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Author Topic:   Molecular Population Genetics and Diversity through Mutation
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 61 of 455 (785053)
05-27-2016 1:19 PM
Reply to: Message 59 by Faith
05-27-2016 1:02 PM


Re: genetic diversity on the ark
Faith writes:
Twelve is really a lot when you are talking about EVERY locus in the genome, or on the ark at least a majority, and when you assume, as I do, that there were lots more functioning genes for a given trait than is now the case, huge numbers having been lost to "junk DNA" since then.
Except, as usual Faith, you have been shown that your assumption that there were lots more functioning genes for a given trait than is now is simply utter, total and complete nonsense.
We have genetic DNA samples from humans, plants and animals that would have been alive at the same time Adam supposedly lived and know for a fact that your assumption is wrong. You have even been shown that evidence numerous times.
Further, we know also have DNA samples from tens of thousands of years before Adam was supposedly created and know for a fact that that DNA is quite similar to what is seen in living critters.
Thank God there never was an Adam & Eve or the Ark.

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 59 by Faith, posted 05-27-2016 1:02 PM Faith has replied

Replies to this message:
 Message 62 by Faith, posted 05-27-2016 1:22 PM jar has replied

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


Message 62 of 455 (785055)
05-27-2016 1:22 PM
Reply to: Message 61 by jar
05-27-2016 1:19 PM


Re: genetic diversity on the ark
Your dating methods are unreliable.

This message is a reply to:
 Message 61 by jar, posted 05-27-2016 1:19 PM jar has replied

Replies to this message:
 Message 64 by jar, posted 05-27-2016 1:33 PM Faith has not replied

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


(1)
Message 63 of 455 (785059)
05-27-2016 1:32 PM
Reply to: Message 54 by Faith
05-27-2016 4:31 AM


Re: You are looking at the wrong part of the system
This quote from the Wikipedia article on Genotype Frequency doesn't treat the H-W equilibrium as an ideal but as a reality.
My statement about Hardy-Weinberg is correct regardless of what you think Wikipedia seems to be saying.
Another point... a population, such as your wildebeests, could be a stable population (not undergoing evolution) and still not be in HW equilibrium, but to show how that would work I would need to use maths... so, you'll just have to take my word for it.
Microevolution means "evolution within a population???" I have NO idea what you are saying. Microevolution IS evolution, it's what is happening wherever new varieties or subspecies are being formed from new gene frequencies.
You quoted a statement from Berkeley but don't even understand how they use the terms they are using?
Defining microevolution
quote:
Biologists who study evolution at this level [microevolution] define evolution as a change in gene frequency within a population.
You have absolutely lost me. You are talking gobbledygook as far as I can tell, making unimportant distinctions as far as my argument is concerned. It is "gene frequency" not "genotype frequency" that is defined as evolution, and it's evolution I'm talking about.
Ok, first of all, I said "genotypes" not "genotype frequency." I am asking what genotypes exist in the daughter population that do not exist in the parental population. Answer: none. In my example (of a loss of alleles due to a sub-population split), all the genotypes in the daughter population exist in the parental population. I am asking you to account for how daughter populations could have unique genotypes (genotypes that do not exist in the parent population). In order for this to occur, there would need to be new alleles introduced, no?
And secondly, this is an example of why I think you are being intentionally obtuse. You claim to understand topics like Hardy-Weinberg better than I, or at the very least you call my points about the subject "gobbledygook" and yet you claim that you don't get the connection between allele frequency, Hardy-Weinberg and genotypic frequency. If you talk about allele frequency and Hardy-Weinberg, you ARE talking about genotypic frequency. Since you obviously know that, your failure to comprehend my point is evidently feigned.
What IS the problem? Extrapolating back from the loss of genetic diversity brought about by selection, random or artificial or natural (it's all the same effect), I add back the genetic diversity lost down the generations and arrive at LOTS of genetic diversity at the starting point from which all the types and breeds descended. A lot more heterozygosity I've many times suggested. WHAT'S THE PROBLEM?
WHAT'S THE PROBLEM? You don't recognize that there is a lot more differences between the genomes of Drosophila melanogaster and Drosophila erecta or between Canis lupus and Canis aureus than a just reduction in heterozygosity. I am asking you to explain how your hypothesis of genetic depletion explains those differences.
It would be if you understood what I'm talking about and looked in the right place for the right evidence.
Of course... that's the problem.
It's obvious that your responses to me are designed to end the discussion between you and I. If you don't wish to further our discussion, then just don't respond to me. Pretending to not understand so that you don't have to address my points is just silly nonsense.
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 54 by Faith, posted 05-27-2016 4:31 AM Faith has replied

