Functions are not so rare at all, and definitely not isolated, in sequence space of biopolymers

[Mercer (John Mercer)]

@Witchdoc

The enzyme active site, is probably the part that can vary LEAST.

Yet that’s precisely what we varied in the papers linked to above. Not merely in the active site, but a tyrosine residue whose side chain is all but contacting the substrate, ATP.

Gil’s claims are utterly falsified by our work.

[Rumraket (Mikkel R.)]

@Giltil

The bindings involve in complex functional proteins such as DNA polymerases or ligand-gated ion channels are not mere unspecified bindings, but highly fine tuned, integrated, coordinated and regulated bindings which can only be established within large proteins exhibiting high functional information.

Well that whole thing with “highly fine tuned, integrated, coodinated and regulated bindings”, with “high functional information” sure sounds complicated, but none of that constitute evidence or an argument that enzymes or ligand-gated ion channels are unevolvable, which is still just a baseless axiom no evidence supports.

We’ve already seen evidence that has basically convinced every expert in the field that membrane channels are rather easy to evolve, and there’s an enormous amount of evidence that new enzymes can evolve by processes described in previous posts.

More rare functions generally evolve from more frequent functions. Pieces of already existing proteins are recombined, shuffled, and fused together into new proteins, so a completely random sampling of sequence space doesn’t have to occur, rather the search is intrinsically biased to things much closer in sequence space to other functional things.

The tornado in a junkyard is a strawman, and the putative isolation of functions is a fantasy.

[Dan_Eastwood]

This thread has been split to move the side discussion to a new topic. Please direct further replies on this topic to the new thread… – Thanks

Raw materials for life

What experiments specifically? As far as I know, many different experiments in abiotic organic chemistry that attempt to mimic early Earth environments of different kinds, yield compounds that bacteria can use as nutrients. Since bacteria evolve, then yes. But of course that depends on the specific experiment and the environment it simulates, and therefore the products produced. Some experiments have shown that iron can reduce CO2 to common metabolites found in the Kreb’s cycle. All life on Earth can eat that. You seem to be asking a much deeper question than what this thread(and the paper in the 2nd post) is trying to address. Here we are discussing(and the purpose for which I am citing that paper) whether genes with new functions can evolve when there is already evolution going on. This whole thread (though not necessarily the scenario conceived as the context in that paper) is based on the premise that life already exists and is evolving. But I get the sense you want to know ho…

/fnord

[Mercer (John Mercer)]

@Mercer

@Giltil

The bindings involve in complex functional proteins such as DNA polymerases or ligand-gated ion channels are not mere unspecified bindings, but highly fine tuned, integrated, coordinated and regulated bindings which can only be established within large proteins exhibiting high functional information.

If it’s that fine tuned, how was it that my colleagues and I could change the specificity of two of the most complex proteins known (myosins) without a significant effect on their normal functions, merely by changing a single amino-acid residue in the active site to one not found in nature?

If you are correct, we could not possibly have succeeded. Link to 5 papers below:

So, Gil, shall we go through these papers together?