Neanderthal genomic DNA

[RonO]

http://science.sciencemag.org/content/early/2017/10/04/science.aao1887

http://www.cell.com/ajhg/fulltext/S0002-9297(17)30379-8

Popular Science articles
http://www.the-scientist.com/?articles.view/articleNo/50571/title/Effects-of-Neanderthal-DNA-on-Modern-Humans/

http://www.sciencemag.org/news/2017/10/your-neandertal-dna-making-your-belly-fat-ancient-genome-offers-clues?utm_campaign=news_daily_2017-10-05&et_rid=338065219&et_cid=1583489

All of the above articles are free to download.

They are getting more DNA out of old Neanderthal bones, and have
assembled the most complete Neanderthal genome to date for a single
individual. It turns out to be more closely related to the Neanderthals
that interbred with modern humans as they left Africa than the Altai
Neanderthal, and they have been able to identify more Neanderthal DNA in
our genomes.

Neanderthals were obviously different from modern humans. The first
paper is about the latest Neanderthal genome sequence and what it tells
us. The second paper is about what some of the Neanderthal variants are
doing in terms of phenotype among modern humans. If your ancestors made
it out of Africa around 60,000 years ago you have a couple percent
Neanderthal DNA in your genome. There was also some interbreeding with
Denisovans that can be detected in some Asians, Indonesians and Australians.

The genome paper is basically a brief summary of what they did and what
they found. They can get a lot of information from these ancient
genomes. Modern humans split from the Neanderthals and Densovans over
half a million years ago and these genomes are allowing a refinement in
how Neanderthals and Denisovans are related to each other and the
various Neanderthal individuals to each other. They now estimate the
split between the Denisovans and Neanderthals at around 400,000 years ago.

What should be of interest to people interested in the topic (whether
you believe it or not) is that they can relate the time at which these
individuals died (their genomes stopped evolving). They knew that the
Altai Neanderthal was more ancient than the Vindija individual and the
DNA reflects that. They can tell how much longer the Vindija
individual's lineage evolved than the Altai. They could estimate that
the Altai individual had died around 60,000 years before the Vindija
individual. With whole genome sequence they could estimate evolution
equivalent to about 1% of the distance between chimps and humans. It is
just an example of how consistent the data is with estimates by other means.

Some TO readers may remember the Discovery Institute project on trying
to figure out if all the variation in the extant human population could
have been derived from Adam and Eve last year. So far they haven't
published on what they found even though this years Bio Complexity issue
is out. They acknowledged the existence of the Neanderthal sequence,
and would have to deal with it somehow. My guess is that the follow up
paper will never be published because as I stated before a half million
years is enough time so that the majority of variation in the human
population is new variation due to mutation since that time. They would
also have to explain how the Neanderthals and Denisovans became so
different from us, and why we have pieces of Neanderthal DNA in our
genomes that exist in around 50,000 base-pair pieces (around 60,000
years worth of genetic recombination).

This paper also notes that there is now more data indicating that there
was an earlier interbreeding event between modern humans and
Neanderthals that occurred around twice as long ago as the migration out
of Africa 60,000 years ago. The only evidence that this earlier
migration event occurred is the DNA retained by the Neanderthals. That
modern human population went extinct before making much of an impact on
Neanderthals and Denisovans.

The second paper is finding what phenotypes are associated with the
Neanderthal DNA in our genomes. Skin color, hair color, immune response
etc. As previous research has indicated it looks like most of the
Neanderthal functional variants are deleterious, and have been selected
against in the modern human population. This may be of interest to
those interested in speciation. It looks like separation of half a
million years in a different environment (ice age Europe and Asia
compared to equatorial Africa) selected for genomes that were becoming
incompatible. When a population becomes isolated it is evolving
independently and as we see with the Thorton paper that I just put up
this week, later functional variation is dependent on the mutations that
have already occurred. It seems that Neanderthals had selected for
different variants that worked together and modern humans in Africa did
not select for the same interacting variants. The Neanderthal and
modern human genetics don't get along very well. The Neanderthal and
modern human hybrids may have been at a disadvantage. It could be a
reason why there is so little evidence of interbreeding, and we only
have a couple percent Neanderthal DNA in our genomes even though we co
existed with Neanderthals for around 30,000 years in Europe and Asia.

Ron Okimoto

[Robert Carnegie]

Does "not having dark skin" come from Neanderthals?
The "modern human" diaspora from Africa presumably
achieved it pretty quick, so, maybe got it by
I'm going to say marriage.

[RonO]

The second paper discusses this issue. They found counter variants
coming from Neanderthal. A pale skin variant that is detrimental in
modern humans because it makes the skin too pale, but Neanderthals also
had a variant of another gene that darkened the skin. So together the
skin color was probably lighter than Africans, but they got there one
way and modern humans developed another that when the Neanderthal pale
skin allele is expressed the skin is too pale and subject to sun damage.

Ron Okimoto

[jillery]

Do you remember the movie "Quest For Fire"? They got the skin colors
right, perhaps deliberately so.

OTOH "Clan of the Cave Bear" got it wrong, where blond blue-eyed
Darryl Hannah represented the more advanced H.sapiens.

OTGH it's no surprise that human skin color so rapidly evolves to fit
a particular latitude. After all, skin is the largest organ and most
often directly contacting the environment. For people in primitive
cultures, absorbing too much *or* too little sunlight can have fatal
consequences, so selection is strong for a Goldilock solution.

--
I disapprove of what you say, but I will defend to the death your right to say it.

Evelyn Beatrice Hall
Attributed to Voltaire

[RonO]

Neanderthal likely had evolved a lighter shade of skin than African
Modern humans at the time of the migration out of Africa around 60,000
years ago, but my guess is that the African skin color was already
around the lighter shade of the San. The modern humans that made it out
of African seemed to have come from the Nile Delta region and they only
had to travel a couple hundred miles to meet up with the Neanderthals in
Israel. That couple hundred miles must have been desolate because it
was some type of barrier for thousands of years. My guess is that there
wasn't enough fresh water to make a crossing possible during the ice age.

There is one allele for blue eyes that around 80% of the people with
blue eyes have and it did evolve in modern humans and not Neanderthals,
but my guess is that, that allele evolved in Europe. The modern humans
that the Neanderthals first met likely didn't have the blue eyed
variant. It could have evolved after the Neanderthals went extinct.

The surprising thing is that we did get some beneficial variants from
Neanderthals, but nothing like the lactase mutation and dairy
populations. The Neanderthal alleles may show some positive selection,
but none of them that I know of got fixed in the modern human
population, or even rose to a really high frequency. We have examples
of the lactase mutation that likely occurred and was selected for after
the rise of agriculture just 10,000 years ago and it is already at 90%
frequency among northern Europeans. There are no Neanderthal alleles
like that even though we got those alleles 60,000 years ago. As the
paper states most of the Neanderthal genetics was deleterious among
modern humans. Half a million years of independent evolution seems to
have resulted in mostly incompatible genomes, even if it is just
slightly deleterious.

The Thorton paper that I recently put up in a thread indicates this is
expected. Biological evolution is contingent on what evolved before and
you can take different paths depending on what mutations occur first.
the African and Neanderthal and Denisovan populations had over half a
million years where they were evolving independently and it looks like
they had begun evolving their separate ways and were coming to different
solutions to various selection issues. Vitamin D metabolism was
something that is associated with skin color and is something that the
Neanderthals were dealing with in different ways than modern humans
according to the paper. For a good part of the year during the ice age
the northern populations of Neanderthal were likely dressed like eskimos
and vitamin D metabolism was likely pretty important to them. You can
extract vitamin D from what you eat. We still fortify milk with a
standard amount of vitamin D.

Ron Okimoto

[jillery]

On Sun, 8 Oct 2017 07:12:06 -0500, RonO <roki...@cox.net> wrote:

[...]

>There is one allele for blue eyes that around 80% of the people with
>blue eyes have and it did evolve in modern humans and not Neanderthals,
>but my guess is that, that allele evolved in Europe. The modern humans
>that the Neanderthals first met likely didn't have the blue eyed
>variant. It could have evolved after the Neanderthals went extinct.

It's interesting that you mention the origin of blue eyes just now.
Recently there was a flurry of popular news articles which claimed
"new research" showed that *all* blue eyes in humans are from a single
common ancestor:

<https://www.sciencedaily.com/releases/2008/01/080130170343.htm>

But then I noticed the actual science article cited by all of those
pop sci articles is about 10 years old, hardly breaking news. Plus I
was skeptical that the scientists did the fieldwork necessary to show
that in fact all blue-eyes people originated from a common ancestor.
After all, even if the mutation were the same everywhere, ISTM as
likely that mutation happened in different populations, and multiple
occurrences would be indistinguishable from just one. So their
exaggeration of breaking news reinforced my pre-existing skepticism of
a claim for a single common ancestor.

The above Sciencedaily article quotes one of the authors:
******************************************
"From this we can conclude that all blue-eyed individuals are linked
to the same ancestor," says Professor Eiberg. "They have all inherited
the same switch at exactly the same spot in their DNA."
******************************************

One of the nice things about Sciencedaily is they almost always cite
the original work:

<https://link.springer.com/article/10.1007%2Fs00439-007-0460-x>

which is paywalled, but the abstract says this:
*****************************
One single haplotype, represented by six polymorphic SNPs covering
half of the 3' end of the HERC2 gene, was found in 155 blue-eyed
individuals from Denmark, and in 5 and 2 blue-eyed individuals from
Turkey and Jordan, respectively. Hence, our data suggest a common
founder mutation in an OCA2 inhibiting regulatory element as the cause
of blue eye color in humans.
******************************
which supports the Sciencedaily article claim.

AIUI OCA2 is one of the genes responsible for melanin coloration in
all mammals, mutations to which cause albinism, while HERC2 regulates
OCA2. A specific mutation in HERC2 suppresses OCA2 melanin production
only in the eyes, causing blue eyes. The articles don't say, but this
may also be the same mechanism for green and hazel eye colors, which
are different amounts of melanin.

So, on the one hand, it's not just a single SNP, but a specific
haplotype in a specific location in HERC2, which is known to cause
blue eyes in three different populations. My understanding is it
would be very unlikely such a specific combination would happen more
than once.

On the other hand, ISTM a sample of only three separate populations is
rather sketchy evidence to conclude that all blue-eyed people
everywhere in the world have this same exact haplotype.

You say above a figure of only about 80% of the population have this
haplotype. Is that based on research older or newer than the above?

Also, the Science article says the authors estimated the mutation
happened about 6-10kya, but I didn't see anything which supported that
claim. Do you know how they came up with that estimate?

