Quote Originally Posted by Slartibartfas
Ok, I hope you excuse if I do not precisely answer your points but present two fascinating mechanisms eukaryotic cells are capable of:

One being micro RNA (miRNA). This is a very recent discovery. Only ten years ago it was found out that very short non coding RNA sequences show regulatory functions in protein expression. This was a big surprise and 10 years later we still only start to grasp the full scale of their importance. Numbers vary but it is expected that miRNAs (co-)regulate the expression of as many as 1/3 or even 2/3 of human genes. They can not only regulate one specific gene but often can influence the expression of many genes. Not only that they can influence different genes to different but precise extends. You can think of them as small programs or list of settings for expression levels for bigger groups of proteins. Add on top of that they are cooperative which means various miRNAs can also act on the same expression of the same gene. It is mind blowing what they could possibly regulate and in which complex ways at the same time by being only 22 bp long on average they are rather simple. It is thought so far that miRNAs have an especially large role to play in development of higher organisms and especially in aspects of morphology where fine tuning of certain gene expressions is possibly leading to substantial differences in morphology.

So far so good. What about evolution of these miRNAs and therefore development of higher organisms due to that? miRNAs mutate as it seems at a common rate like coding genes. So new versions are being created at a certain rate continously in populations and can be also inherited. Of course only few mutations will lead to functional miRNAs also doing a job of expression regulation. Research is still going on there but as it seems functional miRNAs which have a role to play are extremely conserved and hardly ever lost over many generations. This conservation seems to be a functionally self enforcing one. Non-functional miRNAs on the other side are easily lost again. What you end up with is a self selection of functional miRNAs. Higher organisms therefore constantly try out new regulation factors but only keep those that work in certain ways. Bacteria don't have that capability. They can't select that way.

The other mechanism is targeted protein degradation by proteosomes, something bacteria are not capable of either. On one side, functional proteins have a defined life span (which can also depend on various factors), which makes sense but also non-functional proteins are recognized and targeted for degradation by that system. So what happens when a protein randomly mutates and looses its ability of being a properly folded protein? It will get degraded and be not present much at all in the cytoplasma even if one of the two gene copies gets mutated. At the same time, this mutation likewise won't have a big effect on the fitness of the organism. I am not quite sure, but I think there exists even a mechanism of DNA repair based on detection of defect proteins. So most of the dangerous mutations won't have much effect on the cell as the own repair mechanisms can cope with them. If a mutation however leads to a correctly folded enzyme, it will be able to pass the control systems. Folding is just one aspect that gets checked as well.

So these are just two mechanisms but they show two aspects, a selective mechanism for functional mutations at the level of gene expression regulation and on the level of protein mutation. Both are not present in bacteria. They have to compensate with their ability of growing and proliferating extremely fast with huge numbers of individual cells.
That's interesting. And I see no reason to object to any of it.

Except, to say that granting a scenario where there is sufficient RNA around to start self-regulated replication comprises a pretty significant concession. RNA, as you probably know, is a pretty complex molecule in its own right. It is comprised of a sugar component and a set of nucleotides. And each nucleotide is comprised of several components. And of course, all of these components aren't apt to join together to form an RNA molecule on their own.

It takes a competent chemist some effort to synthesize these molecules. The separate components have to be synthesized, pureified and then reacted together in precise ways in order to bring about the desired product. The reason I say all of this is because I don't want the readers to get the impression that simply because the early earth may have had a reducing atmosphere that it neccessarily means the early earth was awash in neucleotides.

Even some origin of life researchers would consider that a near-miracle.