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Author Topic:   How novel features evolve #2
Tangle
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Posts: 9504
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Joined: 10-07-2011
Member Rating: 4.8


Message 1 of 402 (663325)
05-22-2012 10:17 AM


There was an interesting discussion started by RAZD on another thread here:
EvC Forum: How do "novel" features evolve?
about the evolution of novel features, but it got sidetracked by technical discussions about information theory and died an early death in summation mode.
There seemed to be some support for having another attempt at it but without getting into entropy, thermodynamics, information theory or other exotica. ie, let's stick to biology, and the simpler the better (for me at least.)
I think that if we could answer this challenge in an easily understandable way we could make some progress.
"I accept that natural selection does occur and that it can cause a population to change, but you need now to show me how the genome created those novel features because, until you do, I can say that the genome must have had them to start with."
My example was peppered moth observations that show selection for a trait can and does occur but doesn't answer the question about how the trait arose in the first place so that it could then be selected for.
The creationist could argue that the genome carries a complete set of genes that can be selected for when necessary. The biologist even has a name for this - it's called gene plasticity and in the example of the Italian Wall Lizard the claim that the novel feature evolved there - the cecal valve - could simply be an example of that.
So how do we progress from here?

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

Replies to this message:
 Message 3 by jar, posted 05-23-2012 10:14 AM Tangle has replied
 Message 4 by RAZD, posted 05-23-2012 10:44 AM Tangle has replied
 Message 6 by Wounded King, posted 05-23-2012 12:11 PM Tangle has not replied

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 5 of 402 (663335)
05-23-2012 11:36 AM
Reply to: Message 3 by jar
05-23-2012 10:14 AM


Re: Super Genome the Sequel?
I don't think it's necessary to claim a super genome, all that a creationist has to claim is that there's a butterfly genome and a lizard genome (etc) and that what natural selection is doing is swopping around the genes it already has in order to adapt to environmental change.
It all comes down to imperfect copies
Which is a claim that needs to be backed with evidence - and that's where it gets sticky. Because as far as I know, we can't trace a set of mutations in something big enough for a creationist to regard as immutable. Or can we? (The lizards look like a good bet to me.)

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

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 Message 3 by jar, posted 05-23-2012 10:14 AM jar has replied

Replies to this message:
 Message 7 by jar, posted 05-23-2012 12:23 PM Tangle has replied

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 8 of 402 (663349)
05-23-2012 1:12 PM
Reply to: Message 7 by jar
05-23-2012 12:23 PM


Re: Super Genome the Sequel?
Jar writes:
If the genome of a daughter is different than the parent, isn't that sufficient evidence?
Nope. Still H.sapiens and her hair colour was already in the H.sapiens genome etc etc etc

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

This message is a reply to:
 Message 7 by jar, posted 05-23-2012 12:23 PM jar has replied

Replies to this message:
 Message 9 by jar, posted 05-23-2012 2:50 PM Tangle has replied

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 11 of 402 (663360)
05-23-2012 3:40 PM
Reply to: Message 4 by RAZD
05-23-2012 10:44 AM


Re: DNA sequences and Phenotype selection
RAZD writes:
Personally I think we need to focus on the phenotype and selection forces, and that we need to look for further development that what has been discussed so far, with the dogs and with the lizards.
Certainly we need to look at phenotype, but I think we can accept selection pressures; or assume or ignore it. The problem isn't the motive, it's the method.
In my 48 hours on a creationist web site before I was chucked off, the word "inference" was used a lot. It would be good to show the smoking gun.

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

This message is a reply to:
 Message 4 by RAZD, posted 05-23-2012 10:44 AM RAZD has replied

Replies to this message:
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Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 12 of 402 (663361)
05-23-2012 3:47 PM
Reply to: Message 9 by jar
05-23-2012 2:50 PM


Re: Super Genome the Sequel?
Jar writes:
In the example of the doggies the daughter population showed a trait that had not been in the parent population, namely webbed feet.
Yes, but we know that the genes for webbed feet are already in the genome - they pop up regularly even in people. No-one is suggesting - I think - that a mutation causes the webbed feet?