Replies to this message:
 Message 65 by Faith, posted 05-27-2016 1:48 PM herebedragons has replied

  
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 64 of 455 (785060)
05-27-2016 1:33 PM
Reply to: Message 62 by Faith
05-27-2016 1:22 PM


Re: genetic diversity on the ark
Faith writes:
Your dating methods are unreliable.
You often make such silly and unsupported claims yet so far no one including you has ever shown the dating methods to be unreliable and in fact every new method develops has simply increased the accuracy of those dating methods. Further, those very dating methods you claim unreliable are used by Biblical scholars to date recent archeological finds.
Sorry Charley but you don't get to swing both ways or expect anyone to accept your nonsense assertions until you present the model, method, procedure, process or thingamabob used to determine that the dating methods are invalid. Reference to what the Bible says is not such evidence, only evidence of the ignorance of the folk that wrote the Bible stories.

Anyone so limited that they can only spell a word one way is severely handicapped!

This message is a reply to:
 Message 62 by Faith, posted 05-27-2016 1:22 PM Faith has not replied

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


Message 65 of 455 (785064)
05-27-2016 1:48 PM
Reply to: Message 63 by herebedragons
05-27-2016 1:32 PM


Re: You are looking at the wrong part of the system
Ok, first of all, I said "genotypes" not "genotype frequency." I am asking what genotypes exist in the daughter population that do not exist in the parental population. Answer: none. In my example (of a loss of alleles due to a sub-population split), all the genotypes in the daughter population exist in the parental population. I am asking you to account for how daughter populations could have unique genotypes (genotypes that do not exist in the parent population). In order for this to occur, there would need to be new alleles introduced, no?
No. Just new allele frequencies, which we have as result of the population split, which will become the basis for the new genotypes as they get worked through the population down the generations.
ABE: You aren't going to get "new" genotypes, just a new frequency of genotypes. Where you had, say, 90% bb, 8% Bb and 2% BB in the original population, you could have 20% bb, 70%Bb and 10% BB. Parent lots of blue eyes, daughter an increase in brown eyes which should increase even more down the generations.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 63 by herebedragons, posted 05-27-2016 1:32 PM herebedragons has replied

Replies to this message:
 Message 70 by Modulous, posted 05-27-2016 3:01 PM Faith has replied
 Message 78 by herebedragons, posted 05-28-2016 9:20 AM Faith has replied

  
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 66 of 455 (785068)
05-27-2016 2:06 PM
Reply to: Message 53 by 14174dm
05-26-2016 4:46 PM


Re: Some very simple maths.
Instead of arguing math and semantics, could we find examples?
Otzi the Iceman and King Tutankhamun & family have had dna analyses. I've tried but haven't found what I'm looking for.
Good thinking, but better than looking at individuals like Oetzi would be to look a samples from multiple members of ancient populations. And if we stick to historical periods even better since the dating cannot be as easily dismissed, as a YEC would be bound to do for anything claimed to be Palaeolithic in age.
Thankfully we have many such samples, so it should be simple to check whether they have much higher allelic diversity than modern populations. Frustratingly, though, I can't find anything that addresses the question directly, since studies of historical DNA samples are usually addressing questions other than creationist fantasies. I'll let you know if I have any luck.

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Replies to this message:
 Message 67 by Faith, posted 05-27-2016 2:16 PM caffeine has replied

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


Message 67 of 455 (785071)
05-27-2016 2:16 PM
Reply to: Message 66 by caffeine
05-27-2016 2:06 PM


Re: Some very simple maths.
Thankfully we have many such samples, so it should be simple to check whether they have much higher allelic diversity than modern populations.
What you would look for is a higher percentage of heterozygosity throughout the genome. Perhaps significantly less junk DNA.
But I don't believe Oetzi is that old. He ate "highly processed" grains for one thing. Not that I think he bought his cereal at the supermarket, but it suggests something a little more modern than is usually imputed to him. Give up on the radiometric dating and it's all guesswork.

This message is a reply to:
 Message 66 by caffeine, posted 05-27-2016 2:06 PM caffeine has replied

Replies to this message:
 Message 69 by caffeine, posted 05-27-2016 2:46 PM Faith has replied
 Message 72 by Coyote, posted 05-28-2016 12:17 AM Faith has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 68 of 455 (785072)
05-27-2016 2:20 PM
Reply to: Message 59 by Faith
05-27-2016 1:02 PM


