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Author Topic:   Molecular Population Genetics and Diversity through Mutation
NoNukes
Inactive Member


(1)
Message 316 of 455 (785857)
06-12-2016 12:35 PM
Reply to: Message 312 by Faith
06-12-2016 6:57 AM


Re: Mutations are not alleles
Then there was that Wikipedia article that pretty much defined polymorphic genes as disease-causers.
Nope. It says may. That is not a definiton.
Trusting you guys in a sense, not realizing that you don't distinguish between disease-causing alleles and normal variants.
What's hilarious about this is that you've been given about a dozen examples of observed mutations, none of which meet the definition of 'disease-causing alleles.' Beyond that, the article simply does not define things as you claim. It discusses a possible outcome of mutation. Then in the best kettle/pot fashion you complain of having to address straw men.
In fact as I think about it now ALL mutations of alleles create polymorphic genes. That's what the mutations DO to alleles.
Wow, let's examine this chain of logic. You "learned" that mutations to polymorphic genes may, I mean "are defined" as causing disease. You have decided that they always lead to disease, and then you decide that all mutations create polymorphic genes. You reached this conclusion despite knowing of contrary examples.
Let's review another thought path. You've been trying for years to tell us that evolution must inevitably reduce diversity and for that reason evolution cannot produce the results claimed by the theory of evolution even if mutations do work. That is the basis of this particular thread. But somehow it is our fault that you've tricked into discussing mutations as a possible answer? Really, Faith? Is it accurate to say what you are saying.
Finally, you are so far off of your original premise, that you cannot even keep straight whether breeding or any other evolution does or does not involve new genotypes. It's okay to change your mind. I've been urging you to do this throughout the thread, but you ought to at least be honest about "refocusing" rather than blaming others.
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

This message is a reply to:
 Message 312 by Faith, posted 06-12-2016 6:57 AM Faith has not replied

  
herebedragons
Member (Idle past 885 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


(1)
Message 317 of 455 (785916)
06-13-2016 1:11 PM
Reply to: Message 312 by Faith
06-12-2016 6:57 AM


Re: Mutations are not alleles
All the straw man misrepresentations of my argument after all this time are really disappointing.
The reality is that your argument is not very well detailed, it is pretty much a vague set of generalizations about a limited range of topics that broadly cover evolution. Little wonder that we "straw man" your arguments. Besides, your complaints about "straw men" is designed to simply avoid having to address the rebuttals. I mean it would be a different thing if you weren't creating caricatures of your own and of the processes you discuss; such as:
Then there was that Wikipedia article that pretty much defined polymorphic genes as disease-causers.
That is not what the article says. That is your spin on it based on your own person bias.
Being so surprised by that is my own fault of course because I shouldn't have been assuming they were normal variants. Trusting you guys in a sense, not realizing that you don't distinguish between disease-causing alleles and normal variants. I should have realized it, it's been said before here, I guess I just couldn't believe it because it's too irrational -- wow, I guess I learned THAT lesson.
This is disingenuous and even dishonest. There are alleles that cause disease. There are alleles that make on organism less fit in a particular environment. There are alleles that make an organism more fit in a particular environment. There are alleles that have little to no effect on the organism, but are just different. There are alleles that cause morphological changes but that don't really affect fitness much. We have not been deceptive about these facts. Just because you have been trying to define 'allele' in a way that supports your premise is not the fault of any of us. In fact, I have pointed out to you on several occasions that your idea of what alleles are is misinformed.
Alleles are different variants of a gene at a specific locus. This is the definition you will find just about everywhere. From that definition it should be abundantly clear that a disease allele is, in fact, an allele.
Now, describe which of the Runx-2 alleles is a disease allele; and which of the human ABO gene alleles are disease alleles. Both are polymorphic genes and neither are defined as "disease-causers" as you claim.
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 312 by Faith, posted 06-12-2016 6:57 AM Faith has replied

Replies to this message:
 Message 318 by Faith, posted 06-13-2016 2:08 PM herebedragons has replied

  
Faith 
Suspended Member (Idle past 1472 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 318 of 455 (785921)
06-13-2016 2:08 PM
Reply to: Message 317 by herebedragons
06-13-2016 1:11 PM