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

This message is a reply to:
 Message 9 by jar, posted 05-23-2012 2:50 PM jar has replied

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Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 17 of 402 (663366)
05-23-2012 4:44 PM
Reply to: Message 16 by jar
05-23-2012 4:10 PM


Re: Super Genome the Sequel?
Jar writes:
If a Creationist does not want to accept the fact of Evolution, then evidence will seldom sway them.
I agree. But the more facts we have, the harder it is to deny. And anyway, I'd love to be able to demonstrate it from direct evidence myself just for its own sake.
N

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

This message is a reply to:
 Message 16 by jar, posted 05-23-2012 4:10 PM jar has replied

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Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


Message 28 of 402 (663414)
05-24-2012 11:46 AM
Reply to: Message 27 by Taq
05-24-2012 11:41 AM


Taq writes:
If a B-cell binds to an antigen then it is told to make more of that antibody and replicate. This is not anticipation. This is reaction.
It's also pretty damn cool

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

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 Message 27 by Taq, posted 05-24-2012 11:41 AM Taq has not replied

  
Tangle
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Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(1)
Message 32 of 402 (663429)
05-24-2012 2:53 PM


Chaps, can I suggest that we stick to Taq's mouse paper for a while. It seems to me that we have something there - a novel feature and an observed genetic change that appears causal. So what's wrong with it?
Z, let's not get sidetracked into speciation events - that's another topic entirely. and we needn't concern ourselves with a mechanism for the mutation unless we can agree that it has actually occurred. I don't want us to start chasing rabbits again.

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

  
Tangle
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Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(2)
Message 34 of 402 (663434)
05-24-2012 4:01 PM
Reply to: Message 31 by zaius137
05-24-2012 2:20 PM


Z writes:
I would say that this is only modification of existing alleles. What would you say this is?
This caught my eye in your post because it seemed to me that the modification of existing alleles is exactly what it is and exactly what we're looking for. Why do you shrug it off?

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

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 Message 31 by zaius137, posted 05-24-2012 2:20 PM zaius137 has not replied

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Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(2)
Message 37 of 402 (663496)
05-25-2012 4:00 AM
Reply to: Message 10 by Taq
05-23-2012 3:07 PM


Re: Melanism in Pocket Mice
I was relieved to read this in your paper, Taq:
A key problem in evolutionary biology is to connect genotype with phenotype for fitness-related traits (1, 2). Finding the genes underlying adaptation has been difficult for a number of reasons. First, it requires that we identify traits that are ecologically important and that we have some understanding of how these traits affect fitness in different environments. Second, phenotypic variation of ecological relevance has often been studied in species for which we have little genetic information, making the genetic basis of the traits difficult to analyze. For example, one of the best known cases of adaptation involves color morphs of the peppered moth, Biston betularia. Yet, after more than a half-century of study, the genes responsible for these color differences remain unknown (3). Finally, many fitness-related traits are quantitative and are unlikely to have a simple genetic basis. Because of these difficulties, the molecular basis for adaptation is known in only a handful of cases. Most involve either biochemical polymorphisms (4—6) or response to human disturbance, such as heavy metal tolerance in plants, insecticide resistance, warfarin resistance in rats, or antibiotic resistance (7), and in many cases, the specific nucleotide changes have not been identified.
I thought it was just me that was missing something - it turns out that finding direct evidence for mutation leading to new features is tough (but not impossible).
I suppose it does mean that finding the audit trail in genes for speciation is orders of magnitude more difficult and may never be seen.

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

This message is a reply to:
 Message 10 by Taq, posted 05-23-2012 3:07 PM Taq has replied

Replies to this message:
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Tangle
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Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(1)
Message 41 of 402 (663669)
05-26-2012 4:10 AM
Reply to: Message 40 by zaius137
05-26-2012 2:30 AM


Zaius writes:
Your statement implies that these existing alleles just magically appeared in the first place. They are in the right place at the right time to accept moderate modifications to create novel functionality. I have seen no evidence from you or anyone else demonstrating any new novel phylogenic functions arising in the genome except by genetic recombination.
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, even though they having demonstrated that the changes to the mice genes resulted in a change of colouration which was then selected for in the wild, 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?

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

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Tangle
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Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(2)
Message 45 of 402 (663849)
05-27-2012 3:43 AM
Reply to: Message 44 by zaius137
05-27-2012 2:11 AM


zaius writes:
Or is this pushing the thread outside the limits of discussion
Yes it is.
a convenient escape for the harder questions.
No it isn't. It's a necessary first step.
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?

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

This message is a reply to:
 Message 44 by zaius137, posted 05-27-2012 2:11 AM zaius137 has replied

Replies to this message:
 Message 46 by zaius137, posted 05-27-2012 2:41 PM Tangle has replied

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(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

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


(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:
 Message 48 by zaius137, posted 05-28-2012 2:04 PM zaius137 has replied

Replies to this message:
 Message 51 by Wounded King, posted 05-29-2012 8:59 AM Tangle has replied
 Message 54 by zaius137, posted 05-29-2012 4:04 PM Tangle has replied

  
Tangle
Member
Posts: 9504
From: UK
Joined: 10-07-2011
Member Rating: 4.8


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

This message is a reply to:
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