How much of the genome is involved in gene regulation of relevance?

[RonO]

http://www.ncbi.nlm.nih.gov/pubmed/26682651

The paper is free to download and they come to a different conclusion
than the ENCODE project. They found evidence for only a small fraction
of the genome being involved in regulating genes across lineages.

Certain lineages evolve faster than others in their genomic DNA
sequence, but what the researchers seem to have found out is that no
matter what the evolutionary rate of most of the genomic sequence is the
part of the genome that regulates genes seems to be on an independent
clock that was not different across lineages.

So, even though mammals tend to evolve faster in most of their genomic
sequence the parts of the genome involved in gene regulation evolved at
the same rate as lineages whose genomic DNA is apparently evolving at a
slower rate than mammals.

This indicates that most of the genome is evolving at a different rate
than the regulatory sequences, and is more evidence that only a fraction
of the genomic DNA is functional.

It isn't unexpected since most molecular biologists likely didn't
believe the ENCODE claims anyway.

For those that do not know the controversy, there was a major project to
document transcribed regions (RNA producing regions of the genone) and
claims came out of the project that most of the genome was involved in
regulating genes even though less than 5% of the genome coded for known
genes. There is a lot of slop in the system and a lot of the genome
that doesn't need to be transcribed is transcribed for one reason or
another, but most of it is just waste.

As to relevance to this group the IDiots at the Discovery Institute have
a claim that there is no junk DNA (my guess is that they think that
their IDiot designer would not put junk into the genome even when we can
tell that it is junk such as knock out pseudo genes). The IDiots took
the ENCODE claims to heart, but it looks like the IDiots jumped the gun
and should have listened to the guys that actually know what the score is.

In terms of gene regulation the paper above indicates that not a whole
lot of the genome is involved in gene regulation. A lot less than the
ENCODE claims would indicate. There is the caveat that they were
looking at regulation changes across lineages. There could still be
important regulation that evolved within a lineage that would not be
reflected in the regulation shared between lineages. Beats me how much
that could be, but it is the type of differential regulatory behavior
that we expect to contribute to speciation.

Ron Okimoto

[Steady Eddie]

EXCELLENT EXAMPLE of the First DARWINIAN DEFENCE - DD1:
"
1. HOMOLOGY - All similarities are automatically credited to Universal Common Ancestry, whereas
"Universal Common Design" is just as credible an explanation.
- Darwinists avoid at all costs discussing the DIFFERENCES within the biosphere, because they only
have one explanation for the differences: (...)
"

[A.Carlson]

Someone needs to go back to school. Homologies best reflect *shared*
ancestry. There is also nothing 'universal' about it. In fact
homologies wouldn't be credited to the "last universal ancestor"
because such an ancestor, which would only be found way back in
history, is not the least bit likely to reflect your more typical
types of homologies found abundantly throughout the animal kingdom.

The strength of *actual* homologies lies in the fact that they reflect
similarities or variations that can be arranged in nested hierarchies
which themselves are independently reflected in the distribution of
species, both globally and throughout the fossil record. Furthermore,
such hierarchies can also be independently verified (and falsified if
untrue) by comparative genetics.

Your "universal common design", on the other hand, fails miserably
unless your premise is that life was "designed" to appear evolved.

>- Darwinists avoid at all costs discussing the DIFFERENCES within the biosphere, because they only
>have one explanation for the differences: (...)
>"

Variation? I always thought that to be a core component of the ToE.

[Steady Eddie]

Excellent point.
Oh, and don't forget to add that, once you rise higher in the taxonomy than the level of created kinds,
these "hierarchies" are just as much an indiction of common design as common descent.
Within created kinds, you will indeed find nested hierarchies formed, indeed, by common ancestry.
And that's not Darwinism.

> Your "universal common design", on the other hand, fails miserably
> unless your premise is that life was "designed" to appear evolved.

Are all "appearances" as they appear?

> >- Darwinists avoid at all costs discussing the DIFFERENCES within the biosphere, because they only
> >have one explanation for the differences: (...)
> >"
>
> Variation? I always thought that to be a core component of the ToE.

