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Author Topic:   How novel features evolve #2
zaius137
Member (Idle past 2644 days)
Posts: 407
Joined: 05-08-2012


Message 46 of 402 (663887)
05-27-2012 2:41 PM
Reply to: Message 45 by Tangle
05-27-2012 3:43 AM


Tangle my friend..

So if you wouldn't mind answering my earlier question we might make faster progress.

If I understand you correctly, what your are saying now is that you DO accept that changes to alleles can lead to novel features.
But this isn't good enough because ......... it was a result of mixing together genes that already exist in the genome not creating an entirely new gene or set of genes.
Is this correct?

Creationists have always maintained the need for adaptation but the adaptation is not fixed permanently and irreversibly into the genome of a population (speciation). Creationists also believe that there are specific areas in genome that can accept this variation without fatal effects to the genome. We cannot deny that since the fall of mankind in the garden such deleterious mutations happen all the time but as you know humans are diploid and can absorb a heavy loading of the genome. These deleterious mutations may continue to propagate in a particular race of individuals and are not necessarily reversible when outside the adaptive mechanism of the genome (they persist because of the curse of the fall).

The burden of the Evolutionists have been to explain the connection between genotype and phenotype by a number of proposed mechanisms. One important principle is called “classic sweeps” which hopes that variations eliminate heterozygosity so that the change in phenotype is made permanent in the genome and irreversible in a breeding population (fixed permanently).

About fruit flies:

Empirical evidence has shown Darwinian evolution is inadequate in bolstering evolution by natural selection. Consider the following examining “Classic Sweeps” in fixation of traits in a population.

quote:
"Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficial mutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size."

http://www.arn.org/.../experimental_evolution_in_fruit_flies

In other words the old alleles remain present in subsequent generations and are not swept clean from subsequent generations. Stasis in a species is the observable evidence. Species of fruit flies have always been a species of fruit flies.

Fixation in the genome must be discussed when talking about “New and Unique traits appearing by evolution”.


This message is a reply to:
 Message 45 by Tangle, posted 05-27-2012 3:43 AM Tangle has replied

Replies to this message:
 Message 47 by Tangle, posted 05-27-2012 3:55 PM zaius137 has replied

  
Tangle
Member
Posts: 8487
From: UK
Joined: 10-07-2011
Member Rating: 2.5


(2)
Message 47 of 402 (663892)
05-27-2012 3:55 PM
Reply to: Message 46 by zaius137
05-27-2012 2:41 PM


Zalus writes:

Creationists have always maintained the need for adaptation etc etc

Maybe I didn't phrase the question correctly or you didn't understand it or maybe you're ahead of me. In any case, I'd just like this point cleared up before we move on.

We are looking at the mouse paper, do you accept that a mutation to a gene has occurred and that the mutation has given this mouse strain an advantage in its habitat which has been selected for?


Life, don't talk to me about life - Marvin the Paranoid Android

This message is a reply to:
 Message 46 by zaius137, posted 05-27-2012 2:41 PM zaius137 has replied

Replies to this message:
 Message 48 by zaius137, posted 05-28-2012 2:04 PM Tangle has replied

  
zaius137
Member (Idle past 2644 days)
Posts: 407
Joined: 05-08-2012


Message 48 of 402 (664008)
05-28-2012 2:04 PM
Reply to: Message 47 by Tangle
05-27-2012 3:55 PM


Tangle my friend,

Maybe I didn't phrase the question correctly or you didn't understand it or maybe you're ahead of me. In any case, I'd just like this point cleared up before we move on.
We are looking at the mouse paper, do you accept that a mutation to a gene has occurred and that the mutation has given this mouse strain an advantage in its habitat which has been selected for?

Maybe it is my problem in not being specific about my statements…

Talking specifically about the “mouse paper” I do commit to the following statements. I hope you are not expecting a yes or no about this. There were findings in the paper but I purpose the conclusions to be all wrong.

I do not believe that the authors of this “mouse paper” correctly identified all the genes and types of mutations involved or even a connection between the color adaptation and a molecular mechanism for the selection pressure of coat coloration.

Without doubt, some mutations add beneficial adaptations to the genome when they occur in the proper positions (I think everyone here can agree on that). The big question is exactly how many mutations are necessary and how many genes are involved to create these adaptations; new discoveries are now breaking news in genetics (the fruit fly citation).

http://www.genomeweb.com/...lution-fruit-fly-evolution-human

It is clear in your cited “mouse paper” that the authors are making assumptions that a single mutation to a single gene is changing coat color. The authors made further speculation that a different mutation in another gene in a separate group of mice was responsible for similar coloration change in that group. However, they drew their conclusions without identifying that particular gene or type mutation. In my opinion, this “mouse paper”, on that basis, is total nonsense.

