Sunfish genome

[RonO]

http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0144-3

They have sequenced the sunfish genome. This is the largest extant bony
fish species.

https://en.wikipedia.org/wiki/Ocean_sunfish

This is part of the 10,000 vertebrate genome project. The goal is to
sequence the genomes of 10,000 vertebrates by 2020.

These are huge odd looking fish, but their closest relatives are puffer
fish like the fugu.

Reading this paper should give people some concept of what science is
going to get from these 10,000 genomes. As with the human and
Neandertal genome sequences we can tell a lot about a species from the
genome sequence. By looking at how the variation (you can call them
mutations because that is what they were at one time) scattered through
the genome of this single individual they can do population analyses.
If you read the section "Population size and history" you can get some
idea that they can tell things like about when population constrictions
occurred. This is sort of amazing, but is a consequence of evolution.
George has harped on mutation rate and there is no doubt that mutations
keep happening. There is also genetic recombination where the
chromosomes are scrambled every generation by recombination between
pairs of chromosomes that you inherited from your two parents. Well the
steady accumulation of mutations and the creation of new haplotypes can
tell you something about the history of that particular genome.

We use this type of information to estimate population size in humans
over time. It is why we can backtrack and determine that only a portion
of the variation in modern humans went into Europe and estimate a time
frame for it. It is why most of the genetic variation in modern humans
is in Africa because only part of that population managed to leave
Africa and move out into the rest of the world. We can tell that before
we were able to leave Africa something happened and we suffered a
population bottleneck around 80,000 years ago. Our population decreased
to ominous levels. Some estimates go down to around 1,000. We were an
endangered species at one time, but we somehow made it. We are just
left with around 1/5 the genetic variation found in most other species.

So pretty soon we will have 10,000 vertebrate genomes and like the
giraffe and okapi genome sequences there will be much more for
creationists to deny. Whole genome sequences demonstrating the
evolution of vertebrates. We also will have more invertebrate genome
sequences and plant genome sequences. An associate just told me that
there are a couple thousand Salmonella and E. coli genome sequences in
the database. Those are just two related types of bacteria. Denton has
already given up and just claims that everything unfolded as planned
after the initial creation. For the rest it is just different degrees
of denial.

Ron Okimoto

[jillery]

So the founding population of non-African humans was just a fraction
of the surviving fraction of African humans, with just a sprinkling of
Neanderthal and Denisovan adventurers.

>So pretty soon we will have 10,000 vertebrate genomes and like the
>giraffe and okapi genome sequences there will be much more for
>creationists to deny. Whole genome sequences demonstrating the
>evolution of vertebrates. We also will have more invertebrate genome
>sequences and plant genome sequences. An associate just told me that
>there are a couple thousand Salmonella and E. coli genome sequences in
>the database. Those are just two related types of bacteria. Denton has
>already given up and just claims that everything unfolded as planned
>after the initial creation. For the rest it is just different degrees
>of denial.

My impression is ID supporters have been running on nothing but
willful stupidity fumes for decades, as recently illustrated by Axe's
book. There is no logical path from an observation that human design
involves intelligence, to a conclusion that non-human design must also
involve intelligence.
--
This space is intentionally not blank.

[RonO]

The times have changed from the initial estimates, but it is starting to
look like the population that became the Neandertals and Denisovans in
Europe and Asia left Africa half a million years ago, maybe out to
800,000. The human population in Africa has fluctuated over the last
150,000 years in some large swings as the ice age was ending, though the
glacial maximum was only 25,000 years ago. For some reason we had a
major population bottle neck around 80,000 years ago. The Neandertal
genomes show evidence that their population was also affected and
crashed around the same time. For some reason the other apes were not
as affected and managed to maintain larger effective population sizes
and so chimps have around 3 times the genetic variation found among the
modern humans.

Around 60,000 years ago there was a wave of migration out of Africa, so
there was around 20,000 years for our population in Africa to recover
before the migration out of Africa, but only a fraction of the
population left Africa, so there was a loss of variation among the
migrants that left Africa, and Africans show a greater genetic
diversity. Neandertals and Denisovans likely outnumbered the migrants,
but that doesn't seem to have mattered and though we coexisted with
Neandertal for another 25,000 years there seems to have been minimal
interbreeding. We have identified three instances that they are calling
pulses of Neandertal genetics into modern humans. The modern humans
that made it out to Indonesia seem to have encountered some Denisovans
and interbred with them, but again the mix is highly one sided and only
a few percent Denisovan DNA has been retained by some populations.

