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Author Topic:   How novel features evolve #2
Tangle
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Message 1 of 402 (663325)
05-22-2012 10:17 AM


There was an interesting discussion started by RAZD on another thread here:

http://www.evcforum.net/dm.php?control=msg&t=16241

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 responded
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Message 2 of 402 (663327)
05-23-2012 9:51 AM


Thread Copied from Proposed New Topics Forum
Thread copied here from the How novel features evolve #2 thread in the Proposed New Topics forum.
    
jar
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Message 3 of 402 (663330)
05-23-2012 10:14 AM
Reply to: Message 1 by Tangle
05-22-2012 10:17 AM


Super Genome the Sequel?
Is this another hunt for the super genome? I thought we put that absurdity to bed long ago?

We have come a long way in a fairly short period of time in sequencing various genomes. There are grape and cow and human and ancient human and neanderthal and bee and chimp genome sequencing projects and one factor has become pretty much a universal characteristic and that is that the genomes can be identified.

Send a lab an unknown sample and they send back a short note saying "That's a goat." or "That's a human." or "That's a elm tree".

We have samples from ancient folk and modern folk, from here and from there.

Novel features evolve over time in populations by changes in the genome that then get filtered by natural selection.

It all comes down to imperfect copies.


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

This message is a reply to:
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RAZD
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Message 4 of 402 (663333)
05-23-2012 10:44 AM
Reply to: Message 1 by Tangle
05-22-2012 10:17 AM


DNA sequences and Phenotype selection
Hi Tangle,

Hopefully we can keep this one focused on the development of novel features.

The creationist could argue that the genome carries a complete set of genes that can be selected for when necessary. ...

In a sense this is true, just because there are only 4 letters used in DNA and sequences are so long, that the likelihood of a specific sequence already existing is high.

It is also difficult to point out where a specific mutation makes a new combination in a particular location.

The creationist\idologist argument, however, is a post hoc ergo propter hoc fallacy that conveniently ignores all the other mutations that don't result in new traits or beneficial results and all the individuals in the population that are not "gifted" with the mutation.

The counter argument to the creationist\idologist supergenome claim is that not all the population select the new gene to be generated, so this shows that the mutation is not generated or designed mutation but a random one.

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.

Selection operates on the phenotype rather than the genotype, and while the phenotype is the expression of the genotype not all of the genotype is expressed in any specific individual.

For this thread I would suggest that the cause (random or designed) of a mutation is not an issue for discussion, rather that we start with accepting that a different mutation exists in the population that is expressed in the phenotype.

... 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?

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.

These have initiated a potential for new traits, but perhaps we need to discuss speciation (phyletic and divergent), and possibly even the formation of genus or family level diversity.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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This message is a reply to:
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Tangle
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Posts: 6248
From: UK
Joined: 10-07-2011
Member Rating: 2.4


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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Wounded King
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Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 6 of 402 (663338)
05-23-2012 12:11 PM
Reply to: Message 1 by Tangle
05-22-2012 10:17 AM


Others are dealing with some of the basic issues you have brought up so I thought I might look in more detail with a specific case, the Melanic Moths.

Since the last time this topic was discussed here on EvC a couple of new papers have been published, both from the same lab.

The first, (van't Hof and Saccheri, 2010) took what is known as a 'candidate gene' approach, looking at genes known to be associated with melanisation biosynthesis in other insects. They looked at 16 'candidates' and found that none of them were associated with the locus linked to melanism in Biston betularia.

I would suggest that the very fact that there are several different gene candidates associated with melanism would argue against the sort of front loading scenario you suggested. Surely if there was a pre-existing adaptive program in insect we would expect it to target the same gene, if no tproduce the exact same mutation, in the various instances of melanism that we have studied?

The second paper follows on by going through further genetic crossing to refine the localisation of the region linked to the carbonaria phenotype (van't Hof et al., 2011). In this paper they manage to narrow the region down to a 200kb stretch, still quite large, which is associated with wing patterning. This paper raises another issue with the call for some sort of definitive proof for the origin of a novel feature. When they arise in closely associated populations in which there is reduced or no reproductive isolation then there is a possibility for introgression to reintroduce genetic variation into the wild type population making it very hard to distinguish this introgression from existing low frequency standing variation.

