Gene duplication and multifunctional proteins

[RonO]

Since Eddie has gone on about gene duplication and the denial about it
at the Discovery Institute it just so happens that there is a review
that just came out. It covers gene duplication and specifically
"moonlighting" proteins. These are gene products that can do multiple
functions. Some of these functions have evolved after the gene is
duplicated, some not.

http://journal.frontiersin.org/article/10.3389/fgene.2015.00227/abstract

The paper should be free to download.

Some basic facts about gene duplication are that it is more common than
we expected, and that most of the duplication events don't amount to
anything. As the review states the extra gene usually becomes a
nonfunctional pseudogene and slowly degrades in sequence as the lineage
evolves. This means that one of the best features supporting biological
evolution that gene duplication provides is not the new functions that
sometimes evolve, but the gene fossils that are left in the genomes.
Once a gene becomes nonfunctional it slowly mutates its DNA sequence
until the duplicated sequence is so different that you can't tell it
from random sequence. Two closely related species will share the same
mutation events until the two split and become separate species and from
then on the duplicated sequence can change independently. We have
examples of pseudogenes like the defective vitamin C gene. We share
mutations that would have destroyed the activity of the gene with
monkeys (The gene became defective in the common ancestor of simians),
and we share more mutations in common with other apes than we do with
monkeys. The simple reason for this is that we have shared a common
ancestor with other apes longer than we shared a common ancestor with
most monkeys because we split off from other apes more recently.

When we look in the genome we find a lot of duplicated sequence in
various stages of decay. Until the sequence drops below around 40%
similarity we can detect the duplicated sequence, but once you change
over 60% of a DNA sequence (there are only 4 bases) it gets difficult to
say that two sequences were once the same. The fact is that it takes
millions of years for the duplicated sequence to slowly degrade to this
level, but since gene duplication is common we can have duplicated
sequences at all stages of decay that have obviously happened at
different times during the evolution of that species.

We can see what species share the same duplication and look at how the
DNA sequence has changed. So the denial at the Discovery Institute
doesn't do them any good because other aspects of gene duplication
obviously support biological evolution. The ID perps can only say that
gene duplication is not likely to amount to anything. Science has
already demonstrated that, but it has also demonstrated that most of the
duplications can still tell you something about biological evolution.
Real science has the fact that gene duplication happens. We have the
winners that amounted to something new, and we have the majority of
losers that still evolve as expected. What do the IDiots have?

Ron Okimoto

[jillery]

On Wed, 15 Jul 2015 06:47:46 -0500, RonO <roki...@cox.net> wrote:

>Since Eddie has gone on about gene duplication and the denial about it
>at the Discovery Institute it just so happens that there is a review
>that just came out. It covers gene duplication and specifically
>"moonlighting" proteins. These are gene products that can do multiple
>functions. Some of these functions have evolved after the gene is
>duplicated, some not.
>
>http://journal.frontiersin.org/article/10.3389/fgene.2015.00227/abstract
>
>The paper should be free to download.

It was for me, as a PDF or a web page.

Many of the points that Mr. Eddie said Meyer said are flat-out
contradicted by this article. I wonder how long before EN&V posts an
article "proving" that your cited article is wrong and its authors are
delusional. I should start a betting pool.
--
This space is intentionally not blank.

[Steady Eddie]

Excellent reasoning by very intelligent scientists, without a doubt.
The speculations of how the evolutionary scenario could have produced
multi-functional proteins are very imaginative and make sense as the
most likely evolutionary explanation for the phenomenon to date.

So, as an evolutionary explanation, this is excellent material. But as a true
explanation, this has a major flaw:
It's based on the unverified assumption of common ancestry and/or its antecedent, macroevolution.

When trying to find the TRUTH about a historical event or process, you need to
be open to all plausible explanations. Here these scientists fail - they are
limiting themselves to naturalistic explanations only, and trying their level
best to provide the best explanation they can think of under that paradigm.

What these researchers fail to realize is that the existence of mulit-functional proteins is yet more evidence of the handywork of a highloy
intelligent designer.
They've completely closed their minds to this possibility.
Now, if Intelligent Design were previously dismissed after lengthy and impartial
investigation, they would be correct to concentrate on only naturalistic
explanatioins. But this isn't the case; Intelligent Design is still solidly
on the table of scientific investigation.
Until the jury is out on that topic, the conclusions proffered by these and
other evolutionists are simply an exercise in partisan politics.