What it looks like is that Neandertals and Denisovans existed as smaller
groups than modern humans. The individuals that we have sequenced are
more inbred than most modern humans are. Though we might have been
inbreeding to the same extent in Ice Age Europe and Asia. Beats me how
large a population could be maintained in any given area during that
time period.

>
>
>> So pretty soon we will have 10,000 vertebrate genomes and like the
>> giraffe and okapi genome sequences there will be much more for
>> creationists to deny. Whole genome sequences demonstrating the
>> evolution of vertebrates. We also will have more invertebrate genome
>> sequences and plant genome sequences. An associate just told me that
>> there are a couple thousand Salmonella and E. coli genome sequences in
>> the database. Those are just two related types of bacteria. Denton has
>> already given up and just claims that everything unfolded as planned
>> after the initial creation. For the rest it is just different degrees
>> of denial.
>
>
> My impression is ID supporters have been running on nothing but
> willful stupidity fumes for decades, as recently illustrated by Axe's
> book. There is no logical path from an observation that human design
> involves intelligence, to a conclusion that non-human design must also
> involve intelligence.

None of the ID perps have had anything worth talking about since they
started running the bait and switch on their own creationist support
base in 2002. IC and Specified complexity predated the bait and switch
and only the new IDiot law of thermodynamics seems to have been put up
since, and everyone should know how well that turned out. You might
count CSI, but that is just restating Dembski's older specified
complexity junk. No one ever got the promised ID science when they
needed it, and that is apparent to anyone with a brain by this point in
time. It has already been more than 3 years since the last bait and
switch had to go down on both Texas and Louisiana IDiots that wanted to
teach IDiocy in their public schools. It is hard to believe that there
were still IDiots stupid enough to try back in 2013. The bait and
switch had already been going down for over a decade by that time. In 6
more months it will be 15 years since the ID perps decided to start
running the bait and switch instead of putting up any ID science. No
creationists have ever gotten the ID science all they get is an
obfuscation scam that doesn't even mention that ID ever existed.

My guess is that no one expects IDiocy to amount to anything at this
point in time. The IDiot science society (ISCID) closed their doors and
quit the ID scam 8 years ago. Just that fact should be enough for anyone.

Ron Okimoto

[Glenn]

"RonO" <roki...@cox.net> wrote in message news:nr13nl$kel$1...@dont-email.me...

Stop being so dishonest, Ron. Denton has not "given up". The only people you fool are fools.

"Denton still accepts design and embraces a non-Darwinian evolutionary theory. He denies that randomness accounts for the biology of organisms; he has proposed an evolutionary theory which is a "directed evolution" in his book Nature's Destiny (1998)."

https://en.wikipedia.org/wiki/Michael_Denton

[Bill Rogers]

On Saturday, September 10, 2016 at 10:05:03 AM UTC-4, Ron O wrote:
> http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0144-3
>
> They have sequenced the sunfish genome. This is the largest extant bony
> fish species.
>
> https://en.wikipedia.org/wiki/Ocean_sunfish
>
> This is part of the 10,000 vertebrate genome project. The goal is to
> sequence the genomes of 10,000 vertebrates by 2020.
>
> These are huge odd looking fish, but their closest relatives are puffer
> fish like the fugu.

I first saw a picture of an ocean sunfish in "The How and Why Wonder Book of Fish for Kids" and was amazed at the size and the appearance of being all head and no body. Nothing like the "sunnies" I was catching in the local pond (and obviously unrelated).
>
<snip>
> Ron Okimoto

[RonO]

Beats me what you are objecting to. Denton's alternative will always be
consistent with what we discover if life evolved naturally on this
planet. If that isn't giving up on trying to figure out what happened
nothing is giving up. If the designer designed everything to work and
things evolved just like science is figuring out what is the future of
IDiocy?

The fool would seem to be anyone that ever thought Denton had anything
worth talking about.