On a somewhat related note, here's an article which describes how
brown-eyed parents can still have blue-eye children sans hanky-panky,
using standard Mendelian genetics:

<http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children>

<http://tinyurl.com/oway8ne>

On another somewhat related note, I'm unaware of any environmental
disadvantages to blue eyes, unlike fair skin. Some people have a
naive misunderstanding that blue eyes are "weaker", a term usually
applied to focusing problems, a characteristic having nothing to do
with eye color.

[jillery]

On Sun, 8 Oct 2017 07:12:06 -0500, RonO <roki...@cox.net> wrote:

>On 10/7/2017 11:10 PM, jillery wrote:
>> On Sat, 7 Oct 2017 16:24:11 -0700 (PDT), Robert Carnegie
>> <rja.ca...@excite.com> wrote:
>>
>>> Does "not having dark skin" come from Neanderthals?
>>> The "modern human" diaspora from Africa presumably
>>> achieved it pretty quick, so, maybe got it by
>>> I'm going to say marriage.
>>
>>
>> Do you remember the movie "Quest For Fire"? They got the skin colors
>> right, perhaps deliberately so.
>>
>> OTOH "Clan of the Cave Bear" got it wrong, where blond blue-eyed
>> Darryl Hannah represented the more advanced H.sapiens.
>>
>> OTGH it's no surprise that human skin color so rapidly evolves to fit
>> a particular latitude. After all, skin is the largest organ and most
>> often directly contacting the environment. For people in primitive
>> cultures, absorbing too much *or* too little sunlight can have fatal
>> consequences, so selection is strong for a Goldilock solution.
>>
>>

Most seafoods are a good source of Vitamin D, as are most animal
livers and egg yolks. Although many dairy products nowaday are
artificially fortified with vitamin D, that wasn't an option available
to our ancestors.

Becoming a naked ape created a lot of problems.

[RonO]

It isn't all the blue eyed modern humans around 80% of them have the
same haplotype. This just means that there are multiple polymorphisms
in the region that are linked to the causative mutation. That is how we
know that they all share the same common ancestor. If there were
multiple similar mutations causing blue eyes that had independently
evolved in different family lineages the causative mutation would likely
be in more than one haplotype (associated with other linked polymorphisms.

Ron Okimoto

[jillery]

>It isn't all the blue eyed modern humans around 80% of them have the
>same haplotype. This just means that there are multiple polymorphisms
>in the region that are linked to the causative mutation. That is how we
>know that they all share the same common ancestor. If there were
>multiple similar mutations causing blue eyes that had independently
>evolved in different family lineages the causative mutation would likely
>be in more than one haplotype (associated with other linked polymorphisms.
>
>Ron Okimoto

AIUI all the people they tested have "one single haplotype" which is
evidence they have the same common ancestor with blue eyes. But they
only tested people from three different populations. What evidence is
there that *all* blue-eyed individuals from *other* populations have
that same haplotype and so also have that same common ancestor? Is it
an extrapolated inference? Even Svante Pääbo sampled more groups than
that.

And I *still* don't understand what your 80% is a percentage of.

[Robert Carnegie]

I might be continuing to misunderstand arguments, but,
if Neanderthal humans didn't keep cattle (and they
didn't), then they wouldn't produce a mutation to
tolerate lactose as adults.

[RonO]

I was just saying that no Neanderthal variants were as selectively
advantageous as some of the mutations known to occur more recently.
There isn't a Neanderthal variant that has taken over the population as
far as I know. Most of the ones with selective value seem to be
frequency dependent and selection to a high frequency seems to be not an
option.

The lactase example was just an example where a recent mutation has been
selected for more rapidly than any Neanderthal variant we inherited long
ago.

Ron Okimoto

[RonO]

More recent research has determined that the majority of people with
blue eyes have this variant haplotype, but other causes of blue eyes are
known.

Ron Okimoto

[Bob Casanova]

On Sun, 8 Oct 2017 10:45:59 -0700 (PDT), the following
appeared in talk.origins, posted by Robert Carnegie
<rja.ca...@excite.com>:

To be exact, they might produce such a mutation (in fact, if
the mutation is possible they almost certainly would), but
it wouldn't be conserved other than by accident. I think...
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[jillery]

>More recent research has determined that the majority of people with
>blue eyes have this variant haplotype, but other causes of blue eyes are
>known.
>
>Ron Okimoto

Are you referring to variants other than albinism? Or some other
disadvantageous mutation? If so, that would show the article's claim
is factually incorrect. Will you cite?

Or will you cite more recent research which shows this "one single
haplotype" to exist in all human populations?

And, one more time, 80% of what?

[jillery]

On Sun, 08 Oct 2017 12:06:42 -0700, Bob Casanova <nos...@buzz.off>
wrote:

>On Sun, 8 Oct 2017 10:45:59 -0700 (PDT), the following
>appeared in talk.origins, posted by Robert Carnegie
><rja.ca...@excite.com>:
>
>>I might be continuing to misunderstand arguments, but,
>>if Neanderthal humans didn't keep cattle (and they
>>didn't), then they wouldn't produce a mutation to
>>tolerate lactose as adults.
>
>To be exact, they might produce such a mutation (in fact, if
>the mutation is possible they almost certainly would), but
>it wouldn't be conserved other than by accident. I think...

Quite correct. So the more appropriate phrase would be "wouldn't fix

a mutation to tolerate lactose as adults."

[RonO]

80% of the people with green or blue eyes. What did you think? The
rest likely does include some forms of albinism, but I wouldn't think
the various albinisms are a high enough of a frequency to account for
all of the rest.

Ron Okimoto

[jillery]

I think you have no intention of answering with a coherent sentence.

>The
>rest likely does include some forms of albinism, but I wouldn't think
>the various albinisms are a high enough of a frequency to account for
>all of the rest.

And the more recent cites which support that 80%, did you forget them
as well?

[RonO]

http://www.cell.com/current-biology/fulltext/S0960-9822(09)00597-1?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982209005971%3Fshowall%3Dtrue

It was 88% blue associated with the HERC2 haplotype.

Ron Okimoto

[jillery]

On Sun, 8 Oct 2017 21:31:52 -0500, RonO <roki...@cox.net> wrote:

>http://www.cell.com/current-biology/fulltext/S0960-9822(09)00597-1?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982209005971%3Fshowall%3Dtrue
>
>It was 88% blue associated with the HERC2 haplotype.
>
>Ron Okimoto

From your cite:
*************************************
To investigate the power of DNA-based eye color prediction, we
genotyped 37 SNPs from eight genes, representing all currently known
genetic variants with statistically significant eye color association
(Supplemental Data), in a large population sample of 6168 Dutch
Europeans from the Rotterdam Study
*************************************

That's a more restricted population than my cite. Thanks anyway.

[Bob Casanova]

On Sun, 08 Oct 2017 18:49:03 -0400, the following appeared
in talk.origins, posted by jillery <69jp...@gmail.com>:

>On Sun, 08 Oct 2017 12:06:42 -0700, Bob Casanova <nos...@buzz.off>
>wrote:
>
>>On Sun, 8 Oct 2017 10:45:59 -0700 (PDT), the following
>>appeared in talk.origins, posted by Robert Carnegie
>><rja.ca...@excite.com>:
>>
>>>I might be continuing to misunderstand arguments, but,
>>>if Neanderthal humans didn't keep cattle (and they
>>>didn't), then they wouldn't produce a mutation to
>>>tolerate lactose as adults.
>>
>>To be exact, they might produce such a mutation (in fact, if
>>the mutation is possible they almost certainly would), but
>>it wouldn't be conserved other than by accident. I think...
>
>
>Quite correct. So the more appropriate phrase would be "wouldn't fix
>a mutation to tolerate lactose as adults."

OK; thanks. I like your phrase better than my paragraph...
;-)

[RonO]

On 10/9/2017 12:46 PM, Bob Casanova wrote:
> On Sun, 08 Oct 2017 18:49:03 -0400, the following appeared
> in talk.origins, posted by jillery <69jp...@gmail.com>:
>
>> On Sun, 08 Oct 2017 12:06:42 -0700, Bob Casanova <nos...@buzz.off>
>> wrote:
>>
>>> On Sun, 8 Oct 2017 10:45:59 -0700 (PDT), the following
>>> appeared in talk.origins, posted by Robert Carnegie
>>> <rja.ca...@excite.com>:
>>>
>>>> I might be continuing to misunderstand arguments, but,
>>>> if Neanderthal humans didn't keep cattle (and they
>>>> didn't), then they wouldn't produce a mutation to
>>>> tolerate lactose as adults.
>>>
>>> To be exact, they might produce such a mutation (in fact, if
>>> the mutation is possible they almost certainly would), but
>>> it wouldn't be conserved other than by accident. I think...
>>
>>
>> Quite correct. So the more appropriate phrase would be "wouldn't fix
>> a mutation to tolerate lactose as adults."
>
> OK; thanks. I like your phrase better than my paragraph...
> ;-)
>

Unfortunately, this ignores what the argument actually was.

Ron Okimoto

[RonO]

This is a review from 2009. It acknowledges that the early studies did
find a 1:1 correspondence with blue eyes (in fact, the author of the
review was an author on one of those earlier papers), but that did not
hold up, and in the review he cites the paper that I cited.

http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2009.00606.x/full

This is someones commentary on the misinformation of the time and he
cites other more recent research indicating the same thing from 2010 and
2011.

https://udel.edu/~mcdonald/mytheyecolor.html

Things just are the way they are.

Ron Okimoto

[jillery]

It isn't that the above ignored an actual argument, as much as moved
from one pedantic point to another pedantic point, which is fair game.

My impression is there was no argument per se in this thread. The
actual issue was about skin pigmentation among ancestral humans.

IIUC you raised the question to what degree Neanderthal hybridization
might have contributed to H.sapiens skin color, and your point was
likely not very much.

The point I raised is that, with the rise of the naked ape, inherent
human skin pigmentation became sensitive to latitude. So, given their
respective geographic origins of the two species, the recently
out-of-Africa H. sapiens were almost certainly darker-skinned than the
native Levant H. neanderthalensis, and also the native Eurasian
Denisovan. This conclusion is contrary to some extant humans'
cherished but somewhat racist beliefs.

