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Author Topic:   The "Digital Code" of DNA
Rob 
Suspended Member (Idle past 3196 days)
Posts: 2297
Joined: 06-01-2006


Message 136 of 143 (410529)
07-15-2007 4:53 PM
Reply to: Message 135 by kuresu
07-15-2007 3:54 PM


Re: Getting downright logical...
Kuresu:
Your argument about theory and theology was that they have the root word "theo" in them. If we look at their etymologies, we see that theory comes from, "thea" + "horan". Theology comes from "theo" + "logos". Thea is not theo. Possibly similar, but not the same. Your argument that the root is "theo" is false.

My argument that 'theo' is the root of both is correct. You found the Latin but not the Greek Etymology.

The spelling coincidence is no coincidence at all...

Main Entry: the·o·ry
Pronunciation: 'thE-&-rE, 'thir-E
Function: noun
Inflected Form(s): plural -ries
Etymology: Late Latin theoria, from Greek theOria, from theOrein
(http://www.m-w.com/dictionary/theory)

But... even if it were the case that you made (which it is not), their meanings (which was the point) are the same, as I showed in the previous post.

Kuresu:

I do not need faith to know that logic is valid. I can see it right in front of me.

Very good...

Then you can see 'right in front of you' the problem with our current convention of science, not being ultimately concerned with philosophical coherence as Susan Kruglinski confesses in her critique of Intellignet Design.

After a searching review of the record and applicable caselaw, we find that while ID arguments may be true, a proposition on which the Court takes no position, ID is not science....

...Expert testimony reveals that since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena. This revolution entailed the rejection of the appeal to authority, and by extension, revelation, in favor of empirical evidence. Since that time period, science has been a discipline in which testability, rather than any ecclesiastical authority or philosophical coherence, has been the measure of a scientific idea's worth.

(http://discovermagazine.com/2005/dec/intelligent-design/?searchterm=bacterial%20flagellum)

The only authority, is the revelation given by logic itself. And neither you nor I invented it. So our 'own words' are really irrelevant. Our minds and words must conform to logic.

Do I give up my own imagination in the process?

Partially... because everything that fails the coherency test (though I may have given my life and reputation to it) must be given up.

Logic doesn't stop me from thinking creatively... it just gives me a valid lens with which to judge myself and the world around me.

For the record, I don't hink you are a bad debater, or preacher, or whatever... I just think I treated you too harshly in the past because of my own immaturity. So your lashing out...

Two proud men, acting like children.

I'll take a few lashes in exchange for your friendship. I have been wrong and have said some terrible things, losing sight of the goal... Forgive me.

Edited by Rob, : No reason given.

Edited by Rob, : No reason given.


This message is a reply to:
 Message 135 by kuresu, posted 07-15-2007 3:54 PM kuresu has responded

Replies to this message:
 Message 137 by Dr Adequate, posted 07-15-2007 7:44 PM Rob has not yet responded
 Message 138 by kuresu, posted 07-16-2007 2:58 AM Rob has not yet responded

    
Dr Adequate
Member
Posts: 15468
Joined: 07-20-2006
Member Rating: 3.8


Message 137 of 143 (410548)
07-15-2007 7:44 PM
Reply to: Message 136 by Rob
07-15-2007 4:53 PM


Re: Getting downright logical...
My argument that 'theo' is the root of both is correct. You found the Latin but not the Greek Etymology.

He provided both, and following the links, I find:

"From Greek θεωρία "contemplation, speculation", from θεωρός "spectator," literally "one looking at a show", from *θεᾱ+ϝορός > θε(ε)ωρός."

Nothing to do with God, you note. In fact, the English word with which it plainly has a relationship is theater.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 136 by Rob, posted 07-15-2007 4:53 PM Rob has not yet responded

  
kuresu
Member (Idle past 2622 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 138 of 143 (410593)
07-16-2007 2:58 AM
Reply to: Message 136 by Rob
07-15-2007 4:53 PM


Re: Getting downright logical...
You found the Latin but not the Greek Etymology.

So you apparently can't read. Thanks for the confirmation. Really funny, too, given that "thea" is greek.
quote:
The english word "theory" comes from the latin "theoria" and the greek "θεωρία".