>
> "Denton still accepts design and embraces a non-Darwinian evolutionary theory. He denies that randomness accounts for the biology of organisms; he has proposed an evolutionary theory which is a "directed evolution" in his book Nature's Destiny (1998)."

When was this design? What good will it ever to any IDiot?

> https://en.wikipedia.org/wiki/Michael_Denton

So Denton is an IDiot at the Discovery Institute. That isn't big news.
This link claims that Denton has lied about being an agnostic. An
agnostic IDiot? His position would be more like a Deist instead of an
agnostic. Do you believe that Denton is an agnostic? Someone that
claims that some designer created everything with the big bang and then
let it all unfold is not an agnostic.

Ron Okimoto


>

[William Hyde]

I read that book and had exactly the same reaction. Except that I only caught sunfish on vacation. There were no surviving vertebrates in the local river - though now there are.

William Hyde

[Glenn]

"RonO" <roki...@cox.net> wrote in message news:nr1p6p$umm$1...@dont-email.me...

This link does not claim Denton has lied about anything.

[Bob Casanova]

On Sat, 10 Sep 2016 11:55:51 -0700, the following appeared
in talk.origins, posted by "Glenn" <g...@invalid.invalid>:

Really? Let's see who's the fool here...

>"Denton still accepts design and embraces a non-Darwinian evolutionary theory. He denies that randomness accounts for the biology of organisms; he has proposed an evolutionary theory which is a "directed evolution" in his book Nature's Destiny (1998)."

Not to put too fine a point on it, this isn't 1998. Anything
more recent to show that Ron is incorrect *now*? Or did you
think you could slip that one past?

>https://en.wikipedia.org/wiki/Michael_Denton
--

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

[Bob Casanova]

On Sat, 10 Sep 2016 13:27:10 -0700 (PDT), the following
appeared in talk.origins, posted by William Hyde
<wthyd...@gmail.com>:

Sunfish (the bluegill sort) are tenacious; the saying "Spit
on the sidewalk and in 10 minutes there'll be bluegills
breeding in it" is only a minor exaggeration. ;-)

I suspect, unless the entire watershed was *completely* dead
(which is almost impossible to accomplish) there was a
remnant population in the river or in one of its
tributaries. Or somewhere else in the watershed.

[William Hyde]

You are correct. When we spoke of "The River" we meant the deeper part near us and downstream from that. But the watershed was twenty or so miles away, in protected land.

About a mile upstream there was vertebrate life in shallow streams, minnows and tadpoles. Farther upstream still there may have been deeper pools in which larger fish still existed.

Now the main threat to the fish is being stepped on by the deer. Well, that and the otters, I suppose. Pollution control worked, even though there are ten times as many people in the area now, and far more upstream.

William Hyde

[RonO]

Is Denton an agnostic? Why did Denton lie about being an agnostic? Who
would believe him? Do you believe that Denton is an agnostic?

Ron Okimoto

[RonO]

The sunfish genome under discussion is also known as the Mola Mola. It
is not a panfish.

I did give the wiki link.

Ron Okimoto

[Glenn]

"RonO" <roki...@cox.net> wrote in message news:nr4jvo$vh7$1...@dont-email.me...

You place a lot of faith in your beliefs. Where does the Wiki article claim Denton lied about anything?

[RonO]

What an IDiot Glenn.

QUOTE:
Denton describes himself as an agnostic.[3][4]
END QUOTE:

Is Denton an agnostic? He obviously lied.

Do you believe that Denton is an agnostic?

He has written three books describing what he thinks that his designer
is responsible for and he joined a creationist organization not just
once, but twice. He quit the Discovery Institute around the time the
bait and switch started to go down, but he likely quit because the other
ID perps didn't like his second book. The book where he admitted that
common descent was a fact of nature. They all liked his first book
where he was so wrong that he changed his mind about common descent in
his second book. He rejoined the Discovery Institute after IDiocy went
into the toilet. What does that mean?

What does he claim in his last book? He claims that the designer
created things so that everything could unfold over billions of years as
it has. Do you remember the thread about his latest book?

Ron Okimoto

[Glenn]

"RonO" <roki...@cox.net> wrote in message news:nr62u1$ii6$1...@dont-email.me...

