Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 79 (8964 total)
46 online now:
PaulK, Tangle, xongsmith (3 members, 43 visitors)
Newest Member: javier martinez
Post Volume: Total: 872,990 Year: 4,738/23,288 Month: 1,643/1,286 Week: 310/615 Day: 2/42 Hour: 0/1


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Cytachrome C and neutral drift
Wounded King
Member (Idle past 2543 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 16 of 26 (193621)
03-23-2005 5:22 AM
Reply to: Message 9 by NosyNed
03-23-2005 12:52 AM


Re: Help? From me?
This paper is about Cytochrome C Oxidase (COX), not about Cytochrome C. I don't know that it makes any difference in terms of the current discussion but I thought it was a neccessary distinction to make.

TTFN,

WK

This message has been edited by Wounded King, 03-23-2005 05:31 AM


This message is a reply to:
 Message 9 by NosyNed, posted 03-23-2005 12:52 AM NosyNed has responded

Replies to this message:
 Message 20 by NosyNed, posted 03-23-2005 8:39 PM Wounded King has not yet responded

  
pink sasquatch
Member (Idle past 4471 days)
Posts: 1567
Joined: 06-10-2004


Message 17 of 26 (193675)
03-23-2005 11:22 AM
Reply to: Message 8 by judge
03-23-2005 12:46 AM


why Cytochrome C... why neutral...
I was under the impression that the various versions of Cytochrome C were used as evidence of common descent. That they display a kind of nested heirarchy.

Hi judge,

I think this is an important point - the reason Cytochrome C is commonly used to examine common descent doesn't really have anything to do with whether or not genetic change is exclusively the result of neutral drift.

The reason Cytochrome C is used is because it is required for life in all prokaryotes and eukaryotes, and is simply available for comparison. That is, most other genes would simply not exist in a portion of the "Tree of Life", and thus would make analysis of the Tree of Life incomplete.

Also, Cytochrome C is not the only gene used to examine common descent; other genetic data is used.

If there is no evidence that Cytochrome C does in fact undergo neutral drift within species then this may question whether it ever really neutrally drifts at all, and hence whether it can be used as evidence for common descent.

Perhaps more importantly, the examination of common descent does not require solely neutral mutations. In fact, researchers have little way of knowing if mutations are detrimental, beneficial, or neutral - unless they perform extensive functional studies, and these are not done for most such common descent studies.

In any case, the existence of a detrimental or beneficial mutation in two related species is just as much evidence for common descent as a neutral mutation. An oft-cited example is the "GLO" gene, which is mutated to non-functionality in four known species - fruit bats, guinea pigs, chimps, and humans. Humans and chimps have an identical detrimental mutation in the GLO gene, which is a different mutation than the one in the GLO gene of the fruit bats and the guinea pigs. This is evidence for humans and chimps being more closely related than to other species without that specific mutation. Thus a non-neutral mutation also can demonstrate common descent.

Perhaps you are confusing the idea of determining the "molecular clock" with that of determing common descent. The molecular clock method does use assumed neutral mutations to determine when two species diverged from a common ancestor (but not whether or not they did so...)

Hopefully this is helpful, let me know if you have questions.


This message is a reply to:
 Message 8 by judge, posted 03-23-2005 12:46 AM judge has responded

Replies to this message:
 Message 18 by judge, posted 03-23-2005 6:15 PM pink sasquatch has not yet responded

  
judge
Member (Idle past 4892 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 18 of 26 (193744)
03-23-2005 6:15 PM
Reply to: Message 17 by pink sasquatch
03-23-2005 11:22 AM


Re: why Cytochrome C... why neutral...
quote:
Hopefully this is helpful, let me know if you have questions.

Firstly thanks for all the replies.

