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Author Topic:   Molecular Population Genetics and Diversity through Mutation
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 136 of 455 (785376)
06-03-2016 7:38 PM
Reply to: Message 78 by herebedragons
05-28-2016 9:20 AM


Re: You are looking at the wrong part of the system
I added this to my Message 124 because it was becoming clear from subsequent discussion of genotypes that I misunderstood you:
*****************************************
AbE: I think I misunderstood what you meant about genotypes. Now I think you were just saying I'm wrong about phenotypes because of course genotypes underlie phenotypes. In which case my answer is of course you can get new genotypes the same way you get new phenotypes, from the changed gene/allele frequencies. You keep thinking more is needed to get a new breed or subspecies but it's not, changed gene frequencies is all it takes. Remember again that evolution itself has been defined as nothing more than a change in gene frequencies. That ought to show how much change you can get from nothing more than "shuffling alleles." Changing genotypes in this context is just getting a new frequency of genotypes from the new frequencies of alleles. Not new in the sense of absolutely novel, just new in the sense of new frequencies of some combinations -- that's all it takes to make a population characterized by different phenotypes from the parent population. /AbE
*********************************************

This message is a reply to:
 Message 78 by herebedragons, posted 05-28-2016 9:20 AM herebedragons has not replied

Replies to this message:
 Message 137 by NoNukes, posted 06-03-2016 8:57 PM Faith has not replied
 Message 138 by Asgara, posted 06-03-2016 10:08 PM Faith has replied

  
NoNukes
Inactive Member


(1)
Message 137 of 455 (785380)
06-03-2016 8:57 PM
Reply to: Message 136 by Faith
06-03-2016 7:38 PM


Re: You are looking at the wrong part of the system
Remember again that evolution itself has been defined as nothing more than a change in gene frequencies. That ought to show how much change you can get from nothing more than "shuffling alleles.
I think we all understand that you don't believe mutation is part of evolution. But the above quoted statement is not confirmation that the theory of evolution is in agreement with your proposal. Yes you can get changes in the population of phenotypes from generation to generation just by selection pressures and without any new variation. But that is not the same thing as claiming that no other factor is part of evolution.
I know you won't take the advice, but your presentation would likely be much stronger if you simply denied that the theory of evolution was correct than if you continue on the road of denying that the theory of evolution actually encompasses those things we can read in any biology text book. Your 'mutation destroys the species or the breed' is not cutting it.
Consider this, if a new dominate allele appeared that caused humans possessing it to become immune to HIV, or left handed, or to have creases in the back of their neck, would that mutation make a person non-Caucasian? If not, then how would such mutations ruin the breed/race if they occurred after the race formed? If so, then would this not be an example of a race becoming more diverse after formation? Can you really not make up your own similar examples?
As has been illustrated to you many times by direct quotes from origin of species, and also with quotes from modern sources, common descent requires much more than than your own proposal allows. The theory of evolution is that the source of variation includes mutations. Darwin is quoted as saying that without the source of variation, evolution would cease exactly as you have argued.
Beyond that, at this point between this thread and the Great Debate thread, examples of mutations fueling variation has been demonstrated with direct evidence. You of course are free to deny it. But your denials have zero basis.
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

This message is a reply to:
 Message 136 by Faith, posted 06-03-2016 7:38 PM Faith has not replied

  
Asgara
Member (Idle past 2302 days)
Posts: 1783
From: Wisconsin, USA
Joined: 05-10-2003


(4)
Message 138 of 455 (785383)
06-03-2016 10:08 PM
Reply to: Message 136 by Faith
06-03-2016 7:38 PM


Re: You are looking at the wrong part of the system
Forgive what may be a neophyte question but I don't understand just where you are going with this.
If all you are doing is changing the frequencies of alleles being expressed without adding in mutations, then what is causing speciation. All the alleles being expressed in the daughter population are still present in the original population. What is there to cause an inability to interbreed?

This message is a reply to:
 Message 136 by Faith, posted 06-03-2016 7:38 PM Faith has replied

Replies to this message:
 Message 139 by Faith, posted 06-04-2016 7:48 AM Asgara has replied

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


Message 139 of 455 (785401)
06-04-2016 7:48 AM
Reply to: Message 138 by Asgara
06-03-2016 10:08 PM


