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Author | Topic: Molecular Population Genetics and Diversity through Mutation | |||||||||||||||||||||||||||||||||||||||
RAZD Member (Idle past 1433 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Thanks Genomicus for an excellent topic that I have been interested in for some time. Hopefully I can tweak it back to your topic ...
Particularly appropriate as I am reading a book gleaned from my dads library when we sold the old mansion ...
An Introduction to Population EcologyG. Evelyn Hutchinson New Haven and London Yale Press 1978 I'm through chapter 1 so far, and I ran across this section:
F.E.Smith was my dad, and I remember visiting his office at UofM and seeing the tanks of daphnia. This paper was published in 1963, so I was still in High School. Several of the other references involve people we knew (Larry Slobodkin for example parties and annual department picnics. Another paper dad did with Larry is "Why the Earth is Green" ... good times. My point here is that population biology\ecology deals with mechanics of growth\spread and limitations on that growth\spread in the population. I have also been considering species as individual units for evolution in ecologies, and these 'logistic' type curves would also be applicable to species diversity in a specific ecology. When an extinction event causes an vacancy in an ecology the number of species would diversify rapidly and first and then slow down until they reach an equilibrium number of species that fill the niches. Island biogeography also comes back to this with a limitation on the number of species that can exist within a specific ecology. This also brings in the "Why the Earth is Green" paper. Enjoyby our ability to understand Rebel☮American☆Zen☯Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
Right. I am bad at explaining things. All I know is I really wanted to understand what on earth cytochrome C has to do with anything, and I ended up understanding nothing.
I have a bad personality. I am a bad psychologist. I am a bad Christian. What else did I miss? You might at least not make up stuff I didn't say. You seemed to be angry, and you accused me of trying to get an emotional reaction out of you, which I've never done. And I still don't understand anything about cytochrome C.
How about responding to the arguments rather than attacking my character. I find it hard to believe you don't have a clue what I am talking about. Yeah I guess I'm making that up.
mtDNA is also a "true situation." The inheritance patterns for cytC don't have the same problems as nuclear genes do, that is, they aren't affected by the same evolutionary forces as nuclear genes are - they are pretty much only affected by mutation. I'm sorry, your point absolutely escapes me. Edited by Faith, : No reason given.
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Tangle Member Posts: 9512 From: UK Joined: Member Rating: 4.8
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RAZD writes: See -- it really was a "built-in" gene and it just needed the right recombination of the genes to become a realized phenotype ... Yes, a 'real' mutation should use an entirely different chemistry set. Edited by Tangle, : No reason given.Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed.Faith is the denial of observation so that Belief can be preserved." - Tim Minchin, in his beat poem, Storm.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
I didn't say that, RAZD did. Please change the quote reference.
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Tangle Member Posts: 9512 From: UK Joined: Member Rating: 4.8
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Faith writes: I didn't say that, RAZD did. "You wiil, Faith, you will."Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien. Life, don't talk to me about life - Marvin the Paranoid Android "Science adjusts it's views based on what's observed.Faith is the denial of observation so that Belief can be preserved." - Tim Minchin, in his beat poem, Storm.