Re: Mutations are not alleles
There is no excuse whatever for your straw man versions of my argument, and Dr. A's are even worse. NN does the same, but then he does it on every subject imaginable.
The Wikipedia article concerned ONLY disease processes, why is that? You'd think such an article would make an attempt to be inclusive of all the forms but no it only mentions three diseases. ONE mention of a normal variant in the fur color illustrated by the mice in the picture.
My reaction was quite honest to that article.
Defining a disease allele as an allele is what is dishonest even if every geneticist does it. All it proves is that the ToE has a stranglehold on you all.
Here is a link to a couple of pages discussion the ABNORMALITIES connected with Runx-2. You asked, I'm answering:
Runx2 Targeted Allele Detail MGI Mouse (MGI:3043791)
Perhaps you can show that other versions do not produce abnormalities?
craniofacial
abnormal cranium morphology
large anterior fontanelle
absent occipital bone
absent zygomatic arch
abnormal hyoid bone morphology
abnormal nasal bone morphology
growth/size/body
decreased birth body size
decreased birth weight
limbs/digits/tail
abnormal phalanx morphology
abnormal tibia morphology
mortality/aging
postnatal lethality, incomplete penetrance
premature death
skeleton
Edited by Faith, : No reason given.

This message is a reply to:
 Message 317 by herebedragons, posted 06-13-2016 1:11 PM herebedragons has replied

Replies to this message:
 Message 319 by Dr Adequate, posted 06-13-2016 2:24 PM Faith has replied
 Message 320 by NoNukes, posted 06-13-2016 2:30 PM Faith has not replied
 Message 322 by PaulK, posted 06-13-2016 2:47 PM Faith has not replied
 Message 336 by herebedragons, posted 06-13-2016 11:06 PM Faith has replied

  
Dr Adequate
Member (Idle past 312 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 319 of 455 (785925)
06-13-2016 2:24 PM
Reply to: Message 318 by Faith
06-13-2016 2:08 PM


Re: Mutations are not alleles
The Wikipedia article concerned ONLY disease processes, why is that?
It doesn't, as you admit later in the same paragraph.
Defining a disease allele as an allele is what is dishonest even if every geneticist does it. All it proves is that the ToE has a stranglehold on you all.
Faith. This is how the English language works. Nouns are modified by adjectives. We do not have one word for a red boat, and another for a blue boat. Instead we qualify the word "boat" by the words "blue" or "red", as the case may be. We do not have one word for a broken hairdryer and another word for a functioning hairdryer. Rather, we speak of "a broken hairdryer" and "a functioning hairdryer" respectively. And instead of having three different nouns for beneficial alleles, neutral alleles, and deleterious alleles, we speak of "beneficial alleles", "neutral alleles", and "deleterious alleles".
You may think that this is dishonest, Faith, but given that the English language has in current usage about 80,000 nouns and 40,000 adjectives, if we did things your way the English language would have to have a vocabulary consisting of over three billion words, which would make it insuperably difficult to learn.

This message is a reply to:
 Message 318 by Faith, posted 06-13-2016 2:08 PM Faith has replied

Replies to this message:
 Message 328 by Faith, posted 06-13-2016 4:11 PM Dr Adequate has replied

  
NoNukes
Inactive Member


Message 320 of 455 (785926)
06-13-2016 2:30 PM
Reply to: Message 318 by Faith
06-13-2016 2:08 PM


Reading is fundamental...
Emphasis added by me.
The Wikipedia article concerned ONLY disease processes, why is that? You'd think such an article would make an attempt to be inclusive of all the forms but no it only mentions three diseases. ONE mention of a normal variant in the fur color illustrated by the mice in the picture.

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 318 by Faith, posted 06-13-2016 2:08 PM Faith has not replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


(1)
Message 321 of 455 (785929)
06-13-2016 2:46 PM
Reply to: Message 224 by Faith
06-08-2016 7:16 PM


