Mutations

[Brunetmj]

Someone had posted this on another testing site: very interesting

http://www.sciencedaily.com/releases/2011/06/110613012758.htm

[JohnLloydScharf]

No Extra Grasping or Walking Appendages

"60 out of three billion does not sound like I am going to grow an extra arm..."

At least that his how I responded to Bob May's posting of that in my DNA-Testing Yahoo Group:

http://tech.groups.yahoo.com/group/DNA-Testing/message/2113

It does not mention if these are SNiPs or allelles or genes.

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.862.html

"They looked at almost 6000 possible mutations in the genome sequences," hints they meant alleles, but it could have been genes.

SNPs are single basepairs. Alleles are multiple repetitions of a sequence of basepairs like we see in regard to the CODIS and yDNA markers. Genes are a very complex section of molecules designed for a biological purpose.

[nathanm]

For more analysis of the article, Razib and Dienekes both have commentary on it.

It does not mention if these are SNiPs or allelles or genes.

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.862.html

"They looked at almost 6000 possible mutations in the genome sequences," hints they meant alleles, but it could have been genes.

SNPs are single basepairs. Alleles are multiple repetitions of a sequence of basepairs like we see in regard to the CODIS and yDNA markers. Genes are a very complex section of molecules designed for a biological purpose.

The repetitions you're referencing are short tandem repeats (STRs). Allelles are the possible variations of a gene.

[JohnLloydScharf]

First, your "Razib" is actually Donald Conrad who says:
There’s a new letter in Nature Genetics on de novo mutations in humans which is sending the headline writers in the press into a natural frenzy trying to “hook” the results into the X-Men franchise. I implicitly assume most people understand that they all have new genetic mutations specific and identifiable to them. The important issue in relation to “mutants” as commonly understood is that they have salient identifiable phenotypes, not that they have subtle genetic variants which are invisible to us. Another implicit aspect is that phenotypes are an accurate signal or representation of high underlying mutational load. In other words, if you can see that someone is weird in their traits, presumably they are rather strange in their underlying genetics. This is the logic behind models which assume that mutational load has correlates with intelligence or beauty, and these naturally tie back into evolutionary rationales for human aesthetic preferences (e.g., “good genes” models of sexual selection).
I do not consider your other resource reputable.

I suspect he has the same issue with "6000 mutations" as I do.

[JohnLloydScharf]

STRs are also alleles of a marker.

http://www.cstl.nist.gov/strbase/str_TH01.htm

http://www.hartnell.edu/faculty/jhughey/Files/primersfgatyping.pdf

http://www.cstl.nist.gov/biotech/strbase/str_y392.htm

Not all changes in alleles make a difference in genetic outcomes. If you change a gene, it does. A SNP is just a single nucleotide out of an allele, whch may, or may not be, a short tandem repeat.

The human genome has three billion basepairs. A change in one is a SNP. A change in a group is an allele, which may or may not be a STR. A change in a gene is likely a change in function. All are mutations. If you have 6,000 basepairs change out of 3 billion, it is not significant. If you have 6,000 GENES change, that could be real trouble.

The repetitions you're referencing are short tandem repeats (STRs). Allelles are the possible variations of a gene.

[nathanm]

First, your "Razib" is actually Donald Conrad who says:
...

No, Donald Conrad was the lead author of the original letter in Nature Genetics referenced by both Razib's post and the article at the top of this thread. The paragraph you quoted is entirely Razib's writing.

I do not consider your other resource reputable.

Are you saying you know more than Dienekes? He has a couple thousand blog posts over the past seven years, in which he's demonstrated he knows what he's talking about. He may entertain some theories that oppose the current fashion within the scientific community, but that doesn't make him disreputable. His work got a rather glowing review in Nature News. On what do you base your opinion?

STRs are also alleles of a marker.

http://www.cstl.nist.gov/strbase/str_TH01.htm

http://www.hartnell.edu/faculty/jhughey/Files/primersfgatyping.pdf

http://www.cstl.nist.gov/biotech/strbase/str_y392.htm

Not all changes in alleles make a difference in genetic outcomes. If you change a gene, it does. A SNP is just a single nucleotide out of an allele, whch may, or may not be, a short tandem repeat.

The human genome has three billion basepairs. A change in one is a SNP. A change in a group is an allele, which may or may not be a STR. A change in a gene is likely a change in function. All are mutations.

