Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
4 online now:
Newest Member: popoi
Post Volume: Total: 915,817 Year: 3,074/9,624 Month: 919/1,588 Week: 102/223 Day: 13/17 Hour: 0/0


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   On the proportion of Nucleotides in the Genome and what it can tell us about Evolutio
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 1 of 61 (524288)
09-15-2009 5:13 PM


I love giving long 'old-School' titles
Anyhow, as I hope everyone that will join this discussion knows, statistics is a very interesting subject. One of the properties of a random sequence is that, given enough repetitions, it will always tend to go towards a certain %. I may not be clear, so here is an example:
_ If I flip a coin for a very long time, the amount of heads and tails I should register should be close to 50% each.
Now, if we start with a simplistic model of mutations where they are a totally random and apply this fact, then given enough time and mutations, the % of each nucleotides in the genome should tend towards 25%. Natural selection, of course, gives no advantage to either of the nucleotides and therefore should not influence this ratio.
I have searched for data on this ratio in different animals and I have come close to nothing in terms of actual numbers. From my biology book:
- In humans: A=30,3%. T=30,3% G=19,5% C=19,9%
- In E.Coli: A = 26%. (And so probably T=26%, but it is not explicitly said).
I intend this discussion to be more of a knowledge learning for me, and so it is NOT a debate. Please try to keep this in mind everyone. I'll start off with a couple questions:
1- Can mutations be approximated as totally random, and if not, can/does this change the expected proportions of the nucleotides in the Genome ?
2- Does anyone have more information on such proportions from other species ? The more information we have, the more interesting this will be.
3- Has such an analyses of proportions been done and published in the past ?
4- In the hypothetical situations that it turns out that there is a common trend in the different species to favor the A and T base, what could be the possible explanations, from an evolutionnary perspective, for this ?
I consider that if there would be a natural mechanism that favors significantly some nucleotides over others, than this would be a powerful mechanism analog to natural selection in a certain way, and that it's discovery would merit the Nobel Prize ... haha
Hopefully, with all the brilliant minds on this forum who have worked in biology and genetics all their life, I will be able to obtain moe information on this idea I had while eating my cereals 2 weeks ago.
PS I keep the copright on this idea and anything that stems from it lol

Replies to this message:
 Message 3 by New Cat's Eye, posted 09-15-2009 5:44 PM slevesque has replied
 Message 4 by Wounded King, posted 09-15-2009 5:58 PM slevesque has replied
 Message 12 by Dr Adequate, posted 09-15-2009 11:15 PM slevesque has not replied
 Message 13 by Dr Adequate, posted 09-15-2009 11:50 PM slevesque has not replied
 Message 15 by Dr Jack, posted 09-16-2009 6:30 AM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 5 of 61 (524300)
09-15-2009 6:00 PM
Reply to: Message 3 by New Cat's Eye
09-15-2009 5:44 PM


I start with the supposition that each nucleotides has the same amount of information, and also that none of them is statistically favored to be a beneficial mutation. Therefore, natural selection, which favors beneficial mutations, has an equal amount of chance to favor one nucleotides or another, and so its effect on the long term proportion of each in the genome is zero.
Of course, if we were to discover that natural selection favors some nucleotides over others it would probably also merit a Nobel prize ...

This message is a reply to:
 Message 3 by New Cat's Eye, posted 09-15-2009 5:44 PM New Cat's Eye has replied

Replies to this message:
 Message 7 by Wounded King, posted 09-15-2009 6:25 PM slevesque has not replied
 Message 8 by New Cat's Eye, posted 09-15-2009 6:47 PM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 6 of 61 (524301)
09-15-2009 6:04 PM
Reply to: Message 4 by Wounded King
09-15-2009 5:58 PM


Very interesting, any numbers attached to this ?
Also you seem to be the one most knowledgeable on these subjects on EvC, any chance you have other proportions from other species ?