Re: You are looking at the wrong part of the system
Faith writes:
There are two different theories here about the cause of "differences in DNA sequence." MUTATIONS are not responsible for them, BUILT-IN NATURALLY OCCURRING ALLELES, or differences in DNA sequence, are responsible for them.
We observe mutations producing new and naturally occurring alleles all of the time.
You have a serious problem with your argument. You want to claim that any change to the DNA sequence of a species' genome will cause irreparable harm. However, there are millions of changes that separate species, and they aren't harmful. How can you say that mutations producing those changes will cause harm?
We are not genetically related to chimps. There are no mutations that could possibly occur to form one species from another.
Again, you have the same problem. First, you haven't produced a single criteria for determining genetic relatedness, so your claim is hollow. Second, the reason that humans and chimps are different from one another is because of the DNA sequence differences between their genomes. How can you claim that changes in DNA sequence can not produce new species when that is exactly what we observe?
In the best possible scenario mutations would only substitute one ordinary allele for another, which is redundant and unnecessary, but in reality they don't do even that much, they either manage not to do anything good or bad, or they render an allele unfunctional, or they produce an actual disease process. The ToE needs mutations but the mutations it needs don't exist.
Then how do you explain the physical differences between species? What is the cause if it isn't a difference in DNA sequence?
And if you understand my argument the formation of phenotypes has to lose genetic diversity so even if all your genetic diversity is made up of mutations when phenotypes are selected most of that diversity is excluded from the new population anyway, NECESSARILY excluded or you don't get the new phenotypes that are supposedly the evidence of evolution. Perhaps it would help if you assumed the lotus position and meditated on this for a while. {ABE: Sorry, trying to be amusing. Seriously, if you prayed to the living God of the Bible you'd probably start understanding these things. /ABE}
Then how do you explain the physical differences between species if it isn't due to a difference in DNA sequence within their respective genomes? Take any of the 40 million mutations that separate humans and chimps and show us how the observed mechanisms of mutation could not produce those differences. Can you do that?
This statement is what is meaningless. Did you mean "living dead species?" Anyway I have NO idea what you are talking about. The loss in genetic diversity occurs when new phenotypes are developing. It MUST occur. This should be obvious just from knowing how breeding works. The only explanation of all of this is that living things did not evolve from a common ancestor but belong to their own particular genetic Kind or Species, within which much variation is possible. For this variation to occur the evolving population must lose genetic diversity so that it can't vary beyond the point where there is no more diversity left. There may be plenty of genetic diversity in other subspecies or breeds of the same Kind, but where it is varying or evolving it has to lose diversity. This is the built-in limit to evolution that defines the limit to the Kind as well.
Increases in genetic diversity also have to occur due to new mutations in each and every generation and in each and every individual. If two populations are kept apart and do not interbreed, this will necessarily result in each population become less like the other one over time. This is due to the accumulation of population specific mutations. We have directly observed this process occurring. For example, captive breeding populations of lab mice have diverged from one another over the last 60 years.
As I described before, you would describe this divergence as a loss in genetic diversity. Therefore, your description is meaningless. Multiply this process over and over until you have millions of diverging species we have today, and you would call each and every step a loss in genetic diversity.
What you are calling mutations are not mutations, they are naturally occurring built-in genetic differences.
What's the difference? If a mutation turns AGG into AGC, how would the effect be any different than if a supernatural creator turned that same AGG into AGC?
You consistently confuse natural allelic forms with mutations. But when I'm talking about mutations coming along to mess up a breed I'm talking hypothetically for the sake of argument, that once the breed is formed, which requires reduction in geneitic diversity, it would wreck the breed for there to be any new genetic input, whether from mutations, (which I include only for the sake of argument because I believe they are predominantly destructive) or resumed gene flow due to immigration of other individuals. The only reason I emphasize the preservation of a breed or species is to make the point that the ToE claims new species or phenotypes to be evidence of evolution and I'm showing that it can't be because it's genetically limited.
As already shown, humans and chimps are not wrecked, even though they are separated by 40 million differences. Reality proves you wrong.
There aren't any mutations happening in these dogs, period. It's all hypothetical for the sake of argument. The dog breeds are developed from natural built-in genetic variability.
Evidence?
In humans, we observe that every human is born with about 50 mutations. Why would dogs be any different?
Oh but it does, it makes a perfect analogy. Even Darwin understood that much.
Really? Let's use the peppered moths as an example. If you were breeding white moths, the mutation that produced black moths would "wreck the breed". However, in the real world that mutation was very beneficial to the moths when they found themselves in an environment darkened by soot from factories. Your analogy completely fails. What breeders want has nothing to do with what is and could be selected for in nature.
My basic argument proves that the ToE doesn't work. That leaves design.
Your basic argument doesn't have the basics, like a falsifiable list of criteria for determine what genetic relatedness is evidenced by.