Re: You are looking at the wrong part of the system
Forgive what may be a neophyte question but I don't understand just where you are going with this.
If all you are doing is changing the frequencies of alleles being expressed without adding in mutations, then what is causing speciation. All the alleles being expressed in the daughter population are still present in the original population. What is there to cause an inability to interbreed?
The change in frequencies is a powerful changer of phenotypes and their genotypes, which may not be too noticeable if the frequencies aren't dramatically different from the parent population, but becomes quite dramatic if they are. It's not about different alleles it's about frequencies.
A high frequency of the allele for gray fur in the new population can, after some number of generations of reproductive isolation, change the whole look of that population to gray from, say, black, if the parent population had appreciably more of the allele for black fur. There is probably more than just one gene involved for that trait too and you'll get different frequencies for each locus; but besides fur you've got new allele frequencies for EVERY trait of the animal, which is how you can get dramatic new dog breeds for instance. If you get a very high frequency of an allele that was very rare in the parent population you could get a surprising new trait. But the changes may not be dramatic -- you may get a new population of raccoons with slightly new facial markings -- or may be fairly pronounced -- getting a whole population of wildebeests with completely different coloring from the original population plus different antlers plus a different body build. All that is possible from mere changes in gene frequencies at many hundreds of different gene loci.
Then if you get another population split from the new daughter population you will reduce the numbers even further and very likely bring out even more dramatic phenotypic differences. This would occur just because you have fewer genetic possibilities in the second population overall than the original population had which brings out phenotypes that either didn't show up at all in the original population or so rarely they didn't affect the overall phenotypic appearance. Now all these may combine in such a way that you get some really unique phenotypic expressions.
You don't need mutations, and if you got them they would only act the same way built-in alleles would act, being selected the same way, occurring in the same gene frequencies, and what would they be anyway but an alternate version of a particular trait, just as they would be if built in. '
The smaller the new population the fewer genetic possibilities will be available so that the phenotypes that emerge could be quite dramatically different from those in the previous populations. I've argued that the changes in this case can be dramatic enough to bring about inability to interbreed with other populations of the same species, which is the definition of speciation. Genomicus has said on our great debate thread that in some species it only takes change in two genes to bring about inability to interbreed with other populations of the same species, which makes my point even better since I thought more changes were probably needed.
I hope this is clarifying, but it is difficult to get all this across.

This message is a reply to:
 Message 138 by Asgara, posted 06-03-2016 10:08 PM Asgara has replied

Replies to this message:
 Message 141 by NoNukes, posted 06-04-2016 11:49 AM Faith has not replied
 Message 142 by Asgara, posted 06-04-2016 12:05 PM Faith has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(3)
Message 140 of 455 (785416)
06-04-2016 11:42 AM
Reply to: Message 124 by Faith
06-03-2016 1:52 AM