I was looking at a creationist site so i wanted to check the ideas there.

http://www.evolutionisdegeneration.com/book/06Adoption.htm#6.4.2.9g

As you can see

quote:
The fact that a protein like cytochrome c differs between non-related species, but is the same within one species, shows that the non-related species do not have a common ancestry. The point of the different versions of cytochrome c is that they all do the same thing: transport electrons. Natural selection can thus never choose one version over another, because they all do exactly the same thing. A term has also been thought up for that: neutral drift. But it is then strange that different versions of cytochrome c are not also found within the same species (such as perhaps the sharks, which have not changed in millions of years)! It could be called extraordinarily coincidental, if not to say miraculous, that these neutral changes always and only take place around the diverging of two species. What does that indicate? Either the non-related species have no common ancestry and each species received their own variant of cytochrome c, which then theoretically (or by genetic manipulation) could change. Or cytochrome c, in combination with the protein with which it reacts, does not permit any mutations, which means that the non-related species do not have a common ancestry. (This was concluded earlier, but now we see it confirmed in practice.)

This creationist seems to argue that Cytachrome C indicates common descent is not true, but it is difficult for me to know whether what he writes is correct as I am an amateur in this area.


This message is a reply to:
 Message 17 by pink sasquatch, posted 03-23-2005 11:22 AM pink sasquatch has not yet responded

Replies to this message:
 Message 19 by Sylas, posted 03-23-2005 7:21 PM judge has not yet responded
 Message 21 by Ooook!, posted 03-24-2005 6:00 AM judge has not yet responded

  
Sylas
Member (Idle past 3708 days)
Posts: 766
From: Newcastle, Australia
Joined: 11-17-2002


Message 19 of 26 (193765)
03-23-2005 7:21 PM
Reply to: Message 18 by judge
03-23-2005 6:15 PM


Re: why Cytochrome C... why neutral...
No, the writer is not correct.

First, sharks are not a species; they are many species.

Second, sharks most certainly have changed over millions of years. They are very successful in their niche, and so ancient sharks are still very clearly sharks, so the basic body form we recognize as "shark" has been around for a long time; but it is not unchanging.

Third, I would expect there will be some minor differences in cytochrome C sequences within some species; but that this will be unusual. This is because the sequence is so highly conserved. To test this would require many sequences from a single species. I do not believe the writer has such data. Most species, however, will tend to have a single uniform cytochrome C sequence, because of the strong conservation.

Fourth, actually, I think there is cytochrome C variation within sharks. As has been pointed out, your other reference was actually for COX (I missed that, oops!). I can't find a reference for several shark species and cytochrome C; but someone with a bit of time might like to trawl the databases and find out directly. There is certainly variation in cytochrome B; reported in Protein evolution in different cellular environments: cytochrome b in sharks and mammals, by AP Martin and SR Palumbi, in Molecular Biology and Evolution, Vol 10, 873-891. (July 1993).

Cheers -- Sylas


This message is a reply to:
 Message 18 by judge, posted 03-23-2005 6:15 PM judge has not yet responded

  
NosyNed
Member
Posts: 8901
From: Canada
Joined: 04-04-2003
Member Rating: 4.2


Message 20 of 26 (193788)
03-23-2005 8:39 PM
Reply to: Message 16 by Wounded King
03-23-2005 5:22 AM


Oxidase
Oh well I did disclaim to death about my knowledge.

It seems reading should have been included. Thanks.


This message is a reply to:
 Message 16 by Wounded King, posted 03-23-2005 5:22 AM Wounded King has not yet responded

  
Ooook!
Member (Idle past 4263 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 21 of 26 (193942)
03-24-2005 6:00 AM
Reply to: Message 18 by judge
03-23-2005 6:15 PM


Re: why Cytochrome C... why neutral...
Hi judge,

This statement in the paragraph you quoted rang alarm bells for me :

quote:
It could be called extraordinarily coincidental, if not to say miraculous, that these neutral changes always and only take place around the diverging of two species.

The author seems to have based it on information that probably doesn't exist. How do they know that cytochrome C doesn't vary within the same species of shark? What study is this based on? How much individual sequence data is there on the shark genome?

Cytochrome C seems to vary in humans for example. I've just queried "cytochrome C NOT oxidase" here and I found that items 7-49 had variations in the cytochrome C gene (the first 6 were from another gene with cytochrome C in it's name). That's quite a lot of variation for genetic drift to play with.