[RonO]

What is this alternative and how does it work? Real science has cell
theory, basic genetic evidence and all of extant life consistent with
what is known. What do you have?

>
> What these researchers fail to realize is that the existence of mulit-functional proteins is yet more evidence of the handywork of a highloy
> intelligent designer.

Why? We can observe these duplications. We can even know some of the
mechanisms by which they happen because we can take clonal cells and
look before and after the event.

We can look within species like humans and see that many such
duplications have occurred in the current population. We even have a
new name for them copy number variants (CNV) because they are so
numerous once we were able to sequence whole genomes and compare them.

> They've completely closed their minds to this possibility.
> Now, if Intelligent Design were previously dismissed after lengthy and impartial
> investigation, they would be correct to concentrate on only naturalistic
> explanatioins. But this isn't the case; Intelligent Design is still solidly
> on the table of scientific investigation.
> Until the jury is out on that topic, the conclusions proffered by these and
> other evolutionists are simply an exercise in partisan politics.
>

Unlike you, someone that actually understand the evidence and has a
system to evenly weigh it and come to your bogus conclusions. Who could
possibly believe that?

Where is that science of intelligent design? What do you currently get
from the ID perps that sold you that scam when the science is needed?
What has happened to every creationist that needed that ID science? Why
isn't ID even mentioned in the switch scam that you get from the guys
that sold you the ID scam?

In terms of intelligent design there never was a jury because a court
case was never called. No testable hypotheses were presented and
tested. There never was anything worth considering or even calling a
jury to decide. Demonstrate otherwise. Put up the testable hypotheses
and how they were tested.

It has to be pretty lame to be you at this time. What do you think
happened to the ID scam's international science society (ISCID). If the
jury is still out why did they give up and quit? What happened to the
Intelligent design network that was supposed to be an organization of
"academics" that supported the ID scam? Why do you think that those
organizations gave up after the bait and switch went down, and the
reason was obvious after Dover? With intelligent design in the name of
your organization is is pretty tough to bend over and take a switch scam
that doesn't even mention that ID ever existed. If there ever was a
competitive IDiot alternative to the real science why did Philip Johnson
(one of the guys that supposedly got the ID scam rolling) quit the ID
scam and admit that no such alternative existed at this time? Philip
Johnson is still alive and as far as I know he has never returned to
support the ID scam after making that admission.

So what do you think that you are doing at this time? You are over a
decade late to this party and making a fool of yourself.

Ron Okimoto

[Earle Jones27]

> best to provide the best explanation they can think of under that paradigm....

*
At this point, you need to give your definition of "plausible."

Do "plausible" explanations include the faith-based writings of
religious indoctrinations?

Does "plausible" include explanations that depend on the non-evidenced
existence of some intelligent designer that has neither been defined
nor described in any manner?

Who or what is this intelligent designer? If there is not a plausible
explanation based on a hundred years of physical and scientific
evidence, why should we consider this etherial and non-existent
intelligent designer?

earle
*

[Steady Eddie]

The Intelligent Designer is the God of the Bible, whose name is Jehovah.
He has used the Bible to communicate a brief account of his creation of the
Universe, and life on Earth.
His Word the Bible also tells us that Jehovah expects us to use our powers of
investigation and reason to come to the correct conclusion that Earth and the life on it was designed, and to give Him due praise and credit for His work.
Romans 1:19,20, New World Translation:
... what may be known about God is clearly evident among (deniers), for God
made it clear to them. For his invisible qualities are clearly seen from the
world`s creation onward, because they are perceived by the things made, even
his eternal power and Godship, so that they (deniers) are inexcusable.

Hebrews 3:4 says `Every house is constructed by someone, but he that constructed
all things is God.`

Revelation 4:11 says: `You are worthy, Jehovah our God, to receive the glory
and the honor and the power, because you created all things, and because of
your will they came into existence and were created.`

[Earle Jones27]

*
I asked you, Eddie, for your definition of 'plausible.'

You answer with some irrelevant quote from the Bible.

Does the word 'plausible' appear in the Bible?

earle
*

[Steady Eddie]

You don't even know what you asked with your own keyboard:

"Who or what is this intelligent designer?"

THAT was the question I was answering, not some red herring.

