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Author Topic:   On the proportion of Nucleotides in the Genome and what it can tell us about Evolutio
Dr Jack
Member (Idle past 268 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 31 of 61 (524406)
09-16-2009 11:05 AM
Reply to: Message 29 by Dr Adequate
09-16-2009 11:01 AM


Re: Statistics --- ur doin it rong
So, you are not merely wrong, you're also calculating the wrong thing.

You're not humpty-dumpty, words don't mean what you choose them to mean. Touching and crossing are different concepts.


This message is a reply to:
 Message 29 by Dr Adequate, posted 09-16-2009 11:01 AM Dr Adequate has responded

Replies to this message:
 Message 33 by Dr Adequate, posted 09-16-2009 11:09 AM Dr Jack has responded

  
Dr Adequate
Member
Posts: 16095
Joined: 07-20-2006


Message 32 of 61 (524407)
09-16-2009 11:07 AM
Reply to: Message 28 by Dr Jack
09-16-2009 11:01 AM


Re: Statistics --- ur doin it rong
After looking it up, I realise I have erred. In fact, the result I stated holds for a finite random walk, but it does not hold for an infinite random walk.

I'm not sure that you realize quite how badly you have erred, but yes, you frickin' well have.

Now go in peace my child.


This message is a reply to:
 Message 28 by Dr Jack, posted 09-16-2009 11:01 AM Dr Jack has acknowledged this reply

  
Dr Adequate
Member
Posts: 16095
Joined: 07-20-2006


Message 33 of 61 (524408)
09-16-2009 11:09 AM
Reply to: Message 31 by Dr Jack
09-16-2009 11:05 AM


Re: Statistics --- ur doin it rong
You're not humpty-dumpty, words don't mean what you choose them to mean. Touching and crossing are different concepts.

According to your definition, perhaps. And you were being wrong about the wrong one.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 31 by Dr Jack, posted 09-16-2009 11:05 AM Dr Jack has responded

Replies to this message:
 Message 34 by Dr Jack, posted 09-16-2009 11:15 AM Dr Adequate has responded

  
Dr Jack
Member (Idle past 268 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 34 of 61 (524411)
09-16-2009 11:15 AM
Reply to: Message 33 by Dr Adequate
09-16-2009 11:09 AM


Re: Statistics --- ur doin it rong
You used the wrong word. Funnily enough, since I'm not psychic I figured you meant the word you used.
This message is a reply to:
 Message 33 by Dr Adequate, posted 09-16-2009 11:09 AM Dr Adequate has responded

Replies to this message:
 Message 35 by Dr Adequate, posted 09-16-2009 12:14 PM Dr Jack has responded

  
Dr Adequate
Member
Posts: 16095
Joined: 07-20-2006


Message 35 of 61 (524421)
09-16-2009 12:14 PM
Reply to: Message 34 by Dr Jack
09-16-2009 11:15 AM


Re: Statistics --- ur doin it rong
I used a word conventional in mathematics which you failed to understand, and since you didn't read my posts you attributed a meaning to my words that was (a) contrary to what I said (b) contrary to mathematical usage (c) contrary to the context in which I used it (d) obviously stupid (e) not actually relevant to the truth of what I was saying even if you misinterpreted me.

Have you ever thought of becoming a creationist?


This message is a reply to:
 Message 34 by Dr Jack, posted 09-16-2009 11:15 AM Dr Jack has responded

Replies to this message:
 Message 36 by jacortina, posted 09-16-2009 12:59 PM Dr Adequate has not yet responded
 Message 37 by Dr Jack, posted 09-16-2009 1:44 PM Dr Adequate has not yet responded

  
jacortina
Member (Idle past 3246 days)
Posts: 64
Joined: 08-07-2009


Message 36 of 61 (524428)
09-16-2009 12:59 PM
Reply to: Message 35 by Dr Adequate
09-16-2009 12:14 PM


Re: Statistics --- ur doin it rong
I don't believe 'cross' is a conventional term when relating to an axis.

Were you trying for 'intercept'? This would usually include simply 'touching' the line along with 'crossing' it.

Edit: D'oh. Vocab correction post needed its own vocab correction.

Edited by jacortina, : No reason given.

Edited by jacortina, : No reason given.


