This is fantastic!

[Rolf]

Science trudges on, exploring the "Dark Matter" of the genome.

http://preview.tinyurl.com/3c6wybm

Rolf

[r norman]

On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.a...@tele2.no>
wrote:

>Science trudges on, exploring the "Dark Matter" of the genome.
>
>http://preview.tinyurl.com/3c6wybm
>
>Rolf
>

The paper is
A high-resolution map of human evolutionary constraint using 29
mammals

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10530.html

The abstract says:
The comparison of related genomes has emerged as a powerful lens for
genome interpretation. Here we report the sequencing and comparative
analysis of 29 eutherian genomes. We confirm that at least 5.5% of the
human genome has undergone purifying selection, and locate constrained
elements covering ~4.2% of the genome. We use evolutionary signatures
and comparisons with experimental data sets to suggest candidate
functions for ~60% of constrained bases. These elements reveal a small
number of new coding exons, candidate stop codon readthrough events
and over 10,000 regions of overlapping synonymous constraint within
protein-coding exons. We find 220 candidate RNA structural families,
and nearly a million elements overlapping potential promoter, enhancer
and insulator regions. We report specific amino acid residues that
have undergone positive selection, 280,000 non-coding elements exapted
from mobile elements and more than 1,000 primate- and
human-accelerated elements. Overlap with disease-associated variants
indicates that our findings will be relevant for studies of human
biology, health and disease.

[T Pagano]

On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.a...@tele2.no>
wrote:

>Science trudges on, exploring the "Dark Matter" of the genome.
>
>http://preview.tinyurl.com/3c6wybm
>
>Rolf
>

Higly imaginative scientific exploration and descriptive of what's
there. But doesn't explain, in the least, how it got there in the
first place. Perhaps Harshman will show how the Archeopteryx explains
it or Lethe will show how population genetics predicted it.

Rolf's batting average is near zero. But at least he's not nearly as
angry as the Boikat and the yappy RAM troll.


Regards,
T Pagano

[Boikat]

On Oct 16, 9:03�am, T Pagano <not.va...@address.net> wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

> wrote:
>
> >Science trudges on, exploring the "Dark Matter" of the genome.
>
> >http://preview.tinyurl.com/3c6wybm
>
> >Rolf
>
> Higly imaginative scientific exploration and descriptive of what's
> there. �But doesn't explain, in the least, how it got there in the
> first place. �Perhaps Harshman will show how the Archeopteryx explains
> it or Lethe will show how population genetics predicted it.
>
> Rolf's batting average is near zero. �But at least he's not nearly as
> angry as the Boikat and the yappy RAM troll.

How you mistake amusement for anger is beyond me. I find it funny
that you'll spit out your usual denialisms and claim victory, but for
some reason you turn tail and run and dive under your rock when you
are challenged to explain away the transitional nature of Tiktaalik,
without resorting to various strawman excuses.

Boikat

[Frank J]

On Oct 16, 10:03 am, T Pagano <not.va...@address.net> wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

> wrote:
>
> >Science trudges on, exploring the "Dark Matter" of the genome.
>
> >http://preview.tinyurl.com/3c6wybm
>
> >Rolf
>
> Higly imaginative scientific exploration and descriptive of what's
> there.  But doesn't explain, in the least, how it got there in the
> first place.  Perhaps Harshman will show how the Archeopteryx explains
> it or Lethe will show how population genetics predicted it.
>
> Rolf's batting average is near zero.  But at least he's not nearly as
> angry as the Boikat and the yappy RAM troll.

And neither is nearly as angry as the one who has slipped back to the
cheap trick of changing subject lines.

>
> Regards,
> T Pagano

[Rolf]

T Pagano wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.a...@tele2.no>
> wrote:
>
>> Science trudges on, exploring the "Dark Matter" of the genome.
>>
>> http://preview.tinyurl.com/3c6wybm
>>
>> Rolf
>>
> Higly imaginative scientific exploration and descriptive of what's
> there. But doesn't explain, in the least, how it got there in the
> first place.

Right. isn't that too bad? With your interest in science, haven't you found
any credible theory abou how things got there either?

If you can't, nobody can. Guess that's why you can't say anythting sbout
Tiktaalik

[r norman]

On Sun, 16 Oct 2011 10:03:23 -0400, T Pagano <not....@address.net>
wrote:

This time you revert to your usual nonsense.

Of course it doesn't explain how it got there because that is not what
the researchers were attempting. However it is difficult to explain
the shared hidden features in the genome of 29 very different mammals
without the notion of common descent. This is just one more addition
to the now incredibly complex scheme of nested hierarchies. Incredible
that is without the notion of common descent but trivially obvious
with it.

Alternatively, if goddidit, can you explain why the method of doing it
so compellingly argues for evolution? God the trickster?