If new studies with fruit flies is correct this single point mutation paradigm in a single gene to cause a change or the proposed permanent change is completely wrong (see “soft sweeps” in genetics). There is observed evidence that there are far more complicated connections between genes and mutations than evolutionists currently understand. Evolution in fruit flies is inhibited by these new findings, which only demonstrates the claims made by creationists all along.


This message is a reply to:
 Message 47 by Tangle, posted 05-27-2012 3:55 PM Tangle has replied

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Dr Adequate
Member (Idle past 286 days)
Posts: 16112
Joined: 07-20-2006


(2)
Message 49 of 402 (664013)
05-28-2012 3:40 PM
Reply to: Message 48 by zaius137
05-28-2012 2:04 PM


Have you ever noticed that creationists only know what they've been claiming "all along" just after evolutionists tell them what the facts are?

One pictures the scene at Creationist HQ.

BJ: Hey, Jim-Bob!
JB: Yes, Bobby-Joe?
BJ: You'll never guess what we been claimin' all along this time!
JB: Reckon you're right there, I never does know what we been a-claimin' all along.
BJ: Well, we all do have been claimin' ... wait, I got it written down right here ... seems like this week we been claimin' all along that ... uh ... if scientists investigate the genetic changes underlying the phenotypic adaptations laboratory fruit-flies have undergone as a result of their lineage being kept in a laboratory environment for sixty years or so, they will find that few if any of those changes will be attributable to a classic selective sweep.
JB: Do you know what all them big words are a-meanin'?
BJ: Naw, but it don't matter. Jus' remember that we been claimin' it all along.
JB: Since when?
BJ: Startin' right now!
JB: Praise Jesus!

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


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Tangle
Member
Posts: 8487
From: UK
Joined: 10-07-2011
Member Rating: 2.5


(2)
Message 50 of 402 (664015)
05-28-2012 3:54 PM
Reply to: Message 48 by zaius137
05-28-2012 2:04 PM


zaius writes:

I hope you are not expecting a yes or no about this.

yup, I was. it seems black and white to me.

I do not believe that the authors of this “mouse paper” correctly identified all the genes and types of mutations involved ..........

That would be a no then. (Like I said, black and white.)
What evidence do you have to say that they haven't identified the genes necessary for the colour change. They did the work, they think they have, they have presented their evidence - why do you disagree? You need to be specific here.

.........or even a connection between the color adaptation and a molecular mechanism for the selection pressure of coat coloration.

The selection pressure is natural selection and the molecular mechanism is sexual reproduction. Maybe it's too obvious? If you know of any other reason why brown mice live on brown rocks and beige mice live on beige rocks, now is the time to mention it.

Edited by Tangle, : Spelling....


Life, don't talk to me about life - Marvin the Paranoid Android

This message is a reply to:
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Replies to this message:
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Wounded King
Member (Idle past 3329 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 51 of 402 (664130)
05-29-2012 8:59 AM
Reply to: Message 50 by Tangle
05-28-2012 3:54 PM


The selection pressure is natural selection and the molecular mechanism is sexual reproduction.

This is a really bad answer to an admittedly badly constructed question.

Natural selection is not a selective pressure itself, it is a term which captures the action of all the varied selective pressures acting upon a population. In the paper the authors suggest that the relevant selective pressure acting on coat colour is predation, principally by owls.

Secondly sexual reproduction is hard to class as a molecular mechanism and is also not a very tenable explanation for the origin of these mutations. Are you suggesting that the 4 separate Mc1r mutations that were identified as highly associated with the melanic phenotype were brought together to form this trait due to allelic recombination?

The actual molecular mechanism giving rise to these mutations originally was probably any one of a number that cause point mutations, although the fact that 3 of the changes are C->T transitions (see Fig. 3) suggests that deamination could have been an important factor.

TTFN,

WK


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Tangle
Member
Posts: 8487
From: UK
Joined: 10-07-2011
Member Rating: 2.5


Message 52 of 402 (664159)
05-29-2012 2:26 PM
Reply to: Message 51 by Wounded King
05-29-2012 8:59 AM


Wounded King writes:

This is a really bad answer to an admittedly badly constructed question.

Sorry boss :-)

Natural selection is not a selective pressure itself, it is a term which captures the action of all the varied selective pressures acting upon a population. In the paper the authors suggest that the relevant selective pressure acting on coat colour is predation, principally by owls.

