Genuine Puzzles In Biology?

Because asexual reproduction has the disadvantage of only passing on one's genes to the next generation.

I'm a biochemistry major with a focus in genetics and even I had to look up "genetic equidistance":

quote:

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The genetic equidistance phenomenon was first noted in 1963 by E. Margoliash, who wrote: "It appears that the number of residue differences between cytochrome C of any two species is mostly conditioned by the time elapsed since the lines of evolution leading to these two species originally diverged. If this is correct, the cytochrome c of all mammals should be equally different from the cytochrome c of all birds. Since fish diverges from the main stem of vertebrate evolution earlier than either birds or mammals, the cytochrome c of both mammals and birds should be equally different from the cytochrome c of fish. Similarly, all vertebrate cytochrome c should be equally different from the yeast protein."[2] For example, the difference between the cytochrome C of a carp and a frog, turtle, chicken, rabbit, and horse is a very constant 13% to 14%. Similarly, the difference between the cytochrome C of a bacterium and yeast, wheat, moth, tuna, pigeon, and horse ranges from 64% to 69%. Together with the work of Emile Zuckerkandl and Linus Pauling, the genetic equidistance result directly led to the formal postulation of the molecular clock hypothesis in the early 1960s.[3] Genetic equidistance has often been used to infer equal time of separation of different sister species from an outgroup.[4][5]

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Molecular clock - Wikipedia

Using only conserved proteins with identical function in both species ensures that it's the former and not the latter. That's why protein phylogenies are usually performed on genes for proteins like cytochrome c, or the 16S ribosomal subunit. It's not really a puzzle.Also, you're frequently using "equidistance" when what you mean is "distance."

Well, no, we're not. The function of proteins like cytochrome c or ribosomal subunit 16S aren't related to cell type, because the function is so basic every kind of cell in every kind of organism needs to perform it. All of your cells, regardless of type, are engaging in protein synthesis and electron transport activity, or else they're dead.Cell type and cell diversity is going to have no effect whatsoever on these highly conserved proteins, and that's how we know that accumulated differences between homologous genes in different organisms really do reflect evolutionary time. For other proteins, that's not going to be the case, but those aren't the proteins being used to construct phylogenies.

Well, but it's not. We know it's not because, again, genetic distance is being measured only on genes that have nothing to do with cell type, cell diversity, or epigenetic complexity. Genetic distance is measured on the genes for cytochrome c and ribosomal subunit 16S (among others) and the function of those proteins is identical in all species and all cell types, regardless of the complexity of the cell or of the organism.That's why they're such a useful basis for constructing phylogenies; selection for different function in different species is utterly taken out of the equation. Thus we can conclude with certainty that the genetic distance observed between these homologous genes is not related to the complexity of the organism. Regardless of how complex an organism you are, your mitochondria engage in electron transport and your cells express proteins. By only measuring the genetic distance on proteins that have identical function between the compared species regardless of complexity, like cytochrome c and ribosomal subunit 16S. Yes, I have. In many cases you do mean "equidistance." But in most cases what I think you actually mean is "distance", as in the genetic distance between two species. Equidistance is an observation about the genetic distance between each of two different species to a third outgroup, and the fact that this pattern is observed in highly conserved genes supports the concept of molecular clocks and, by extension, evolution.