UB takes down the “life is only fancy chemistry” shibboleth:
AVS:
The transcription and translation processes are entirely based on chemistry. Can you explain why functional sequence specific DNA cannot be reduced to chemistry?
UB:
Because there is a chemical discontinuity between the nucleic medium and the amino acid effect that must be preserved in order for translation to be obtained.
AVS:
And what is this chemical discontinuity exactly, Upright?
UB:
There is nothing you can do to the nucleic pattern GCA to relate it to Alanine, except translate it. Which is what the cell does.
AVS:
It’s related by another nucleic pattern, bound to alanine, that has a specific sequence that associates with that GCA.
UB:
The base pairing that enables transcription between nucleotides does not establish a relationship to alanine. That relationship is established by the protein aaRS before the transfer RNA ever enters the ribosome.
UB:
AVS, is there an inexorable chemical relationship between pattern GCA and alanine, or is it a contingent relationship? [UD Editors: Instead of “contingent” one might say “arbitrary”]
AVS:
But there is a relationship. You just explained it. The amino acid is associated with the aaRS, which associates with tRNA, which associates with mRNA. This relationship is the product of the evolution of these molecules.
UB:
Correct. The relationship is established in spatial and temporal isolation by the protein aaRS.
So, there is a physical discontinuity between the nucleic pattern and the amino acid, which is contingent on the structure of the protein aaRS. Therefore, there is nothing about the pattern that determines the amino acid, and consequently, chemistry cannot explain the association. It can only explain the operation of the system with the association in place.
AVS:
The association of the tRNA with aaRS determines the amino acid as I said. The chemical evolution that occurred would explain the why these molecules associate in our cells now, an ultimately arbitrary decision, driven by chemical interactions that occurred in early cells.
UB:
The cells decided huh? cool
AVS, there is a chemical discontinuity between the nucleic medium and the amino acid effect, and that discontinuity must be preserved in order for translation to be obtained.
Do you know why?
(…think about it)
AVS:
That chemical discontinuity between nucleotide and protein is bridged by more chemical interactions though, UB, which as I said are the product of evolution. Yes the cells “decided” for lack of a better word. This is one of the problems with you guys, scientists try to put things in the simplest terms an you completely blow these terms out of proportion.
UB:
I’m glad you now recognize the discontinuity.
My question is: Do you know why it’s there, and why the system must preserve it during translation?
(hint: it’s not evolution)
AVS:
It is evolution UB. Early organisms evolved this translating system to carry out more diverse functions with better efficiency. The system we see today is the result of the chemical evolution that occurred in these early organisms and has been conserved to this day.
UB:
This is not an answer to the question. Do you know why it’s there, and why the system must preserve it during translation? There is an identifiable reason. What is it?
AVS:
UB, there obviously needs to be a connection to nucleotide and amino acid that is conserved. The system we have been talking about does this and it does this based on chemical interactions. And the evolution of this system was based on chemical interactions. That’s it. Make your point already.
UB:
AVS,
I was giving you the benefit of the doubt, hoping you could think for yourself. Why would a physical discontinuity be required in a chemo/mechanical system in order to get a particular amino acid presented at the peptide binding site? Why would such a system need to preserve that discontinuity in order to produce the effect?
…
The physical effect of having a particular amino acid presented at a binding site at a particular point in time is not something that can be derived from physical law – it’s not some innate property to be drawn from, or activated in, the atomic composition of matter. So a discontinuity will naturally exist in any system that produces such an effect. That discontinuity is required in order to allow the input of formal constraint (information) into the system, where it can produce an effect that operates under physical law, but is not determined by it. In other words, it’s an operational necessity to achieve the result.
And the system must preserve that discontinuity for much the same reason. From a purely mechanical standpoint, if the effect were derivable directly from the physical properties of the medium, then it would be so by the forces of inexorable law, and those inexorable forces would limit the system to what can be physically derived from that medium, thus making the input of form (not derived from that medium) impossible to achieve.
However, incorporating the discontinuity by preserving it allows the effect to be determined by a second arrangement of matter operating in the system. This second arrangement establishes a local relationship between the medium and its effect (bridging the discontinuity while preserving it). This relationship then becomes an identifiable regularity of the system, allowing the system the capacity to produce lawful effects not determined by physical law.
UB:
…by the way.
This entire arrangement is a necessary precondition of the genotype-phenotype distinction. It must be in place prior to the onset of Darwinian evolution. To say this system is the product of Darwinian avolution, is to say that a thing that does not yet exist on a pre-biotic earth can cause something to happen.
Which is obviously false.
*crickets*
AVS, where are you? You’re letting down your side. Come on back and tell UB why he’s wrong!