I believe this can be quickly answered. I’m not looking for an apologetic argument. I’m just trying to understand something. So, feel free to explain in as much detail as you think is neccessary, but please keep in mind that I have no background in chemistry, or microbiology. I am a paramedic. We went over some things, like ATG and energy production, but it was a brief look. The focus was prodomenately on saving lives in the field. One of the things that changed in the way EMS operated after 9/11 was the use of common talk over the radio. It became painfuly clear that different agencies, some in the same districts, used different codes. So, when one agency tried to communicate with the other agency using codes the messages were misinterpreted, coordination was lost, and maybe some lives. So plain talk was determined to be the best way to communicate, because simple & common speach means everyone will understand. So, if you can, please follow the acronym, KISFSPLM. Keep It Simple For Stupid People Like Me.
As I understand it, there are a number of possible nitrogenous base pair combonations that DNA can use to code for the same protein. This is a neutral drift that can occur where one of the bases is substituted with no change-- like alternative spelling of a word that has no effect on its meaning. What causes this drift is what my curriosity is about right now. Is this, or can this be the same as codon bias that is affected by enviromental availability of materials needed for the senthesis of the nitrogenous bases? As far as I know the codon usage bias was seen in microorganisms, not in larger animals like rats. I’m not sure if the genetic drift has been observed in rats or bacteria, but I believe it has been seen in larger animals. And I assume that this is all transferable from microorganism to all levels or organism.
As I imagine it, there are prefered synthesis “ingredients” that are not always available, maybe not available in addequate consentration, but there is another way for it to be done that works, maybe not as well, but sufficient (kind of like playing scrabble, and there are not enough Ts to spell Letter but there are enough to spell Note). Would this be what was driving the neutral drift?
First off, nothing drives neutral drift. That’s why it’s neutral. Codon bias would be caused not by drift but by selection. Some areas of the genome are, for reasons unclear to me but presumably due to selection operating on bulk composition, AT rich, and others are GC rich. Selection can also operate on other features. tRNAs may be unequal in abundance, and codons associated with rare tRNAs may be avoided if selection favors fast translation, or preferred if it favors slow translation. If I recall, some codons are also more quickly transcribed than others.
Drift is the random change from generation to generation in the frequency of a variant in the population. What causes it is just random sampling. If you have one copy of a variant, it’s 50-50 whether to pass it on to each child you have. And some individuals have more offspring than others. So the number of copies of a variant will fluctuate from generation to generation, even if the variant has no effect on fitness.
This has nothing to do with codon bias, which is a form of selection: some codons are slightly fitter in a particular species than others.
There are websites that have some pretty amazing interactive simulations for genetic drift. Some hands on experience might help you wrap your head around it.
@Cris_DeLoach, my impression is that you have gotten neutral mutations confused with neutral drift. If you read a bit on each of those very separate topics, you will see why they have nothing to do with each other.
10/4. I am looking over the link a kind gentelman provided above. I’m sure I will have more questions by the time I get done with this, but that is the point for me. I am just trying to understand it beyond what I see at the popular level. So, any free and not too wordy sources you want to point me towards I will be happy to read.
Thanks for the link. I had problems with loading on all but the basic simulation. I probably misstated my question a bit. I get how an allele can become distributed through the population. I was shooting more for why that allele (if I am using allele correctly) occurs. I assume it is in response to environment.
An allele (that is, an alternate bit of genetic sequence) is created when a mutation occurs. Mutations can be caused by environmental factors – ionizing radiation, mutagenic chemicals – or spontaneous processes within an organism, like an error in DNA replication or a spontaneous chemical change. What particular mutation occurs isn’t determined by the environment or by the needs of the organism.