I find it hard to believe that whatever the genetic basis within that 200KB stretch that it will be something impossible to produce from known mutational mechanisms. That said it is hard to see how outwith catching such a feature arising under laboratory conditions the exact nature of the actual causative mutation can be known, we are really limited to making informed inferences from known mechanisms in the most part, but if such mechanisms are sufficient I don't really see the need for any sort of special pleading.

TTFN,

WK

P.S. What you call gene plasticity is normally called phenotypic plasticity .


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jar
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Posts: 30934
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.3


Message 7 of 402 (663340)
05-23-2012 12:23 PM
Reply to: Message 5 by Tangle
05-23-2012 11:36 AM


Re: Super Genome the Sequel?
If the genome of a daughter is different than the parent, isn't that sufficient evidence?

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

This message is a reply to:
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Tangle
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Posts: 6248
From: UK
Joined: 10-07-2011
Member Rating: 2.4


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

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 Message 7 by jar, posted 05-23-2012 12:23 PM jar has responded

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jar
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Posts: 30934
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.3


Message 9 of 402 (663356)
05-23-2012 2:50 PM
Reply to: Message 8 by Tangle
05-23-2012 1:12 PM


Re: Super Genome the Sequel?
In the example of the doggies the daughter population showed a trait that had not been in the parent population, namely webbed feet.

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

This message is a reply to:
 Message 8 by Tangle, posted 05-23-2012 1:12 PM Tangle has responded

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Taq
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(2)
Message 10 of 402 (663358)
05-23-2012 3:07 PM


Melanism in Pocket Mice
Found an article that may be of value:

quote:
Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5268-73. Epub 2003 Apr 18.
The genetic basis of adaptive melanism in pocket mice.
Nachman MW, Hoekstra HE, D'Agostino SL.
SourceDepartment of Ecology and Evolutionary Biology, Biosciences West Building, University of Arizona, Tucson, AZ 85721, USA. nachman@u.arizona.edu

Abstract
Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here, we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice, Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However, populations of dark (melanic) mice are found on dark lava, and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene, Mc1r, that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly, another melanic population of these mice on a different lava flow shows no association with Mc1r mutations, indicating that adaptive dark color has evolved independently in this species through changes at different genes.


Full paper can be found here:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC154334/

Another interesting quote from the paper:

quote:
In most places, these mice have a sandy dorsal pelage and white underbelly, and they inhabit light-colored rocks. In several different regions, however, these mice are found on lava flows. The mice from these lava sites are typically melanic, with dark-colored dorsal hairs and white underbellies. Most of the lava flows are surrounded by light-colored substrate and are isolated from one another by hundreds of kilometers, raising the possibility that melanic mice have evolved independently on different lava flows.
emphasis mine


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Tangle
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From: UK
Joined: 10-07-2011
Member Rating: 2.4


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

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Tangle
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Posts: 6248
From: UK
Joined: 10-07-2011
Member Rating: 2.4


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

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jar
Member
Posts: 30934
From: Texas!!
Joined: 04-20-2004
Member Rating: 1.3


Message 13 of 402 (663362)
05-23-2012 3:53 PM
Reply to: Message 12 by Tangle
05-23-2012 3:47 PM


Re: Super Genome the Sequel?
HUH?

How do we know that the genes for webbed feet were in the parent doggie population?


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

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Taq
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Member Rating: 3.4


Message 14 of 402 (663363)
05-23-2012 3:54 PM
Reply to: Message 12 by Tangle
05-23-2012 3:47 PM


Re: Super Genome the Sequel?
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?

Dachsunds were possibly mentioned in the previous iteration of this thread, and they are worth mentioning here again. Dachsunds have achondroplasia, otherwise known as dwarfism. It is caused by a mutation in the FGFR3 gene, just as it is in humans. Presumably, the wild ancestors of dachsunds did not carry this mutation. As far as I know, there is not a wild population of wolves with stunted legs.


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Taq
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Posts: 7594
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Member Rating: 3.4


(1)
Message 15 of 402 (663364)
05-23-2012 3:56 PM
Reply to: Message 13 by jar
05-23-2012 3:53 PM


Re: Super Genome the Sequel?
How do we know that the genes for webbed feet were in the parent doggie population?

The question is whether webbed feet are heritable or not. It could be argued that some webbed feet are due to poor development and not genetics (e.g. Thalidomide). However, webbed feet breed true in many dog breeds so I think it is safe to assume that it is heritable in that case.


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