Trying to clarify cytochrome C
Ok, first off I made a mistake in describing the situation with cytochrome C. CytC is a mitochondrial gene which means it is haploid, so there would not be two copies in each organism, but only 1. It is also inherited primarily through the maternal line, so there is no recombination with the male counterpart. So in reality we would expect only 1 haplotype to exist in the original ark pair - although I could be open to the idea that multiple sequences existed in the same organism.
This explains, in part, why the study Genomicus cited showed increasing genetic diversity while other reports suggest that the population has not recovered from their genetic bottleneck. Elephant seals are highly polygamous, meaning that a single dominant male will fertilize between 30 and 100 females. This greatly reduces the effective population which in a population with only a few dominant males getting all the action, the effective population could be as low as 1/10th the actual population. In addition, the dominant male would be breeding with his own daughters and granddaughters further increasing homozygosity. Mitochondrial DNA does not have these problems. So it should be clear why the discrepancy between the two systems.
But I digress...
So back to cytC.
So each separate breed of dog has its own unique cytC sequence? You can identify, say, a spaniel from a wolfhound from a poodle by their own unique sequence?
Yes and No. Theoretically you should be able to trace a lineage through the maternal line, so in that way, yes, each breed or more precisely, each breeding population should have its own identifying sequence. However, the amount of differentiation between sequences is probably not sufficient to identify a specific breed. The other complication is that contrary to what you are suggesting, the main way that new breeding lines are developed is by the introgression of desirable traits into a preferred genetic background and then selecting for those desirable traits (think 'gene flow'). Rather than 'muddying the waters', gene flow provides variation for which further evolution can operate. How this complicates the cytC situation with dogs, or other breeding programs, is that if a trait was introduced from a male parent, there would be no mitochondrial record of that introgression. So mtDNA (mitochondrial DNA) has its uses in breeding programs, but it is not used for ID.
Or a Persian cat from Siamese? Or from a lion, or a lion from a tiger?
A grizzly from a polar bear?
Persian from Siamese - Probably not. Same deal as with dogs above - although I don't think cat breeding history is as complicated as dogs.
House cat from a lion - Yes
Lion from a tiger - Yes
Grizzly from a polar bear -Yes
Rat from a mouse - Yes
Below is an alignment of a rat sequence and a mouse sequence. Where there are not vertical bars between the sequences indicates a difference in sequences - ie. a mutation.
IIRC, the sequences had 95% or 96% identity. So if I had a sequence and wasn't sure what it was, I could compare it to a database and I might find that it matched 99% with a mouse sequence and 95% with a rat sequence and I could conclude the sequence was from a mouse.
If I did the same thing with a dog sequence, I would probably return dozens of sequences from many different breeds that had 99% identity, so while they may be different and even unique, it would not be conclusive enough to assign the sequence to a specific breed. However, it may be different enough from a wolf and certainly would be from a coyote or a fox.
*******Side topic alert*********
You can eliminate drosophila from the list because God didn't command Noah to save insects or bacteria, or even plants for that matter, although I'm willing to think about plants.
This is what puzzles me about literalists.
quote:
Gen 7:21 - 23
And all flesh died that moved upon the earth, both of fowl, and of cattle, and of beast, and of every creeping thing that creepeth upon the earth, and every man: All in whose nostrils was the breath of life, of all that was in the dry land, died. And every living substance was destroyed which was upon the face of the ground, both man, and cattle, and the creeping things, and the fowl of the heaven; and they were destroyed from the earth: and Noah only remained alive, and they that were with him in the ark.
*Literally* "every living substance was destroyed" and "all that was in the dry land, died." which includes "every creeping thing that creepeth on the earth,". I guess I understand plants not being on the list, but insects? It is abundantly clear that ALL animal life was completely wiped off the face of the earth, yet literalists want to interpret this in some other manner than a simple, straightforward, literal reading.
******end of side topic******
The more I think about this the less sense it makes.
The problem is that rather then looking at the evidence at determining what it tells you, you are trying to get it to fit the narrative you have created. I can understand why it would not make much sense.
1) These alleles are species identifiers, you say, so how is it that two individuals of the same Kind/Species would have four different species-identification alleles among them?
They wouldn't. I was trying to fit these observations into an imaginary scenario (and by imaginary here I simply mean that rather than being able to go somewhere and learn about this hypothesis of yours, I have to imagine what it means. Whether it is imaginary in the sense of being not real is what we are discussing).
2) When that pair mates, say they are dogs, they aren't going to have four new species or even one new species, they are going to have a litter of puppies. Which should all have the same cytC identifier since they are all of the same Kind/Species, shouldn't they?
3) After they grow in numbers to a sizeable population then they might split off into subpopulations and eventually become new subspecies of dogs. But they'd all still have the cytC identifier for Dogs, wouldn't they?
What are you saying? That when a new subspecies emerges, at some point it gets a new cytC identifier? What would bring that about? At what point would you expect it to emerge in the process of its evolution?
Just to be clear, cytC does not determine the species, it identifies it. Meaning there is nothing about the sequence that gives an organism its unique phenotype. cytC sequence changes occur independently of what is happening in the nuclear genome.
Mutations in the cytC gene accumulate in step-wise fashion. Within a breeding population, there will be some variations in sequence; not all members will have identical sequences. Perhaps a sub-population splits off from the main population. This sub-population will continue to accumulate changes, but these accumulated changes will be different from the parent population. Over time the sequences of the two populations will be recognizably different. During this same time, changes are also occurring in the nuclear genome. When these changes in nuclear genes are sufficient to prevent (or minimize) interbreeding with the parent population, the changes in cytC have diverged sufficiently to be used to be identified with that new species or subspecies.
Another thing to clarify, there is nothing specific about a cytC sequence that allows one to identify the species, it is comparison to known samples from a database that provides identity. If no representatives from a species has ever been sequenced, a search may present no close matches. It this case, you may be able to say that it is closely related to some other species, but not a close enough match to identify it as a specific species.
This can be a powerful tool in understanding the history of a species and what has driven its evolution. If a pattern and pace of nucleotide changes have occurred in the cytC gene since a population diverged, one would expect similar changes to have occurred in similar nuclear regions. If they haven't, if the pattern and pace is significantly different that expectation, it is an indication of one of the evolutionary forces at work. Often a gene tree will be developed based on a region such as cytC (the standard now is 4 or more independent regions) and other traits will be overlaid on the tree to study how they have changed or how they vary in different species.
I know you probably think this is completely irrelevant to your argument, but its is relevant. The patterns we observe require an explanation. Here's where that comes in...
All I can think is that if it is a species-identifier then it is a Dog identifier, not a dog-breed identifier, in other words it is an identifier of the Biblical Kind or Species. If that's the case then it would make a wonderful way of defining what a Kind is.
Yes, that would be the expectation, wouldn't it. Based on what I have said about the system in this post (hopefully it is a bit clearer) how would you predict that one could distinguish between "kinds" using this method? Saying that the sequence of a dog should be more similar to another member of the dog kind than it would be to a cat kind is not enough, since that is also what the ToE would predict. How would you predict that there would be disparity between the kinds? How would you recognize different kinds?
I think if nothing else, this should make it clear that mutations do occur and accumulate. I know you have allowed for "some kind of mutation" meaning... I don't know what. Yes, the mutations in cytC are essentially neutral, which is maybe the "some kind" that you allow for. But, the bigger point is that we see this same pattern at play in nuclear coding genes. But we'll have to cover that later, once you understand the point about cytC and how it is used.
HBD

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.