This message is a reply to:
 Message 4 by Wounded King, posted 09-15-2009 5:58 PM Wounded King has replied

Replies to this message:
 Message 9 by Wounded King, posted 09-15-2009 7:02 PM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 40 of 61 (524461)
09-16-2009 5:23 PM


Wow, two pages of statistics, that wasn't expected.
I can't help you guys unfortunately, since well I haven't done any statistics yet, and mathematican-physicians don't usually do any unless you take it as an optional course.
Anyways, can't we agree that the ratio of heads/tails will tend to one when the number of n repetition tends to infinity ?
Which goes back to my original post where, if we assume no effects by natural selection, random mutations in the genome should bring the ratio of nucleotides in the genome to about 25% each.
Ok so now is the time to clear a little misunderstanding, which I was not precise enough in my original post. I posited a simplistic view of the phenomenon I was trying to research. Hence why I posited that natural selection's effect on the nucleotides' ratios was zero. I do not know if this is how researchers usually start off, but this is how I decided to do it for the simple reason that I have a very limited knowledge of the subject. However, this does not mean that I was stupid enoughto think that this simple starting point was the actual reality of things,
Someone talked about the difference in the strength of the A-T double bond and the G-C triple bond. I remembered this fact from my biology class. Now, in order to evaluate the extent of the effects of this fact on the mutational ratios, we would need to observe a trend in the Genomic sequences of various species, favoring the G and C letters.
However, I feel that this effect should be rather small. Because, if I remember correctly, mutations happen during transcription and technically the double strand of DNa has already been seperated by the ADN-polymerase (by memory, probably wrong about the name) and so the actual strength of the bond between G and C doesn't really impact te mutations during transcription.
About the impact of natural selection, we must not forget that EVEN IF, for example, GC mutations had a higher probability of being favorable than AT, than it does not readily follow that NS will be able to favor GC mutations to a high degree. This is because natural selection does not act upon the genotype, but the phenotype. And even though some mutations do have an observable impact on the phenotype, the vast majority of them are nearly-neutral and so natural selection cannot act upon them. Thus these mutations become fixed in a population through genetic drift, which is a random process. This is without counting that, from an evolutionary point of view, the majority of the genome is composed of junk DNA, and so mutations inside this DNA are not affected whatsoever by NS.
PS. The two links provided by Dr.A are great, but like he said it would be even better if we could have similar statistics about eukaryotic genomes.

Replies to this message:
 Message 41 by Dr Adequate, posted 09-16-2009 5:46 PM slevesque has replied
 Message 42 by Wounded King, posted 09-16-2009 6:32 PM slevesque has replied
 Message 43 by Dr Jack, posted 09-17-2009 4:42 AM slevesque has replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 44 of 61 (524582)
09-17-2009 3:40 PM
Reply to: Message 41 by Dr Adequate
09-16-2009 5:46 PM


ratio, yes.
Consider the following two cases.
Case #1 : We have a genome. We keep tossing a coin, and every time it comes up heads we add an AT base-pair, and every time it comes up tails we add a CG base-pair.
Now, this is not what you're trying to model. But it's what you're modeling. When you appeal to the Law Of Large Numbers in the way that you do, that's what you're modeling.
Case #2 : We have a genome of a fixed length. We keep tossing a coin, and every time it comes up heads we change a CG base-pair into an AT base-pair, and every time it comes up tails we change an AT base-pair into a CG base pair.
You probably shouldn't be modeling that, either. But that would be a "random walk" and wouldn't tend to anything
Ok, I see the nuance between the two cases.
But will it realy make a difference in the long term ? I mean, if we take a genome and look at it mutate for a long time. Will not every nucleotide position, after several mutations, have a 50% chance of being AT or GC, and so when we consider the total ratio of the genome, we should expect to find approximately a 50/50 combination of AT and GC in it ?
But what about mutations the rest of the time?
I would suppose that technically, the inherited mutations are those that are in the sperm or the ovule, and so are those who occur during the production of the two. A totally intuitive and random guess of mine would suggest that the vast majority of these mutations happen when the DNA is copied and so when it is unfolded, so that the strength of the GC bon does not play a role in the % of mutations. ( said transcription, but after reading WK post I remembered that transcription was when they unfold a part to make an RNA brand. I was rather thinking of the copying of the entire genome during Meiosis)
Yes, but consider a reductio ad absurdum. If natural selection didn't count, and neutral genetic drift was all we had to think about, then it would be perfectly possible for this process to result in 100% AT. Now count how many amino acids can be produced by nucleotides just going ATTTATATATTTTATTATTATTTATAAAT ...
Yeah, that's quite right. So NS would prohibit the genome of a population from coming near that 100% mark. In any case I think it would not favor GC over AT, or vice-versa, which is the point.
That or the population in question would develop a binary system like we have in our computers ...
This is true of eukaryotic genomes, but I hardly see how it applies to bacterial genomes.
If, as I have shown, one bacterium has only 25.1% AT, and another has 84.3% AT, then the difference between them is more than half of the genome --- none of which, apparently, can be easily written off as "junk".
Yeah well which is why I'm still looking for more information on eukaryotic genomes ...

