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Author Topic:   The "Digital Code" of DNA
Brad McFall
Member (Idle past 4024 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


(1)
Message 140 of 143 (562788)
06-01-2010 7:03 PM
Reply to: Message 1 by kuresu
04-26-2007 2:17 PM


metaphysical codes
Just yesterday while thinking through the content and criticism of Kant's OPUS POSTUMUM I realized a way to cognize the origin of the genetic code from within Kant's ostensive construction of dynamics.

This may be a significant use of a priori reasoning or just another of my seeminglyl endless speculations and thoughts but in case it is important I want you all to know you heard it first!

I had been trying on EVC to explain why I did not agree to much with ID and this if real is really good!

Brad

Here is the content of a new page on my website

http://aexion.org/codemetaphysics.aspx
Metaphysics and the Genetic Code

Francis Crick (1966) has written

“Why a Triplet?
We have argued that the code must have been basically a triplet code from a very early stage, so that one is not entitled to use sophisticated arguments which would apply only to a later stage, although one could argue that early organisms with doublet or quadruplet codes actually existed but became extinct, only the triplet code surviving.

However, we are inclined to suspect that the reason in this case may be a structural ‘ one. If indeed there is no direct stereochemical relationship between an amino acid and a triplet, the problem of constructing an adaptor to recognize the codon may be a difficult one to solve.

In effect, one wants to perform a rather complicated act of recognition within a rather limited space, since two adaptors need to lie side by side, and attached to adjacent codons on the mRNA, during the act of synthesis. This is probably very difficult to perform if protein is used for the adaptor. On the other hand, nucleic acid, by employing the base-pairing mechanism, can do a very neat job in a small space.

For various reasons the adaptor cannot be too simple a molecule. For example, the amino acids on adjacent adaptors need to be brought together—this is probably done at the present using the flexible ... CCA tail. It must have, to some extent, a definite structure and this is likely to be based on stretches of double-helix. Thus .the diameter of a double-helix (since two may have to lie side by side) may have dictated the size of the codon, in that a doublet-code (moving along two bases at a time) would present an impossible recognition problem."

I have suggested that the code arose in fulfillment of Kant’s construction of dynamics, namely that the triplet question posed above is not one of simple recognition but rather by logical constraint to circumscribe any possible balance of general repulsions and attractions (two fundamental metaphysical force kinds).

Thus the amino acids represent the filling of biological space so as to resist other bodies from entering the same reproductive continuum. Different code systems thus represent different systems of resistance and thus target different sets of impact/environmental/mutation forces. This means that there should be classes of mutagens that do not merely affect rates of mutations (randomly) as understood by Wright, but this is the maximal extent that the code can “evolve”.

Crick also said,

“The evolution of the code sketched here has the property that it could produce a code in which the actual allocation of amino acid to codons is mainly accidental and yet related amino acids would be expected to have related codons. The theory seems plausible but as a theory it suffers from a major defect: it is too accommodating.

In a loose sort of way it can explain anything. A second disadvantage is that the early steps needed to get the system going seem to require rather a lot of chance effect. A theory of this sort is not necessarily useless if one can get at the facts experimentally. Unfortunately, in this problem this is just what is so difficult to do.”

The metaphysical reading does not permit accidental relations but may express something like the principle of substance stability (Gladyshev) as the volume of resistance is enlarged (during possible growth).and it does not suggest “chance effect” but rather simply a better logic of the infinite in positing.

On this reading, evolution in Mendelian populations occurs because of the logical bifurcation that any pair of repulsions and attractions can compose phoronomically. Life is the dyad of this kinematics. Sex can double the impact forces dealt with in the dyad.

Thus, this organon indicates that notions of bacterial sex confuse the substance of resistance with the thermostat of the dyad. This understanding however should not be read as implicating in any way “intelligent design” of the genetic code.


This message is a reply to:
 Message 1 by kuresu, posted 04-26-2007 2:17 PM kuresu has not yet responded

Replies to this message:
 Message 141 by Iblis, posted 06-01-2010 7:22 PM Brad McFall has responded

  
Brad McFall
Member (Idle past 4024 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 142 of 143 (562793)
06-01-2010 7:33 PM
Reply to: Message 141 by Iblis
06-01-2010 7:22 PM


Re: metaphysical codes
The idea is way to nascent for me to have thought extensively with it. There would be some relation what amino acids go on what codons if this is correct but whether that should be thought from metaphysical or physical principles (such as substance stability) I have not worked on. I used some empirical thoughts to drill down into Kant's reasoning (as against critics) but this can not be the way it should be written if the interpretation is correct. I would need to explicate the positing of being in outersense without ID for instance. I have not tried to think of this.

The reason I was able to think this was because the notion of chemistry for Kant is transitive (relative to physics and teleology) which is supported by phoronomics and the angle other than an orthogonal one ("rectum") is out of the "picture". It is clear to me if this idea is correct DNA is not"digital" in anyway. I have not even begun to think about RNA much yet. It has some relation to 1-D symmetry in the density as I started to talk about in a page linked to the one I put in the post above.


This message is a reply to:
 Message 141 by Iblis, posted 06-01-2010 7:22 PM Iblis has not yet responded

  
Brad McFall
Member (Idle past 4024 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 143 of 143 (565546)
06-17-2010 6:26 PM
Reply to: Message 141 by Iblis
06-01-2010 7:22 PM


Re: metaphysical codes
It is begining to appear to me even more subjectively that the idea here may be of value. It would mean that Crick’s idea of a “frozen” accident is wrong, and that Kaufmann’s simple network beyond the algorithm notion of the genetic code is also off. The circularity(supposed) in the notion of Density (of Kant) may be possiblly cognized in the different codon triples for the same amino acid.

Historically, the idea would make sense of Orested’s JUDGeMENT that gavalnic forces are between electric and magnetic (thought by him before he observed deviation of the mag needle under a moving current) and this would be DNA.

RNA using a different base would imply that a slightly different relation to volumes (of attraction and repulsion) is possible to be figured in the proteins rather than in the any construction from the DNA itself and it may be that this is the macrothermodynamic use of substance stability.\

I am beginning to be able to think of translation phoronomically. RNA would enable “re-programming” of case one and two phoronomic situations under a given angle of case 3 but this would not be like digital algorithms in computers nor simple networks as understood by Kaufmann with switches. The programming would change the relative 1-D symmetry effects per gene. The difficulty is that the unity of the concept is not thought by single base mutations but rather by supramolecular interactions of a larger dimension.

The real stumbling block for many will be that the metaphysics requires some thought of absolute space, which since Mach and even Poincare has been deprecated.

The idea is not dead in the water nor red carded but it would be of such huge importance if true that I refrain from anything but the most mild indulgence in the thought.

I have begun to think with this notion on the following pages
http://axiompanbiog.com/CroizatMethod.aspx
http://aexion.org/eeintroduction.aspx
http://aexion.org/codemetaphysics.aspx
http://axiompanbiog.com/ingentracks.aspx
http://axiompanbiog.com/basics.aspx


This message is a reply to:
 Message 141 by Iblis, posted 06-01-2010 7:22 PM Iblis has not yet responded

  
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