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NoNukes Inactive Member |
but the versions of the traits are nothing special, nothing new, all business as usual in the world of alleles. Except that they are versions that did not exist in the population prior to the mutation, accordingly, with respect to the entire population, they are an increase in diversity. Some members carrying the new version while others carry the old is no more of a 'breaking of the species' than is some people having brown eyes while others have blue eyes. The entire idea that mutations ruin the breed not to be taken seriously. Yet is apparently and idea that is vital to your proposition. It ought to be completely unnecessary to say such things, but such a mutation of a single trait, can conceivably spread through a percentage of the population without displacing any other alleles in members who did not have inherit the new allele. If so, the diversity within the population has increased. If it never turns out that the trait has an advantage, then the entire population remains a single species with increased diversity. Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
Except that they are versions that did not exist in the population prior to the mutation, accordingly, with respect to the entire population, they are an increase in diversity Thank you for that recitation of the Evo Creed, Article Whatever. That's all it is, just the usual Evo Statement of Faith. Cuz you do not know for sure that it didn't exist in the population already. The way added mutations could mess up a breed is by changing major characteristics. If you've been working for decades to get a perfect purebred Whozit you don't want a mutation to pop up for a Whatzit. You DO NOT WANT this new trait in your breed. What's so hard to understand about that? And this is after the Whozit breed has been pretty well established, so that it's ALREADY lost genetic diversity in its formation, which is NECESSARY to its formation. What you've got is a LARGE net decrease in genetic diversity with respect to former populations from which it was derived. The idea that one mutation could come along and increase its genetic diversity in any meaningful sense of the term is quite laughable. 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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herebedragons Member (Idle past 886 days) Posts: 1517 From: Michigan Joined: |
The way added mutations could mess up a breed is by changing major characteristics. If you've been working for decades to get a perfect purebred Whozit you don't want a mutation to pop up for a Whatzit. You DO NOT WANT this new trait in your breed. Easy solution. Don't use your newly mutated Whatzit to breed your next generation of Whozits. It happens. Breeders have good breeding stock and stock that they don't breed because it has a Whatzit look to it. ABE:
And this is after the Whozit breed has been pretty well established, so that it's ALREADY lost genetic diversity in its formation, which is NECESSARY to its formation. What you've got is a LARGE net decrease in genetic diversity with respect to former populations from which it was derived. What if I had a Whozit breed and I wanted develop a new breed from that called a Howzit? What would I do to go from a Whozit to a Howzit? HBD Edited by herebedragons, : No reason given.Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem. Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.
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NoNukes Inactive Member |
Thank you for that recitation of the Evo Creed, Article Whatever. That's all it is, just the usual Evo Statement of Faith. Cuz you do not know for sure that it didn't exist in the population already. Well no. My statement was not intended to be a statement of proof that some allele already did or did not already exist. Instead it is a response to your claim that if mutation did produce a new allele, that would not matter. Clearly your labeling the point of discussion that you yourself brought up as something reflecting on me makes no sense at all. If there is any silliness involved here it is your own. It appears you are losing track of exactly what is being discussed and on what basis we are arguing. If you want to assume that mutations do not produce new alleles, that's one thing. But here you claimed that any new alleles would not make a difference because they are just like the old ones. You've simply jumped the shark here in an extremely transparent fashion. As has been mentioned dozens of times, what you attack here is not the theory of evolution, but is instead some weaker theory that Darwin already said does not work. Your much better of just denying that mutations do not create new alleles. Edited by NoNukes, : No reason given. Edited by NoNukes, : No reason given. Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams
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Dr Adequate Member (Idle past 313 days) Posts: 16113 Joined: |
The way added mutations could mess up a breed is by changing major characteristics. If you've been working for decades to get a perfect purebred Whozit you don't want a mutation to pop up for a Whatzit. You DO NOT WANT this new trait in your breed. What's so hard to understand about that? And if the laws of nature conformed to the desires of people trying to produce a perfect purebred Whozit ... then the world would be a very different place, and your point would have some relevance to the discussion. But they don't, it isn't, and it doesn't; and mutations occur.