[Will in New Haven]

On Oct 16, 11:37�ｿｽam, r norman <r_s_nor...@comcast.net> wrote:
> On Sun, 16 Oct 2011 10:03:23 -0400, T Pagano <not.va...@address.net>
> wrote:
>
>
>
> >On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

> >wrote:
>
> >>Science trudges on, exploring the "Dark Matter" of the genome.
>
> >>http://preview.tinyurl.com/3c6wybm
>
> >>Rolf
>
> >Higly imaginative scientific exploration and descriptive of what's

> >there. �ｿｽBut doesn't explain, in the least, how it got there in the
> >first place. �ｿｽPerhaps Harshman will show how the Archeopteryx explains

> >it or Lethe will show how population genetics predicted it.
>

> >Rolf's batting average is near zero. �ｿｽBut at least he's not nearly as

> >angry as the Boikat and the yappy RAM troll.
>
> This time you revert to your usual nonsense.
>
> Of course it doesn't explain how it got there because that is not what

> the researchers were attempting. �ｿｽHowever it is difficult to explain

> the shared hidden features in the genome of 29 very different mammals

> without the notion of common descent. �ｿｽThis is just one more addition

> to the now incredibly complex scheme of nested hierarchies. Incredible
> that is without the notion of common descent but trivially obvious
> with it.
>
> Alternatively, if goddidit, can you explain why the method of doing it

> so compellingly argues for evolution? �ｿｽGod the trickster?

Yep, god wants the people smart enough to study the evidence in the
natural world and come to the obvious conclusions to go to Hell. That
is because the god Tony (and Ray and many other morons) believes in is
the god of stupid and/or willfully ignorant people. He is their
instrument for vengeance on people smarter than themselves, which is
most people.

--
Will in New Haven

[Glenn]

"Will in New Haven" <bill....@taylorandfrancis.com> wrote in message
news:f2d8bae7-46c8-4ef0...@k2g2000yqh.googlegroups.com...

> On Oct 16, 11:37 am, r norman <r_s_nor...@comcast.net> wrote:
> > On Sun, 16 Oct 2011 10:03:23 -0400, T Pagano <not.va...@address.net>
> > wrote:
> >
> >
> >
> > >On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>
> > >wrote:
> >
> > >>Science trudges on, exploring the "Dark Matter" of the genome.
> >
> > >>http://preview.tinyurl.com/3c6wybm
> >
> > >>Rolf
> >
> > >Higly imaginative scientific exploration and descriptive of what's

> > >there. But doesn't explain, in the least, how it got there in the
> > >first place. Perhaps Harshman will show how the Archeopteryx explains

> > >it or Lethe will show how population genetics predicted it.
> >

> > >Rolf's batting average is near zero. But at least he's not nearly as

> > >angry as the Boikat and the yappy RAM troll.
> >
> > This time you revert to your usual nonsense.
> >
> > Of course it doesn't explain how it got there because that is not what

> > the researchers were attempting. However it is difficult to explain

> > the shared hidden features in the genome of 29 very different mammals

> > without the notion of common descent. This is just one more addition

> > to the now incredibly complex scheme of nested hierarchies. Incredible
> > that is without the notion of common descent but trivially obvious
> > with it.
> >
> > Alternatively, if goddidit, can you explain why the method of doing it

> > so compellingly argues for evolution? God the trickster?

>
> Yep, god wants the people smart enough to study the evidence in the
> natural world and come to the obvious conclusions to go to Hell. That
> is because the god Tony (and Ray and many other morons) believes in is
> the god of stupid and/or willfully ignorant people. He is their
> instrument for vengeance on people smarter than themselves, which is
> most people.
>

You don't look smart enough to spit in a bucket.

[Charles Brenner]

On Oct 16, 1:42 pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "Will in New Haven" <bill.re...@taylorandfrancis.com> wrote in messagenews:f2d8bae7-46c8-4ef0...@k2g2000yqh.googlegroups.com...

Thanks, I sort of wondered what Will looks like. Interesting fact.

But his point is valid isn't it?

[Glenn]

"Charles Brenner" <cbre...@berkeley.edu> wrote in message
news:fc80e483-ee6d-4eac...@t38g2000prg.googlegroups.com...

[Friar Broccoli]

On Oct 16, 9:49�am, r norman <r_s_nor...@comcast.net> wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

I am more interested in the implied percent of the human genome that
is coding. The article Rolf pointed to refers to "360 million DNA
letters" which would give 360,000,000/3,000,000,000 = ~12%. That
roughly agrees with the size of the Puffer Fish genome which has 365
million base-pairs. So why does the above article refer to ~4.2% and
5.5%?