I did think that it was obvious that predation was the selection pressure - ie natural selection at work. (Particularly as it's spelled out in the paper and heavily implied in my "If you know of any other reason why brown mice live on brown rocks and beige mice live on beige rocks, now is the time to mention it." remark.)

But I suppose it doesn't harm to be precise.

Secondly sexual reproduction is hard to class as a molecular mechanism and is also not a very tenable explanation for the origin of these mutations. Are you suggesting that the 4 separate Mc1r mutations that were identified as highly associated with the melanic phenotype were brought together to form this trait due to allelic recombination?

I have no opinion on the origin the mutation and didn't express one - that's well above my pay grade. My reference to sexual reproduction is as an answer to his - as you say, badly expressed - request for a molecular mechanism "for the selection pressure of coat coloration"

Which I took to mean something like "how does selection pressure create a molecular mechanism to transmit the genes for coat colour to create a brown population.

Sexual reproduction is the molecular method used to transmit the genes that natural selection (via predation) has selected into the next generation.


Life, don't talk to me about life - Marvin the Paranoid Android

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RAZD
Member (Idle past 640 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 53 of 402 (664161)
05-29-2012 2:41 PM
Reply to: Message 52 by Tangle
05-29-2012 2:26 PM


Hi Tangle,

But I suppose it doesn't harm to be precise.

Especially in debates like this where some people have trouble comprehending the basic concepts (for whatever reason of many possibles).

Sexual reproduction ...

Is also part of sexual selection and thus of natural selection, which can lead to confusions as well. Better to talk about allelic recombination with errors and other random mutations as the source/s.

One of the problems here is the creationist "clutching at straws" assertion that the particular gene sequence comes from "storage" somewhere else on the genome (ie - zaius137's comment about whether or not the whole genome was sequenced).

This of course ignores the fact that mutations are random and not all mice got the mutations.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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zaius137
Member (Idle past 2644 days)
Posts: 407
Joined: 05-08-2012


Message 54 of 402 (664171)
05-29-2012 4:04 PM
Reply to: Message 50 by Tangle
05-28-2012 3:54 PM


Tangle my friend….
The selection pressure is natural selection and the molecular mechanism is sexual reproduction. Maybe it's too obvious? If you know of any other reason why brown mice live on brown rocks and beige mice live on beige rocks, now is the time to mention it.

Unfortunately, you mix up what comes first in selective pressure. You see there must be certain coloration of mice first before there is any kind of selection to take place. Therefore, if you talk about sexual selection then the mutation or alleles are already expressed in the population and all the predators have to do is select those individuals that do not express the beneficial coloration (Concentration of specific alleles).
You see mouse coloration is pre –existing so you cannot say it has arisen because of natural selection. Remember, “survival of the fittest is not creation of the fittest”.

Let’s see some ware in this thread one of has claimed that the genetic structure was “pre-existing. Who was that?

Now you have a population of selected individuals with concentrations of beneficial alleles for camouflage. Was the development of beneficial coloration a “new and novel trait”? No because it had to show up before selection could even work on it. Is other populations of this species devoid of these alleles? No again, because other members occasionally show up with the desired coat color under lower selective pressure (or neutral pressure) because of Mendelian genetics.

Again the crux of your argument must consider fixation of these mutations in a population before you can actually say these “Novel Traits” arose and are not just deformed individuals.

By the way, when I refer to molecular mechanisms it is not sexual reproduction.

quote:
Environmental stresses and stimuli cannot exercise the creative causation of highly complex pre-coded genetic information that underlies irreducibly complex systems of adaptation.

http://www.icr.org/article/6727/
Keep the thought process going there is always room for one more creationist around here.

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jar
Member
Posts: 33893
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.8


(1)
Message 55 of 402 (664174)
05-29-2012 4:19 PM
Reply to: Message 54 by zaius137
05-29-2012 4:04 PM


the mutation comes first.
Natural selection always operates after the fact, it never causes any change.

Anyone so limited that they can only spell a word one way is severely handicapped!

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Tangle
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From: UK
Joined: 10-07-2011
Member Rating: 2.5


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Message 56 of 402 (664177)
05-29-2012 4:39 PM
Reply to: Message 54 by zaius137
05-29-2012 4:04 PM


The order things happen in is:

Mutation of a gene that affects hair colouration occurs in a mouse
Mouse can sit on a dark rock without being eaten by predators
Mouse mates and passes on its brown genes
More brown mice are born and can sit on brown rocks unmolested
Any beige mice born are eaten by preditors
Brown mice breed
Etc

ie the standard theory.