[Steady Eddie]

On Thursday, 16 July 2015 23:45:40 UTC-6, Earle Jones27 wrote:

My definition of "plausible" is synonymous with "operationally possible" in information theory.
That is, something that has been DEMONSTRATED to be possible.

I like the example from the video "Programming of Life" where it says:
If you say it is "possible" for two dice to end up balanced on their edges upon being rolled, you have to
DEMONSTRATE that this could happen, either by observation, or by inference to similar events occurring
in our uniform and consistent observation.

Now, a SCIENTISTS should not claim ANYTHING to be "possible", simply on the grounds that anything's, well, possible.
Rather, the SCIENTIFIC usage of the term "possible" is the special meaning of "operationally possible" or
"plausible".

So, in my opinion, "plausible" means "demonstrated to be possible" by some method.

[RonO]

Too bad Eddie, it looks like you have gone back to July and still
haven't found what you claimed exists. I am not perfect Eddie. I mess
up from time to time. The last that I recall was something about turtle
evolution, but you had nothing to do with that.

Keep looking. I want you to go back and determine just what kind of
person that you have been, and how senseless and dishonest it all has
been in your case.

Ron Okimoto

[Steady Eddie]

ID has the findings of real science.
And an open mind.

> >
> > What these researchers fail to realize is that the existence of mulit-functional proteins is yet more evidence of the handywork of a highloy
> > intelligent designer.
>
> Why? We can observe these duplications. We can even know some of the
> mechanisms by which they happen because we can take clonal cells and
> look before and after the event.

Okay, you might prove me wrong here -
Put up your DIRECT observations of these duplications occurring.

> We can look within species like humans and see

(read "speculate")

[Steady Eddie]

...crickets...

[RonO]

Eddie, eternal september does not tell you when someone is posting to an
old thread, at least the way I have it set up. I only see these type of
posts if I go to google to look something up.

ID was just a creationist scam run on creationist rubes like yourself.
Demonstrate that any ID science was ever accomplished. All you will
find for over a decade is the bait and switch going down. Where is the
wonderful ID science?

>
>>>
>>> What these researchers fail to realize is that the existence of mulit-functional proteins is yet more evidence of the handywork of a highloy
>>> intelligent designer.
>>
>> Why? We can observe these duplications. We can even know some of the
>> mechanisms by which they happen because we can take clonal cells and
>> look before and after the event.
>
> Okay, you might prove me wrong here -
> Put up your DIRECT observations of these duplications occurring.

They do the research in slngle celled organisms like yeast where they
have a single colony that has been derived from one organism and they
can do research on that culture and determine how it changes.

http://www.genetics.org/content/172/4/2211.full

Eddie you have gene duplications in your genome that I likely do not
have. Where did they come from?

>
>> We can look within species like humans and see
> (read "speculate")
>> that many such
>> duplications have occurred in the current population. We even have a
>> new name for them copy number variants (CNV) because they are so
>> numerous once we were able to sequence whole genomes and compare them.

It isn't speculation after it has been observed in the lab. We have
models to explain it, but that doesn't mean that it doesn't happen.

What a boneheaded IDiot.

Apologize for lying and get it over with.

Ron Okimoto

[Steady Eddie]

"Spontaneous duplications of large chromosomal segments have been experimentally demonstrated in yeast. HOWEVER, THE DYNAMICS OF INHERITANCE OF SUCH STRUCTURES AND THEIR EVENTUAL FIXATION IN POPULATIONS REMAIN LARGELY UNSOLVED."(emphasis mine)

Read your own science, idiot.
This statement proves that you have NO WAY OF KNOWING that these duplications work for evolution
the way you think they do.
It's called an ASSUMPTION until it becomes "largely solved".

> >> We can look within species like humans and see
> > (read "speculate")
> >> that many such
> >> duplications have occurred in the current population. We even have a
> >> new name for them copy number variants (CNV) because they are so
> >> numerous once we were able to sequence whole genomes and compare them.
> It isn't speculation after it has been observed in the lab.

DID YOU SEE THE GENE DUPLICATION HAPPENING IN THE LAB, IDIOT?

[RonO]

Idiot, no stupid degenerate idiot. Read the paper for comprehension.
You asked if we had observed gene duplication, and we have. Why would
we need all the answers? What a jerk Eddie. You lied. Apologize for
lying about me and get it over with.