This message is a reply to:
 Message 124 by Faith, posted 06-03-2016 1:52 AM Faith has replied

Replies to this message:
 Message 143 by Faith, posted 06-04-2016 3:01 PM herebedragons has replied

  
NoNukes
Inactive Member


Message 141 of 455 (785417)
06-04-2016 11:49 AM
Reply to: Message 139 by Faith
06-04-2016 7:48 AM


Re: You are looking at the wrong part of the system
here is probably more than just one gene involved for that trait too and you'll get different frequencies for each locus; but besides fur you've got new allele frequencies for EVERY trait of the animal, which is how you can get dramatic new dog breeds for instance.
This explanation is total crap. You get dog breeds by supplying intense selective pressure, namely by not allowing dogs who don't have most or all of the desired traits to remain in the gene pool. The point you have yet to address is that such selective pressures are extremely artificial and generally do not exist in nature. For example, the dark moths appear to have only minor differences from the white moths, and if we remove the predators, we would expect to see white moths increase in percentage.
It is also the case that dog breeders, in general do not simply start with a couple of animals with a trait and breed them together and then simply continue to breed their offspring. That they, of necessity bring in other animals during the breeding process in their attempt to eliminate recessive traits. What breeders accomplish simply does not happen naturally. And you have yet to successfully argue that it does.
If you get a very high frequency of an allele that was very rare in the parent population you could get a surprising new trait.
Could you? The evidence for this is what?
You don't need mutations, and if you got them they would only act the same way built-in alleles would act
Assuming that this statement is true, we would have to note that such things while acting the same as built-in alleles, would be an additional of variation, and diversity. So mathematically, and for the point of this debate, the result would not be the same.
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

This message is a reply to:
 Message 139 by Faith, posted 06-04-2016 7:48 AM Faith has not replied

  
Asgara
Member (Idle past 2302 days)
Posts: 1783
From: Wisconsin, USA
Joined: 05-10-2003


(3)
Message 142 of 455 (785418)
06-04-2016 12:05 PM
Reply to: Message 139 by Faith
06-04-2016 7:48 AM


Re: You are looking at the wrong part of the system
But you aren't explaining how just a change i frequency, with no mutation, can give you anything that isn't already in the parent population. Just because you might have more black wolves than grey in the daughter population they are still able to breed with the parent population.
What actually causes speciation? There is nothing in the new population that isn't already in the parent population. How does a change in frequency achieve what you're proposing?
When Genomicus is discussing cases where only 2 changes can bring about speciation she is talking about mutations. You aren't making any changes other than the frequency of things that are already there.

This message is a reply to:
 Message 139 by Faith, posted 06-04-2016 7:48 AM Faith has replied

Replies to this message:
 Message 144 by Faith, posted 06-04-2016 3:30 PM Asgara has not replied

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


Message 143 of 455 (785422)
06-04-2016 3:01 PM
Reply to: Message 140 by herebedragons
06-04-2016 11:42 AM