[Bob Casanova]

On Sun, 11 Sep 2016 12:27:19 -0700 (PDT), the following

OK, with the proviso that "the watershed" includes the
river, all its tributaries *and* any river into which it
flows before reaching its destination, usually the ocean but
sometimes a major lake.

>About a mile upstream there was vertebrate life in shallow streams, minnows and tadpoles. Farther upstream still there may have been deeper pools in which larger fish still existed.
>
>Now the main threat to the fish is being stepped on by the deer. Well, that and the otters, I suppose. Pollution control worked, even though there are ten times as many people in the area now, and far more upstream.

Pollution control is always a benefit. Look at the history
of the Cuyahoga River; it no longer catches fire.

[Bob Casanova]

On Sun, 11 Sep 2016 17:02:29 -0500, the following appeared
in talk.origins, posted by RonO <roki...@cox.net>:

>The sunfish genome under discussion is also known as the Mola Mola. It
>is not a panfish.
>
>I did give the wiki link.

Yes, you did, and the difference was noted above by William.

[Bob Casanova]

On Mon, 12 Sep 2016 06:18:24 -0500, the following appeared

in talk.origins, posted by RonO <roki...@cox.net>:

Give it up, Ron. Glenn is just being Glenn, and claiming
that unless the words "Denton lied about..." are in the Wiki
article your statement is wrong. Documenting that Denton
made contradictory claims doesn't count.

>Do you believe that Denton is an agnostic?
>
>He has written three books describing what he thinks that his designer
>is responsible for and he joined a creationist organization not just
>once, but twice. He quit the Discovery Institute around the time the
>bait and switch started to go down, but he likely quit because the other
>ID perps didn't like his second book. The book where he admitted that
>common descent was a fact of nature. They all liked his first book
>where he was so wrong that he changed his mind about common descent in
>his second book. He rejoined the Discovery Institute after IDiocy went
>into the toilet. What does that mean?
>
>What does he claim in his last book? He claims that the designer
>created things so that everything could unfold over billions of years as
>it has. Do you remember the thread about his latest book?
>
>Ron Okimoto
>

[RonO]

Where did your functioning brain go? Years ago you used to actually try
to put up an argument. Now all you can do is ask stupid questions that
you already know the answer to.

Where did that Glenn go? Why was he replaced by this pathetic pretender?

Ron Okimoto

[Glenn]

"RonO" <roki...@cox.net> wrote in message news:nr7fsa$kkf$1...@dont-email.me...

Yes, I know the answer. You lie.

[jillery]

On Mon, 12 Sep 2016 20:41:00 -0700, "Glenn" <g...@invalid.invalid>

Oh, the paradox of a technically correct but substantially irrelevant
point vs a technically incorrect but substantially valid point.

[Glenn]

"jillery" <69jp...@gmail.com> wrote in message news:fs0ftblatlhsublov...@4ax.com...

Vote Hillary.

[RonO]

Are you even able to tell yourself the truth? Is someone like Denton
telling the truth when they claim to be agnostic? Why lie to yourself
about stupid things like that? If Denton were an agnostic would you
even be trying to support the IDiot?

Why have you degenerated so badly? What happened to the argument that
you thought that you had years ago?

Ron Okimoto

[Earle Jones27]

*
I was wondering the same thing. There used to be a Glenn (Glenn
Sheldon) who could put up some semi-rational arguments. Is this the
same Glenn?

And rational men everywhere need to know: Did Steady Eddie really go
back to God?

earle
*

[RonO]

That is Glenn. What used to be is no more. It may be more than a
decade since Glenn tried to put up any type of argument. Now all he
does is what he is doing.

Ron Okimoto

Ron Okimoto

[Earle Jones27]

*
Ron: That is truly sad. Do you think he is beyond any of the type of
help or encouragement that we could provide? I remember him fairly
positively. Is he a young guy? I had the impression that he, back in
the day, was a student making some (weak) attempt to learn something.

Now he is a sound-bite pot-shot artist. Very sad.

earle
*

[RonO]

I do not think that there is anything that anyone on this forum can do
at this time. I do not know how old Glenn is, but I recall he indicated
that he was retired from whatever he had been doing. I could be mixing
him up with someone else, it has been a pretty long time since Glenn has
put forward much of anything worth discussing.

Ron Okimoto