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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 Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
You'll find G-C figures easier to get hold of, probably, because they're the one's traditionally used. G-C %ages were long used as a means of classifying microbial species, so there's a lot out there about them. They're increasingly being replaced by more sophisticated phylogenies based on actual sequences.
As others have noted your assumption that the %ages are not adaptive is simply false. A-T pairs have a double bond, G-C pairs have a triple bond; this means that A-T pairs are easier to seperate, and G-C are harder. So, for example, the origins of replication on genomes (of which there are many on eukaryotic chromosomes, and some archael chromosomes and one on bacterial and most archael chromosomes) have a very high proportion of A-T pairs because these can be easily seperated. Thermophillic bacteria have higher levels of G-C pairings that their mesophilic relatives (that is, bacteria adapted to higher temperatures have more of the triple bonding G-C pairs which is thought to aid DNA stability). However, among archaea (the true kings of high temperature living), this link between temperature and G-C content doesn't hold. Species such as Pyrolobus fumarii (which can survive at up to 113 oC and grows best at 106) use protein and enzyme chaperones to mphilic relA stability instead. Finally, there are also specific sequences that perform non-coding functions that can be higher or lower in the two - e.g. the TATA box which indicates gene starts. So, you see, the picture is much more complicated than a simple random variation between the letters.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
The
The reason for this is quite obvious if you think about it: because all future flips occur independently of those flips that have already happened, the chances are that there will not be a trend reversing any initial discrepency from zero. Edited by Mr Jack, : Added explaination Edited by Mr Jack, : Meant mode not median
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
How can zero be the median? Sorry, I meant mode. My bad.
I think you're still confusing the average difference from zero as n tends to infinity with the path of a particular random walk. No, I'm not. More paths will not ever cross the zero line than any other particular number of crosses; what is more as the number of crosses increases, the number of paths that have that number of crosses decreases.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
Nosy, it correct, I was discussing crossings, not meetings.
And, as I said, I meant mode not median. Again, my bad.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
Mean is an extremely poor choice for a situation such as this - especially when considering the infinite limit - because of the large value distortion effect, and the non-normal distribution of the probabilities.
The most probable number of crosses is 0, followed by 1, followed by 2, followed by 3, etc.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
But you've not crossed it unless the next toss is the same.
HTH meets the zero line, it does not cross itHTT meets and then crosses the zero line. Of the possible 3 toss sequences, then, HTT and THH cross the line once; the other six do not cross it at all.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
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.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
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.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
You used the wrong word. Funnily enough, since I'm not psychic I figured you meant the word you used.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
You used the word wrongly. Crossing in maths means crossing, just like you'd expect.
Man up and admit your error.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
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.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
Because of deamination (in which cytosine loses an amine group, and is converted to uracil which then binds to thymine rather than guanine during DNA replication) it sees quite probable that GC -> AT point mutations are more likely than AT -> GC point mutations.
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Dr Jack Member Posts: 3514 From: Immigrant in the land of Deutsch Joined: Member Rating: 8.4 |
Yes, sorry, binds to uracil, thus replacing the cytosine with thymine *sigh*
That needs to be 5-methyl cytosine for it to really work. There are enzymes which specifically excise and replace uracil bases in the DNA. The repair system may still allow a few through though. And, yes, most such changes are caught, but not all. Which should provide a bias to the probability to GC->AT vs. AT->GC changes.
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