Most deleterious mutations will indeed be lost because of purifying selection. We really don’t know the number of beneficial mutations, but tens of thousands doesn’t strike me as impossible.
Sure, but the response to those triggers is still dependent on the DNA sequence.
As far as we know, all of the differences between humans and chimpanzees stem from differences in our DNA. The degree of genetic difference is more than adequate to cause the observed differences and there is no evidence and no reason to think any other kind of difference is involved. That doesn’t conclusively rule out some other kind of difference, but when we have no evidence for something and no reason to think the something exists, we tend not to worry about it. We also haven’t ruled out the possibility that 16.86 miles directly below your feet there is a small chamber containing nothing but turnips and light bulbs, for example, but I’m not going to spend a lot of time contemplating that possibility.
How did you go from “some nucleotide differences contribute to phenotypic differences, and so do some other factors” to “nucleotide differences don’t contribute much to phenotypic differences”?
I didn’t make that leap. I was pointing out that looking at the similarity does not tell us how much of the difference in phenotypes is caused by differences in nucleotides and how much due to rearrangement of existing genetic materials.
I.e interpreting the impact of a number such as 84% similarity or 98% similarity in terms of what causes the phenotypic differences is difficult.
I think most scientists agree. Mutations which change gene expression are most likely the bulk of mutations responsible for phenotypic differences. There are many targets within functional DNA that can affect gene expression, be it promoter regions, copy number variants, protein sequence of transcription factors, micoRNA, the 3’ UTR in mRNA that bind microRNA, transposon insertion, and so on.
Differences in DNA sequence is what causes the differences in gene expression. Genomes with identical sequence will have identical gene expression profiles.
If I get what you are saying, the genome of the organism completely determines how cells differentiate and form the organism. When and where every gene is expressed is already determined. Is this what you are claiming?
Excluding environmental factors, yes that is what I am saying. Of course, environment also has an affect on organisms, but if two organisms with identical genomes are put in identical environments their response to that specific environment will be identical. This is why identical twins look identical, because their genomes are identical (except for a few mutations that occurred after the initial zygote split into two zygotes). I have brothers who are identical twins, and no one can tell them apart except for close friends and family.
Ok thanks for the clarification. I have read papers/scientists who disagree with your view. (For ex Noble et al).
Noble doesn’t disagree with this view. He is mainly focused on niche construction which fully embraces mutations being the cause of differences in phenotype. There are some who think epigenetics plays a role in transgenerational differences in addition to changes in DNA sequence (at least for vertebrates), but evidence has yet to come through.
As I said before, this is trivially true. That’s why I said that people (like me) have to actually investigate the specific nucleotide differences in detail to see how they might affect phenotype.