Re: Trying to clarify cytochrome C
Ok, first off I made a mistake in describing the situation with cytochrome C. CytC is a mitochondrial gene which means it is haploid, so there would not be two copies in each organism, but only 1. It is also inherited primarily through the maternal line, so there is no recombination with the male counterpart. So in reality we would expect only 1 haplotype to exist in the original ark pair - although I could be open to the idea that multiple sequences existed in the same organism.
Then how could it possibly be a species identifier?
This explains, in part, why the study Genomicus cited showed increasing genetic diversity while other reports suggest that the population has not recovered from their genetic bottleneck. Elephant seals are highly polygamous, meaning that a single dominant male will fertilize between 30 and 100 females. This greatly reduces the effective population which in a population with only a few dominant males getting all the action, the effective population could be as low as 1/10th the actual population. In addition, the dominant male would be breeding with his own daughters and granddaughters further increasing homozygosity. Mitochondrial DNA does not have these problems. So it should be clear why the discrepancy between the two systems.
One saying no increased genetic diversity, the other saying yes increased genetic diversity. Fine, you've explained the discrepancy but not solved the problem of whether there is increased genetic diversity or not. Seems to me that the mitochondrial DNA measure in fact says nothing about the true situation, which in reality is that increasing homozygosity brought about by the mating patterns, which would be severe enough even if the seals mated for life but of course exacerbated by the dominant male pattern. Obviously the mitochrondrial DNA method is useless as a measure of genetic diversity so why is it used at all?
But I digress...
Maybe, but that discrepancy is of paramount importance in this discussion, and what you've illuminated is that it makes zero sense to use mitochondrial DNA as an indicator of genetic diversity. It could say there's a big increase in genetic diversity while the creature goes extinct from all that increasing homozygosity.
So back to cytC.
So each separate breed of dog has its own unique cytC sequence? You can identify, say, a spaniel from a wolfhound from a poodle by their own unique sequence?
Yes and No. Theoretically you should be able to trace a lineage through the maternal line, so in that way, yes, each breed or more precisely, each breeding population should have its own identifying sequence.
Huh? Why would its being passed on through the maternal line produce a different sequence/species identifier in the offspring?
However, the amount of differentiation between sequences is probably not sufficient to identify a specific breed.
How are you getting any "differentiation between sequences" at all in the first place?
The other complication is that contrary to what you are suggesting, the main way that new breeding lines are developed is by the introgression of desirable traits into a preferred genetic background and then selecting for those desirable traits (think 'gene flow'). Rather than 'muddying the waters', gene flow provides variation for which further evolution can operate. How this complicates the cytC situation with dogs, or other breeding programs, is that if a trait was introduced from a male parent, there would be no mitochondrial record of that introgression. So mtDNA (mitochondrial DNA) has its uses in breeding programs, but it is not used for ID.
That entire paragraph is absolute gobbledygook to me. I have NO idea what this means: "the main way that new breeding lines are developed is by the introgression of desirable traits into a preferred genetic background and then selecting for those desirable traits (think 'gene flow')." Absolutely zip. Not only does it not tell me anything about why I'm wrong about breeding practices, it doesn't tell me anything at all about breeding methods, period. What is an "introgression?" what is a "preferred genetic background?" What I've described of breeding practices is so well known, not only is this statement undecipherable, but insofar as it aims to contradict what is well known it's ridiculous.
Or a Persian cat from Siamese? Or from a lion, or a lion from a tiger?
A grizzly from a polar bear?
Persian from Siamese - Probably not. Same deal as with dogs above - although I don't think cat breeding history is as complicated as dogs.
House cat from a lion - Yes
Lion from a tiger - Yes
Grizzly from a polar bear -Yes
Rat from a mouse - Yes
But you've said absolutely nothing about how these different species get or don't get a particular species identifier. Ordinary reproduction should pass on the same identifier indefinitely, so in related species how do they get different identifiers?
Below is an alignment of a rat sequence and a mouse sequence. Where there are not vertical bars between the sequences indicates a difference in sequences - ie. a mutation.
1) I can't read it because it blinds me, and 2) I have no idea what I'd be looking for if I could read it, why the supposed mutations matter, how the rat and the mouse got different sequences and so on.
IIRC, the sequences had 95% or 96% identity. So if I had a sequence and wasn't sure what it was, I could compare it to a database and I might find that it matched 99% with a mouse sequence and 95% with a rat sequence and I could conclude the sequence was from a mouse.
If I did the same thing with a dog sequence, I would probably return dozens of sequences from many different breeds that had 99% identity, so while they may be different and even unique, it would not be conclusive enough to assign the sequence to a specific breed. However, it may be different enough from a wolf and certainly would be from a coyote or a fox.
I'm sure this makes sense to you, and you think you are explaining something to me, but if anything it's making the whole issue more mystifying.
*******Side topic alert*********
You can eliminate drosophila from the list because God didn't command Noah to save insects or bacteria, or even plants for that matter, although I'm willing to think about plants.
This is what puzzles me about literalists.
quote:
Gen 7:21 - 23
And all flesh died that moved upon the earth, both of fowl, and of cattle, and of beast, and of every creeping thing that creepeth upon the earth, and every man: All in whose nostrils was the breath of life, of all that was in the dry land, died. And every living substance was destroyed which was upon the face of the ground, both man, and cattle, and the creeping things, and the fowl of the heaven; and they were destroyed from the earth: and Noah only remained alive, and they that were with him in the ark.