What do you not get about what you quoted? What does "experimentally
demonstrated" mean? When you have the cells before and after the event
what do you have? Really, they start with clones of cells that do not
have the duplication and then they find rare mutations (duplications) in
newly reproduced cells. Why does that not count as observing gene
duplication?

QUOTE:
In a previous work, we developed a gene dosage selection assay to
recover spontaneous duplications from the right arm of chromosome XV in
a haploid yeast strain (Koszul et al. 2004).
END QUOTE:

These guys aren't just studying the after math of gene duplication, they
have developed assays to identify when gene duplications occur. That is
how they can find so many of them to study.

We did not know how common gene duplication was until we could sequence
whole genomes. Most gene duplications amount to nothing, just like most
other mutations. The fact is that they do happen and look what we can
tell after the fact.

>
>>>> We can look within species like humans and see
>>> (read "speculate")
>>>> that many such
>>>> duplications have occurred in the current population. We even have a
>>>> new name for them copy number variants (CNV) because they are so
>>>> numerous once we were able to sequence whole genomes and compare them.
>> It isn't speculation after it has been observed in the lab.
>
> DID YOU SEE THE GENE DUPLICATION HAPPENING IN THE LAB, IDIOT?

What a stupid idiot. Read the paper for comprehension. What else do
you need? It is just a fact that gene duplications happen.

Apologize for lying about me and apologize for the stupid and dishonest
juvenile behavior that you just exhibited. It took me less than 5
minutes to find this example, and there are others. You can use PubMed
and related articles to get more. Gene duplication is a fact of nature.
You can't keep it from happening.

Ron Okimoto

[Steady Eddie]

I agree that duplications of large chromosomal segments of yeast have been observed in the lab. Thank
you for the information.
Does this mean that these duplications were INHERITED, then became FIXED IN POPULATIONS, in order
for them to mutate into new, different instruction sets for building new proteins?

As the above quote FROM YOUR PAPER demonstrates, YOU DON'T KNOW.

So why have you been beaking off about how gene duplications PRODUCE NOVEL FUNCTIONS AND
STRUCTURES IN ORGANISMS?

[RonO]

So was it so hard to admit that you were wrong?

>
> I agree that duplications of large chromosomal segments of yeast have been observed in the lab. Thank
> you for the information.
> Does this mean that these duplications were INHERITED, then became FIXED IN POPULATIONS, in order
> for them to mutate into new, different instruction sets for building new proteins?

They are inherited just like any other mutation in your genome. You
have gene duplications that you have a chance of passing onto your children.

As the paper that I gave you indicates there is a difference in that
tandem duplications have a higher back reversion rate than their forward
mutation rate. This just means that duplications can be undone more
often than other mutations like base substitutions that would basically
have the same reversion rate as their mutation rate. The paper notes
that this higher reversion rate is nullified by translocating the
duplicated sequence to another chromosome, and this was also observed by
the researchers, so that they could do the analysis and come to that
conclusion.

I talked about this elevated reversion rate in another thread somewhere.
It is due to aberrant recombination. Genetic recombination happens
every meiosis at a certain frequency, and if the duplicated segments do
not match up correctly you can lose a copy. You can also gain a copy.
That is why we can explain things like the HOX tandem duplication. We
have observed how you gain and lose duplicated copies.

As other mutations can be fixed in the population so can duplications.
Neutral mutations are fixed basically at the rate of mutation, but if
the duplication has a selective advantage like the duplications of
starch metabolizing genes that you likely have if you are of Asian or
European descent (an adaptation to cereal grain agriculture) they can
increase rapidly in a population due to positive selection.

>
> As the above quote FROM YOUR PAPER demonstrates, YOU DON'T KNOW.

What don't we know?

>
> So why have you been beaking off about how gene duplications PRODUCE NOVEL FUNCTIONS AND
> STRUCTURES IN ORGANISMS?
>

Eddie, remember that estrogen receptor paper that you talked about in
one of your threads. There was a gene duplication, one copy acquired
two new mutations that altered the active site and allowed the receptor
to recognize a new hormone, both hormone receptors have duplicated many
times and do multiple different things in extant organisms. What don't
you understand. How do you think that the researchers were able to
backtrack and figure out the original protein sequence.