This message is a reply to:
 Message 224 by Faith, posted 06-08-2016 7:16 PM Faith has not replied

  
PaulK
Member
Posts: 17827
Joined: 01-10-2003
Member Rating: 2.3


Message 322 of 455 (785930)
06-13-2016 2:47 PM
Reply to: Message 318 by Faith
06-13-2016 2:08 PM


A private definition of honesty ?
Apparently gross misrepresentation is "honest" while simply not inventing the jargon Faith wants is "dishonest". I do not think that further commentary is necessary.

This message is a reply to:
 Message 318 by Faith, posted 06-13-2016 2:08 PM Faith has not replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


Message 323 of 455 (785932)
06-13-2016 3:04 PM
Reply to: Message 302 by Faith
06-11-2016 7:11 PM


Re: Mutations are not alleles
Yeah sickle cell anemia exchange for malaria. Wonderful. The occasional fluke like the moths and the pocket mice, which is still not easy to explain despite the insistence here, doesn't save mutations from the opprobrium they deserve.
And "neutral" mutations are killers of normal alleles. At least they set the stage for their complete killing when another mutation comes along. There is nothing benign about "neutral" mutations.
I picked out some random human DNA and searched for that same sequence in the chimp genome. This is what I got:
Query  133   ACATACAGACTGTACATGTAAGCAAATTTAAAATGCAGTATTAAATCATAGCTCTATAGC  192
             |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
Sbjct  1     ACATACAGACTGTACATGTAAGCAAATTTAAAATGCAGTATTAAATCATAACTCTATAGC  60

Query  193   CGCCACTGTCTGGCCACAGCCCCGCGCTCCTCGCTGTCGCTTGTCATCTCGCACAGGGTG  252
             |||||||||||||||||||||||||||||||||||||| ||||||||| ||  |||||||
Sbjct  61    CGCCACTGTCTGGCCACAGCCCCGCGCTCCTCGCTGTCACTTGTCATCGCGTGCAGGGTG  120

Query  253   GTTCCGTTTCTGGTATTTGGTGCCGGAATTAAGCAACCACCATGTTGAGCAAAAAGGCAA  312
             |||||| ||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct  121   GTTCCGGTTCTGGTATTTGGCGCCGGAATTAAGCAACCACCATGTTGAGCAAAAAGGCAA  180
Now, which of those differences are you saying that the observed processes of mutation could not produce?

This message is a reply to:
 Message 302 by Faith, posted 06-11-2016 7:11 PM Faith has replied

Replies to this message:
 Message 330 by Faith, posted 06-13-2016 4:16 PM Taq has replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


Message 324 of 455 (785933)
06-13-2016 3:09 PM
Reply to: Message 312 by Faith
06-12-2016 6:57 AM


Re: Mutations are not alleles
I may yet come back and answer the rest of your post as originally planned, but for now I kind of got the wind knocked out of me. All the straw man misrepresentations of my argument after all this time are really disappointing.
Then why don't you help us out. We start with Population A, which has a DNA sequence of "AAAAAAAAA" at a specific point in their genome for all members of the population.
A new river forms and it splits the population in two. Since the species can't swim that well, there is no interbreeding between the pouplations. We call them Population B and Population C (or PB and PC for short).
In PB, a mutation occurs in the genetic locus, resulting in the sequence "AAAATAAAA". This mutation is selected for, and it replaces the old allele. The same mutation is not selected for in PC.
We now have two populations with a different allele at the same orthologous position.
PB= AAAATAAAA
PC= AAAAAAAAA
Now, would you define this as a loss in genetic diversity?
Edited by Taq, : No reason given.

This message is a reply to:
 Message 312 by Faith, posted 06-12-2016 6:57 AM Faith has replied

Replies to this message:
 Message 325 by Dr Adequate, posted 06-13-2016 3:14 PM Taq has replied
 Message 327 by Faith, posted 06-13-2016 3:38 PM Taq has replied

  
Dr Adequate
Member (Idle past 312 days)
Posts: 16113
Joined: 07-20-2006


Message 325 of 455 (785935)
06-13-2016 3:14 PM
Reply to: Message 324 by Taq
06-13-2016 3:09 PM


Re: Mutations are not alleles
Then why don't you help us out. We start with Population A, which has a DNA sequence of "AAAAAAAAA" at a specific point in their genome for all members of the population.
A new river forms and it splits the population in two. Since the species can't swim that well, there is no interbreeding between the pouplations. We call them Population B and Population C (or PB and PC for short).
In PB, a mutation occurs in the genetic locus, resulting in the sequence "AAAATAAAA". This mutation is selected for, and it replaces the old allele. The same mutation is not selected for in PC.
We now have two populations with a different allele at the same orthologous position.
PB= AAAATAAAA
PC= AAAAAAAAA
Now, would you define this as a loss in genetic diversity?
Oh, that's easy. In the Faith Theory Of Evolution And Not Reading Good, the only bit that counts is the bit highlighted in red, which is a loss of genetic diversity. The other stuff is irrelevant, as is the fact that genetic diversity has increased.