*Literally* "every living substance was destroyed" and "all that was in the dry land, died." which includes "every creeping thing that creepeth on the earth,". I guess I understand plants not being on the list, but insects? It is abundantly clear that ALL animal life was completely wiped off the face of the earth, yet literalists want to interpret this in some other manner than a simple, straightforward, literal reading.
Huh? We all figure insects died too. We also figure they managed to survive in much reduced numbers without Noah's help, as hitchhikers on the ark or some other way, and that there were plenty of seeds for plants on the ark, as well as some that survived in the land to sprout after the Flood. But that is not the same thing as Noah's being specifically required to save them. He also was not commanded to save sea creatures, so although obviously huge numbers of them died, some also survived the Flood. So for whatever reason the creeping things are not identified with insects, and I'm just going by what most theologians say about them. I don't get why you have a problem with any of this.
The more I think about this the less sense it makes.
The problem is that rather then looking at the evidence at determining what it tells you, you are trying to get it to fit the narrative you have created. I can understand why it would not make much sense.
That is a completely gratuitous unfair accusation. I'm doing my best to understand your completely garbled presentation of these things.
1) These alleles are species identifiers, you say, so how is it that two individuals of the same Kind/Species would have four different species-identification alleles among them?
They wouldn't. I was trying to fit these observations into an imaginary scenario (and by imaginary here I simply mean that rather than being able to go somewhere and learn about this hypothesis of yours, I have to imagine what it means. Whether it is imaginary in the sense of being not real is what we are discussing).
Maybe you should just try explaining what you know instead of making up straw men.
2) When that pair mates, say they are dogs, they aren't going to have four new species or even one new species, they are going to have a litter of puppies. Which should all have the same cytC identifier since they are all of the same Kind/Species, shouldn't they?
3) After they grow in numbers to a sizeable population then they might split off into subpopulations and eventually become new subspecies of dogs. But they'd all still have the cytC identifier for Dogs, wouldn't they?
What are you saying? That when a new subspecies emerges, at some point it gets a new cytC identifier? What would bring that about? At what point would you expect it to emerge in the process of its evolution?
Just to be clear, cytC does not determine the species, it identifies it. Meaning there is nothing about the sequence that gives an organism its unique phenotype. cytC sequence changes occur independently of what is happening in the nuclear genome.
It never occurred to me to think it would determine the species. What a strange idea. Also the fact that these sequences change independently makes it hard to link them at all to the species. How they become species identifiers is still unexplained.
Mutations in the cytC gene accumulate in step-wise fashion.
No idea what that means. Sounds rather programmed for an accidental or random replication mistake.
Within a breeding population, there will be some variations in sequence; not all members will have identical sequences. Perhaps a sub-population splits off from the main population. This sub-population will continue to accumulate changes, but these accumulated changes will be different from the parent population. Over time the sequences of the two populations will be recognizably different. During this same time, changes are also occurring in the nuclear genome. When these changes in nuclear genes are sufficient to prevent (or minimize) interbreeding with the parent population, the changes in cytC have diverged sufficiently to be used to be identified with that new species or subspecies.
Another thing to clarify, there is nothing specific about a cytC sequence that allows one to identify the species, it is comparison to known samples from a database that provides identity. If no representatives from a species has ever been sequenced, a search may present no close matches. It this case, you may be able to say that it is closely related to some other species, but not a close enough match to identify it as a specific species.
???
This can be a powerful tool in understanding the history of a species and what has driven its evolution. If a pattern and pace of nucleotide changes have occurred in the cytC gene since a population diverged, one would expect similar changes to have occurred in similar nuclear regions. If they haven't, if the pattern and pace is significantly different that expectation, it is an indication of one of the evolutionary forces at work. Often a gene tree will be developed based on a region such as cytC (the standard now is 4 or more independent regions) and other traits will be overlaid on the tree to study how they have changed or how they vary in different species.
I know you probably think this is completely irrelevant to your argument, but its is relevant. The patterns we observe require an explanation. Here's where that comes in...
All I can think is that if it is a species-identifier then it is a Dog identifier, not a dog-breed identifier, in other words it is an identifier of the Biblical Kind or Species. If that's the case then it would make a wonderful way of defining what a Kind is.
Yes, that would be the expectation, wouldn't it. Based on what I have said about the system in this post (hopefully it is a bit clearer) how would you predict that one could distinguish between "kinds" using this method? Saying that the sequence of a dog should be more similar to another member of the dog kind than it would be to a cat kind is not enough, since that is also what the ToE would predict. How would you predict that there would be disparity between the kinds? How would you recognize different kinds?
I think if nothing else, this should make it clear that mutations do occur and accumulate. I know you have allowed for "some kind of mutation" meaning... I don't know what. Yes, the mutations in cytC are essentially neutral, which is maybe the "some kind" that you allow for. But, the bigger point is that we see this same pattern at play in nuclear coding genes. But we'll have to cover that later, once you understand the point about cytC and how it is used.
Now MAYBE if I read all this a few dozen times some kind of light would be shed on it, but as it is I'm afraid I'm no less in the dark than I was before.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 140 by herebedragons, posted 06-04-2016 11:42 AM herebedragons has replied