Well, you could certainly say it's a core REQUIREMENT of the ToE...

[RonO]

Beats me where you get this junk. You should start reading some real
science instead of the lame and bogus creationist claptrap. You know
that the lie to you, so why repeat the crap? Why would all similarities
be automatically credited to a universal common ancestor? Answer that
question and you will be on your way to figuring out how you were lied to.

What about biological evolution do you just not get? Isn't it stupid to
attribute homologous traits to some universal common ancestor if
biological evolution is the fact of nature that it is?

Why are humans vertebrates when the common ancestor with our genetic
code did not have bones and was not even mutlicellular? Why don't
nematodes have bones or insects? Why are we terrestrial tetrapods like
lizards, alligators, birds and other mammals when that common ancestor
way back when did not have legs and arms, and why aren't all vertebrates
such as fish terrestiral tetrapod vertebrates?

Just think for a moment and reality might take hold. I know that would
be a stretch for someone as bigoted and willfully as ignorant as you
are, but you might give it a try.

You started a recent thread about some mythical "Darwinism" when your
real beef is just with real science. What you should do is use your
stupidity about homology to start to understand the difference between
real science and pseudoscience such as IDiocy/creationism.

Real science works, and your creationist stupidity about homology ends
up in the waste basket. Once you figure that out and reason through why
that happens there may be hope that you might understand what reality
actually is at this time.

Ron Okimoto

[Steady Eddie]

This is my "original junk", inspired by a brief alleged comment by a biologist, but who I won't name
because I can't confirm the accuracy of the account.

> What about biological evolution do you just not get? Isn't it stupid to
> attribute homologous traits to some universal common ancestor if
> biological evolution is the fact of nature that it is?

The devil's in the details.
It all depends on which "facts" of nature you're talking about.
You'd be surprised what Darwinists use for facts these days.

> Why are humans vertebrates when the common ancestor with our genetic
> code did not have bones and was not even mutlicellular? Why don't
> nematodes have bones or insects? Why are we terrestrial tetrapods like
> lizards, alligators, birds and other mammals when that common ancestor
> way back when did not have legs and arms, and why aren't all vertebrates
> such as fish terrestiral tetrapod vertebrates?

Oh! And don't forget: Why are you an innie or an outie?

> Just think for a moment and reality might take hold. I know that would
> be a stretch for someone as bigoted and willfully as ignorant as you
> are, but you might give it a try.
>
> You started a recent thread about some mythical "Darwinism" when your
> real beef is just with real science. What you should do is use your
> stupidity about homology to start to understand the difference between
> real science and pseudoscience such as IDiocy/creationism.
>
> Real science works, and your creationist stupidity about homology ends
> up in the waste basket. Once you figure that out and reason through why
> that happens there may be hope that you might understand what reality
> actually is at this time.
>
> Ron Okimoto

I like you. You and Matzke should produce the Nick N' Ron show.

[Ernest Major]

Last time your posted those falsehoods it was explained to you that they
were false. Why are you repeating them?

--
alias Ernest Major

[August Rode]

Steady Ed reads from a creationist script and doesn't think for himself. Explaining why his talking points are wrong will have no effect on him.

[Vincent Maycock]

On Tue, 29 Dec 2015 01:14:07 -0800 (PST), Steady Eddie
<1914o...@gmail.com> wrote:

snip

>> >EXCELLENT EXAMPLE of the First DARWINIAN DEFENCE - DD1:
>> >"
>> >1. HOMOLOGY - All similarities are automatically credited to Universal Common Ancestry, whereas
>> >"Universal Common Design" is just as credible an explanation.
>>
>> Someone needs to go back to school. Homologies best reflect *shared*
>> ancestry. There is also nothing 'universal' about it. In fact
>> homologies wouldn't be credited to the "last universal ancestor"
>> because such an ancestor, which would only be found way back in
>> history, is not the least bit likely to reflect your more typical
>> types of homologies found abundantly throughout the animal kingdom.
>>
>> The strength of *actual* homologies lies in the fact that they reflect
>> similarities or variations that can be arranged in nested hierarchies
>> which themselves are independently reflected in the distribution of
>> species, both globally and throughout the fossil record. Furthermore,
>> such hierarchies can also be independently verified (and falsified if
>> untrue) by comparative genetics.
>
>Excellent point.
>Oh, and don't forget to add that, once you rise higher in the taxonomy than the level of created kinds,
>these "hierarchies" are just as much an indiction of common design as common descent.

