So when you claimed
What you actually meant was ‘I’m not aware of any’. So this is a burden shift.
To your question, I already said it.: Binding ATP is a function. What function does ATP binding serve? It binds ATP. You are confusing function with utility.
I have a pretty good idea which is a pattern where the new genes or changes to existing can be explained by reproduction. @Michael_Okoko came up with a possibility with fruit flies where common descent was a possible cause.
Sals flower…not so much 
Done for the day…
Yes. I should have repeated the qualifier I used earlier in this discussion i.e. those ID’ers who do not affirm common descent (which is most of them).
Binding is not separable from catalysis. It is integral.
I’m talking about binding ATP and anything else.
Please provide your other instances, but only with citations to the primary literature.
I’ll ask again: have you ever read a basic biochemistry textbook? Do you know what “Kd” means?
This?
This seems to take us back to John’s idea of:
I suppose this is an answer of sorts, but not really a satisfactory answer. It would appear to replace “replication with modification” with “replication with no modification whatsoever”. Whilst it has been (reasonably in my opinion) argued on another thread that common descent does not require mutation, I have seen nothing to suggest that the two are incompatibile (and in fact the standard Evolutionary explanation involves an interplay of them both).
This would leave us with “Howe’s Venn Diagram is inconsistent with common descent”, if you first stipulate the impossibility of new genes being gained, or old genes being lost, through evolution". This stipulation would however, I would suggest, be a case of Begging the Question, in that it rules out Evolutionary mechanisms a priori.
Ever heard of cooperativity, where the binding of one substrate to an enzyme enhances the binding of another substrate due to conformational changes in the enzyme induced by the first substrate?
Ever heard of the induced-fit model of substrate binding, which postulates that a substrate will loosely bind an enzyme causing that enzymes to undergo conformational shifts that optimizes binding with that substrate, kickstarting its catalysis? Some enzymes have been observed to conform to this model.
You really should take John’s advice and go learn basic biochemistry.
No, that’s literally impossible. The maximum amount of mutations that can separate two proteins must correspond to the length of the longest of the two. If two proteins are 200 amino acids long and have zero sequence-similarity, it can take at most 200 mutations(amino acid substitutions) to turn one into the other.
Of course, that’s a meaningless statement because what matters are functions, not the particular sequence that carries it out, and nobody is saying any arbitrary extant protein can be turned directly into another extant protein by point mutations.
What we know from evidence is that all proteins, all proteins without exception, have other potential functions nearby in sequence space. Usually within a distance of one or two mutations. And we also know from evidence is that there are many kinds of ways to evolve new proteins from old proteins beside just point mutations. For example, gene fusion:
That’s just one way to gain genes. Another is good old gene duplications and divergence. Copy a gene, make a mutation in it = new gene.
This is an important point. To say it is easy to evolve a new function is not the same as saying evolving that arbitrarily picked function is unconditionally useful to all organisms. That doesn’t mean it’s not a function. Giving E coli that lives in your gut an enzyme that has the ability to degrade nerve-gas, which is definitely an enzyme function, is of no use to E coli in your gut. Chances are if they’re ever exposed to a useful amount of nerve gas, the host organism with which they live in symbiosis is dead.
All known organisms currently use ATP for many roles in the cell, so just giving them an ATP binding protein is likely to interfere with something rather than help the organism.
But it’s trivial to see there are alternative examples where simple binding activity can be useful. Binding a toxic molecule so a chemically reactive functional group is blocked and can’t wreak havoc within the cell could be one way that simple small molecule binding could be useful.
The point is that evolving the binding activity, which is a function all by itself, is easy. ATP binding is really just a stand in for small-molecule binding, of which there are innumerable kinds.
Well technically Rum it can take 10^100 mutations to change one protein to a completely different one, if both proteins were 10^100 long. However, proteins that ridiculously long don’t exist making SCD’s question totally irrelevant.
Heh, well such a protein couldn’t possibly exist even theoretically. A protein 10100 amino acids long would contain more mass than all baryonic matter in the entire observable universe(it’s been estimated there’s “only” about 1080 atoms in the universe), and would immediately begin collapsing into a black hole should one be somehow brought into existence.
i will try to make it simple.
not if we are talking about specific sequence in this theoretical case. if we need a specific sequence then we will indeed need 20^200 mutations on average to get that sequence since we are talking about specific sequence out of 20^200. anyway, i remind you that ATP binding by itself should not benefit the organism since ATP binding by itself will be meaningless for the survival of the organism.
You are entirely correct.
You’re talking past each other. @scd is trying to talk about, well, who knows, but he’s assuming that you have to try all all possible mutations at every site before you arrive at the exact sequence you want. Aside from exemplifying the Texas sharpshooter, that’s just a silly number even for estimating the expected number of mutations needed to produce an exact sequence, which is what I think he’s aiming for.
The rest of you are talking about the minimum number.
Remind us? You mean you reassert your entirely baseless, and clearly false, claim.
Gee thanks. Go draw me another one of your phylogenies of vehicles.
None of that makes any sense. You’ve made it so simple it’s completely meaningless. There is no starting point defined, no average distance between the starting point and a functional sequence, and in any case you seem to have went for the one-true-sequence-fallacy simultaneously with the Texas sharpshooter.
Rather than consider the distance between any adaptively functional sequence and the current position in sequence space you’re treating this as a sort of tornado in a junkyard where a specific target sequence has to emerge de novo by randomly hooking up amino acids one at a time with no feedback from selection, with each being equally probable. And you’re working exclusively with substitutions, no insertions or deletions, duplications, shufflings, gene fusions, recombination.
None of all that has anything to do with evolution.
I remind you that this reminding was completely refuted by @CrisprCAS9.
but that was your scenario:
which isnt realy true if there is no functional stepwise. and in the ATP binding case this is probably the case since even if we will evolve the first ATP binding site it should not improve the species survival. but lets take a look at what we see in human population. one in how many births we see a new anatomical trait? how many of those traits are beneficial?
Right, but I wrote more didn’t I? I specifically wrote:
Of course, that’s a meaningless statement because what matters are functions, not the particular sequence that carries it out, and nobody is saying any arbitrary extant protein can be turned directly into another extant protein by point mutations.
So if you can seizure up some fever dream scenario where evolution has to occur by having some specific protein evolve into some other, completely unrelated specific protein, through unfathomable quintillions of nonfunctional intermediates, then go right ahead.
Evolution within a few billion years is effectively impossible if this protein X has to evolve into this protein Y and all the intermediates are nonfunctional. Okay, yes. I agree. If that was true it would be effectively impossible. But what evidence do you have that this delusion is true? None. Zero.
In Rum’s hypothetical, the starting point is an existing protein that is 200 amino acids long, so we would need just 200 mutations to transform it to any completely different protein molecule. That makes your 20^200 estimate irrelevant.
More so, even if we were looking for a specific sequence of amino acids in the universe of 200 AA long protein sequences, there are mechanisms that shorten nature’s search for that sequence in sequence space. Nature doesn’t always have to traverse through sequence space randomly.
again lets go to my last question: one in how many births we see a new anatomical trait? how many of those traits are beneficial? if we can estimate that we can also estimate how many mutations we need.