You were using that paper as an example of where two mutations were
required, but as Behe himself calculated those two mutations may have a
low probability of occurring, but would be expected to occur among the
number of organisms in a cubic meter of pond mud every generation.
Remember that calculation that came out during the Dover testimony?

The tRNA synthases required to make proteins are all duplicated from
just two original synthases, do you remember that example?

This is the type of real science that you are up against, and why ID is
just a scam.

Apologize for lying about me to another poster. You will likely feel
better about your lousy pathetic self. Just look at the pathetic junk
that you have resorted to doing, and you know that you were lying.

Ron Okimoto

[czeba...@gmail.com]

It seems like Eddie is trying to claim that some invisible being came along, did something mysterious and voila! a gene dupe. And since you didn't see it, it must be true.

gregwrld

[RonO]

On 11/29/2015 6:25 PM, czeba...@gmail.com wrote:
> It seems like Eddie is trying to claim that some invisible being came along, did something mysterious and voila! a gene dupe. And since you didn't see it, it must be true.
>
> gregwrld
>

You are giving Eddie too much credit. Eddie doesn't even have an
alternative that is what is the most stupid thing about his argument.

Ron Okimoto

[Bob Casanova]

On Sun, 29 Nov 2015 16:25:44 -0800 (PST), the following
appeared in talk.origins, posted by czeba...@gmail.com:

>It seems like Eddie is trying to claim that some invisible being came along, did something mysterious and voila! a gene dupe. And since you didn't see it, it must be true.

The classic, "We don't (yet) know exactly how this occurred,
therefore Goddidit."

Since science operates by investigation rather than by
dogma, the "yet" is assumed to equal "and never will".
--

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

[Steady Eddie]

Can you read?

> You were using that paper as an example of where two mutations were
> required, but as Behe himself calculated those two mutations may have a
> low probability of occurring, but would be expected to occur among the
> number of organisms in a cubic meter of pond mud every generation.
> Remember that calculation that came out during the Dover testimony?

No, I don't remember it. Please put up a link to it.

> The tRNA synthases required to make proteins are all duplicated from
> just two original synthases, do you remember that example?

No, I don't remember it. Please put up a link to it.

> This is the type of real science that you are up against, and why ID is
> just a scam.

This is the type of rhetoric you are famous for, but do you ever give a link or citation to your assertions?

[RonO]

Can you read? What was the paper about? They addressed the issue of
inheritance in that paper. What a boneheaded idiot IDiot. The quote is
just them telling you why they did the research. They wouldn't have
done the study if they didn't think that it was something that would be
useful to know.

>
>> You were using that paper as an example of where two mutations were
>> required, but as Behe himself calculated those two mutations may have a
>> low probability of occurring, but would be expected to occur among the
>> number of organisms in a cubic meter of pond mud every generation.
>> Remember that calculation that came out during the Dover testimony?
>
> No, I don't remember it. Please put up a link to it.

It was a year ago and bad memories tend to get lost on your part routinely.

https://groups.google.com/d/msg/talk.origins/oRdLd1bHccU/CqoaOBwVwwgJ

This is one example where I tried to explain the facts of life to you
about the Thorton paper that you put up.

https://groups.google.com/d/msg/talk.origins/1dUQUCClblo/tttmkeWoTlMJ

>
>> The tRNA synthases required to make proteins are all duplicated from
>> just two original synthases, do you remember that example?
>
> No, I don't remember it. Please put up a link to it.

You may still be posting to that translation thread. Just more running
away in denial on your part.

https://groups.google.com/d/msg/talk.origins/qsqGMhXeX-E/QYVAHG38JcUJ

>
>> This is the type of real science that you are up against, and why ID is
>> just a scam.
>
> This is the type of rhetoric you are famous for, but do you ever give a link or citation to your assertions?

They are the type of facts that you can only deal with by your stupid
denial of this type. How sad can you possibly be? What do you ever do
with the links and citations that I do put up, but run and come back
with more stupidity like this?

>
>> Apologize for lying about me to another poster. You will likely feel
>> better about your lousy pathetic self. Just look at the pathetic junk
>> that you have resorted to doing, and you know that you were lying.
>>
>> Ron Okimoto
>

Apologize for lying and get it over with. You know that you lied so why
carry on like this?

Really, "Can you read?" How sad is that when you obviously did not know
what the paper that you were quoting from was about?

Ron Okimoto