Are the similarities between you and your siblings the result of a
common stork rather than common descent?

>Within created kinds, you will indeed find nested hierarchies formed, indeed, by common ancestry.
>And that's not Darwinism.
>
>> Your "universal common design", on the other hand, fails miserably
>> unless your premise is that life was "designed" to appear evolved.
>
>Are all "appearances" as they appear?

If it looks like a duck, walks like a duck, and quacks like a duck ...

[A.Carlson]

On Tue, 29 Dec 2015 01:14:07 -0800 (PST), Steady Eddie

<1914o...@gmail.com> wrote:

>On Monday, 28 December 2015 22:02:05 UTC-7, A.Carlson wrote:
>> On Mon, 28 Dec 2015 20:08:50 -0800 (PST), Steady Eddie
>> <1914o...@gmail.com> wrote:
>>

<< Clip >>

>> >
>> >EXCELLENT EXAMPLE of the First DARWINIAN DEFENCE - DD1:
>> >"
>> >1. HOMOLOGY - All similarities are automatically credited to Universal Common Ancestry, whereas
>> >"Universal Common Design" is just as credible an explanation.
>>
>> Someone needs to go back to school. Homologies best reflect *shared*
>> ancestry. There is also nothing 'universal' about it. In fact
>> homologies wouldn't be credited to the "last universal ancestor"
>> because such an ancestor, which would only be found way back in
>> history, is not the least bit likely to reflect your more typical
>> types of homologies found abundantly throughout the animal kingdom.
>>
>> The strength of *actual* homologies lies in the fact that they reflect
>> similarities or variations that can be arranged in nested hierarchies
>> which themselves are independently reflected in the distribution of
>> species, both globally and throughout the fossil record. Furthermore,
>> such hierarchies can also be independently verified (and falsified if
>> untrue) by comparative genetics.
>
>Excellent point.
>Oh, and don't forget to add that, once you rise higher in the taxonomy than the level of created kinds,
>these "hierarchies" are just as much an indiction of common design as common descent.

You conveniently dismiss the fact that it's nested hierarchies all the
way down. Not only that but the fossil record shows that there were
far more dead ends than successes and that it is an ongoing process,
taking place over an extended period of time and not the one-off event
reflected in that fictional book of yours.

Your "common design calls for an omnipotent, omniscient, and
omnipresent being who is alleged to have the power to create the
entire universe in one fell swoop and yet the majority of his
creations regarding life forms appear to have been in error.. Occam's
razor must come into play here, especially given that there is no
empirical evidence that such a creature actually exists. IOW, given
the totality of facts here your pleading for common design appears to
be nothing more than a desperate attempt to salvage a bankrupt
theology.

>Within created kinds, you will indeed find nested hierarchies formed,
>indeed, by common ancestry. And that's not Darwinism.

Since your musings seem to be little more than desperate
rationalizations there is really nothing of significance to consider
here. And, no, your religious fantasies are not 'Darwinism'. They're
not science either.

>> Your "universal common design", on the other hand, fails miserably
>> unless your premise is that life was "designed" to appear evolved.
>
>Are all "appearances" as they appear?

Not if you have a particularly devious creator.

>> >- Darwinists avoid at all costs discussing the DIFFERENCES within the biosphere, because they only
>> >have one explanation for the differences: (...)
>> >"
>>
>> Variation? I always thought that to be a core component of the ToE.
>
>Well, you could certainly say it's a core REQUIREMENT of the ToE...