In any case this is all a big surprise to me, since I thought only 2%
was coding/used. (For me, control genes are coding, even if not for
proteins.)

[r norman]

I gave a link to the full paper that is referred to in that article.
Nowhere does the number 360 appear. It does say "With 29 mammals, we
pinpoint 3.6 million elements spanning 4.2% of the genome". The
abstract refers to 5.5% being subject to strong selection and hence is
probably functional. That leaves almost 95% of the genome to account
for.

I have no idea what the ScienceDaily article is doing. You may recall
a separate thread Rolf cited where ScienceDaily titles the article
"How the Zebra got its stripes" when the paper addressed says
absolutely nothing about zebras. Press releases are notoriously
unreliable sources of scientific information. Popular press magazines
purporting to be about science, like ScienceDaily, are even worse.
That is why I also go directly to the published paper and only to the
published paper. You simply cannot accept magazine stories as correct
and informative without checking.

[Vend]

On 16 Ott, 15:49, r norman <r_s_nor...@comcast.net> wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

What do "purifying selection" and "constrained elements" mean?

[Will in New Haven]

On Oct 16, 5:59 pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "Charles Brenner" <cbren...@berkeley.edu> wrote in message

What a brilliant and interesting comment, asshole.

--
Will in New Haven

"At least an ad-hominem acknowledges ones opponent's humanity." Bill
Reich on Fido Net 1993

[Will in New Haven]

On Oct 16, 4:42 pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "Will in New Haven" <bill.re...@taylorandfrancis.com> wrote in messagenews:f2d8bae7-46c8-4ef0...@k2g2000yqh.googlegroups.com...

What a brilliant and well-reasoned comment.

[Glenn]

"r norman" <r_s_n...@comcast.net> wrote in message
news:2qpm97hk15r8g38l0...@4ax.com...

ScienceDaily simply reprinted the release from MIT Press, so consider that
source to be even worse.
Who may have originated the story is unknown, though it appears to be a
writer from Broad. But why the writer would include such a statement piqued
my interest, since I doubt that many writers would come up with something
all on their own. So here is where my little internet research project led
me, google for - "copy number variations" "360 million" -Here's from one
search result:

"The extent of the variation was breathtaking: these relatively common CNVs
cumulatively affected 360 million nucleotides, or about 12% of the human
genome"
http://www.cmaj.ca/content/176/4/441

This may have originally been claimed by Redon et al Nature 2006 or a
previous paper in '96, although I find no reference for this in the paper.
Nor did I find in the paper any instances of "CNV", "copy number", "12%" or
"360". The MIT article seems to have got this from an entirely different
source than from anyone connected to the actual paper.

[r norman]

On Sun, 16 Oct 2011 16:38:21 -0700 (PDT), Vend <ven...@virgilio.it>
wrote:

"Purifying selection" is negative selection: the removal of
deleterious variants. "Constrained elements" are sections of the
genome that are not able to vary freely by mutation but are conserved
over time. They are exactly the part of the genome that is "purified"
by natural selection removing any changes.

In short, that is the part of the DNA that is almost certainly truly
significant regions: real junk has no constraints on change and there
is no selection to remove deleterious changes because changes there
don't matter.

[Friar Broccoli]

Thanks very much.
I downloaded a copy of the paper for safe keeping against a future
paywall.

[RAM]

On Oct 16, 9:03 am, T Pagano <not.va...@address.net> wrote:
> On Sun, 16 Oct 2011 11:45:07 +0200, "Rolf" <rolf.aalb...@tele2.no>

Why Pags the yappy RAM troll seems to always be on your radar screen.

Could it be he is getting your goat about your moral flaws like
plagiarizing and lying about it and your dubious religious beliefs
like a global flood, special creation and a young earth?

Why yes it could be seems to be obvious to me.

[Glenn]

"RAM" <ramat...@gmail.com> wrote in message
news:6df115f5-99dc-48a7...@u2g2000yqc.googlegroups.com...

You probably have your own goat.

[William Hughes]

On Oct 16, 12:37 pm, r norman <r_s_nor...@comcast.net> wrote:

> Alternatively, if goddidit, can you explain why the method of doing it
> so compellingly argues for evolution?  God the trickster?

Perhaps not. God may have other reasons for creating a universe in
which evolution seems logical. It may be that he does not want
to create a universe in which it is possible to prove that he exists
[1].
This is of course the babel fish argument so you may consider it
to be a load of dingo's kidneys.

- William Hughes

[1] I don't know. I am a disciple of Pope.

[Friar Broccoli]

On Oct 16, 9:18 pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "r norman" <r_s_nor...@comcast.net> wrote in message

I just realized that this is a clear case of evolution (descent with
modification constrained by Natural Selection) being used to discover
something that would otherwise have been impossible to determine.

[Vend]

Thanks.