[jillery]

On Tue, 10 Oct 2017 06:40:07 -0500, RonO <roki...@cox.net> wrote:

>On 10/8/2017 11:19 PM, jillery wrote:
>> On Sun, 8 Oct 2017 21:31:52 -0500, RonO <roki...@cox.net> wrote:
>>
>>> http://www.cell.com/current-biology/fulltext/S0960-9822(09)00597-1?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982209005971%3Fshowall%3Dtrue
>>>
>>> It was 88% blue associated with the HERC2 haplotype.
>>>
>>> Ron Okimoto
>>
>> From your cite:
>> *************************************
>> To investigate the power of DNA-based eye color prediction, we
>> genotyped 37 SNPs from eight genes, representing all currently known
>> genetic variants with statistically significant eye color association
>> (Supplemental Data), in a large population sample of 6168 Dutch
>> Europeans from the Rotterdam Study
>> *************************************
>>
>> That's a more restricted population than my cite. Thanks anyway.
>>
>

>This is a review from 2009. It acknowledges that the early studies did
>find a 1:1 correspondence with blue eyes (in fact, the author of the
>review was an author on one of those earlier papers), but that did not
>hold up, and in the review he cites the paper that I cited.
>
>http://onlinelibrary.wiley.com/doi/10.1111/j.1755-148X.2009.00606.x/full

The above is interesting in pointing out that human irises are often
not solid colored, but can have rings and spots and other patterns
which don't necessarily follow standard Mendelian inheritance rules.

>This is someones commentary on the misinformation of the time and he
>cites other more recent research indicating the same thing from 2010 and
>2011.
>
>https://udel.edu/~mcdonald/mytheyecolor.html

The above affirms the point my cite made, that human eye color is
controlled by the interaction of multiple genes.

Unfortunately, NOTA say anything about whether *all* human blue-eyes
(excluding albinism and other maladaptive genes) derive from a single
common ancestor, which is a conclusion asserted in my cite, which is
the point I challenged, which is the question you continue to ignore.

>Things just are the way they are.

Whatever that means, perhaps a carryover from your fine-tuning posts.

[Bob Casanova]

On Tue, 10 Oct 2017 10:24:00 -0400, the following appeared

Agreed; Usenet is famous (notorious?) for that.

>My impression is there was no argument per se in this thread. The
>actual issue was about skin pigmentation among ancestral humans.
>
>IIUC you raised the question to what degree Neanderthal hybridization
>might have contributed to H.sapiens skin color, and your point was
>likely not very much.
>
>The point I raised is that, with the rise of the naked ape, inherent
>human skin pigmentation became sensitive to latitude. So, given their
>respective geographic origins of the two species, the recently
>out-of-Africa H. sapiens were almost certainly darker-skinned than the
>native Levant H. neanderthalensis, and also the native Eurasian
>Denisovan. This conclusion is contrary to some extant humans'
>cherished but somewhat racist beliefs.
--

[Robert Carnegie]

My quibble with the theory that our non-Neanderthal
ancestors left Africa and then evolved from "black" skin
to "white" skin on their own is along the lines that
this hasn't happened yet to black people in North America
with more recent African ancestors. Or perhaps it does
happen and we aren't noticing when it does.

I think somewhere back there another argument was made
or implied that now that we can all drink cow milk which
contains vitamin D (unless we can't, or we don't want to),
being black isn't as big a drag as it used to be.

[RonO]

Beats me what you are trying to argue. The original citation clearly
indicates in the figure that only 88% of the blue eyed phenotypes are
explained by the HERC2 haplotype. The review acknowleges this to be the
case even though the author of the review participated in one of the
earlier studies that found a 1:1 correspondence. What more do you want?
The citation that you want to ignore above calls it a myth that a
single gene accounts for blue eyes and provides more recent citations.

Ron Okimoto

[RonO]

As I wrote the modern humans that left Africa were likely already pretty
light skinned. Probably more like the San than central Africans. The
modern human migrants likely came from the Nile delta region and were
only a couple hundred miles from the Neanderthals living in Israel. The
ice age had been going on for a couple million years and my guess is
that the modern humans that far north in Africa already were wearing
quite a bit of clothing in the winter time. There would have been
selection for lighter skin long before they migrated out of Africa.

Ron Okimoto

[jillery]

Interesting you mention that. Richard Pryor did a stand-up where he
talked about his first visit to Africa. He couldn't get over how
"really black" everybody was. And there was another program where
some African-American fashion models went to Africa, but couldn't get
a job because they weren't "black enough".

The point being that most African-Americans have a large percentage of
European genes, thanks in large part to the habits of slaveowners, and
so are substantially lighter-skinned than their African relatives.

>I think somewhere back there another argument was made
>or implied that now that we can all drink cow milk which
>contains vitamin D (unless we can't, or we don't want to),
>being black isn't as big a drag as it used to be.

Umm... no. Milk doesn't naturally contain vitamin D. Modern dairy
products are artificially fortified with vitamin D in the U.S.
Besides, milk would be worse than useless to those largely
lactose-intolerant African slaves.

[jillery]

There are other good reasons to think ancestors of extant San people
were the H.sapiens to first successfully leave Africa. But even
though San are lighter-skinned than modern central Africans, they are
still substantially darker-skinned than modern Eurasians, and so don't
completely answer Robert Carnegie's quibble.

Average solar albedo changes with the sine of the latitude. Between
the tropical latitudes, there is almost no change. But as one goes
progressively farther north or south, albedo drops ever rapidly.
Problems from maladaptive skin color, whether too dark or too light,
would effect most strongly growing children and their mothers,
especially from cultures which relied on restricted diets.

[jillery]

>Beats me what you are trying to argue.

Really? Then what are you trying to argue?

>The original citation clearly indicates in the figure that only 88% of the blue eyed phenotypes are
>explained by the HERC2 haplotype.

Actually, your OP specified 80%. And I *still* have no idea what
"original citation" your talking about.

OTOH my original citation explicitly claims that *all* blue-eyed
humans got that mutation from a common ancestor. Just to refresh your
convenient amnesia:

<https://www.sciencedaily.com/releases/2008/01/080130170343.htm>

"Blue-eyed humans have a single, common ancestor"

You can't get more explicit than that.

You're welcome.

>The review acknowleges this to be the
>case even though the author of the review participated in one of the
>earlier studies that found a 1:1 correspondence. What more do you want?

Since apparently you don't read your own cites *or* my posts, I say
again, I would like to read a cite which identifies the genes of
blue-eyed individuals from around the world, or at least from multiple
regions, not just Europe. Why is that so unreasonable to you?

> The citation that you want to ignore above calls it a myth that a
>single gene accounts for blue eyes and provides more recent citations.

I have no idea what citation you think I want to ignore. Be specific.

[RonO]

I didn't remember the exact number so I said around 80%, check it out.

"There is one allele for blue eyes that around 80% of the people with
blue eyes have"

This doesn't matter because not all blue eyes are due to the HERC2
haplotype.

>
> OTOH my original citation explicitly claims that *all* blue-eyed
> humans got that mutation from a common ancestor. Just to refresh your
> convenient amnesia:
>
> <https://www.sciencedaily.com/releases/2008/01/080130170343.htm>
>
> "Blue-eyed humans have a single, common ancestor"
>
> You can't get more explicit than that.
>
> You're welcome.

Except that is a myth. A myth based on the first two studies. What
happened later with more analysis and more loci checked?

Ron Okimoto

[jillery]

I accept your lack of response to my question above as your tacit
admission that you have no idea what you're talking about.

>>> The original citation clearly indicates in the figure that only 88% of the blue eyed phenotypes are
>>> explained by the HERC2 haplotype.
>>
>>
>> Actually, your OP specified 80%. And I *still* have no idea what

>> "original citation" you're talking about.

>
>I didn't remember the exact number so I said around 80%, check it out.
>
>"There is one allele for blue eyes that around 80% of the people with
>blue eyes have"
>
>This doesn't matter because not all blue eyes are due to the HERC2
>haplotype.

And you *still* haven't identified what "original citation" you're
talking about.

>> OTOH my original citation explicitly claims that *all* blue-eyed
>> humans got that mutation from a common ancestor. Just to refresh your
>> convenient amnesia:
>>
>> <https://www.sciencedaily.com/releases/2008/01/080130170343.htm>
>>
>> "Blue-eyed humans have a single, common ancestor"
>>
>> You can't get more explicit than that.
>>
>> You're welcome.
>
>Except that is a myth. A myth based on the first two studies.

According to my cited article, their claim is based on a distinctive
haplotype, which includes a specific mutation in HERC2. Apparently
you *still* haven't read my cited article.

And to refresh your convenient amnesia, I said I suspected their
conclusion is incorrect. But unlike you, I would like to see results
of studies based on a broader sampling of the world's blue-eyed
individuals.

>What
>happened later with more analysis and more loci checked?

I have no idea. AFAICS you haven't identified any later studies of
more loci checked.

>Ron Okimoto
>>
>>
>>> The review acknowleges this to be the
>>> case even though the author of the review participated in one of the
>>> earlier studies that found a 1:1 correspondence. What more do you want?
>>
>>
>> Since apparently you don't read your own cites *or* my posts, I say
>> again, I would like to read a cite which identifies the genes of
>> blue-eyed individuals from around the world, or at least from multiple
>> regions, not just Europe. Why is that so unreasonable to you?

I accept your lack of response to my question above as your tacit
admission that you're being unreasonable here.

>>> The citation that you want to ignore above calls it a myth that a
>>> single gene accounts for blue eyes and provides more recent citations.
>>
>>
>> I have no idea what citation you think I want to ignore. Be specific.

I accept your failure to specify your alleged cite as your tacit
admission that you provided no such cite.

[RonO]

I accept your inability to state what you want me to discuss.

What more do you want until you tell me what we are supposed to be
discussing?

>
>
>>>> The citation that you want to ignore above calls it a myth that a
>>>> single gene accounts for blue eyes and provides more recent citations.
>>>
>>>
>>> I have no idea what citation you think I want to ignore. Be specific.
>
>
> I accept your failure to specify your alleged cite as your tacit
> admission that you provided no such cite.

Read for comprehension and look up the citatations that you have been given.

Ron Okimoto

[Robert Carnegie]

But if it's due to "intermarriage" then that's just
what we were saying hadn't taken place between "us" and
Neanderthals, at least as far as transferring non-blackness
from one to the other. So why didn't that transfer occur?

Having said that, a simple gene to "not be black" is just
melanin-producing gene that doesn't work. Like our busted
vitamin C gene. But there doesn't seem to be strong
selection to "not be black" for health reasons after all.

> >I think somewhere back there another argument was made
> >or implied that now that we can all drink cow milk which
> >contains vitamin D (unless we can't, or we don't want to),
> >being black isn't as big a drag as it used to be.
>
>
> Umm... no. Milk doesn't naturally contain vitamin D. Modern dairy
> products are artificially fortified with vitamin D in the U.S.