Replies to this message:
 Message 145 by herebedragons, posted 06-04-2016 7:46 PM Faith has replied

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


Message 144 of 455 (785424)
06-04-2016 3:30 PM
Reply to: Message 142 by Asgara
06-04-2016 12:05 PM


Re: You are looking at the wrong part of the system
But you aren't explaining how just a change i frequency, with no mutation, can give you anything that isn't already in the parent population.
It doesn't and why should it? This is a very strange expectation. All any new variety or breed or species has is new combinations of what was passed on from the previous population. They may not have shown up in the original population because it took the new genetic combinations to bring them to expression.
Just because you might have more black wolves than grey in the daughter population they are still able to breed with the parent population.
Maybe, maybe not. There is nothing obvious about this. There are many different genes involved, all with their new gene frequencies, not just one trait like grey or black fur, and after many generations of breeding in isolation, developing new genetic combinations, losing some alleles in the process, the daughter population can become genetically incompatible with the parent. And that isn't inevitable either. It may or may not happen.
What actually causes speciation? There is nothing in the new population that isn't already in the parent population. How does a change in frequency achieve what you're proposing?
When Genomicus is discussing cases where only 2 changes can bring about speciation she is talking about mutations. You aren't making any changes other than the frequency of things that are already there.
But if the original population had a fair amount of genetic diversity there's a ton of stuff that's "already there" that didn't get expressed in the parent population, some of which is now getting expressed in the daughter, and there's still more for future populations to bring out. The large heads of the Pod Mrcaru lizards that developed within thirty years probably represent combinations of many different genes that occurred through many reproductive cycles. Darwin got exaggerated characteristics in his pigeons just by breeding them generation after generation for the same trait so that the genetic material kept accumulating in some way that wasn't present in that form to begin with. Dramatic change from same genetic material over generations.
Also, mutations really don't add anything anyway even according to those who believe in them. So you get a black moth besides the white moths, but it's just an allele, which is just a variation of a trait. All species have alleles for different versions of their traits, for black or white or many other colors or different markings that come out over generations. All a mutation does is replace one allele with another and all that allele does is what all alleles do: it provides a specific version of the trait. Since alleles are theoretically all the product of mutations anyway, you've already got an established collection of different possible versions of various traits that can combine in lots of different ways, but the versions of the traits are nothing special, nothing new, all business as usual in the world of alleles. There's no possible way of distinguishing a mutated allele from a built-in allele; they do the same thing in the same way no matter what their origin. You NEVER get anything completely new in the new population, it's all just new combinations of possibilities already available in the species as a whole.

This message is a reply to:
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 Message 156 by NoNukes, posted 06-05-2016 8:36 PM Faith has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 145 of 455 (785432)
06-04-2016 7:46 PM
Reply to: Message 143 by Faith
06-04-2016 3:01 PM


Re: Trying to clarify cytochrome C
Then how could it possibly be a species identifier?
Maybe you could try reading the whole post before you begin replying?
Fine, you've explained the discrepancy but not solved the problem of whether there is increased genetic diversity or not. Seems to me that the mitochondrial DNA measure in fact says nothing about the true situation,
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.
Obviously the mitochrondrial DNA method is useless as a measure of genetic diversity so why is it used at all?
Did you read the paper that Genomicus cited? What did they use it for? What sort of things did they detect from their study.
Maybe that study wasn't the best example to show an increase in genetic diversity because of the confounding factors, but it does nicely show an increase in genetic diversity that is due to ONLY mutations.
How are you getting any "differentiation between sequences" at all in the first place?
Mutation. If you would have read the entire post before replying it would have been clear.
That entire paragraph is absolute gobbledygook to me.
Standard go to response. I am still convinced you are being deliberately obtuse.
What I've described of breeding practices is so well known, not only is this statement undecipherable, but insofar as it aims to contradict what is well known it's ridiculous.
I take it you have experience with a breeding program, since breeding is "so well known" to you? If so, then you should know what introgress and genetic background means. But... introgress means to introduce a trait from a different species, breed, or a wild relative and then backcrossing until it is a fixed part of the target genome. Genetic modification is an example of this where a specific gene (and only a specified gene) is introduced into a breeding line. If you have a line that say has high yield and high protein content, this would be the genetic background. These are the traits you want to maintain in your new variety.
But say this line is susceptible to a disease that is becoming an increasing problem. And say there is another variety that does not have the desirable yields or has some other undesirable characteristics but is resistant to the disease in question. A breeder will breed the two varieties together and do several backcrosses until that desirable trait (disease resistance) has 'introgressed' into the desirable genetic background. Then they will use selection to develop the new variety.
Not only does it not tell me anything about why I'm wrong about breeding practices, it doesn't tell me anything at all about breeding methods, period.
You only focus on the selection part, but where does the variation come from? You claim the variation is always there, built in, but you have NO support for that idea other than your narrative that it must be so. You have also claimed that gene flow "muddies" the breed, but in fact that is not the case. A breeder will introduce new variation into a breeding line so that new traits can be selected. The creation of new breeds or varieties requires new variation not reduced genetic variation. Breeders introduce this variation artificially while in nature variation is introduced via mutations (although mutation does play some role in breeding and crossbreeding does play some role in nature).
But you've said absolutely nothing about how these different species get or don't get a particular species identifier. Ordinary reproduction should pass on the same identifier indefinitely, so in related species how do they get different identifiers?
Mutations that are passed on to the offspring which then accumulate new mutations which are passed down to their offspring which then accumulate more mutations which are passed on to their offspring, etc... over many generations the sequences are distinguishable from the original parental sequences. I already said this...
That is a completely gratuitous unfair accusation.
I didn't mean it as an insult, I can see why this would not make sense to you... it doesn't fit you idea of how genetics work.
I'm doing my best to understand your completely garbled presentation of these things.
No you're not. You are trying to find reasons to dismiss it, to ignore it. Claiming it is completely undecipherable is the only thing you can come up with at this point.
Maybe you should just try explaining what you know instead of making up straw men.
Make up your mind.
Faith writes:
Perhaps you could try thinking like a YEC for a moment, maybe you'd come up with the explanation.
But then when we do...
Faith writes:
Maybe you should just try explaining what you know instead of making up straw men.
Ok. Here's what I know... Your idea about how genetics works is totally crap and has absolutely no explanatory power. It matches nothing we observe in population genetics and doesn't even work mathematically.
HBD

