Neutral Mutations

The_Fragile
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Neutral Mutations

I've been curious about this certain topic for some time now. Are there neutral mutations and how does natural selection "view" them? I suppose because natural selection doesn't "view" them as negative then it simply lumps them into the positive pile. So I guess what I'm trying to say is, are neutral mutations meaningless? Sort of like how Mike views the terms macro and micro evolution as meaningless terms. Simply because their both evolution and one fuels the other through cumlative selection. A co-worker of mine, who is majoring in biology, said these are the most common types of mutations. I wasn't sure on how credible this statement was since he hasn't been studying in the field that long. Anyhow, thanks in advanced for whoever puts forth their expertise.

 

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deludedgod
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The_Fragile wrote: I've

The_Fragile wrote:

I've been curious about this certain topic for some time now. Are there neutral mutations and how does natural selection "view" them? I suppose because natural selection doesn't "view" them as negative then it simply lumps them into the positive pile.

 

Indeed there are. Many, many mutations are neutral. One of the reasons for this is something known as Silent Codon Shuffling, because most amino acids can be represented by four codons, although there is now new research suggesting that SCS can be quite harmful. At any rate, many mutations are not deletrious, but are also not harmful, and as such, they merely accumulate, but have no effect on evolution.

However, they are infuriating for geneticists, when we try to determine homologous relationships between different protein domains in diverged cell lines, we often find that knowing the precise sequencing is not good enough. We need to know the 3D structure too, because of all the damn "noise mutations", which can affect the results so much that two proteins could only share 30% amino acids and still be structurally almost identical. Fortunately, there is a way around this. There are short sequences in proteins called "signature sequences" which are so sensitive that they refuse to change at all, even in 3 billion years (an example of how sensitive they are, replacing a glutamic acid with an aspartic acid in the binding site of a hexokinase molecule can shift the position of the carboxylate ion by the radius of a proton, and this is enough to decrease catalysis 1000 times).

 

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Yellow_Number_Five
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Most mutations are neutral.

Most mutations are neutral.

Point mutations can easily change the lettering but not the content of a genetic codon. Many nucleotide sequences code for the SAME amino acid. For example, UCU, UCA, UCC and UCG ALL code for serine. A neutral mutation could be considered one that changes the codon, but not the actual genotype.

Furthur, there is a lot of "junk" DNA out there - basically all of the genome that, as far as we can tell, doesn't actually code for anything phenotypically or affect biological processes. Now going into why there is junk DNA and what, if anything it does would be a lecture unto itself, but for the purposes of this question, the answer is obvious. Mutations in such DNA should not have manifestations phenotypically - IOW, it should not change how an organism looks or functions or works on the biological level.

 Junk DNA is GREAT stuff. Comparitive genomics allows us to locate genes and infer how selective pressures have been incorporated - genetic elements that are responsible for the differences between species will be divergent (and conserved), those responsible for similarity will be covergent or similar (and conserved), and those that don't do a damn thing will be unconserved - they should change at random.

That random nature of the uncoserved "junk" is wonderful. If we can (and we have) find ways to gauge rates of mutation, we can look at "junk" markers in related species and gauge how long ago they diverged. We've had rather good success with this in fact.

For example there is a strong correlation between population decreases or extinctions of mastodons, bison and other large animals around the time of the last ice age. Population is typically determined via fossil density, and the fossils are indexed by geological strata and radiometric dating.

Stronger evidence exists in the DNA of organisms whose ancestors experienced these bottlenecks. If one compares the DNA of ancestral populations to current populations and models the differences they see in the DNA of the two populations they can determine when bottlenecks occurred. This involves looking for molecular sequence variations in the form of polymorphisms. Bottlenecks in populations are indicated by increases in allelic association by non-uniform sampling of haplotypes. Allelic association is a measure of the non-random assortment between alleles.

What we are after here is a measure of linkage disequilibrium, a measure of the deviation from random assortment of alleles at a pair of polymorphic DNA sites.

Additional reading:

http://www.genome.gov/Pages/Research/HapMap/Goldstein.pdf

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=11346797&dopt=Citation

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deludedgod
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Yellow_Number_Five

Yellow_Number_Five wrote:

Junk DNA is GREAT stuff.

 

Yellow_Number_Five wrote:

That random nature of the uncoserved "junk" is wonderful

LOL. Differences of field, I suppose. Junk DNA is extremely useful for the molecular clock test, tracking of evolutionary flows and of course, for disproving creationism. However, part of my work involves the protein folding problem, so I for one cannot stand junk DNA, it makes life so much more difficult when trying to ID structural homology in conserved protein domains. 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

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Yellow_Number_Five
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deludedgod

deludedgod wrote:

Yellow_Number_Five wrote:

Junk DNA is GREAT stuff.

 

Yellow_Number_Five wrote:

That random nature of the uncoserved "junk" is wonderful

LOL. Differences of field, I suppose. Junk DNA is extremely useful for the molecular clock test, tracking of evolutionary flows and of course, for disproving creationism. However, part of my work involves the protein folding problem, so I for one cannot stand junk DNA, it makes life so much more difficult when trying to ID structural homology in conserved protein domains. 

 

LOL, yeah, I always forget about you poor saps sorting through billions of base pairs Eye-wink

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

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The_Fragile
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Thanks for the responses

Thanks for the responses guys very helpful. By the way, my co-worker also told me about a math formula used to judge if a species is evolving or not. I can't remember what the formula is called. Maybe due to the fact its a rather long complex title. Anyway, I was curious of how accurate it is.

I hope they cannot see
the limitless potential
living inside of me
to murder everything.
I hope they cannot see
I am the great destroyer.