Re: genetic diversity on the ark
You act as if I'd never discussed this.
Not at all, I'm just pointing out that from an allele standpoint you have the issue of there being fewer as you go back so you still need some way for them to have got here one way or another
I do need to account for the extra alleles that now exist for a single locus nevertheless, so I've considered the possibility that there is some kind of mutation, just not the random accidental kind.
Indeed. Or as I said
quote:
Indeed, the problem is that you need to introduce variability into the system one way or another to explain what we see.
You have *something God related no doubt*
We have observed random noise.
not the random accidental kind.
But why not? At least for microevolutionary events. As a real example take this:
quote:
The body hairs on the dorsal surface of Salukis and Afghan Hounds have both phaeomelanin and eumelanin portions, even though they had an a(t)/a(t) genotype at ASIP. In addition, all had at least one copy of a newly identified mutation in MC1R, g.233G>T, resulting in p.Gly78Val. This new allele, that we suggest be designated as E(G), is dominant to the E and e (p.Arg306ter) alleles at MC1R but recessive to the E(M) (p.Met264Val) allele.
A new mutation in MC1R explains a coat color phenotype in 2 "old" breeds: Saluki and Afghan hound - PubMed
In English, they note a gene that affects coat colour have a point mutation from a G to a T. You can see this further here:
UniProt
10         20         30         40         50
MNIFRLLLAT LLVSLCFLTA YSHLAEEKPK DDRSLRSNSS VNLLDFPSVS
        60         70         80         90        100
IVALNKKSKK ISRKEAEKKR SSKKKASMKN VARPRPPPPT PCVATRNSCK
       110        120        130
SPAPACCDPC ASCQCRFFRS ACTCRVLSPR C            
a mutation that turns this into
10         20         30         40         50
MNIFRLLLAT LLVSLCFLTA YSHLAEEKPK DDRSLRSNSS VNLLDFPSVS
        60         70         80         90        100
IVALNKKSKK ISRKEAEKKR SSKKKASMKN VARPRPPPPT PCVAT[color=red]C[/color]NSCK
       110        120        130
SPAPACCDPC ASCQCRFFRS ACTCRVLSPR C       
Arginine -> Cysteine will make an Alsatian/German Shephard black.
Interesting if maximum heterozygosity is 50% as you say.
Basically, yes.
Imagine there are two heterozygotic individuals, call them Adam and Eve. OK, I've proven the thesis wrong as there is 100% heterozygosity. But they mate what are their babies?
GG
gg
gG
Gg
50% of them will be heterozygotic. Obviously chance plays a role, but the trend is biased towards 50% heterozygotic as a maximum.

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caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


Message 69 of 455 (785076)
05-27-2016 2:46 PM
Reply to: Message 67 by Faith
05-27-2016 2:16 PM


Re: Some very simple maths.
What you would look for is a higher percentage of heterozygosity throughout the genome. Perhaps significantly less junk DNA.
But I don't believe Oetzi is that old. He ate "highly processed" grains for one thing. Not that I think he bought his cereal at the supermarket, but it suggests something a little more modern than is usually imputed to him. Give up on the radiometric dating and it's all guesswork.
Knowing that your response would be along these lines is precisely why I suggested looking to historical populations rather than to someone like Oetzi. Thankfully we have plenty of DNA from historical contexts, from individuals who lived during the Roman Empire, for example, which I think we can all agree about about 2,000 years old.
Looking at heterozygosity in a single individual doesn't tell us a great deal. If we can look at allelic diversity across a large sample and see if it differs from today.

This message is a reply to:
 Message 67 by Faith, posted 05-27-2016 2:16 PM Faith has replied

Replies to this message:
 Message 73 by Faith, posted 05-28-2016 12:18 AM caffeine has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 70 of 455 (785078)
05-27-2016 3:01 PM
Reply to: Message 65 by Faith
05-27-2016 1:48 PM


Re: You are looking at the wrong part of the system
ABE: You aren't going to get "new" genotypes, just a new frequency of genotypes. Where you had, say, 90% bb, 8% Bb and 2% BB in the original population, you could have 20% bb, 70%Bb and 10% BB. Parent lots of blue eyes, daughter an increase in brown eyes which should increase even more down the generations.
This isn't how it works. The situation of '90% bb, 8% Bb and 2% BB' is not in Hardy Equilibrium. If this population has children, they will have different frequencies, which is why it is not equilibrium. Let's say 90% of the population has blue eyes. To get this the 'b' allele has to be 95% of all alleles. About 9% of the population will have Brown Heterozygous and 1% will be homozygous. This is the only way for blue eyes to be in Hardy Weinberg Equilibrium and be expressed in 90% of the population. So the real Hardy equilibrium is either 90% blue 10% brown OR more accurately 90%bb 9%Bb 1%BB
You pick a subgroup which has 20% blue eyes and 70% brown heterozygous. This isn't Hardy Weinberg so it tends towards this equilibrium. Let's say it settles down to 16% blue eyes and 48% brown eye heterozygous. This is a new equilibrium and instead of b having a frequency of 95%, b now has a frequency of 40%.
That's Hardy-Weinberg. The gene frequencies change between these two states, but that is because of emmigration, something which can interfere with the equilibrium and yes, emmigration is ONE of the things which causes frequency change but it is not the only one, and it its not a big one because other than random chance the only way for a large group to have disproportionally blue eyed people is if there is some naturally occurring selective force.
Adding to Hardy Weinberg with only natural selection, sexual selection drift and emmigration will result in subgroups having certain alleles unavailable to them, resulting in a tendency towards nothing.
You can have 1% blue eyes, 90% blue eyes and anything else in Hardy Weinberg equilibrium. Darwin's contribution was essentially to say (though he didn't know it at the time) that although any Hardy Weinberg equilibria is possible in nature, nature prefers some equilibria over others. Sometimes nature's preferred equilibria is 100% 0%, sometimes it is something else. This 'preference' is natural selection.