Vitamin D may be added but this
<http://www.milkfacts.info/Nutrition%20Facts/Nutrient%20Content.htm>
implies it is already naturally present, although
I do notice that the different types of milk considered
include "reduced", "low fat", and "skim". These are
footnoted as having vitamin A added, not D. The page
also indicates that goat milk provides vitamin D.
Sheep and water buffalo are "don't know". This may not be
a document of peer-review standard.

> Besides, milk would be worse than useless to those largely
> lactose-intolerant African slaves.

There are cows in Africa. Or, they could try cheese.
<https://www.healthyeating.org/Milk-Dairy/Nutrients-in-Milk-Cheese-Yogurt/Nutrients-in-Cheese>
indicates that vitamin D in cheese varies widely,
with cheddar top and American bottom - apparently zero.

[jillery]

What part of "I would like" do you not understand?

>>>>> The citation that you want to ignore above calls it a myth that a
>>>>> single gene accounts for blue eyes and provides more recent citations.
>>>>
>>>>
>>>> I have no idea what citation you think I want to ignore. Be specific.
>>
>>
>> I accept your failure to specify your alleged cite as your tacit
>> admission that you provided no such cite.
>
>Read for comprehension and look up the citatations that you have been given.

Sez the troll who doesn't read his own cites.

Why are you aping the village IDiot?

[jillery]

On Wed, 11 Oct 2017 16:33:32 -0700 (PDT), Robert Carnegie

You previously mentioned black people in North America becoming less
black without it being noticed. I pointed out that it be noticed.

And since your mention has nothing to do with our ancient ancestors, I
just followed your train of thought as you jumped the track.

>Having said that, a simple gene to "not be black" is just
>melanin-producing gene that doesn't work. Like our busted
>vitamin C gene.

Of course, there are multiple genes which control human skin color,
else there wouldn't be such a broad range across different
populations. I assumed you understood that. My bad:

<https://en.wikipedia.org/wiki/Human_skin_color>

>But there doesn't seem to be strong
>selection to "not be black" for health reasons after all.

How so?

>> >I think somewhere back there another argument was made
>> >or implied that now that we can all drink cow milk which
>> >contains vitamin D (unless we can't, or we don't want to),
>> >being black isn't as big a drag as it used to be.
>>
>>
>> Umm... no. Milk doesn't naturally contain vitamin D. Modern dairy
>> products are artificially fortified with vitamin D in the U.S.
>
>Vitamin D may be added but this
><http://www.milkfacts.info/Nutrition%20Facts/Nutrient%20Content.htm>
>implies it is already naturally present, although
>I do notice that the different types of milk considered
>include "reduced", "low fat", and "skim". These are
>footnoted as having vitamin A added, not D. The page
>also indicates that goat milk provides vitamin D.
>Sheep and water buffalo are "don't know". This may not be
>a document of peer-review standard.

Something is wrong with your cited chart. Vitamin D is fat-soluble. I
would expect its amount to decrease with decreasing amounts of fat.
Instead the chart has the amount increasing. Also, the amount given
is approximately what fortified milk provides. I suspect this chart
does not describe raw milk, but the USDA approved stuff found in U.S.
stores.

>> Besides, milk would be worse than useless to those largely
>> lactose-intolerant African slaves.
>
>There are cows in Africa. Or, they could try cheese.
><https://www.healthyeating.org/Milk-Dairy/Nutrients-in-Milk-Cheese-Yogurt/Nutrients-in-Cheese>
>indicates that vitamin D in cheese varies widely,
>with cheddar top and American bottom - apparently zero.

Look at your cited chart. You would have to cut a lot of cheese to
get enough vitamin D from it.

There are populations in Africa which are lactose tolerant, and have a
strong pastoral tradition. However, the vast majority of slaves to
the New World came from central east Africa, which IIUC didn't have
any dairy culture at the time.

OTOH the discussion is about populations out of Africa, so cows in
Africa is just another train derailment.

[RonO]

You would like what? This is getting ridiculous. Just tell me what you
want to discuss. I was responding to all your stupidity. Go up and
read it.

Why should I respond to this junk?

QUOTE from above:

>>>>>> Beats me what you are trying to argue.
>>>>>
>>>>>
>>>>> Really? Then what are you trying to argue?
>>>
>>>
>>> I accept your lack of response to my question above as your tacit
>>> admission that you have no idea what you're talking about.

END QUOTE:

What kind of response was that? Why not just state what you are trying
to argue so that we can discuss it?

Why should I bother with any of this junk until you tell me that? What

are you trying to argue?

As far as I'm concerned I have given you the correct citations for
whatever you have asked for and you have just blown them off. My
original citation was the same one that the review I gave you cited. Go
through everything that I have given you and determine that for
yourself. I have even given you a reference that tells you that what
you are trying to defend is a myth and that reference gives even more
recent references than I have given.

So what are you trying to argue? You started that stupidity, why not
end it by just stating what we are supposed to be discussing? To me we
have already discussed it and you can't accept reality. I could be
wrong, but it doesn't look like it. Just go up and read your responses
to my answers. They just ignore what you don't want to deal with and
make some excuse for ignoring it. Actually read my first reference
about the 88%. They looked at many more genes and found that their
variants were all segregating in Hardy-Weinberg equilibrium. Do you
know what that means? It means that all the variants were well mixed in
the population and they were looking at established polymorphisms and
their sample wasn't biased in any way that would alter the expected
Mendelian segregation. People can have blue eyes for different genetic
reasons. You already know this because things like albinism results in
what people classify as blue eyes.

Go to my reference that calls the single gene for blue eyes a myth. It
is just a fact that the HERC2 polymorphism does not account for all
cases of blue eyes. If you don't want to believe my original reference
he gives several others.

Ron Okimoto

[jillery]

Since you asked, I will refresh your convenient amnesia by copying
from the quoted text above:

***************************************

Since apparently you don't read your own cites *or* my posts, I say
again, I would like to read a cite which identifies the genes of
blue-eyed individuals from around the world, or at least from multiple
regions, not just Europe.

**************************************

How many times do you have to be asked? Do I have to say pretty
please?


>This is getting ridiculous.


To the contrary, you went past ridiculous many posts ago.

>Just tell me what you want to discuss. I was responding to all your stupidity. Go up and
>read it.
>
>Why should I respond to this junk?

Since you asked, why should *I* respond to this junk:

>QUOTE from above:
> >>>>>> Beats me what you are trying to argue.
> >>>>>
> >>>>>
> >>>>> Really? Then what are you trying to argue?
> >>>
> >>>
> >>> I accept your lack of response to my question above as your tacit
> >>> admission that you have no idea what you're talking about.
>END QUOTE:
>
>What kind of response was that?

Since you asked, it was exactly the kind of response your comment
deserved.

>Why not just state what you are trying
>to argue so that we can discuss it?

Since you asked, once again:

***************************************

Since apparently you don't read your own cites *or* my posts, I say
again, I would like to read a cite which identifies the genes of
blue-eyed individuals from around the world, or at least from multiple
regions, not just Europe.

**************************************

How many times do you have to be asked? Do I have to say pretty
please?

>Why should I bother with any of this junk until you tell me that?

Since you asked, once again:

***************************************

Since apparently you don't read your own cites *or* my posts, I say
again, I would like to read a cite which identifies the genes of
blue-eyed individuals from around the world, or at least from multiple
regions, not just Europe.

**************************************

How many times do you have to be asked? Do I have to say pretty
please?

>What are you trying to argue?

Since you asked, I argue nothing.

>As far as I'm concerned I have given you the correct citations for
>whatever you have asked for and you have just blown them off.

Of course, that's a lie. I can cite where I quoted your cites and
commented on them. Too bad you can't say the same.

>My
>original citation was the same one that the review I gave you cited.

I have no idea what review you're talking about. Be specific.

>Go
>through everything that I have given you and determine that for
>yourself.

I have. As far as I can tell, what you say is there doesn't exist.
Prove me wrong.

>I have even given you a reference that tells you that what
>you are trying to defend is a myth and that reference gives even more
>recent references than I have given.

Since I defend nothing, myth or otherwise, your statement above merely
reaffirms you have no idea what you're talking about.

>So what are you trying to argue?

Since you asked, I argue nothing here.


>You started that stupidity,


You mean your stupidity? That was you.

>why not
>end it by just stating what we are supposed to be discussing?

Since you asked, one more time:

***************************************

Since apparently you don't read your own cites *or* my posts, I say
again, I would like to read a cite which identifies the genes of
blue-eyed individuals from around the world, or at least from multiple
regions, not just Europe.

**************************************

How many times do you have to be asked? Do I have to say pretty
please?

>To me we
>have already discussed it and you can't accept reality.

Since we have "discussed" nothing, your statement above merely
reaffirms you have no idea what you're talking about.

>I could be wrong, but it doesn't look like it.

But of course it does.

>Just go up and read your responses to my answers.

Been there, done that, bought the shirt. Still waiting for a real
answer.

>They just ignore what you don't want to deal with and
>make some excuse for ignoring it.

Right here would have been a good place for you to have said what you
think I don't want to deal with. But you didn't, which shows you have

no idea what you're talking about.

>Actually read my first reference about the 88%.

I have no idea what first reference you're talking about. Be
specific.

>They looked at many more genes and found that their
>variants were all segregating in Hardy-Weinberg equilibrium. Do you
>know what that means?

Don't you know? Do I have to say what Hardy-Weinberg equilibrium
means in order to turn you back into a real boy?

>It means that all the variants were well mixed in
>the population and they were looking at established polymorphisms and
>their sample wasn't biased in any way that would alter the expected
>Mendelian segregation.

Since you answered your own question, why bother asking me?

>People can have blue eyes for different genetic
>reasons. You already know this because things like albinism results in
>what people classify as blue eyes.
>
>Go to my reference that calls the single gene for blue eyes a myth.

I have no idea what reference you're talking about. Be specific.

>It
>is just a fact that the HERC2 polymorphism does not account for all
>cases of blue eyes. If you don't want to believe my original reference
>he gives several others.

I have no idea what original reference you're talking about. Be
specific.

>>>>>>> The citation that you want to ignore above calls it a myth that a
>>>>>>> single gene accounts for blue eyes and provides more recent citations.
>>>>>>
>>>>>>
>>>>>> I have no idea what citation you think I want to ignore. Be specific.
>>>>
>>>>
>>>> I accept your failure to specify your alleged cite as your tacit
>>>> admission that you provided no such cite.
>>>
>>> Read for comprehension and look up the citatations that you have been given.
>>
>>
>> Sez the troll who doesn't read his own cites.
>>
>> Why are you aping the village IDiot?

