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Author Topic:   Do only advantageous mutations fuel evolution?
Huntard
Member (Idle past 467 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


Message 16 of 28 (499534)
02-19-2009 5:30 AM
Reply to: Message 15 by Darwinist
02-19-2009 5:19 AM


Darwinist writes:

But how then, if a mutation is beneficial in one environment, but deleterious in another, do we define exactly what an advantageous mutation is?


That all depends on teh environment.


I hunt for the truth

What you can do in my country and get away with:

Softdrugs? Legal!
Legal drinking age? 16!
Birth control (the pill)? Free!
Gay marriage? Legal!
Abortion? Legal!
Euthanasia? Legal!
Age of consent? 16 (14 if you have the parents permission)!

Yep, only one way down for us!


This message is a reply to:
 Message 15 by Darwinist, posted 02-19-2009 5:19 AM Darwinist has not yet responded

    
Parasomnium
Member (Idle past 868 days)
Posts: 2191
Joined: 07-15-2003


Message 17 of 28 (499536)
02-19-2009 5:40 AM
Reply to: Message 15 by Darwinist
02-19-2009 5:19 AM


Hindsight
Well, clearly a mutation can only be called advantageous or deleterious with hindsight. A mutation is advantageous if it has conferred (note the the use of the present perfect tense here) an advantage to the organism.


"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.

Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

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shalamabobbi
Member (Idle past 1021 days)
Posts: 397
Joined: 01-10-2009


Message 18 of 28 (499537)
02-19-2009 5:51 AM
Reply to: Message 15 by Darwinist
02-19-2009 5:19 AM


it's relative
But how then, if a mutation is beneficial in one environment, but deleterious in another, do we define exactly what an advantageous mutation is?

That which survives in an environment is beneficial by definition. That which perishes in an environment is deleterious by definition.
When you go shopping you pick the best fruits and vegetables available to purchase.
It is all relative to what else is around to compete.
I might be able to kick snot on an elementary school kid(deleterious) but be placed in my casket by Mike Tyson(beneficial).
Again as I understand it.
This message is a reply to:
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Darwinist
Junior Member (Idle past 3688 days)
Posts: 22
From: Two Rocks, Western Australia
Joined: 02-15-2009


Message 19 of 28 (499539)
02-19-2009 6:15 AM
Reply to: Message 18 by shalamabobbi
02-19-2009 5:51 AM


Re: it's relative
Is there then, no real such thing as a netral mutation?


Always wanting to hear other peoples opinions about God and evolution. Email me.
This message is a reply to:
 Message 18 by shalamabobbi, posted 02-19-2009 5:51 AM shalamabobbi has not yet responded

Replies to this message:
 Message 20 by Parasomnium, posted 02-19-2009 7:10 AM Darwinist has not yet responded
 Message 21 by Wounded King, posted 02-19-2009 7:10 AM Darwinist has not yet responded

    
Parasomnium
Member (Idle past 868 days)
Posts: 2191
Joined: 07-15-2003


Message 20 of 28 (499552)
02-19-2009 7:10 AM
Reply to: Message 19 by Darwinist
02-19-2009 6:15 AM


Re: it's relative
Darwinist writes:

Is there then, no real such thing as a netral mutation?

That's too hasty a conclusion. Neutral mutations are possible. For example, there is such a thing as junk DNA, which is generally not expressed. How this junk DNA got into the genome is another story, but if a mutation happens in a piece of junk DNA, nothing happens as a result of it.

Another example of a neutral mutation would be a mutated codon that codes for the same amino acid as the original codon. Take the amino acid Alanine for example. The codon GCA codes for it. If the A is mutated into a G you get GCG. This also codes for Alanine. The resulting protein would be the same in either case, and you wouldn't notice the mutation in the organism that has it.


"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.

Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 19 by Darwinist, posted 02-19-2009 6:15 AM Darwinist has not yet responded

Replies to this message:
 Message 22 by Wounded King, posted 02-19-2009 7:27 AM Parasomnium has responded

  
Wounded King
Member (Idle past 2267 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 21 of 28 (499553)
02-19-2009 7:10 AM
Reply to: Message 19 by Darwinist
02-19-2009 6:15 AM


Re: it's relative
I think that Shalamabobi is mis-stating the case by oversimplifying it. There are reasons why neutral and even deleterious mutations can survive in a population, such as genetic drift. Similarly beneficial mutations can be lost by drift. But it is true that what we consider beneficial mutations are those that tend to increase in frequency in a population due to selection, potentially up to the point of fixation.

The only way to actually measure the beneficial effect of a mutation is from post-hoc measurements as Parasomnium pointed out.

Most mutations are considered neutral, or nearly neutral, but I would suggest it is not possible to definitively show that there is no possible environment in which a particular mutation might have some beneficial, or deleterious, effect. It is however possible to identify many mutations which have little or no likelihood of having an effect, such as in-frame nucleotide substitutions in a protein coding gene which do not affect the amino acid sequence they code for. Even as I write this I am thinking of scenarios where such a mutation could indeed be non-neutral, but I still think there are lots of cases where we can be confident that the mutation will be neutral in most forseeable environments.

TTFN,

WK


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Wounded King
Member (Idle past 2267 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 22 of 28 (499556)
02-19-2009 7:27 AM
Reply to: Message 20 by Parasomnium
02-19-2009 7:10 AM


nit-picking
For example, there is such a thing as junk DNA, which is generally not expressed. How this junk DNA got into the genome is another story, but if a mutation happens in a piece of junk DNA, nothing happens as a result of it.

