that right or it may not.
Also I don't know of course how the Ark pairs branched off after the Flood. Perhaps many of them ran off to some distance right away, or maybe they stayed around because there was still food available from the Ark for them. As the plant life recovered the animals would have branched out. Predators would have followed the prey. Then their populations multiplied, then after a few generations we get some population splits. All of them go on reproducing, including the original pair; more generations pass, more population splits. Pack animals and herd animals may not undergo as many population splits as, say, cats and bears do. The result of all this is unknowable and uncharitable. I don't see how any tests based on such things would reflect anything I've said.
But if just one allele didn't make it into the new population that's a decrease, and that's very likely to happen with population splits.
A loss of a single allele is not likely to bring about a new subspecies. The situation would be much more complicated than that and require much more significant differences.
You are completely missing my point. The point is that any population is going to bring about a change in gene frequencies, a greater percentage f some alleles, a lower percentage of others by comparison with the original population. This is bound to change the phenotypes in the new group, possibly also the original, depends on the numbers involved. Im trying to make the point that the overall trend will always be to decreased genetic variability, but sometimes all the alleles from the original group will come over to the daughter group and then you don't have that decrease. You DO have new gene frequencies so you DO have new phenotypes if that daughter population remains reproductively isolated over some generations. My point was that you CAN'T have an increase in genetic variability from a population split, but although you might not have a decrease either, you COULD have a decrease, and the loss of even one allele would be a decrease. It's possible there could be a loss of more than one allele. Then if very few of a certain allele come over, eventually that one too could be lost. The point, again, is that the TREND is to a decrease, not an increase. That's the whole point: even the loss of one allele demonstrates the trend.
As long as there is reproductive isolation the only thing that could increase the diversity is beneficial mutations within the new population, and even everybody here agrees that they occur at such a slow rate it would take a very long time for that to make a difference.
But the new gene frequencies themselves should bring about recognizable change within the first few generations.
I wonder, do you think that two identical populations, if kept geographically isolated could eventually be recognized as separate subspecies? What would be the factors that would bring about that change?
Identical in numbers? Like one population splits into two of exactly the same number of individuals? Yes, that is really my argument although I'm usually imagining a daughter population starting with fewer individuals, but even an equal split is going to produce a completely new subspecies given enough generations in reproductive isolation -- because any split is going to change gene/allele frequencies so that there is a greater percentage of some alleles and a lower percentage of others. Both of the new populations should get a completely new mix by comparison with the original population, it would be very unusual if the same mix was retained. THIS is what would bring about the change you are asking about. That's all it takes, the reproductive isolation of a new population with its new allele frequencies.
avoid the implication that the Kind can evolve or vary in any way outside the Kind.
qWe can focus on diversification within the kind.
That's all I'm ever talking about.
In order for your hypothesis to gain acceptance you not only need to show evidence that supports it, but you also need to describe what evidence would falsify it.
I've described the laboratory tests I think would do that job. Or the test of sampling the DNA from each of a series of ring species.
You also need to describe what predictions could be made using this hypothesis. For example, you should be able to arrange all extant canids in a hierarchical pattern based on number of alleles, heterogeneity, number of genes, or some combination of genetic traits.
This doesn't fit with my thinking about this.
In short, develop a model that explains the data better than the current one.
I'd be content for starters if I could just get across this basic scenario I keep describing.
HBD
By the way, on one level I agree with you that population splits can and do reduce genetic diversity, what I disagree with is that it is the whole story.
My argument is that it's the general TREND of all evolutionary processes. But there are of course many different angles that could be pursued.

This message is a reply to:
 Message 142 by herebedragons, posted 02-17-2014 9:53 AM herebedragons has replied

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


Message 179 of 236 (719988)
02-19-2014 2:34 PM
Reply to: Message 177 by Taq
02-19-2014 11:04 AM


Re: Factual versus interpretive tendentious terminology
The problem is that a population that is increasing in number will also be increasing in genetic variability due to the accumulation of mutations in each generation.
Not many of which occur in the germ cells, though, isn't that correct? Not to mention that as usual the idea that the mutations actually accomplish anything for the benefit of the organism is an article of faith rather than shown to be fact.
The chances of a neutral mutation reaching fixation is 1/n where n is the number of individuals in the population. The larger the population the lower the chances are that a neutral mutation will reach fixation meaning that a larger population will have a large number of neutral mutations that have not reached fixation.
The only time we see a drastic reduction in genetic variation within a population is if the population size is drastically reduced.
Can you explain what the benefit is of "a large number of neutral mutations that have not reached fixation" ?
I do realize from this, however, that the tests I've proposed that involve examining the DNA for variability from population to population would be skewed by the counting of mutations that don't do anything toward the development of the phenotypes that define the subspecies. Is there any way to avoid this? Is it possible to focus only on the genes that clearly underlie the new phenotypes? (What is needed is a test to SHOW that mutations don't do what you all think they do. What tests have you done in this direction? That might show that mutations really ARE just mistakes and overall don't benefit the organism at all?)
(I'm thinking of observable traits, clear visible changes from the former population, although I know there would also be changes that wouldn't be observable.)
My point was that you CAN'T have an increase in genetic variability from a population split,
The accumulation of mutations after the population split does increase genetic variability over time. That is what happens in the real world.
But this is a completely artificial idea if the mutations don't actually DO anything to further the development of the character of the subspecies, and what interests me most about this now is if there is any way to differentiate between the mutations and alleles that are determining the new traits. I mean, can you tell for sure what IS a recent mutation, or is this the usual case of just assuming everything is as you assume it to be, such as that all those 40 million mutations are really alleles? That would certainly throw a wrench into the tests I have in mind.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
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 180 of 236 (719990)
02-19-2014 2:43 PM


QUESTION ABOUT PSEUDOGENES
I agree with the person who said this thread isn't really "an introduction to genetics," it was originally for answering questions, mostly about the genome, and I think it got mistitled. But Dr. A said he had plans to do a genuine introductory course in genetics at some point.
=================
Anyway, I have a question about pseudogenes or "junk DNA" again. I understand these occur here and there throughout the genome. I'd like to know
1) if there's anything about them that meets the eye, just in their sequences or how they appear as you are sequencing the genome, to tell you they are not normal genes? Or do you have to do some kind of testing to see if they actually make proteins to find out that they aren't true genes?
2) what it is that has led geneticists to determine that some of them have a "regulatory function," and what that function actually is and how you tell? And how many of them can be described this way?
I think I have another question but I can't remember it right now.

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