I would add that I am not a geneticist so I may have committed a horrendous error here (people are welcome to correct me and make me look daft :)), but I'd still want to see the studies that show that no variation is seen within species.

Cheers

Edit: Dikshunrees, hoo needs 'em?

This message has been edited by Ooook!, 24-03-2005 11:02 AM


This message is a reply to:
 Message 18 by judge, posted 03-23-2005 6:15 PM judge has not yet responded

Replies to this message:
 Message 22 by Wounded King, posted 03-24-2005 6:24 AM Ooook! has responded

  
Wounded King
Member (Idle past 2543 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 22 of 26 (193948)
03-24-2005 6:24 AM
Reply to: Message 21 by Ooook!
03-24-2005 6:00 AM


Re: why Cytochrome C... why neutral...
A better way to view the data is with the cSNP facility. Here is the cSNP view of CYCS.

TTFN,

WK

This message has been edited by Wounded King, 03-24-2005 06:25 AM


This message is a reply to:
 Message 21 by Ooook!, posted 03-24-2005 6:00 AM Ooook! has responded

Replies to this message:
 Message 23 by Ooook!, posted 03-24-2005 6:43 AM Wounded King has responded

  
Ooook!
Member (Idle past 4263 days)
Posts: 340
From: London, UK
Joined: 09-29-2003


Message 23 of 26 (193958)
03-24-2005 6:43 AM
Reply to: Message 22 by Wounded King
03-24-2005 6:24 AM


Re: why Cytochrome C... why neutral...
Yeah...

well...

that is of course another way of doing it. If you wanted to make it easier to do and much more easy to understand.

Cheers Wounded.

Sometimes I wonder why I bother :(

(Shuffles away sheepishly to get back to some real work)


This message is a reply to:
 Message 22 by Wounded King, posted 03-24-2005 6:24 AM Wounded King has responded

Replies to this message:
 Message 24 by Wounded King, posted 03-24-2005 6:55 AM Ooook! has not yet responded
 Message 25 by sfs, posted 03-24-2005 12:02 PM Ooook! has not yet responded

  
Wounded King
Member (Idle past 2543 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 24 of 26 (193963)
03-24-2005 6:55 AM
Reply to: Message 23 by Ooook!
03-24-2005 6:43 AM


Re: why Cytochrome C... why neutral...
I shouldn't be embarrased if I was you, I've been looking at the CYC1 gene all this time instead of CYCS.

TTFN,

WK


This message is a reply to:
 Message 23 by Ooook!, posted 03-24-2005 6:43 AM Ooook! has not yet responded

  
sfs
Member (Idle past 982 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 25 of 26 (194033)
03-24-2005 12:02 PM
Reply to: Message 23 by Ooook!
03-24-2005 6:43 AM


Re: why Cytochrome C... why neutral...
Note that of the variant sites listed for the human CYCS coding sequence, not one has been validated, i.e. seen more than once. The detection method used for finding all of these SNPs is not the most reliable, so it is likely that some of these sites are not really variant, and possible that none of them are. Keep in mind that CYCS is a small gene, with only 312 base pairs of sequence. Even if there were no constraints, you'd only expect to find one reasonably high frequency (> 1%) variant in such a small bit of sequence; in coding sequence there's no reason to expect even one.

This message is a reply to:
 Message 23 by Ooook!, posted 03-24-2005 6:43 AM Ooook! has not yet responded

Replies to this message:
 Message 26 by Wounded King, posted 03-24-2005 12:16 PM sfs has not yet responded

  
Wounded King
Member (Idle past 2543 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 26 of 26 (194039)
03-24-2005 12:16 PM
Reply to: Message 25 by sfs
03-24-2005 12:02 PM


Re: why Cytochrome C... why neutral...
Note that of the variant sites listed for the human CYCS coding sequence, not one has been validated

This is true but if you go to the 'in gene region' view, rather than just looking at the coding sequence, there are a number of validated polymorphisms in the 3' and 5' UTRs.

TTFN,

WK


This message is a reply to:
 Message 25 by sfs, posted 03-24-2005 12:02 PM sfs has not yet responded

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.0 Beta
Innovative software from Qwixotic © 2020