It is also widely observed, both now and in the past.

[Ray Martinez]

For example....

Waiting.

Ray

[A.Carlson]

As clearly mentioned above . . . LOOK AT ALL THE DEAD-ENDS!!!

The majority of species that existed in past eras and epochs are no
longer with us and only a few of them have progeny that currently
exist.

Also, much of what certainly appears to the majority of the scientific
community as being adaptations from pre-existing forms would otherwise
leave a lot to be desired if they were designed as they now exist. The
blind spot in the mammalian eye is just one example.

Also, as the pinnacle of God's creation, as some would believe, humans
are lacking in many other areas compared to other animals, sometimes
even leading to arguably unnecessarily premature break-downs.

>Waiting.

Just pay attention.

>Ray

[Ray Martinez]

Restating the claim. Again, I asked for an example? Why are you pretending that you don't understand? Why are you stalling?

>
> The majority of species that existed in past eras and epochs are no
> longer with us and only a few of them have progeny that currently
> exist.

Nobody denies extinction; surely extinction isn't an example, but the future of every living thing.

>
> Also, much of what certainly appears to the majority of the scientific
> community as being adaptations from pre-existing forms would otherwise
> leave a lot to be desired if they were designed as they now exist. The
> blind spot in the mammalian eye is just one example.
>
> Also, as the pinnacle of God's creation, as some would believe, humans
> are lacking in many other areas compared to other animals, sometimes
> even leading to arguably unnecessarily premature break-downs.
>
> >Waiting.
>
> Just pay attention.
>
> >Ray

Your bluff was called and you failed to produce even one example. Instead you restated your claim while explaining dead-ends as adaptations and alleged sub-optimality.

Simply ridiculous.

General Audience: Goes to show you shouldn't assume Evolutionists know what they're talking about. When one scrutinizes their claims one discovers that they don't know what they're actually talking about. Adaptation, for example, a major scientific concept, has nothing to do with alleged evolutionary dead-ends. Our Evolutionist COULD NOT produce a scholarly quotation if his life depended on it.

Ray

[RonO]

Why would anyone believe you? My guess is that it could be true because
you don't seem to be able to comprehend enough IDiocy/creationism to say
in your own words what the argument is and what makes it science. So
this could be just stupid junk you made up yourself and that you can't
back up or defend.

>
>> What about biological evolution do you just not get? Isn't it stupid to
>> attribute homologous traits to some universal common ancestor if
>> biological evolution is the fact of nature that it is?
>
> The devil's in the details.
> It all depends on which "facts" of nature you're talking about.
> You'd be surprised what Darwinists use for facts these days.

What an IDiot response. Why not really answer the questions?

Name a "Darwinist" and explain why they are a "Darwinist."

>
>> Why are humans vertebrates when the common ancestor with our genetic
>> code did not have bones and was not even mutlicellular? Why don't
>> nematodes have bones or insects? Why are we terrestrial tetrapods like
>> lizards, alligators, birds and other mammals when that common ancestor
>> way back when did not have legs and arms, and why aren't all vertebrates
>> such as fish terrestiral tetrapod vertebrates?
>
> Oh! And don't forget: Why are you an innie or an outie?

Oh! Can't figure out where you went so wrong, so you have to deny
reality and run in any way that you can.

>
>> Just think for a moment and reality might take hold. I know that would
>> be a stretch for someone as bigoted and willfully as ignorant as you
>> are, but you might give it a try.
>>
>> You started a recent thread about some mythical "Darwinism" when your
>> real beef is just with real science. What you should do is use your
>> stupidity about homology to start to understand the difference between
>> real science and pseudoscience such as IDiocy/creationism.
>>
>> Real science works, and your creationist stupidity about homology ends
>> up in the waste basket. Once you figure that out and reason through why
>> that happens there may be hope that you might understand what reality
>> actually is at this time.
>>
>> Ron Okimoto
>
> I like you. You and Matzke should produce the Nick N' Ron show.
>

What you are may be a tragedy, but it isn't much of a show.