That doesn't make any sense. Alleles aren't changes. They're the possible values of a SNP or gene, or range of possible repeats of a STR. In a SNP where C is sometimes substituted for T, the possible alleles are CC, CT, and TT. If a STR can repeat between 5-10 times, the possible alleles are 5, 6, 7, 8, 9, and 10. Genes are more complex, but alleles are just the different forms of that gene.

If you have 6,000 basepairs change out of 3 billion, it is not significant. If you have 6,000 GENES change, that could be real trouble.

Agreed.

[JohnLloydScharf]

Dienekes said “They are not amateurs. They are far from being amateurs.”

Bahar did not say that about Dienekes. Dienekes said that about Donald Conrad.

There are plenty of racist bloggers with many thousand pages. Being prolific about posting the peer reviewed papers of others does not lend any credibility to his arguments. It is not that he contradicts the current theories. It is that he presents faulty arguments using statistics for purposes and comes to conclusions that were not intended by the researchers.

Ultimately, I believe he, or she, has no education in research design, probability and statistics, anthropology, or molecular biology. Since she/he writes under a pseudonym with no credentials to boot, he/she has no credibility.

I consider this blog disreputable because the writer of it claims there is a scientific basis for race.

If you want to believe in that mumbo jumbo, that is fine. You can start reading Storm Front. I suspect you will feel at home with them.

I base everything on genetics. If there is four races, then there are a million of them.

Tasting bitter, having a blood typed, and Human leukocyte antigen types is just as valid, if not more so, than the amount of pigment in your hair, eyes, and skin.

You could claim every yDNA and mtDNA haplogroup is a race as well. How about hat size? I wear a 7 and a half hat. How about the size of arms and legs. I have 36 inch sleeves and inseam. SO, am I a prospective SS, the Elite Guard?

The Nazis were so wrong about this issue they made a Jew, Warner Goldberg, their poster boy as an ideal Aryan. Too late! The posters were out when they found out. Hitler declared Goldberg to be an Aryan to avoid the propaganda issues.

On journalist who typed Hitler's relatives in the US reports the results were E1b1b for the yDNA of the offspring of a nephew in his patriarchal lineage.

I dared the 2011 Census by refusing to complete the form. They came to my place several times attempting to intimidate me into responding. They dared not take me to court on the issue, as I had hoped for.

SO, no. Dienekes has no credibility at all as far as I am concerned. Zero. Zip. Nada.

No, Donald Conrad was the lead author of the original letter in Nature Genetics referenced by both Razib's post and the article at the top of this thread. The paragraph you quoted is entirely Razib's writing.


Are you saying you know more than Dienekes? He has a couple thousand blog posts over the past seven years, in which he's demonstrated he knows what he's talking about. He may entertain some theories that oppose the current fashion within the scientific community, but that doesn't make him disreputable. His work got a rather glowing review in Nature News. On what do you base your opinion?


That doesn't make any sense. Alleles aren't changes. They're the possible values of a SNP or gene, or range of possible repeats of a STR. In a SNP where C is sometimes substituted for T, the possible alleles are CC, CT, and TT. If a STR can repeat between 5-10 times, the possible alleles are 5, 6, 7, 8, 9, and 10. Genes are more complex, but alleles are just the different forms of that gene.


Agreed.

[Max von Pif]

mutations

Darn! I always fancied a prehensile tail... oh well...

[MMaddi]

Dienekes said "They are not amateurs. They are far from being amateurs."

Bahar did not say that about Dienekes. Dienekes said that about Donald Conrad.

You need to read that article more closely. Here's what it says (copied and pasted from the article): "They are not amateurs. They are far from being amateurs," says Doron Behar, a population geneticist at Rambam Health Care Campus in Haifa, Israel, who studies human history. "I cannot stress enough the level of appreciation I have for their efforts." So, it is the case that Doron Behar, a member of FTDNA's scientific board, said that about Dienekes and David Wesolowski. Here's the link again, if you think I'm making this up - http://www.nature.com/news/2010/1012...l/468880a.html

There are plenty of racist bloggers with many thousand pages. Being prolific about posting the peer reviewed papers of others does not lend any credibility to his arguments. It is not that he contradicts the current theories. It is that he presents faulty arguments using statistics for purposes and comes to conclusions that were not intended by the researchers.

I've read Dienekes' blogs on a semi-regular basis. I don't agree with all his assessments and critiques. But he seems to have useful and incisive comments about many peer-reviewed articles. He provides a service by also bringing these articles to the attention of interested laymen. Can you give me an example of his "faulty arguments"?

Ultimately, I believe he, or she, has no education in research design, probability and statistics, anthropology, or molecular biology. Since she/he writes under a pseudonym with no credentials to boot, he/she has no credibility.