This message is a reply to:
 Message 35 by Dr Adequate, posted 09-16-2009 12:14 PM Dr Adequate has not yet responded

    
Dr Jack
Member (Idle past 268 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 37 of 61 (524434)
09-16-2009 1:44 PM
Reply to: Message 35 by Dr Adequate
09-16-2009 12:14 PM


Re: Statistics --- ur doin it rong
You used the word wrongly. Crossing in maths means crossing, just like you'd expect.

Man up and admit your error.


This message is a reply to:
 Message 35 by Dr Adequate, posted 09-16-2009 12:14 PM Dr Adequate has not yet responded

  
AdminModulous
Administrator (Idle past 267 days)
Posts: 897
Joined: 03-02-2006


Message 38 of 61 (524435)
09-16-2009 1:56 PM


You're wrong, no you're wrong
For the sake of moving the debate forward, can someone support their claim that the other person is wrong and put this gainsaying to bed? Thanks.
Replies to this message:
 Message 39 by Dr Adequate, posted 09-16-2009 5:18 PM AdminModulous has not yet responded

    
Dr Adequate
Member
Posts: 16095
Joined: 07-20-2006


Message 39 of 61 (524460)
09-16-2009 5:18 PM
Reply to: Message 38 by AdminModulous
09-16-2009 1:56 PM


Re: You're wrong, no you're wrong
For the sake of moving the debate forward, can someone support their claim that the other person is wrong and put this gainsaying to bed? Thanks.

Done that: I did the work; no-one's quoted me being wrong about anything; I did the work; I have a PhD in math and know what I'm talking about; I did the work; analyzing "crossing" the h = t axis in the weirdo sense would be incredibly dumb because it would just make more useless pointless work for whoever tried to do it; I did the work; my math is correct; I did the work; I did the work rather than standing on the sidelines being wrong about what the result would be if I did the wrong calculation; I did the work; I am right about every mathematical proposition I've actually put forward; I did the sodding work, cheers.

Now, back to slevesque's question about genetics ...


This message is a reply to:
 Message 38 by AdminModulous, posted 09-16-2009 1:56 PM AdminModulous has not yet responded

  
slevesque
Member (Idle past 2803 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 responded
 Message 42 by Wounded King, posted 09-16-2009 6:32 PM slevesque has responded
 Message 43 by Dr Jack, posted 09-17-2009 4:42 AM slevesque has responded

  
Dr Adequate
Member
Posts: 16095
Joined: 07-20-2006


Message 41 of 61 (524465)
09-16-2009 5:46 PM
Reply to: Message 40 by slevesque
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 ?

The 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.

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.

But what about mutations the rest of the time?

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.

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 ...

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.

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".

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 40 by slevesque, posted 09-16-2009 5:23 PM slevesque has responded

Replies to this message:
 Message 44 by slevesque, posted 09-17-2009 3:40 PM Dr Adequate has responded
 Message 51 by sfs, posted 09-17-2009 10:32 PM Dr Adequate has responded

  
Wounded King
Member (Idle past 2257 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 42 of 61 (524468)
09-16-2009 6:32 PM
Reply to: Message 40 by slevesque
09-16-2009 5:23 PM


if I remember correctly, mutations happen during transcription

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.

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.

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'.

TTFN,

WK


This message is a reply to:
 Message 40 by slevesque, posted 09-16-2009 5:23 PM slevesque has responded

Replies to this message:
 Message 45 by slevesque, posted 09-17-2009 3:49 PM Wounded King has responded

    
Dr Jack
Member (Idle past 268 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 43 of 61 (524485)
09-17-2009 4:42 AM
Reply to: Message 40 by slevesque
09-16-2009 5:23 PM


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.

You've misunderstood my point. The differences in strength of bonding are themselves adaptive. Bacteria adapted to high temperature environments have more G-C bonds because this increases the stability of the DNA. Origins of replication have high levels of A-T bonds because these can be more easily seperated.

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.

This is true only of the Eukarya, in Archaea and Bacteria, the majority of their DNA is not junk.


This message is a reply to:
 Message 40 by slevesque, posted 09-16-2009 5:23 PM slevesque has responded

Replies to this message:
 Message 46 by slevesque, posted 09-17-2009 3:51 PM Dr Jack has acknowledged this reply

  
slevesque
Member (Idle past 2803 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 responded

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

  
slevesque
Member (Idle past 2803 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:
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