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NoNukes Inactive Member |
You DO NOT WANT this new trait in your breed. What's so hard to understand about that? It is not hard to understand. You are correct. It would be unwanted. If it occurred, a breeder would be forced to do something about not getting what he wants. Something like having the animal neutered and given to his kids to play with. How is the fact that something is undesirable to breeders a reason why the problem cannot occur. You make a number of statements such as 'mutations are not needed', 'look at the large amount of variation available without mutation', or 'mutations are unwanted'. None of that stuff is even the tiniest bit of an argument that mutations do not produce new alleles. Why you continue to repeat such things, with emphasis no less, or with comments impugning my intelligence is difficult to understand. It does not make you look good. One thing to that might help is understanding that the rate of mutations is low enough that the probability of a significant one in a few individuals is relatively low. If you are working with a few dozen dogs in a breeding program, the overwhelming majority of them won't have issues with mutations. But if a few offspring did have problems, the breeder would remove them from the program. For that matter, the presence of dominant and recessive allele's required removing dogs from the breeding program anyway. Are you also going to answer that there are no such things as recessive genes because that interferes with breeding? Since dogs have multiple pups per birthing over a significant breeding period, the problem you identify may not a big issue. Is that too hard to understand? On the other hand, sometimes breeding programs fail to produce the desired result. "I don't want it" just is not a force that makes nature behave. Sorry, but that's life in the big universe. Edited by NoNukes, : No reason given. Edited by NoNukes, : No reason given. Edited by NoNukes, : No reason given. Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
This discussion has gone weird and I'm not up to trying to correct it. The REAL point, which I probably contributed to garbling as much or more than anyone else, is whether after you get a breed, or in nature a subspecies, the lost genetic diversity will be made up by mutations. I say isn't going to happen and if it did you wouldn't want it to if you were a breeder, from which I conclude it hardly ever happens anyway. But if it did it would never make up for what has been lost in arriving at the breed or species, which is the alleles for ALL the other breeds or subspecies of the Dog Kind or Cat Kind or cattle Kind or whatever it is. And if it did you could never hold on to a breed at all and Nature wouldn't have recognizable species at all.
MEASURING GENETIC DIVERSITY:Anyway I'd like to go on to this other issue that has been bugging me. I still don't get the point about cytochromeC, HBD, and I'm afraid to ask you to try to clarify it again. But it's related to this other question I'd also like to understand if possible, and that is how you can get any true measure of a population's genetic iversity from microsatellites or Mitochondrial DNA, both of which I understand are used for that purpose. You explained a couple of discrepancies between the studies Genomicus posted on the Great Debate thread and known facts: one study that showed no gene flow and high diversity, which was contradicted by a known rich history of gene flow, and the other study found high genetic diversity in the elephant seals although Scientific American just a few years ago discussed the plight of the seals with their known low genetic diversity despite their great population increase. I gather the discrepancy is explained by measuring Mitochrondrial DNA rather than chromosomal DNA? Right? In which case why would that be done at all? I'm sure there's some rational explanation but it completely escapes me.
GENETIC DIVERSITY IN JUTLAND CATTLE:I just went back to a very old thread and read up on the Jutland cattle which had split into four different breeds with distinctive phenotypes. Percy had introduced the subject and gave a link to this journal where you can find the article on page 75. It's full of technical terms so it's hard for me to get through it all, but it's concerned with conservation of these Danish cattle breeds, and of course that would be a concern if their genetic diversity is low, which one might expect to be the case as a result of much splitting into separate populations. I was of course interested at the time in the fact that you can get recognizable new phenotypes from such splits, showing that this can occur in a very short period of time and not take millions of years. A few decades in the case of these four populations of cattle. It also implies loss of genetic diversity, of course, since that's the concern of the conservationists. So it worked well for my argument. But reading through it now I see that they studied the genetic diversity at Mitochondrial DNA and microsatellites. (I read up on these enough at least to know where they are located and what they look like), and they found HIGH GENETIC DIVERSITY IN THESE FOUR CATTLE POPULATIONS. Which is just mindboggling to me. I suspect this is exactly the same situation I ran into with Genomicus' examples -- the high diversity is ONLY in the MtDNA and the microsatellites and NOT in the chromosomal DNA WHERE IT COUNTS. By the way the microsatellite and MtDNA results differed for two of the herds on some point I don't remember and would have to look up again. What good are methods that don't give reliable results? Or is this a fluke? SOMEBODY please explain this in ordinary English. ********************************