So it looks like you are admitting that you don't have an argument, or
can't figure out what it was supposed to be so you are running in denial
again instead of even trying to defend the junk.

Ron Okimoto

[A.Carlson]

On Tue, 29 Dec 2015 14:30:51 -0800 (PST), Ray Martinez

What claim then? Your request for an example immediately followed my
claim that the "majority of his creations" appeared to have been in
error. Your god must have been very short sighted if there was only
one single creation event.

In the context of special creation vs descent through modification how
is pointing out multiple dead ends not a relevant claim? Or do you
even deny this to be a fact? Seen any dinosaurs hanging around
lately?

>> The majority of species that existed in past eras and epochs are no
>> longer with us and only a few of them have progeny that currently
>> exist.
>
>Nobody denies extinction; surely extinction isn't an example, but the future of every living thing.

A lot of wasted effort for a god that is supposed to be omniscient,
omnipotent, and omnipresent. It seems as thought you want things both
ways here. Again, one of the claims that I made that you so
conveniently are ignoring here is that there are multiple dead ends
that do not appear to have any existing progeny in the modern world
(or that were ever contemporaneous to humans).

If you represent them as the progeny of what is to come (IE: "the
future of every living thing") it appears again that you want things
both ways as the claim of imperfection directly relates to the
weakness of special creation and not descent through modification.

>> Also, much of what certainly appears to the majority of the scientific
>> community as being adaptations from pre-existing forms would otherwise
>> leave a lot to be desired if they were designed as they now exist. The
>> blind spot in the mammalian eye is just one example.
>>
>> Also, as the pinnacle of God's creation, as some would believe, humans
>> are lacking in many other areas compared to other animals, sometimes
>> even leading to arguably unnecessarily premature break-downs.
>>
>> >Waiting.
>>
>> Just pay attention.
>>
>> >Ray
>
>Your bluff was called and you failed to produce even one example.
>Instead you restated your claim while explaining dead-ends as
>adaptations and alleged sub-optimality.

So how were dead ends not exercises in futility then if they were
supposedly part of some greater plan? You can't have it both ways.

Remember that my so-called "bluff" was in response to the bogus claim
that the evidence as a whole regarding homologies equally supports
special creation as it does descent through modification and it was in
this light that I pointed out weaknesses relevant to S-P-E-C-I-A-L
C-R-E-A-T-I-O-N!!!!!

- Now how does multiple false starts support the notion of
special creation? Why would an omnipotent deity create
so many seemingly false starts. Remember, this is in
relation to the counter claim about the evidence supporting
special creation.
- How do weaknesses in design support the notion of
special creation by an omnipotent sky fairy?

>Simply ridiculous.

Yes, you seem to want your cake and to eat it too. Either it was all
part of some grand plan or it wasn't. A pretty piss-poor plan if you
ask me. Taking billions of years and far too many false starts to
only finally getting to the pinnacle of creation, the end result, only
to have the final product riddled with unnecessary weaknesses.

>General Audience: Goes to show you shouldn't assume Evolutionists know
>what they're talking about. When one scrutinizes their claims one
>discovers that they don't know what they're actually talking about.

Typical creationist. Selectively sees only what he wants to and then
distorts claims to avoid the blatantly obvious.

>Adaptation, for example, a major scientific concept, has nothing to do
>with alleged evolutionary dead-ends. Our Evolutionist COULD NOT
>produce a scholarly quotation if his life depended on it.

Shifting the goal post now. How unoriginal. You asked for an
example, not a quote.

My relevant claim was that dead-ends occurred, which they clearly did,
far more often than not. In addition they certainly fit the continuum
of adaptation observed throughout nature and the fossil record far
better than a one-off single creation event.

“Geology gave us the immensity of time and taught us how
little of it our own species has occupied.”