No reply. I guess I have to wait for the exorcism to be completed.

[jillery]

On Wed, 11 Oct 2017 23:10:12 -0500, RonO <roki...@cox.net> wrote:

I apologize for my previous reply. I shouldn't harass you to answer a
question you obviously don't want to answer. Perhaps later when you
feel better. I leave it up to you.

[RonO]

How many times does it not matter? Just think for a momment. Not all
blue eyed people are blue eyed for the same genetic reason. It doesn't
matter where they live or what the mutations are. That is just fact.
You take a place like Belgium and over half the population has blue
eyes, but only 88% of those blue eyed individuals have the same genetics
to produce those blue eyes. These people exist and there are obviously
a lot of them. So what more do you need?

>
>
>> To me we
>> have already discussed it and you can't accept reality.
>
>
> Since we have "discussed" nothing, your statement above merely
> reaffirms you have no idea what you're talking about.

Since you don't understand what the issue is, or you have some other
issue than what was being discussed you should tell me what that other
issue is. The issue that I thought that we were discussing is over.
There are obviously multiple genetic reasons for blue eyes. It doesn't
matter that I have checked other populations because that fact doesn't
change and not all blue eyed individuals share the same mutation from
some common ancestor.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934

This is a more recent paper and it is free to download and they use
Belgiums the UK and Australian datasets.

This study is from Poland.

https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf

The are both more recent than my reference and your references, of which
my reference was more recent than the ones that you are depending on.

>
>
>> I could be wrong, but it doesn't look like it.
>
>
> But of course it does.

No it doesn't. Why don't you have any references to refute mine except
for the first two studies on the subject? The review author was
involved in one of those first two studies and what did he claim in his
review? What paper did he used to do it?

>
>
>> Just go up and read your responses to my answers.
>
>
> Been there, done that, bought the shirt. Still waiting for a real
> answer.

You'll keep doing it for as long as the denial lasts.

>
>
>> They just ignore what you don't want to deal with and
>> make some excuse for ignoring it.
>
>
> Right here would have been a good place for you to have said what you
> think I don't want to deal with. But you didn't, which shows you have
> no idea what you're talking about.

I haven't ignored it for your reasons of denial. It never mattered to
what we were discussing. Think about it for a moment and you might get it.

>
>
>> Actually read my first reference about the 88%.
>
>
> I have no idea what first reference you're talking about. Be
> specific.

Then read the posts again.

>
>
>> They looked at many more genes and found that their
>> variants were all segregating in Hardy-Weinberg equilibrium. Do you
>> know what that means?
>
>
> Don't you know? Do I have to say what Hardy-Weinberg equilibrium
> means in order to turn you back into a real boy?

It would help you understand the first reference. Even if you will
never be a real boy.

>
>
>> It means that all the variants were well mixed in
>> the population and they were looking at established polymorphisms and
>> their sample wasn't biased in any way that would alter the expected
>> Mendelian segregation.
>
>
> Since you answered your own question, why bother asking me?

Why not apply that knowledge?

>
>
>> People can have blue eyes for different genetic
>> reasons. You already know this because things like albinism results in
>> what people classify as blue eyes.
>>
>> Go to my reference that calls the single gene for blue eyes a myth.
>
>
> I have no idea what reference you're talking about. Be specific.

Go up and read the posts again because it isn't worth me doing this.

If this is really the case you are a lost cause.

Ron Okimoto

[Robert Carnegie]

Back to melanin... I thought people had blue or green
or grey eyes for one reason - that the gene to put brown
colour in the iris is non-working from both parents.
However, exactly which spelling error there is in the
gene is interesting to trace - when you can.

[RonO]

Read the posts between Jillery and myself and find out how wrong you are.

There isn't a single gene reason for all blue eyed individuals. One
allele is at a very high frequency among blue eyed individuals, but as
one of my references states the single gene notion is a myth. Eye color
is polygenic. There are several single gene mutations that can cause
blue eyes in the human population, and there are gene interactions that
can cause blue eyes in the human population.

Back to melanin the most common allele responsible for blue eyes is also
associated with skin color issues and people with blue eyes are more
susceptible to some forms of skin cancer. People with blue eye color
are also more susceptible to things like snow blindness than are brown
eyed people. My guess is that this is due to decreased melanin
synthesis. There are modifiers that will increase melanin production in
the skin and hair, and you can be brunette with blue eyes and you can
see some fairly dark skinned African Americans with blue eyes. There
are dark skinned Africans that have blue eyes and I have seen it claimed
that it is a different non albino (they have dark skin and hair) blue
eyes, but I haven't seen any genetic analysis.

Ron Okimoto

[jillery]

This is one of the cites I originally posted:

It describes how blue-eyed parents can still have brown-eyed children
sans hanky-panky, using standard Mendelian genetics:

<http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children>

<http://tinyurl.com/oway8ne>

Note that it specifies OCA2 and HERC2 genes. Both are located on
chromosome 15. If both copies of either gene are non-functional
(homozygous recessive), that person will have blue eyes, period. This
has nothing to do with other possible causes of blue eyes.

At first glance, the above might lead one to think blue-eyed parents
can't sire brown-eyed children, since brown eyes are dominant, right?

But because there are two genes which can express blue, so there are
heterozygous combinations which allow that apparently impossible
inheritance.

The example Punnett Square shows that if one parent's genes are
heterozygous OCA2 and homozygous HERC2, while the other parent's genes
are heterozygous HERC2 and homozygous OCA2, then their children have a
25% chance of being brown-eyed, even though both parents are
blue-eyed.

Even more counter-intuitive, their blue-eyed children have a 2 out of
3 chance of carrying a brown-eyed gene.

This would be impossible if blue eyes were controlled by a single
gene.

You also mention other eye colors; green or gray. Here's an article
about gray eyes:

<http://genetics.thetech.org/ask/ask232>

Like blue, gray in eyes isn't from pigment, but from light scattering
through the collagen in the iris.

According to the article above, no one is sure of the difference
between blue and gray eyes. One suggestion is the collagen proteins
are a different structure. Another suggestion is the back layer of the
iris is pigmented differently.

As for green eyes, one merely needs a yellowish pigment to combine
with the blue inherent of irises, yielding green (or hazel). Some
articles say that pigment is lipochrome. Others say it's just a
lesser amount of melanin. Either way, the gene which expresses green
eyes is different from the one which expresses brown eyes, and the
brown-eyed gene dominates over the green-eyed gene.

And in my rummaging, I ran across a Sandwalk article which might shed
some light on this discussion:

<http://sandwalk.blogspot.com/2007/02/genetics-of-eye-color.html>

Interestingly, Larry Moran's explanation for blue-eyed parents having
brown-eyed children is different from the one I cited above.

[jillery]

On Thu, 12 Oct 2017 06:45:59 -0500, RonO <roki...@cox.net> wrote:

<reboot>

>http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934
>
>This is a more recent paper and it is free to download and they use
>Belgiums the UK and Australian datasets.
>
>This study is from Poland.
>
>https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf

You provided these two cites above in reply to one of my posts. You
didn't state what you think these cites show, or how you think they
show it.

So I can only presume that you think they contain information which
disproves my cite's claim, that all blue-eyed humans inherited that
mutation from a single common ancestor who lived between 6K - 10K
years ago, based on a haplotype which includes a specific mutation in
HERC2 which is expressed by unpigmented irises, but not albinism,
which I understand is a different mutation altogether, and so not
relevant here.

So I am looking in your cites for statements which focus specifically
on blue eye color and the genes for it and those genes' distribution
throughout the world. And I am unconcerned about statements which
deal with other eye colors and traits, of which I acknowledge there
are many. If you think my criteria above are incorrect, then state
your alternative criteria here.

Your Plos article describes methods for identifying the entire
spectrum of human eye color, so it's no surprise that they would
identify additional genes than the ones which concern me here. To the
best of my knowledge, there is nothing in this article which fits the
criteria I specified above. If you believe there is something
relevant, then quote it here.

Your Nature article describes the challenges of correlating specific
genes with specific human eye colors, particularly among those of
European descent. It discusses 24 polymorphisms in 11 known genes
involved in pigmentation of human irises. The authors looked for
gene-masking and other interactions.

A problem here is, blue eyes are a consequence of a lack of pigment.
So those genes which control pigment expression are relevant only to
the degree that the blue phenotype has them all disabled. To the best
of my understanding, that isn't relevant here. To the best of my
knowledge, there is nothing in this article which fits the criteria I
specified above. If you believe there is something relevant, then
quote it here.

[RonO]

On 10/12/2017 11:34 PM, jillery wrote:
> On Thu, 12 Oct 2017 14:15:15 -0700 (PDT), Robert Carnegie
> <rja.ca...@excite.com> wrote:
>
>> Back to melanin... I thought people had blue or green
>> or grey eyes for one reason - that the gene to put brown
>> colour in the iris is non-working from both parents.
>> However, exactly which spelling error there is in the
>> gene is interesting to trace - when you can.
>
>
> This is one of the cites I originally posted:
>
> It describes how blue-eyed parents can still have brown-eyed children
> sans hanky-panky, using standard Mendelian genetics:
>
> <http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children>

Just stop. If you understood your own reference you would know that
they are talking about two different mutations. One affecting HERC2
this is the most common. The other affecting OCA2. Knocking down either
one will cause blue eyes, but if a HERC2 blue eyed person mates with an
OCA2 blue eyed person they can have children with brown eyes because
those children inherit a good OCA2 gene from the HERC2 blue eyed parent
and a good HERC2 from the OCA2 blue eyed parent. This is classic gene
complimentation, and has been used for a century to tell if you are
dealing with mutations in different genes that cause similar phenotypes.
For organisms with high recombination rates like yeast they use it to
determine if they are dealing with different mutations in the same gene
by looking at the recombinants.

HERC2 and OCA2 are both known to be involved in melanin biosynthesis.
They happen to be next to each other in the genome. It is common to
have genes in the same biosynthetic pathway in the same region of the
genome.

Just stop this nonsense. It was over multiple posts ago. You obviously
are continuing it for some other reason, and until you tell me what you
actually want to discuss there is no need to continue the discussion.