I consider this blog disreputable because the writer of it claims there is a scientific basis for race.

If you want to believe in that mumbo jumbo, that is fine. You can start reading Storm Front. I suspect you will feel at home with them.

Now you're painting Dienekes and anyone who sees useful things in his work as equivalent to Storm Front. I can tell you that I've never seen any sort of racist or Nazi tinge in anything he's written. I can also assure you that I'm not a racist or Nazi. I happen to believe, as many scientists do, that race is a very weak and not very useful scientific concept, especially as its understood by most non-scientists. So your suspicions that I would feel at home with Storm Front because I admire Dienekes' work are totally unfounded. You should be more careful when trying to portray people you disagree with as Nazis or racists. That sounds like the tactics of someone who doesn't have any sound arguments to offer.

[nathanm]

Dienekes said "They are not amateurs. They are far from being amateurs."

Bahar did not say that about Dienekes. Dienekes said that about Donald Conrad.

You really need to read more carefully. This is the second time on this thread you've mis-attributed a quote. The article I linked in my previous post had nothing at all to do with Donald Conrad. Here's the whole quote in context:

"They are not amateurs. They are far from being amateurs," says Doron Behar, a population geneticist at Rambam Health Care Campus in Haifa, Israel, who studies human history. "I cannot stress enough the level of appreciation I have for their efforts."

So it was Doron Behar, FTDNA's "Chief mtDNA Scientist and member of the Scientific Advisory Board," talking about genome bloggers in general, not anybody specific. However, only two are mentioned in the article: Dienekes and David Wesolowski, who runs the Eurogenes Genetic Ancestry Project.

There are plenty of racist bloggers with many thousand pages. Being prolific about posting the peer reviewed papers of others does not lend any credibility to his arguments. It is not that he contradicts the current theories. It is that he presents faulty arguments using statistics for purposes and comes to conclusions that were not intended by the researchers.

Ultimately, I believe he, or she, has no education in research design, probability and statistics, anthropology, or molecular biology. Since she/he writes under a pseudonym with no credentials to boot, he/she has no credibility.

Do you have any specific examples of Dienekes' poor scholarship? Surely there would be dozens if what you say is correct. The commenters to his blog posts include many "credentialed" scientists, who raise plenty of objections. However, they usually amount to minor quibbles or differences in interpretation.

I consider this blog disreputable because the writer of it claims there is a scientific basis for race.

Anthropologists and scientists still use the term race to classify humans, but in a very narrow, clinical sense. It's not the same thing as the social construct called race, which has been abused for so long. Do you have any specific evidence that Dienekes is racist?

If you want to believe in that mumbo jumbo, that is fine. You can start reading Storm Front. I suspect you will feel at home with them.

I base everything on genetics. If there is four races, then there are a million of them.

Tasting bitter, having a blood typed, and Human leukocyte antigen types is just as valid, if not more so, than the amount of pigment in your hair, eyes, and skin.

You could claim every yDNA and mtDNA haplogroup is a race as well. How about hat size? I wear a 7 and a half hat. How about the size of arms and legs. I have 36 inch sleeves and inseam. SO, am I a prospective SS, the Elite Guard?

The Nazis were so wrong about this issue they made a Jew, Warner Goldberg, their poster boy as an ideal Aryan. Too late! The posters were out when they found out. Hitler declared Goldberg to be an Aryan to avoid the propaganda issues.

On journalist who typed Hitler's relatives in the US reports the results were E1b1b for the yDNA of the offspring of a nephew in his patriarchal lineage.

Wow, it's not everyday I'm accused of being a racist, and without even the slightest evidence. Then the "argument" veers wildly all over the place, ending with Hitler. Haven't you heard of Godwin's law?

I dared the 2011 Census by refusing to complete the form. They came to my place several times attempting to intimidate me into responding. They dared not take me to court on the issue, as I had hoped for.

So in the distant future, your descendants won't be able to find you in the census. You're that guy, who genealogists rightly complain about. I just filled the race question on the census form by writing in "human."

SO, no. Dienekes has no credibility at all as far as I am concerned. Zero. Zip. Nada.

You're entitled to your own opinion.

[Dumbldorf]

Goodwin's law cannot apply here, this has not gone beyond one page yet.

[Darren]

Ah but now it has...

As this thread is starting to border less and less on what is relevant to genetic genealogy and more on personal opinion I am going ahead and closing this down.

-Darren Marin
Family Tree DNA