Expression is not the be all and end all of genomic function. There are probably multiple non-expressed sites in what has been considered putative junk DNA which have a functional role, one already identified group of such regions are the 'conserved noncoding elements' (CNEs)(Woolfe and Elgar, 2008). Although as yet the functional roles of all these regions are not clear some have been shown to mediate regulation of nearby genes (Sabherwal et al., 2007).

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 20 by Parasomnium, posted 02-19-2009 7:10 AM Parasomnium has responded

Replies to this message:
 Message 23 by Parasomnium, posted 02-19-2009 7:41 AM Wounded King has responded

    
Parasomnium
Member (Idle past 868 days)
Posts: 2191
Joined: 07-15-2003


Message 23 of 28 (499557)
02-19-2009 7:41 AM
Reply to: Message 22 by Wounded King
02-19-2009 7:27 AM


Re: nit-picking
Wounded King writes:

Although as yet the functional roles of all these regions are not clear some have been shown to mediate regulation of nearby genes (Sabherwal et al., 2007).

Wouldn't that be a form of expression as well, although indirect?


This message is a reply to:
 Message 22 by Wounded King, posted 02-19-2009 7:27 AM Wounded King has responded

Replies to this message:
 Message 24 by Wounded King, posted 02-19-2009 8:03 AM Parasomnium has responded

  
Wounded King
Member (Idle past 2267 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 24 of 28 (499564)
02-19-2009 8:03 AM
Reply to: Message 23 by Parasomnium
02-19-2009 7:41 AM


Re: nit-picking
Its the regulation of expression but the sequences themselves are never expressed.

You might argue that as functional elements these aren't junk DNA but unfortunately the term is so plastic that there is no easy way to draw a distinct line between what is and what isn't. We suspect that most CNEs have function (or else why are they conserved?) but is conservation enough to mean that a region should no longer be considered junk?

Personally, I don't like the term 'junk DNA'. Its especially unfortunate that so many creationists/IDists seem to have decided that somehow some 'junk DNA' being functional is proof of (divine) design.

TTFN,

WK


This message is a reply to:
 Message 23 by Parasomnium, posted 02-19-2009 7:41 AM Parasomnium has responded

Replies to this message:
 Message 25 by Parasomnium, posted 02-19-2009 8:43 AM Wounded King has responded

    
Parasomnium
Member (Idle past 868 days)
Posts: 2191
Joined: 07-15-2003


Message 25 of 28 (499571)
02-19-2009 8:43 AM
Reply to: Message 24 by Wounded King
02-19-2009 8:03 AM


Re: nit-picking
Its the regulation of expression but the sequences themselves are never expressed.

If the raison d'etre of some piece of DNA is the regulation of neighboring pieces, then if it does so, that would constitute its expression, right? (We are nit-picking after all... Just ignore this.)

[W]hy are [CNEs] conserved?

Because they're good at causing themselves to be copied? Most "functional" genes use the complete organism as a means to get themselves copied and spread around. Maybe the CNEs are just hitching a ride? (Selfish gene talk, Dawkins and all that.)


This message is a reply to:
 Message 24 by Wounded King, posted 02-19-2009 8:03 AM Wounded King has responded

Replies to this message:
 Message 26 by Wounded King, posted 02-19-2009 9:55 AM Parasomnium has not yet responded

  
Wounded King
Member (Idle past 2267 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 26 of 28 (499587)
02-19-2009 9:55 AM
Reply to: Message 25 by Parasomnium
02-19-2009 8:43 AM


Re: nit-picking
If the raison d'etre of some piece of DNA is the regulation of neighboring pieces, then if it does so, that would constitute its expression, right? (We are nit-picking after all... Just ignore this.)

I can't really ignore this, it totally redefines the whole concept of gene expression. A gene is 'expressed' when it is transcribed as mRNA from its DNA template, and in canonical cases then translated into protein. To use 'expressed' in some other way is only going to confuse any familiar with molecular biology. You seem to be conflating gene expression and function.

Because they're good at causing themselves to be copied? Most "functional" genes use the complete organism as a means to get themselves copied and spread around. Maybe the CNEs are just hitching a ride? (Selfish gene talk, Dawkins and all that.)

Being copied is a distinct mechanism from being conserved. There are some 'junk' elements that lend themselves to increased copying, especially highly repetitive sequences where slippage can occur leading to duplications, but CNEs are usually identified from datasets where such repetitive elements have already been screened out. There still needs to be something acting to maintain the conserved sequence from simply degrading. These sequences are not like ERVs or other remnant proto-viral sequences which can sometimes proliferate through reinfection.

If this were merely a case of nearby sequences hitching a ride with selected genes then why do CNEs form islands of such high conservation, why aren't the other nearby sequences conserved?

The fact that we are identifying regulatory functions for CNEs suggests that what is going on is more directly relevant to organismal development/evolution than an artifact of genetic hitchhiking.

TTFN,

WK


This message is a reply to:
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shalamabobbi
Member (Idle past 1021 days)
Posts: 397
Joined: 01-10-2009


Message 27 of 28 (499636)
02-19-2009 2:05 PM
Reply to: Message 21 by Wounded King
02-19-2009 7:10 AM


Re: it's relative
I think that Shalamabobi is mis-stating the case by oversimplifying it.

That would be because shalamabobbi doesn't know that much about it yet. Thanks for all the great input. This site has been very helpful and sets a very high standard. Not all of us are unappreciative of the time spent here by busy scientists. I alas am a lowly engineer but the choice was sort of a toss up for me.
This message is a reply to:
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olivortex
Member (Idle past 2950 days)
Posts: 70
From: versailles, france
Joined: 01-28-2009


Message 28 of 28 (499650)
02-19-2009 3:46 PM


yes.
I think some of the obtuse people i have discussed with on the evolution topic should give this forum a try!

You go quite in the core of the matter here :)


    
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