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.

This message is a reply to:
 Message 143 by Faith, posted 06-04-2016 3:01 PM Faith has replied

Replies to this message:
 Message 146 by Faith, posted 06-05-2016 5:18 AM herebedragons has replied

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


Message 146 of 455 (785437)
06-05-2016 5:18 AM
Reply to: Message 145 by herebedragons
06-04-2016 7:46 PM


Re: Trying to clarify cytochrome C
I often don't read linked papers, they are too hard on my eyes and I expect the poster to put the point in ordinary language.
So the fact that mitochondrial DNA gets a lot of mutations proves that the animal has increased genetic diversity, even if it's on the verge of extinction from all the increasing homozygosity?
What are you so ticked about? You aren't good at explaining things so now you're in a rage at me?

This message is a reply to:
 Message 145 by herebedragons, posted 06-04-2016 7:46 PM herebedragons has replied

Replies to this message:
 Message 147 by herebedragons, posted 06-05-2016 7:19 AM Faith has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 147 of 455 (785438)
06-05-2016 7:19 AM
Reply to: Message 146 by Faith
06-05-2016 5:18 AM


Re: Trying to clarify cytochrome C
Rage????
I realized long ago that one of your strategies for replying to me was to try and elicit an emotional response and I don't allow you to goad me into that kind of response. The most emotion you should get from my response is annoyance. I'm in a rage, really? That's the best response you got????
HBD
Edited by herebedragons, : typo

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.

This message is a reply to:
 Message 146 by Faith, posted 06-05-2016 5:18 AM Faith has replied

Replies to this message:
 Message 148 by Faith, posted 06-05-2016 7:22 AM herebedragons has replied

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


Message 148 of 455 (785439)
06-05-2016 7:22 AM
Reply to: Message 147 by herebedragons
06-05-2016 7:19 AM


Re: Trying to clarify cytochrome C
You're also a very bad psychologist.

This message is a reply to:
 Message 147 by herebedragons, posted 06-05-2016 7:19 AM herebedragons has replied

Replies to this message:
 Message 149 by herebedragons, posted 06-05-2016 8:04 AM Faith has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 149 of 455 (785441)
06-05-2016 8:04 AM
Reply to: Message 148 by Faith
06-05-2016 7:22 AM


Re: Trying to clarify cytochrome C
Right. I am bad at explaining things. I have a bad personality. I am a bad psychologist. I am a bad Christian. What else did I miss?
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.
HBD

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.

This message is a reply to:
 Message 148 by Faith, posted 06-05-2016 7:22 AM Faith has replied

Replies to this message:
 Message 152 by Faith, posted 06-05-2016 12:08 PM herebedragons has not replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 150 of 455 (785450)
06-05-2016 10:19 AM
Reply to: Message 132 by Tangle
06-03-2016 8:57 AM


Re: Finally.
Tangle writes:
Nature writes:
... Our findings fill a substantial knowledge gap in the iconic example of microevolutionary change, adding a further layer of insight into the mechanism of adaptation in response to natural selection. The discovery that the mutation itself is a transposable element will stimulate further debate about the importance of ‘jumping genes’ as a source of major phenotypic novelty.
From Nature
Nature - Not Found
Oo oo nailed it -- door #1 in Message 45 in Iconic Peppered Moth - gene mutation found:
1. an inactive gene section is moved into an active section of the genome and goes to work, ...
See -- it really was a "built-in" gene and it just needed the right recombination of the genes to become a realized phenotype ...
Enjoy

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This message is a reply to:
 Message 132 by Tangle, posted 06-03-2016 8:57 AM Tangle has replied

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