POD MRCARU LIZARDS DON'T NEED ABE: Just have to bring up the Pod Mrcaru lizards too because Percy said this about them:
Unfortunately the phenotypic differences are never described, so there is no way to tell if they're as significant as the head and diet changes of the lizards of Pod Mrcaru, but even without this detail I think we have to grant that the phenotypic changes in these lizards could have been due either drift, selection, mutation or, most likely, some combination. Yes I wish the phenotypic differences between the cattle populations had been described too, though enough is said to indicate that they had distinct differences. But where he goes on to say "we have to grant" that the lizards' large head and diet changes "could have been due" to drift, selection, mutation or a combination, my answer is that they were most probably due ONLY to normal recombination over some number of generations of inbreeding. Selection was accomplished by the initial numbers released on the island anyway, starting the population with a mere five pairs, drift is just a version of selection and could have been a factor in such a small population too, though not needed, and mutation is simply not needed AT ALL. The large heads and different digestive system were NOT present in the original population so how would they emerge in the new population? I would point you to Darwin's pigeons which acquired some dramatically exaggerated characteristics over a number of generations in which he selected for that particular trait. The huge breasts, for one, are not to be found at all in wild pigeons; they emerged due only to sexual recombination over some number of breeding seasons, showing that genetic changes can multiply. So you wouldn't need to have a single allele for the large heads of the Pod Mrcaru lizards either, all you would have to have is a multiplication of the alleles for size down the generations. And the new gut seems to demonstrate a design factor that links characteristics for the good of the animal, IMHO. If it's going to be munching some crunchier food with its big new jaws, it needs to be able to digest it. 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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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
But reading through it now I see that they studied the genetic diversity at Mitochondrial DNA and microsatellites. (I read up on these enough at least to know where they are located and what they look like), and they found HIGH GENETIC DIVERSITY IN THESE FOUR CATTLE POPULATIONS. Which is just mindboggling to me. I suspect this is exactly the same situation I ran into with Genomicus' examples -- the high diversity is ONLY in the MtDNA and the microsatellites and NOT in the chromosomal DNA WHERE IT COUNTS. Have been busy with non-EvC stuff, but I'm presently working on an excoriation of your last posts in the Great Debate thread, and wanted to respond to this bit here. You do realize that microsatellite sequences consists of chromosomal DNA, right? This is pretty basic stuff, so c'mon, you shoulda known that.
By the way the microsatellite and MtDNA results differed for two of the herds on some point I don't remember and would have to look up again. What good are methods that don't give reliable results? Umm, what good is answering a question that doesn't have a reliable way to see what point you're referring to that you don't remember? Do the work and look it up and present the actual, relevant data. Edited by Genomicus, : No reason given.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
Sigh. Yes, microsatellites are chromosomal, should only have contrasted Mitochondrial DNA with chromosomal. Sigh. But they are another thing from the traits that require reduced genetic diversity and from the heterozygosity that would reflect genetic diversity, so why are these separate apparently unrelated segments of chromosomal DNA used to measure genetic diversity?
The point you want me to look up was so minor and secondary I didn't want an answer to it, it was just a by-the-way. There are more important matters in that post. ' ABE: Of course we're debating but why the need to be "excoriating." What's wrong with "Understanding Through Discussion," which IS the slogan for EvC Forums despite the murderous inclinations on both sides of this issue. What's the point of playing Swashbuckling Scientist with a mere creationist? Edited by Faith, : No reason given. Edited by Faith, : No reason given.
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Faith  Suspended Member (Idle past 1473 days) Posts: 35298 From: Nevada, USA Joined: |
Here's the point you wanted me to look up, found on page 79 of the journal
Kortegaard and Vesterboelle were found to be the least differentiated, and Oregaard and Westergaard the most highly differentiated herds based on mtDNA. All pairwise microsatellite FST comparisons were also significant, but in contrast to the mtDNA data, the microsatellite data showed Kortegaard and Oregaard as the least differentiated herds, and Kortegaard and Vesterboelle as the most differentiated. Not sure what this meant at first. I guess it means how different or similar the phenotypes? Edited by Faith, : No reason given. Edited by Faith, : No reason given. Edited by Faith, : No reason given.
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