[qs=kuresu]If we look at their etymologies, we see that theory comes from, "thea" + "horan".[/quote]
www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=121#121 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=121#121">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=121#121
www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=135#135 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=135#135">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=13&t=83&m=135#135

And I'm so glad you found the merriam webster etymology. Try the online etymology dictionary.

theory
1592, "conception, mental scheme," from L.L. theoria (Jerome), from Gk. theoria "contemplation, speculation, a looking at, things looked at," from theorein "to consider, speculate, look at," from theoros "spectator," from thea "a view" + horan "to see." Sense of "principles or methods of a science or art (rather than its practice)" is first recorded 1613. That of "an explanation based on observation and reasoning" is from 1638. The verb theorize is recorded from 1638.

http://www.etymonline.com/index.php?search=theory

If you'll notice, theorien comes from theoros which comes from thea + horan. "thea + horan" is quite different from "theo + logos".

theology
1362, from O.Fr. theologie "philosophical treatment of Christian doctrine" (14c.), from L. theologia, from Gk. theologia "an account of the gods," from theologos "one discoursing on the gods," from theos "god" (see Thea) + -logos "treating of."

So yes, you are quite wrong on "theo" being the root of theory and theology. As they say, spelling counts.

What do do "thea" and "theo" mean? Depending on the dictionary, "thea" is the feminine of "theo". However, in the etymologies I find, "thea" is always connected to the idea of seeing.

Then you can see 'right in front of you' the problem with our current convention of science, not being ultimately concerned with philosophical coherence

This is a problem how? By the way, Susan Kruglinski is not confessing to any problem. In fact, it's not Susan writing this. This is the opinion given by the judge of the Kitzmiller vs. Dover trial. So you should be saying the judge is admitting to this problem. Trouble is, he's not. He's stating what science is.

And I still fail to see how this focus on testability (i would rather use empirical evidence + testability) instead of philosophical coherence is a problem. Why?
It might be philosophically coherent that A = B, but if reality shows that A actually = C, then the truth is that A = C.

So your lashing out...

If I'm lashing out, it's not your past history here toward me per se, it's your continual repitition of refuted and/or irrelevant points. It's your continual preaching. At least this time (yet) you haven't started playing the martyr card.
This message is a reply to:
 Message 136 by Rob, posted 07-15-2007 4:53 PM Rob has not yet responded

    
Chiroptera
Member (Idle past 1926 days)
Posts: 6202
From: Oklahoma
Joined: 09-28-2003


Message 139 of 143 (457617)
02-24-2008 2:08 PM


PZ Meyers weighs in on DNA "codes"
In the lastest post on Pharyngula, PZ Meyers explains why DNA is not really a computer program, and that a computer program is not even a good analogy for the way DNA works in the genome.

I figure this should have some relevance to whether we should recognize DNA as a "digital code".


If I had a million dollars, I'd buy you a monkey.
Haven't you always wanted a monkey?
-- The Barenaked Ladies
  
Brad McFall
Member (Idle past 2380 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 togetherthis 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 Kants 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

    
Iblis
Member (Idle past 1243 days)
Posts: 663
Joined: 11-17-2005


Message 141 of 143 (562791)
06-01-2010 7:22 PM
Reply to: Message 140 by Brad McFall
06-01-2010 7:03 PM


Re: metaphysical codes
Hi Brad, good to see you here again.

Have you got any ideas for experiments to tickle this idea with? The RNA World people have done some things with exo-cellular replication just lately that are continually bothering me. They seem to indicate that reproduction begins as simple linear accretion in strands. This does occur in both directions, though, so perhaps a variation from this (at right angles, as it were) is what produces the triplets you are looking at. Unless I'm missing something important?


This message is a reply to:
 Message 140 by Brad McFall, posted 06-01-2010 7:03 PM Brad McFall has responded

Replies to this message:
 Message 142 by Brad McFall, posted 06-01-2010 7:33 PM Iblis has not yet responded
 Message 143 by Brad McFall, posted 06-17-2010 6:26 PM Iblis has not yet responded

  
Brad McFall
Member (Idle past 2380 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 2380 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 Cricks idea of a frozen accident is wrong, and that Kaufmanns 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 Oresteds 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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