Ron Okimoto

[RonO]

On 10/12/2017 11:38 PM, jillery wrote:
> On Thu, 12 Oct 2017 06:45:59 -0500, RonO <roki...@cox.net> wrote:
>
> <reboot>
>
>> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934
>>
>> This is a more recent paper and it is free to download and they use
>> Belgiums the UK and Australian datasets.
>>
>> This study is from Poland.
>>
>> https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf
>
>
> You provided these two cites above in reply to one of my posts. You
> didn't state what you think these cites show, or how you think they
> show it.

They both determine that there are other ways to produce blue eyes than
the mutation that you are talking about. End of story. Your own
citation above relies on two different mutations in two different genes
producing blue eyes. What do you not get. The other mutations involved
with producing blue eyes do not come from the same common ancestor as
the most common cause for blue eyes.

Just stop this nonsense.

Ron Okimoto

[jillery]

On Fri, 13 Oct 2017 06:17:28 -0500, RonO <roki...@cox.net> wrote:

>On 10/12/2017 11:34 PM, jillery wrote:
>> On Thu, 12 Oct 2017 14:15:15 -0700 (PDT), Robert Carnegie
>> <rja.ca...@excite.com> wrote:
>>
>>> Back to melanin... I thought people had blue or green
>>> or grey eyes for one reason - that the gene to put brown
>>> colour in the iris is non-working from both parents.
>>> However, exactly which spelling error there is in the
>>> gene is interesting to trace - when you can.
>>
>>
>> This is one of the cites I originally posted:
>>
>> It describes how blue-eyed parents can still have brown-eyed children
>> sans hanky-panky, using standard Mendelian genetics:
>>
>> <http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children>
>>

>> <http://tinyurl.com/oway8ne>
>>
>
>Just stop.


Stop what, exactly? What do you think I am continuing? How is what I
wrote nonsense? How is anything I wrote inconsistent with the facts
you specified? How does any facts you specified contradict anything I
wrote? What did I write that in any way suggests that I don't
understand my own reference? Until you start backing up your attacks
against me, you're just another stupid troll.

>If you understood your own reference you would know that
>they are talking about two different mutations. One affecting HERC2
>this is the most common. The other affecting OCA2. Knocking down either
>one will cause blue eyes, but if a HERC2 blue eyed person mates with an
>OCA2 blue eyed person they can have children with brown eyes because
>those children inherit a good OCA2 gene from the HERC2 blue eyed parent
>and a good HERC2 from the OCA2 blue eyed parent. This is classic gene
>complimentation, and has been used for a century to tell if you are
>dealing with mutations in different genes that cause similar phenotypes.
> For organisms with high recombination rates like yeast they use it to
>determine if they are dealing with different mutations in the same gene
>by looking at the recombinants.
>
>HERC2 and OCA2 are both known to be involved in melanin biosynthesis.
>They happen to be next to each other in the genome. It is common to
>have genes in the same biosynthetic pathway in the same region of the
>genome.
>
>Just stop this nonsense. It was over multiple posts ago. You obviously
>are continuing it for some other reason, and until you tell me what you
>actually want to discuss there is no need to continue the discussion.

My post below is a reply to Robert Carnegie, not to you. So I had no
need to even mention you. I replied to you in a separate post which
deletes and ignores all of your ad hominem stupidities. Don't be
insulted that I don't wait for your reply to that. Get over yourself.

[jillery]

On Fri, 13 Oct 2017 06:24:53 -0500, RonO <roki...@cox.net> wrote:

>On 10/12/2017 11:38 PM, jillery wrote:
>> On Thu, 12 Oct 2017 06:45:59 -0500, RonO <roki...@cox.net> wrote:
>>
>> <reboot>
>>
>>> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934
>>>
>>> This is a more recent paper and it is free to download and they use
>>> Belgiums the UK and Australian datasets.
>>>
>>> This study is from Poland.
>>>
>>> https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf
>>
>>
>> You provided these two cites above in reply to one of my posts. You
>> didn't state what you think these cites show, or how you think they
>> show it.
>
>They both determine that there are other ways to produce blue eyes than
>the mutation that you are talking about.

Right here would have been a good place for you to have quoted where
your cites say they determined there are other ways to produce blue
eyes. That you didn't suggests they didn't.


>End of story.


I agree. It's really sad, almost painful, to watch you descend into
incoherence.


>Your own citation above


You're confused. I posted no citation above. Both cites above are
from your post.

>relies on two different mutations in two different genes
>producing blue eyes. What do you not get. The other mutations involved
>with producing blue eyes do not come from the same common ancestor as
>the most common cause for blue eyes.

Right here would have been a good place for you to say what "other
mutations" you're talking about. That you didn't suggests there are
none, and you're just making up stuff because you have nothing
intelligent to say.


>Just stop this nonsense.


Your nonsense disqualifies you from complaining about my alleged
nonsense.

[RonO]

I would do the work for you, but you obviously never understood the
first references that I gave you. You are just a lost cause. Not only
that, but you obviously have no interest in actually learning anything
about this subject and you are just arguing to be arguing. Face the
facts. You just don't have an argument, as your other post today
indcates. If you knew that two different mutations were already known
to produce blue eyes, what do you think that you have been arguing for
multiple posts? To remind you, you are the one that believes the myth
that all blue eyed people share a common ancestor that had "the"
mutation for blue eyes because if they didn't all share the same
mutation they do not have to be related to that individual. Admitting
that you know that more than one mutation causes blue eyes means what
for your argument?

Ron Okimoto

[jillery]

On Fri, 13 Oct 2017 19:49:19 -0500, RonO <roki...@cox.net> wrote:

... more incoherent ranting.

>On 10/13/2017 7:10 AM, jillery wrote:
>> On Fri, 13 Oct 2017 06:24:53 -0500, RonO <roki...@cox.net> wrote:
>>
>>> On 10/12/2017 11:38 PM, jillery wrote:
>>>> On Thu, 12 Oct 2017 06:45:59 -0500, RonO <roki...@cox.net> wrote:
>>>>
>>>> <reboot>
>>>>
>>>>> http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934
>>>>>
>>>>> This is a more recent paper and it is free to download and they use
>>>>> Belgiums the UK and Australian datasets.
>>>>>
>>>>> This study is from Poland.
>>>>>
>>>>> https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf
>>>>
>>>>
>>>> You provided these two cites above in reply to one of my posts. You
>>>> didn't state what you think these cites show, or how you think they
>>>> show it.

And you *still* haven't shown where these cites say what you say they
say.

>>> They both determine that there are other ways to produce blue eyes than
>>> the mutation that you are talking about.
>>
>>
>> Right here would have been a good place for you to have quoted where
>> your cites say they determined there are other ways to produce blue
>> eyes. That you didn't suggests they didn't.

And you *still* haven't shown where these cites say what you say they
say.

>>> End of story.
>>
>>
>> I agree. It's really sad, almost painful, to watch you descend into
>> incoherence.
>>
>>
>>> Your own citation above
>>
>>
>> You're confused. I posted no citation above. Both cites above are
>> from your post.
>>
>>
>>> relies on two different mutations in two different genes
>>> producing blue eyes. What do you not get. The other mutations involved
>>> with producing blue eyes do not come from the same common ancestor as
>>> the most common cause for blue eyes.
>>
>>
>> Right here would have been a good place for you to say what "other
>> mutations" you're talking about. That you didn't suggests there are
>> none, and you're just making up stuff because you have nothing
>> intelligent to say.
>
>I would do the work for you,

They're your cites, to show they say what you say they say, or not.
Aping the village IDiot like this suggests you know you have nothing
intelligent to say.

>but you obviously never understood the
>first references that I gave you.

Right here would have been a good place for you to have said how you
think I never understood your first reference. That you didn't
suggests you know you can't, and are just making up stuff because you

have nothing intelligent to say.

>You are just a lost cause.

Now you're just projecting.

>Not only
>that, but you obviously have no interest in actually learning anything
>about this subject and you are just arguing to be arguing.

I have no need. You're doing enough of that for the both of us.


>Face the facts.


<PING> Dang it.

>You just don't have an argument, as your other post today
>indcates. If you knew that two different mutations were already known
>to produce blue eyes, what do you think that you have been arguing for
>multiple posts?

Since you asked, I copy from the quoted text below where I answered
your question even before you asked it:

****************************************

So I can only presume that you think they contain information which
disproves my cite's claim, that all blue-eyed humans inherited that
mutation from a single common ancestor who lived between 6K - 10K
years ago, based on a haplotype which includes a specific mutation in
HERC2 which is expressed by unpigmented irises

*****************************************

So, the issue is not what I believe, but instead is the evidence for
my cited article's conclusion.

The issue is not how many mutations, but instead is the haplotype my
cited article used to make that conclusion.

That you continue to claim that is not what are the issues shows you

have no idea what you're talking about.

>>To remind you,

>> So I can only presume that you think they contain information which
>> disproves my cite's claim, that all blue-eyed humans inherited that
>> mutation from a single common ancestor who lived between 6K - 10K
>> years ago, based on a haplotype which includes a specific mutation in
>> HERC2 which is expressed by unpigmented irises, but not albinism,
>> which I understand is a different mutation altogether, and so not
>> relevant here.

>you are the one that believes the myth
>that all blue eyed people share a common ancestor that had "the"
>mutation for blue eyes because if they didn't all share the same
>mutation they do not have to be related to that individual. Admitting
>that you know that more than one mutation causes blue eyes means what
>for your argument?

Since you asked, it means:

You have no idea what you're talking about.
Your reading comprehension sucks.
Aping the village IDiot makes you sound really stupid.
You're just a troll arguing just to argue.


One can only wonder how someone with enough working brain cells to
breathe still has so much trouble know what are the relevant issues,
even after I spelled it out really slow and used simple words multiple
times.

Thanks for asking.

Let me know if you ever recover from your acute rectal asphyxiation.
Don't be insulted that I don't wait for you to do so.

>Ron Okimoto
>>
>>
>>> Just stop this nonsense.
>>
>>
>> Your nonsense disqualifies you from complaining about my alleged
>> nonsense.
>>
>>
>>>> So I can only presume that you think they contain information which
>>>> disproves my cite's claim, that all blue-eyed humans inherited that
>>>> mutation from a single common ancestor who lived between 6K - 10K
>>>> years ago, based on a haplotype which includes a specific mutation in
>>>> HERC2 which is expressed by unpigmented irises, but not albinism,
>>>> which I understand is a different mutation altogether, and so not
>>>> relevant here.
>>>>
>>>> So I am looking in your cites for statements which focus specifically
>>>> on blue eye color and the genes for it and those genes' distribution
>>>> throughout the world. And I am unconcerned about statements which
>>>> deal with other eye colors and traits, of which I acknowledge there
>>>> are many. If you think my criteria above are incorrect, then state
>>>> your alternative criteria here.