This message is a reply to:
 Message 41 by Dr Adequate, posted 09-16-2009 5:46 PM Dr Adequate has replied

Replies to this message:
 Message 50 by Dr Adequate, posted 09-17-2009 9:57 PM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 45 of 61 (524584)
09-17-2009 3:49 PM
Reply to: Message 42 by Wounded King
09-16-2009 6:32 PM


They certainly can, and there is some evidence that highly transcribed regions are more prone to mutation, but that is important principally in somatic mutations, in the germ line mutations which actually contribute to heritable variation this effect will be considerably reduced. It is by no means that case that mutations only happen during transcription, perhaps more important in evolutionary terms are meiosis and mitosis which similarly involves the unwinding of DNA to allow DNA synthesis enzymes to have access to single stranded DNA. You are basing your reasoning on a number of huge assumptions.
See previous post, as I should not have used the word 'transcription' I think.
Wow, that is the sort of argument that creationists always use as a strawman of what biology says. I don't think anyone familiar with modern biology really believes this. The majority of the genome is composed of non-coding DNA, but this isn't the same thing.
Unless you specifically define 'Junk DNA' as DNA which is neutral in terms of selection, i.e. non-functional, then any of the commonly used meaning of the term show your statement to be wrong. There are a number of non-coding sequences in the genome that have been targets of selection. Many of these serve structural roles in stabilising the chromosome, see microsatellite DNA, Telomeres, Satellite DNA and probably othe as yet uncharacterised sets of sequences. There are also regulatory elements which are found to be embedde in intergenic regions which might previously have been discounted as 'Junk'.
I used 'junk DNA' in the same sense as Ohno did back in his 1972 paper (So Much Junk DNA in our Genome. Evolution of genetic systems. Brookhaven Symposia In Biology)
Of course, since that time our knowledge of genetics as being moving forward by leaps and bounds, and many regions which were labelled as 'junk DNA' are now known to have functions. Actually, creationists are continuously pointing out to these advancements to show that 'Junk DNA' isn't junk after all. I would often argue that this strawman of modern biology is actually being done by the evolutionists, who often resort to this argument in public debates etc. (It is a bit reminescent of the 'vestigial organ' argument of the 1900's.)
Of course, every time previousl though non-functional DNa is discovered to have a function, it makes it even harder to apply Kimura's theory of neutral evolution to solve Haldane's dilemna. But that's another topic I guess.

This message is a reply to:
 Message 42 by Wounded King, posted 09-16-2009 6:32 PM Wounded King has replied

Replies to this message:
 Message 48 by Wounded King, posted 09-17-2009 4:55 PM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 46 of 61 (524585)
09-17-2009 3:51 PM
Reply to: Message 43 by Dr Jack
09-17-2009 4:42 AM


Well I would like to focus on eukaryotic cells, but I have difficulty finding data on it (Principally because I don't know where to look).
About the GC and AT triple and double bound, should it have an effect on DNA proportions of eukaryotic genomes ? (Considering what I said about inheritable mutations 'probably' happening during Meiosis ? (Which is just an intuitive guess on my part)

This message is a reply to:
 Message 43 by Dr Jack, posted 09-17-2009 4:42 AM Dr Jack has seen this message but not replied

Replies to this message:
 Message 47 by sfs, posted 09-17-2009 4:34 PM slevesque has not replied

  
slevesque
Member (Idle past 4640 days)
Posts: 1456
Joined: 05-14-2009


Message 59 of 61 (524840)
09-19-2009 2:37 PM


So to recap what has been said, can someone answer this question;
What ratio GC/AT should we expect from a mutating genome ?
If we can answer this question, we can add the effects NS later on.
PS. A totally acurate answer is probably to much to ask, an approximte and qualitative answer should do.
EDIT: sfs, are you the same person as sfs1 on Tweb ?
Edited by slevesque, : No reason given.

Replies to this message:
 Message 60 by Dr Adequate, posted 09-19-2009 4:35 PM slevesque has not replied
 Message 61 by sfs, posted 09-20-2009 4:55 PM slevesque has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024