The question we're trying to answer here is whether we can identify the gene that changed. The guys that did the work think they have and have presented their evidence. If you think differently you have to show why.


Life, don't talk to me about life - Marvin the Paranoid Android

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jar
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Posts: 33893
From: Texas!!
Joined: 04-20-2004
Member Rating: 2.8


(4)
Message 57 of 402 (664180)
05-29-2012 5:04 PM
Reply to: Message 54 by zaius137
05-29-2012 4:04 PM


How novel features evolve
There is a population of mice.

The mice have baby mice.

Not all the copies are perfect, some have mutations.

Some baby mice are tan.

Some baby mice are dark gray.

Some baby mice are bright pink with yellow and green stripes.

The baby mice that are tan go out to eat and play. Those that stay on the tan rocks find lots of food and have fun playing. They grow up and marry the mouse next door and have lots of pretty tan baby mice.

Those that play on the dark gray rock though get eaten by predators and don't get to play or have fun or grow up to marry the mouse next door and have lots of pretty tan baby mice.

The baby mice that are dark gray go out to eat and play. Those that stay on the dark gray rocks find lots of food and have fun playing. They grow up and marry the mouse next door and have lots of pretty dark gray baby mice.

Those that play on the tan rock though get eaten by predators and don't get to play or have fun or grow up to marry the mouse next door and have lots of pretty dark gray baby mice.

The baby mice that are bright pink with yellow and green stripes go out to eat and play. They get eaten.

Soon there are two populations of mice, tan mice and dark gray mice and bad little mice are told, "If you do that again you will turn pink with yellow and green stripes and get eaten! And it will make you go blind too!".


Anyone so limited that they can only spell a word one way is severely handicapped!

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Taq
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Posts: 8519
Joined: 03-06-2009


(3)
Message 58 of 402 (664181)
05-29-2012 5:28 PM
Reply to: Message 54 by zaius137
05-29-2012 4:04 PM


You see there must be certain coloration of mice first before there is any kind of selection to take place.

And that is exactly what happened. The mutations in MC1R produced novel coloration that was then selected for. Here is the picture of the two different colorations on the two substrates. It is not that hard to figure out why there is selective pressure through predation:

You see mouse coloration is pre –existing so you cannot say it has arisen because of natural selection.

We are saying that it came about through mutation. That is the whole point. Mutations produce novel phenotypes which are then selected for, otherwise known as evolution. Have you not been listening? This is like the 3rd time I have said this in this thread.

Was the development of beneficial coloration a “new and novel trait”? No because it had to show up before selection could even work on it.

That is a howler, and a symptom of some very serious denial. A novel trait is a trait that was not in the population prior to that point. Once the mutation/s occurred, it was a novel trait. Whether it was selected for has nothing to do with whether it is novel or not. Once more with feeling . . . selection has NOTHING to do with whether a trait is novel or not.

Again the crux of your argument must consider fixation of these mutations in a population before you can actually say these “Novel Traits” arose and are not just deformed individuals.

Novel traits do not need to be fixed in a population in order to be novel.

Environmental stresses and stimuli cannot exercise the creative causation of highly complex pre-coded genetic information that underlies irreducibly complex systems of adaptation.

Evidence please.


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RAZD
Member (Idle past 640 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 59 of 402 (664196)
05-29-2012 7:39 PM
Reply to: Message 55 by jar
05-29-2012 4:19 PM


Re: the mutation comes first.
Hi Jar

Natural selection always operates after the fact, it never causes any change.

It seems so simple, but it seems some people can't grasp it ... perhaps because it is so simple.

That's one reason for this graphic:

It just keeps going around and around ... and whenever you look, evolution is found ...

The only way out of the feedback loop is when all the offspring die before reproduction -- ie extinction happens.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 55 by jar, posted 05-29-2012 4:19 PM jar has seen this message

  
RAZD
Member (Idle past 640 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 60 of 402 (664198)
05-29-2012 7:50 PM
Reply to: Message 58 by Taq
05-29-2012 5:28 PM


another point ...
Hi Taq, nice post.

Loved the "peppered moth" style photos ...

We are saying that it came about through mutation. That is the whole point. Mutations produce novel phenotypes which are then selected for, otherwise known as evolution. Have you not been listening? This is like the 3rd time I have said this in this thread.

Another point to the whole issue is that a novel trait may be deleterious in the "home" ecology, but allow the individual to prosper in a neighboring ecology ... as here with the different colored rocks.

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.

The selection of traits will be different in different ecologies where the opportunities and challenges are different.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

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