This message is a reply to:
 Message 324 by Taq, posted 06-13-2016 3:09 PM Taq has replied

Replies to this message:
 Message 326 by Taq, posted 06-13-2016 3:29 PM Dr Adequate has not replied
 Message 329 by Faith, posted 06-13-2016 4:12 PM Dr Adequate has replied

  
Taq
Member
Posts: 10084
Joined: 03-06-2009
Member Rating: 5.1


Message 326 of 455 (785940)
06-13-2016 3:29 PM
Reply to: Message 325 by Dr Adequate
06-13-2016 3:14 PM


Re: Mutations are not alleles
Oh, that's easy. In the Faith Theory Of Evolution And Not Reading Good, the only bit that counts is the bit highlighted in red, which is a loss of genetic diversity. The other stuff is irrelevant, as is the fact that genetic diversity has increased.
If that is the case, then my accusation in an earlier post stands. If Faith watched each and every mutation and selection event from the universal common ancestor to all of the species diversity we see today, Faith would call that entire process a loss in genetic diversity.

This message is a reply to:
 Message 325 by Dr Adequate, posted 06-13-2016 3:14 PM Dr Adequate has not replied

  
Faith 
Suspended Member (Idle past 1472 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


(1)
Message 327 of 455 (785941)
06-13-2016 3:38 PM
Reply to: Message 324 by Taq
06-13-2016 3:09 PM


Re: Mutations are not alleles
Now, would you define this as a loss in genetic diversity?
That would be an increase in genetic diversity.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 324 by Taq, posted 06-13-2016 3:09 PM Taq has replied

Replies to this message:
 Message 331 by Taq, posted 06-13-2016 5:13 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1472 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 328 of 455 (785947)
06-13-2016 4:11 PM
Reply to: Message 319 by Dr Adequate
06-13-2016 2:24 PM


Re: Mutations are not alleles
THe point, which you have clearly managed to overlook or intentionally garble, is that the adjectives are not used, while the word "allele" is used alone to designate every sequence found at a gene locus no matter what its origin.

This message is a reply to:
 Message 319 by Dr Adequate, posted 06-13-2016 2:24 PM Dr Adequate has replied

Replies to this message:
 Message 333 by Dr Adequate, posted 06-13-2016 5:23 PM Faith has not replied

  
Faith 
Suspended Member (Idle past 1472 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 329 of 455 (785948)
06-13-2016 4:12 PM
Reply to: Message 325 by Dr Adequate
06-13-2016 3:14 PM


Re: Mutations are not alleles
Oh, that's easy. In the Faith Theory Of Evolution And Not Reading Good, the only bit that counts is the bit highlighted in red, which is a loss of genetic diversity. The other stuff is irrelevant, as is the fact that genetic diversity has increased.
Perfect misrepresentation of my argument.

This message is a reply to:
 Message 325 by Dr Adequate, posted 06-13-2016 3:14 PM Dr Adequate has replied

Replies to this message:
 Message 334 by Dr Adequate, posted 06-13-2016 5:26 PM Faith has not replied
 Message 337 by NoNukes, posted 06-13-2016 11:25 PM Faith has replied

  
Faith 
Suspended Member (Idle past 1472 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 330 of 455 (785949)
06-13-2016 4:16 PM
Reply to: Message 323 by Taq
06-13-2016 3:04 PM


Re: Mutations are not alleles
I don't get the point of your example. I also don't doubt that mutations can make all kinds of changes, why not? They're just mistakes that seem to occur more or less willy-nilly, with some apparent preference for certain locations for some reason. But why would I doubt that sequences could not be changed by a single base or any other chunk?

This message is a reply to:
 Message 323 by Taq, posted 06-13-2016 3:04 PM Taq has replied

Replies to this message:
 Message 332 by Taq, posted 06-13-2016 5:15 PM Faith has not replied

  
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