Arbitrary implies unconstrained freedom to map codons to different amino acids by alternative biochemistry. You need to support that assertion; it is not self evident.
1 Like
I don’t think you understand what you are saying.
The codon, AUG, will preferably (because of some physicochemical factors) base pair with the anticodon, UAC, thus largely excluding any charged and uncharged tRNA molecule not carrying that anticodon sequence in its anticodon arm from the “A” site of the ribosome. That’s chemistry fixing which anticodon binds to a specific codon.
If I have a tRNA molecule with an anticodon sequence that base-pairs with a specific codon due to certain physicochemical principles, then it means only that tRNA molecule will recognize that specific codon. Again this is chemistry (and physics) fixing which tRNA molecule with a given anticodon sequence binds to a specific codon.
Of course, we now have to ask why a particular amino acid gets joined to a particular tRNA molecule with an anticodon sequence that recognizes a specific codon in the genetic code and the answer is chemistry! aa-tRNA synthetases are picky (due to several physicochemical factors) about the tRNA molecule they adsorb, thus, one type of aa-tRNA synthetase will typically bind one or two types of tRNA with an anticodon(s) that recognizes a specific codon(s). A specific aa-tRNA synthetase will attach an amino acid to this bound tRNA molecule (with an anticodon that recognizes a specific codon) guided by several physicochemical factors as well. Again, its chemistry choosing which amino acid maps to a specific codon according to the genetic code. Chemistry sets the rules, but nature can twist or modify those rules.
When mutations significantly alter sequence composition then we expect the magnitude and direction of these interactions to change.
There is no relationship between this and the “codon” talk and its also nonsense at least in the context of extant organisms. Recombination and mutation, both biochemical processes, explain why my genome sequence in particular exists, same with every other living organism on this planet.
Nobody:
2nd years biochemistry undergrads: hahahahahha
The context here is the practical coding of messages as it relates to Information Theory. The biochemical coding represented by DNA is not arbitrary in that same sense.
That genetic code in turn is determined by physical and chemical factors. That’s why we can reassign codons by tweaking these physicochemical factors.
Right. I was trying to clarify the context of Dave’s comment. It seems I failed?
1 Like
We may have been speaking past each other, so please explain your point clearly.
I am way out of my element here but it seems to me that @DaveB / @swamidass are saying that chemistry doesn’t require these structures (e.g., codons, DNA, etc.) exist but will constrain them if they do.
I wonder if an analogy would be that a collection of square blocks do not require that a wall be built, but if a wall is built using square blocks, then there are constrains on how the wall will exist. The constraints on how the wall will exist flows from the properties of the square blocks. However, the square blocks don’t “care” about walls and exist just fine without walls and still retain all of their properties if no wall is built. So, it would not be right to say that the walls exist because the square blocks require walls to exist.
@DaveB / @swamidass would that be a fair analogy? @Michael_Okoko What do you think?
Again, I am way out of my element on the chemistry which is why I used square blocks. LOL!
In the context of Information Theory, how the message is coded is arbitrary/irrelevant to the theory. I had to defend Dave a little because that context is somewhat off-topic. I only brought it up because IT pops up in some ID arguments.
In practice, how information is coded is not completely arbitrary, both in communications and biology. Some codes are better than others, depending on the purpose.
1 Like
DaveB also makes a similar mistake when talks about nothing in chemistry requiring a particular amino acid mapping to a a given codon.
There is nothing in chemistry that demands the existence of the genetic code, but once it comes into existence, regardless of how crude it is, what maps or doesn’t map to something else is fundamentally dependent on chemistry and physics.
I agree with this but that’s not exactly how DaveB puts it. He has been asking whether there is any chemical law that necessitates the existence of a particular biomolecular sequence and the answer is yes. My genome sequence is unique, it is “particular” and certain chemical mechanisms and regularities necessitated its existence. However, if we pretend there was a first genome (from which my genome emerged from billions of years later) then there would be nothing in chemistry, AFAIK, that would require it existed.
That’s crystal clear. Thanks.
1 Like
This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.