I accept your lack of response here as your tacit admission that my
criteria as specified are both necessary and sufficient.

>>>> Your Plos article describes methods for identifying the entire
>>>> spectrum of human eye color, so it's no surprise that they would
>>>> identify additional genes than the ones which concern me here. To the
>>>> best of my knowledge, there is nothing in this article which fits the
>>>> criteria I specified above. If you believe there is something
>>>> relevant, then quote it here.

I accept your lack of response here as your tacit admission there is
nothing relevant in your cited article above.

>>>> Your Nature article describes the challenges of correlating specific
>>>> genes with specific human eye colors, particularly among those of
>>>> European descent. It discusses 24 polymorphisms in 11 known genes
>>>> involved in pigmentation of human irises. The authors looked for
>>>> gene-masking and other interactions.
>>>>
>>>> A problem here is, blue eyes are a consequence of a lack of pigment.
>>>> So those genes which control pigment expression are relevant only to
>>>> the degree that the blue phenotype has them all disabled. To the best
>>>> of my understanding, that isn't relevant here. To the best of my
>>>> knowledge, there is nothing in this article which fits the criteria I
>>>> specified above. If you believe there is something relevant, then
>>>> quote it here.

I accept your lack of response here as your tacit admission there is
nothing relevant in your cited article above.

[RonO]

You are obviously not arguing anything in this post except the fact that
you want to argue about something that likely isn't even an issue. Do
you have any doubt that there are other genetic causes of blue eyes?
Since the answer is no, what are you arguing?

There is no lack of response only a lack of understanding on your part.
You are a lost cause. Why would I respond to any of this junk. It
doesn't matter to the issue because your own example is complementation
between two mutations in different genes causing blue eyes. Do you
acknowledge that fact?

What kind of response did you expect. All you are saying is that you
don't care that they found other genes that caused blue eyes. Just take
my first reference. What do you think it means when the mutation that
you are talking about accounts for only 88% of the cases of blue eyes in
a sample size of over 500 blue eyed people?

What more do you expect to argue about? There is obviously more than
one genetic cause of blue eyes. That was the issue and it has been over
for how many posts? It should have ended with my first reference. You
have never countered that reference. You just blew it off and claimed
that it wasn't the same population. Who cares? They were obviously
human. The sample size was around a thousand with more than half of
them having blue eyes. So what is your objective for continuing to
argue about What?

What I said about around 80% was right. You have no counter, so what
are you doing? I've already admitted that I did not remember the exact
percentage, so what is your beef?

Ron Okimoto

[jillery]

On Fri, 13 Oct 2017 23:42:01 -0400, jillery <69jp...@gmail.com>
wrote:


Obviously, you're still suffering from rectal asphyxiation. Wait
until you get that problem fixed.

[RonO]

Still can't accept reality. Until you accept what the first reference
claims why should I do anything more?

Just so that you understand that all the stupidity is on you I will tell
you about the two other references. When are you going to accept reality?

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934

They introduce more genes affecting eye color into their eye color
prediction. The HERC2 mutation, like all other studies is the best
predictor for blue eyes, but it is not the only one and does not account
for all individuals with blue eyes. Even though they add some new genes
they do not go to 100% prediction for blue eyes. This means that they
still do not know all the genes involved in producing blue eyes, and the
HERC2 mutation is not responsible for all individuals with blue eyes.
It is that simple.

This is their summary using all their genes.
QUOTE:
The accuracy in predicting 3-category eye color was 0.92 for blue, 0.74
for intermediate, and 0.93 for brown, which reflects a slight but
statistically significant (P = 2.7×10−4) improvement compared to our
previous attempt using 15 SNPs from 8 genes (AUC 0.91 for blue, 0.73 for
intermediate, and 0.93 for brown) [8].
END QUOTE:

Even adding the additional genes they still could not account for all
the blue eyed individuals. At this time it seems that we still do not
know all the genes involved in making blue eyes.

https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf

In this study they look at several genes (not as many as the study
above) and the HERC2 mutation does not account for all the blue eyes and
apparently less than the first reference that I gave. None of their
different analysis went to 100% (blue vs non blue) when considering the
HERC2 SNP by itself and none of their analyses went to 100% considering
their other genes.

Again the HERC2 mutation does not account for all blue eyes and this
study is still not dealing with all genes involved in making blue eyes.

Just look at table 3 the rs12913832 SNP is the HERC2 mutation and it
obviously does not account for all blue eyes with an accuracy of only
0.83. I haven't figured out how they estimated accuracy (there are
several ways to express it and 0.83 does not have to translate to a
straight percentage of success and failure) but they obviously do not
have an accuracy close enough to 100% to matter.

Things are just that simple. The HERC2 mutation does not account for
all blue eyes, and we still do not know all of the genes responsible for
blue eyes because we still have significant prediction errors using the
genes that have been used so far.

Your own reference has the complementation results indicating more than
one gene is involved in blue eyes. What more do you want? The
reference that I gave that calls what you are claiming a myth uses the
complementation test, the two references above and others to support his
conclusion. What do you not get? This discussion was over with my
first reference. The first reference has only been supported by more
recent work.

Ron Okimoto

[RonO]

On 10/12/2017 1:53 AM, jillery wrote:
> On Wed, 11 Oct 2017 23:10:12 -0500, RonO <roki...@cox.net> wrote:
>
> I apologize for my previous reply. I shouldn't harass you to answer a
> question you obviously don't want to answer. Perhaps later when you
> feel better. I leave it up to you.

The obvious truth of the matter is that you don't want to know the
answer. I have given it to you multiple times in multiple ways and all
you have done is harassement for some other reason because there is
nothing further to discuss on this issue.

So why not answer my question. What do you want to discuss? It
obviously isn't the fact that the HERC2 mutation does not account for
all blue eyes because it obviously doesn't, so what is your real beef?

Ron Okimoto

[jillery]

On Sat, 14 Oct 2017 07:55:17 -0500, RonO <roki...@cox.net> wrote:

>On 10/14/2017 12:59 AM, jillery wrote:
>> On Fri, 13 Oct 2017 23:42:01 -0400, jillery <69jp...@gmail.com>
>> wrote:
>>
>>
>> Obviously, you're still suffering from rectal asphyxiation. Wait
>> until you get that problem fixed.
>>
>>
>>
>

>Still can't accept reality. Until you accept what the first reference
>claims why should I do anything more?

Until you identify what you call "the first reference claims", why

should I do anything more?

It's so easy to deflect your nonsense back on you.

>Just so that you understand that all the stupidity is on you I will tell
>you about the two other references. When are you going to accept reality?

Since you asked, I accept reality just fine. Part of that reality is
that people who cite articles explain why they cited them and how
their cites show what they claim them to show. You're welcome.

And since you continue to clusterfuk with stupid strawmen, I will once
again refresh your convenient amnesia what I'm talking about.

From my post where I first introduced it:
******************************************
<https://link.springer.com/article/10.1007%2Fs00439-007-0460-x>

which is paywalled, but the abstract says this:
*****************************
One single haplotype, represented by six polymorphic SNPs covering
half of the 3' end of the HERC2 gene, was found in 155 blue-eyed
individuals from Denmark, and in 5 and 2 blue-eyed individuals from
Turkey and Jordan, respectively. Hence, our data suggest a common
founder mutation in an OCA2 inhibiting regulatory element as the cause
of blue eye color in humans.
******************************
*****************************************

And since your rectal asphyxiation keeps you from reading for
comprehension, I emphasize for you their phrases "ONE SINGLE
HAPLOTYPE" and "COMMON FOUNDER MUTATION", which means the authors
claim that all blue-eyed humans get them from a single common
ancestor.

Also note there is no mention of HERC2 only. That's your stupid
strawman.

When I cited that article, I expressed my skepticism of the authors'
claim, and sought additional information which would confirm or deny
it.

Your cites below are the same ones you posted in your reply
immediately prior, the ones which you failed to identify why you
posted them, and failed to quote how you think they support what you
say they say. Apparently you pulled your head out of ass long enough
to understand the need to do that. That's some progress toward your
acceptance of reality, however small. Normally I would be grateful
for even that, but at this point it's merely anticlimactic.

>http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000934
>
>They introduce more genes affecting eye color into their eye color
>prediction. The HERC2 mutation, like all other studies is the best
>predictor for blue eyes, but it is not the only one and does not account
>for all individuals with blue eyes. Even though they add some new genes
>they do not go to 100% prediction for blue eyes. This means that they
>still do not know all the genes involved in producing blue eyes, and the
>HERC2 mutation is not responsible for all individuals with blue eyes.
>It is that simple.

No, not that simple. The authors of your article above are concerned
with quantifying the *entire spectrum* of human eye colors, not just
blue, and correlating them to specific haplotypes. The authors'
identify eye colors beyond the standard blue-green-hazel-brown. They
refer to blue eyes only in the context of other eye colors. What the
article says is they didn't find an exact correspondence between
haplotypes and eye colors generally, not just blue

>This is their summary using all their genes.
>QUOTE:
>The accuracy in predicting 3-category eye color was 0.92 for blue, 0.74
>for intermediate, and 0.93 for brown, which reflects a slight but

>statistically significant (P?=?2.7×10?4) improvement compared to our

>previous attempt using 15 SNPs from 8 genes (AUC 0.91 for blue, 0.73 for
>intermediate, and 0.93 for brown) [8].
>END QUOTE:
>
>Even adding the additional genes they still could not account for all
>the blue eyed individuals. At this time it seems that we still do not
>know all the genes involved in making blue eyes.

Your interpretation assumes p=0.92 means there are haplotypes which
exclude the HERC2-OCA2 haplotype but still have phenotype blue eyes.
It's not clear from the article that your assumption is correct. It's
as likely the authors identified haplotypes which include the
HERC2-OCA2 haplotype but do not have phenotype blue eyes.

Also, the article isn't clear if the authors included certain
deleterious genetic diseases such as albinism, or non-genetic causes
such as aging, disease and trauma, which also can cause blue eyes.
These factors are not relevant to disproving my cited article's claim.

My impression is a p=0.92 is a very high correlation, but it doesn't
imply that all blue-eyed individuals, excluding those disease and
non-genetic cases above, did not have the HERC2-OCA2 haplotype. For
that reason, and also because its samples are geographically
restricted, this article is insufficient to disprove my cited
article's claim.

