If the first point is neglected and plays a role, then doesn't that mean that your conclusion is unwarranted because you assume random changes to DNA..? I have no idea what Axes model is or how that relates to the probability you used to determine the probability of proteins evolving.
Who knows how complicated the interplay becomes when you add natural selection and other evolutionary forces into play. It's no longer a simple random number problem. One factor can feedback back into the other... Over aeons...
Anyway..
His is model is the research paper I cited.
2. https://www.differencebetween.com/difference-between-mutation-and-vs-recombination/
Why can't recombination play a role, when it seemingly plays a role in almost all standard evolutionary processes? If it can result in a novel set of genetic information, then why is it not important?
And yes, it plays a role in population dynamics. How did you rule that out? I understand that you're talking about a novel property arising, but I can imagine that happening even just through re-shuffling of the genome, forget even the novel traits for a second... because then the macroscopic properties of DNA are different and the microscopic interactions (random mutations) can differ in their feedback to the macroscopic properties.
Recombination accounts for far less genetic variation than mutations - it can be noted that the same can be said for genetic drift. And I mean far far less.
3. "The possibility that DNA arranges, through selection, in such a way that random mutations tend to cause beneficiel changes. I.e., emergent phenomena. There's even some evidence of this happening in some species that seem to save up mutations for a "rainy day". "
I'm talking about how DNA is arranged and it reacts to microscopic changes.
Let me make some random shit up to demonstrate.. Imagine a strand of DNA is
AAAABCBDAAA
or
ABDAABDBEBA
If you randomly change one of the letters in that chain, imagine the first one has 500 possible macroscopic arrangements such that the change leads to a beneficial trait... The second one has 1. Clearly the first arrangement is then favored.
Imagine that selection tends towards such arrangements that lead to beneficial traits... but you're not taking selection into account. So how did you rule out that possibility, when there's some evidence that this happens in nature?
This is just a simple example... it becomes infinitely more complicated once you take all the other evolutionary forces and agents, and let them feedback on each other at every level.
So how did you rule out selection that creates DNA arrangements which favor beneficial mutations, when there's some evidence that this happens in nature?
Are you speaking of Allele frequency?
Allele frequency (This is the frequency in which those variations occur) is a secondary phenomena to mutation because the variations don't exist without initial mutation.
Pertaining to your example, the majority of all of those changes will lead to instability of the coded protein. This is covered under Axes model, recall they take a specific gene and add small random variations to it to get their results. The set H includes all functional mutations, which beneficial mutations would fall under because they are both functional and stable.
I will look for the frequency of these arrangements that could possible lean towards beneficial functions but they either don't exist or are few because the majority of mutations are neutral meaning they do nothing.
Furthermore the question would arise how often do such sequences even mutate, just because the sequence itself could lean towards a beneficial mutation doesn't mean it will mutate to read that point. I'm sure of the validity of all this though because of how sensitive protein folds - as i said any change usually leads to neutrality.
Do you have sources for the selection you speak of if it's not Allele frequency?