- Stephen Jay Gould,

[Dana Tweedy]

On 12/29/15 2:06 PM, Ray Martinez wrote:
snipping

>>>
>>> Excellent point.
>>> Oh, and don't forget to add that, once you rise higher in the taxonomy than the level of created kinds,
>>> these "hierarchies" are just as much an indiction of common design as common descent.
>>
>> You conveniently dismiss the fact that it's nested hierarchies all the
>> way down. Not only that but the fossil record shows that there were
>> far more dead ends than successes and that it is an ongoing process,
>> taking place over an extended period of time and not the one-off event
>> reflected in that fictional book of yours.
>>
>> Your "common design calls for an omnipotent, omniscient, and
>> omnipresent being who is alleged to have the power to create the
>> entire universe in one fell swoop and yet the majority of his
>> creations regarding life forms appear to have been in error..
>
> For example....
>
> Waiting.
>
> Ray
>

Trilobites.
Entelodonts.
Ceratopsians
Anomalocaris


DJT

[Prince Michael]

On Monday, December 28, 2015 at 8:12:05 PM UTC-8, Steady Eddie wrote:


> EXCELLENT EXAMPLE of the First DARWINIAN DEFENCE - DD1:

The issue with that is the mechanism of the idea, I think.

The substitute words above (that is the ToE, subgroup darwinists, the idea is the first item I mentioned (in the first paragraph section).

[Steady Eddie]

Because Ron repeated the fallacy.

[RonO]

What a boob Eddie. Can you tell me what fallacy I was supposed to have
repeated, demonstrate that I actually did what you claim, and that it is
a fallacy?

Ron Okimoto

[eridanus]

waiting for Godot?
eri

[eridanus]

you had presented some good replies.
eridanus

[eridanus]

thinking about humans, the best work of the creator, what stupid bunch
of animals they are. They are working their best to run towards the next
extinction. It is a little like they are reinventing the universal flood
that kill all humans once more.
And speaking of the Flood, it is clear in this case the utter failure of an
omniscient almighty creator. Do you want a best argument of the failure
of god? He had to destroy all living creatures, because they were bad?
Because they were peeing in the bed? The story of the flood is the ultimate
prove that a god omniscient do not exist at all.
Think of the next glaciation. Seven or 12 billion humans beings down the
drain. 99.9% of them would perish of hunger due to the scarcity. With a drop
of 8 C degrees (14F) most human beings would perish of hunger.
But if there is not any omniscient creator, we cannot blame him. This
occurred because this planet works like this. Sometimes is very cold and dry
sometimes hot and humid, but not everywhere. This is not a planet made for
us as a perfect planet. It is simply a planet, and sometimes it would be
a good place to live, sometimes it would become a nightmare. Like when
the supervolcano Toba, that nearly extinguish the humans beings. On the
other hand humans were merely surviving, because 30,000 years ago the average
temperature of the planet was 8 to 9 C degrees lower. The rains were scarce
and little temperature made the planet almost barren. Humanity was fleeing
out of Africa, for it was almost a desert. Humans were probably living close
to the sea, eating shellfish and seafood, some fishes perhaps. As a piece
of shore become exhausted they that to move on, looking for a different
place to find something to eat. In the mid of the voyage they encountered
met the Volcano Toba, that caused a great havoc. This narrative does not
look the work of an omniscient creator. This world with their swings in temperature, were not the plan of an intelligent god. But if someone tell
me, it was not any god that created this shit of a planet. We are here by
mere chance. This is what we have. We are here now, and in a few more thousand years we will be out of the game. We would be exterminated by the
next glaciation.

If you think god made a perfect planet for the humans think again.
Did go make a good planet for the dinosaurs? It seems that he had not.
The dinosaurs all were exterminated. We do not know yet well what happened
and why it exist today still some life in this planet. Some catastrophe
exterminated most of the living beings. Perhaps as much as 99.99% of them.
Life had to reinvent itself from the limited animals that survived in very
small numbers, in very small and scarce places that were good enough.
The ancestor of humans were probably like rats. From them evolved all mammals
that exist today.
eridanus

[jillery]

...or his book to be published.
--
This space is intentionally not blank.