>https://www.nature.com/jhg/journal/v56/n6/pdf/jhg201138a.pdf
>
>In this study they look at several genes (not as many as the study
>above) and the HERC2 mutation does not account for all the blue eyes and
>apparently less than the first reference that I gave. None of their
>different analysis went to 100% (blue vs non blue) when considering the
>HERC2 SNP by itself and none of their analyses went to 100% considering
>their other genes.
>
>Again the HERC2 mutation does not account for all blue eyes and this
>study is still not dealing with all genes involved in making blue eyes.
>
>Just look at table 3 the rs12913832 SNP is the HERC2 mutation and it
>obviously does not account for all blue eyes with an accuracy of only
>0.83. I haven't figured out how they estimated accuracy (there are
>several ways to express it and 0.83 does not have to translate to a
>straight percentage of success and failure) but they obviously do not
>have an accuracy close enough to 100% to matter.

Table 3 compares blue with non-blue, ie all other eye colors. Given
that the HERC2-OCA2 haplotype has nonfunctioning alleles, It's not
surprising that other genes would modify it's default blue-eye
phenotype. For that reason, and also because the article's population
is geographically restricted, it's insufficient to disprove my cited
article's claim.

>Things are just that simple. The HERC2 mutation does not account for
>all blue eyes, and we still do not know all of the genes responsible for
>blue eyes because we still have significant prediction errors using the
>genes that have been used so far.
>
>Your own reference has the complementation results indicating more than
>one gene is involved in blue eyes. What more do you want? The
>reference that I gave that calls what you are claiming a myth uses the
>complementation test, the two references above and others to support his
>conclusion. What do you not get? This discussion was over with my
>first reference. The first reference has only been supported by more
>recent work.

You *still* don't identify your first reference.
You *still* argue using your stupid strawmen.
You *still* don't address the actual issue I repeatedly identified.

So, even though you finally got around to doing what you should have
done when you first posted your "first reference", whatever that might
be, you still suffer from the effects of rectal asphyxiation.

[jillery]

On Sat, 14 Oct 2017 13:36:42 -0500, RonO <roki...@cox.net> wrote:

>On 10/12/2017 1:53 AM, jillery wrote:
>> On Wed, 11 Oct 2017 23:10:12 -0500, RonO <roki...@cox.net> wrote:
>>
>> I apologize for my previous reply. I shouldn't harass you to answer a
>> question you obviously don't want to answer. Perhaps later when you
>> feel better. I leave it up to you.
>
>The obvious truth of the matter is that you don't want to know the
>answer. I have given it to you multiple times in multiple ways and all
>you have done is harassement for some other reason because there is
>nothing further to discuss on this issue.
>
>So why not answer my question. What do you want to discuss? It
>obviously isn't the fact that the HERC2 mutation does not account for
>all blue eyes because it obviously doesn't, so what is your real beef?
>
>Ron Okimoto

If you had removed your head from your twitching sphincter long enough
to get some oxygen to your brain, you might have noticed that the post
to which you reply above is two days old, and is a response to one of
your posts several iterations previous.

That's the kind of thing that happens when you don't know what you're
talking about. Just sayin'.

[RonO]

On 10/15/2017 12:06 AM, jillery wrote:
> On Sat, 14 Oct 2017 07:55:17 -0500, RonO <roki...@cox.net> wrote:
>
>> On 10/14/2017 12:59 AM, jillery wrote:
>>> On Fri, 13 Oct 2017 23:42:01 -0400, jillery <69jp...@gmail.com>
>>> wrote:
>>>
>>>
>>> Obviously, you're still suffering from rectal asphyxiation. Wait
>>> until you get that problem fixed.
>>>
>>>
>>>
>>
>> Still can't accept reality. Until you accept what the first reference
>> claims why should I do anything more?
>
>
> Until you identify what you call "the first reference claims", why
> should I do anything more?

This is just utter bullshit and you know it. Just go up and figure it
out for yourself because I have done that and it is pretty easy. It is
the reference with accounting for 88% of blue eyes with the HERC2
mutation. Just because you want to deny reality there is no reason to
do it. Really, just try to get yourself to do something that would snap
you back to reality and out of your utter denial.

You are a lost cause. This discussion was over how many posts ago?

Ron Okimoto

[jillery]

On Sun, 15 Oct 2017 06:22:01 -0500, RonO <roki...@cox.net> wrote:

>On 10/15/2017 12:06 AM, jillery wrote:
>> On Sat, 14 Oct 2017 07:55:17 -0500, RonO <roki...@cox.net> wrote:
>>
>>> On 10/14/2017 12:59 AM, jillery wrote:
>>>> On Fri, 13 Oct 2017 23:42:01 -0400, jillery <69jp...@gmail.com>
>>>> wrote:
>>>>
>>>>
>>>> Obviously, you're still suffering from rectal asphyxiation. Wait
>>>> until you get that problem fixed.
>>>>
>>>>
>>>>
>>>
>>> Still can't accept reality. Until you accept what the first reference
>>> claims why should I do anything more?
>>
>>
>> Until you identify what you call "the first reference claims", why
>> should I do anything more?
>
>This is just utter bullshit and you know it.

Yes, I know your post here is utter bullshit, one worthy of a village
idiot, a consequence of rectal asphyxiation. Having once taken your
head out of your ass to finally make a coherent argument, you return
to your old habitat. How sad is that?

> Just go up and figure it
>out for yourself because I have done that and it is pretty easy. It is
>the reference with accounting for 88% of blue eyes with the HERC2
>mutation. Just because you want to deny reality there is no reason to
>do it. Really, just try to get yourself to do something that would snap
>you back to reality and out of your utter denial.
>
>You are a lost cause. This discussion was over how many posts ago?

Since you asked, you only engaged in "this discussion" with your
penultimate post, the one where you finally articulated a coherent
argument. All posts prior were just to get your head out of your ass.

And since you restored your rectal asphyxiation, I suppose I have to
do the math for you; that would make it two posts ago.

You're welcome.

[RonO]

Denial is stupid. Look what you have to do in order to deny reality.

Ron Okimoto

[jillery]

On Sun, 15 Oct 2017 09:55:48 -0500, RonO <roki...@cox.net> wrote:

>Denial is stupid.


I agree. SO stop doing it.

[jillery]

On Sun, 08 Oct 2017 11:39:08 -0400, jillery <69jp...@gmail.com>
wrote:

>On Sun, 8 Oct 2017 07:12:06 -0500, RonO <roki...@cox.net> wrote:
>
>[...]

>
>>There is one allele for blue eyes that around 80% of the people with

>>blue eyes have and it did evolve in modern humans and not Neanderthals,
>>but my guess is that, that allele evolved in Europe. The modern humans
>>that the Neanderthals first met likely didn't have the blue eyed
>>variant. It could have evolved after the Neanderthals went extinct.
>
>
>It's interesting that you mention the origin of blue eyes just now.
>Recently there was a flurry of popular news articles which claimed
>"new research" showed that *all* blue eyes in humans are from a single
>common ancestor:
>
><https://www.sciencedaily.com/releases/2008/01/080130170343.htm>
>
>But then I noticed the actual science article cited by all of those
>pop sci articles is about 10 years old, hardly breaking news. Plus I
>was skeptical that the scientists did the fieldwork necessary to show
>that in fact all blue-eyes people originated from a common ancestor.
>After all, even if the mutation were the same everywhere, ISTM as
>likely that mutation happened in different populations, and multiple
>occurrences would be indistinguishable from just one. So their
>exaggeration of breaking news reinforced my pre-existing skepticism of
>a claim for a single common ancestor.
>
>The above Sciencedaily article quotes one of the authors:
>******************************************
>"From this we can conclude that all blue-eyed individuals are linked
>to the same ancestor," says Professor Eiberg. "They have all inherited
>the same switch at exactly the same spot in their DNA."
>******************************************
>
>One of the nice things about Sciencedaily is they almost always cite
>the original work:

>
><https://link.springer.com/article/10.1007%2Fs00439-007-0460-x>
>
>which is paywalled, but the abstract says this:
>*****************************
>One single haplotype, represented by six polymorphic SNPs covering
>half of the 3' end of the HERC2 gene, was found in 155 blue-eyed
>individuals from Denmark, and in 5 and 2 blue-eyed individuals from
>Turkey and Jordan, respectively. Hence, our data suggest a common
>founder mutation in an OCA2 inhibiting regulatory element as the cause
>of blue eye color in humans.
>******************************

>which supports the Sciencedaily article claim.
>
>AIUI OCA2 is one of the genes responsible for melanin coloration in
>all mammals, mutations to which cause albinism, while HERC2 regulates
>OCA2. A specific mutation in HERC2 suppresses OCA2 melanin production
>only in the eyes, causing blue eyes. The articles don't say, but this
>may also be the same mechanism for green and hazel eye colors, which
>are different amounts of melanin.
>
>So, on the one hand, it's not just a single SNP, but a specific
>haplotype in a specific location in HERC2, which is known to cause
>blue eyes in three different populations. My understanding is it
>would be very unlikely such a specific combination would happen more
>than once.
>
>On the other hand, ISTM a sample of only three separate populations is
>rather sketchy evidence to conclude that all blue-eyed people
>everywhere in the world have this same exact haplotype.


Here's an example of something which could be used to argue against
the authors' claim above:

<https://www.oddee.com/list/5-stunning-people-waardenburg-syndrome/>

<https://en.wikipedia.org/wiki/Waardenburg_syndrome>


The blue in blue eyes are from a lack of pigmentation in the surface
layer of the iris; the blue isn't a pigment, but from Rayleigh
scattering, like blue jays' feathers. So it's unsurprising that
genetic defects which affect pigmentation might also cause blue eyes
along with a number of other features. What is surprising is that
many of those features have nothing to do with coloring, ex. deafness,
intestinal blockage, which suggests those features are a consequence
of a more general regulatory failure.

The genes responsible for Waardenburg syndrome are different from the
genes identified by my cite above, which apparently have no other
distinctive features associated with them. So on the one hand, their
claim is technically incorrect, as there are in fact a number of
individuals with blue eyes from other causes besides the HERC2/OCA2
haplotype they identified.

On the other hand, there is a significant population with HERC2/OCA2
haplotype, and they may all have inherited it from a single common
ancestor, which is a more restrictive form of my cite's conclusion.

[Robert Carnegie]

Anyeway, whatever else goes on in the eyes, if the
melanin genes are in working order then the irises
are brown. Whatever other colour there is underneath
that, the colour that's visible is brown.

[jillery]

Not quite. As another cite I posted shows, some people have perfectly
good brown-eyed alleles but still have blue eyes:

<http://genetics.thetech.org/how-blue-eyed-parents-can-have-brown-eyed-children>

<http://tinyurl.com/oway8ne>