This message is a reply to:
 Message 65 by Faith, posted 05-27-2016 1:48 PM Faith has replied

Replies to this message:
 Message 71 by Faith, posted 05-28-2016 12:03 AM Modulous has replied

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


Message 71 of 455 (785108)
05-28-2016 12:03 AM
Reply to: Message 70 by Modulous
05-27-2016 3:01 PM


Re: You are looking at the wrong part of the system
This isn't how it works. The situation of '90% bb, 8% Bb and 2% BB' is not in Hardy Equilibrium. If this population has children, they will have different frequencies, which is why it is not equilibrium.
Dear dear Moddy, I said nothing about H-W equilibrium. If for some reason it SHOULD be in equilibrium, though I don't know why it should, then adjusting the percentages is fine with me. It was just a collection off the top of my head to describe what I figured was a predominantly blue-eyed population -- from which the daughter population randomly selected most of the B's which would give it a new set of genotypes, which was the point to HBD who keeps insisting that population splits don't change genotypes (or phenotypes.)
I know this makes me a lazy bum, but I like to keep the argument general rather than getting all specific about exact percentages of this that or the other, because the argument is about a general trend and not about specifics.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 70 by Modulous, posted 05-27-2016 3:01 PM Modulous has replied

Replies to this message:
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Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 72 of 455 (785109)
05-28-2016 12:17 AM
Reply to: Message 67 by Faith
05-27-2016 2:16 PM


A challenge for Faith...
Give up on the radiometric dating and it's all guesswork.
Oetzi has been dated by radiocarbon to between 3350 and 3100 BC.
You say "I don't believe Oetzi is that old" and that it is all guesswork?
May I suggest that 1) you don't know anything useful about radiocarbon dating, and that 2) you are basing everything on a religious belief, but that 3) you have to try to invoke science to convince yourself and others that your religious beliefs are accurate.
So, if you disagree lets hear the technical details about why radiocarbon dating is "guesswork." (But be careful--those creationist sites will lie to you.)

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 73 of 455 (785110)
05-28-2016 12:18 AM
Reply to: Message 69 by caffeine
05-27-2016 2:46 PM


Re: Some very simple maths.
Thankfully we have plenty of DNA from historical contexts, from individuals who lived during the Roman Empire, for example, which I think we can all agree about about 2,000 years old.
Looking at heterozygosity in a single individual doesn't tell us a great deal. If we can look at allelic diversity across a large sample and see if it differs from today.
Sounds good to me. Let me know what you find out about the Roman Empire.

This message is a reply to:
 Message 69 by caffeine, posted 05-27-2016 2:46 PM caffeine has not replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 74 of 455 (785113)
05-28-2016 2:01 AM
Reply to: Message 39 by Faith
05-26-2016 3:03 AM


Re: But I'm just as mathematically challenged as ever
See Message 3 of the Great Debate thread.
Edited by Genomicus, : No reason given.

This message is a reply to:
 Message 39 by Faith, posted 05-26-2016 3:03 AM Faith has not replied

  
PaulK
Member
Posts: 17822
Joined: 01-10-2003
Member Rating: 2.2


Message 75 of 455 (785116)
05-28-2016 2:57 AM


Faith - Why the fuss?
Faith you have admitted that you are not interested in the question of long-term trends in diversity, only what happens to diversity in speciation events.
why then, are you claiming to have discovered such a trend when you aren't interested enough to investigate the question properly ?
Wouldn't it be far easier to just admit that you aren't interested and drop the point right at the start instead of spending - literally - years arguing over something you claim not to care about ?

Replies to this message:
 Message 76 by Faith, posted 05-28-2016 3:34 AM PaulK has replied

  
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