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Author Topic:   DNA is not English
AnswersInGenitals
Member
Posts: 509
Joined: 07-20-2006


Message 16 of 26 (372640)
12-28-2006 6:46 PM
Reply to: Message 14 by 12345
12-28-2006 5:26 PM


Re: Useful analogy, but just an analogy.
Thank you for the correction and update. Has bactrial and synthetic insulin totally replaced that derived from animals? In either case, my point is still made, even amplified, that the genomic language has a lot of flexibility and nuances in it, a charactoristic of any 'real' language.
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12345
Inactive Junior Member


Message 17 of 26 (372641)
12-28-2006 7:26 PM
Reply to: Message 16 by AnswersInGenitals
12-28-2006 6:46 PM


Re: Useful analogy, but just an analogy.
I'm not 100% sure but I don't think animal insulin is used anymore-its much cheaper and "cleaner" to make it recombinantly.

I agree that the issue of nuance is extremely important. In my example of transcription factor binding the "context" in which the "word" is found can change its meaning. However there is a sense in which these sequence differ from a language. The sequence itself is what is bound. There is no "translation" from the language into the effect. The "word" is the object. I'm a bit out of my depth in linguistics so I'm not sure if I am being clear. An example of the idea I'm trying to get at is if you think of droping an apple. The apple falls to the ground. Do we say that the mass of the apple is the code or word that is translated by the laws of physics into an acceleration?


This message is a reply to:
 Message 16 by AnswersInGenitals, posted 12-28-2006 6:46 PM AnswersInGenitals has responded

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Chiroptera
Member
Posts: 6532
From: Oklahoma
Joined: 09-28-2003


Message 18 of 26 (372662)
12-28-2006 10:21 PM
Reply to: Message 17 by 12345
12-28-2006 7:26 PM


Re: Useful analogy, but just an analogy.
quote:
I'm a bit out of my depth in linguistics

Heh. So is Hoot. And so are John Maynard Smith and Eörs Szathmáry. I bet real linguists would have a thing or two to say about DNA being a "language".


I have always preferred, as guides to human action, messy hypothetical imperatives like the Golden Rule, based on negotiation, compromise and general respect, to the Kantian categorical imperatives of absolute righteousness, in whose name we so often murder and maim until we decide that we had followed the wrong instantiation of the right generality. -- Stephen Jay Gould
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AnswersInGenitals
Member
Posts: 509
Joined: 07-20-2006


Message 19 of 26 (372691)
12-29-2006 2:09 AM
Reply to: Message 18 by Chiroptera
12-28-2006 10:21 PM


What WOULD linguists say?
But the real question here, Chiro, is what, if anything, would linguists say? What would they add to our understanding of the usefulness of the analogy between genetic codes and languages: where it is enlightening; where it is deceptive? Do you have any inputs from or references to the linguists take on this issue? In particular, can the linguists shed any light on the very confusing and confused issue of discerning information content of the code or a language? Whoops! I mentioned information content, which means we'll soon get a post from Brad McF. That's usually about when I bow out of a thread. Brad certainly adds some interesting insights to the evolution of language.
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AnswersInGenitals
Member
Posts: 509
Joined: 07-20-2006


Message 20 of 26 (372693)
12-29-2006 2:16 AM
Reply to: Message 17 by 12345
12-28-2006 7:26 PM


Re: Useful analogy, but just an analogy.
12345 writes:

The apple falls to the ground. Do we say that the mass of the apple is the code or word that is translated by the laws of physics into an acceleration?

But the apple doesn't fall to the ground. It just follows its world line through space as that space is warped by the mass of the ground (earth), until it is stopped by its interaction with the ground (or some Englishman's head). So the question is: are the geometric constraints of space analogous to lanquage syntax? Or maybe the real question is: have we gotten off the road to total enlightenment and onto the road to total silliness?


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alexcj
Inactive Member


Message 21 of 26 (372706)
12-29-2006 6:22 AM
Reply to: Message 20 by AnswersInGenitals
12-29-2006 2:16 AM


Re: Useful analogy, but just an analogy.
Firstly, my humble apologies to admin for having two logins. I'm also 12345. I couldn,t remember the password I used on the work computer now that I'm at home.

Yes it has gotten silly but isn't that the point? The analogy has broken down when pushed.

OK I was using Newtonian physics instead of Einsteinian (I have no idea how I should spell or even use this word). I responded to this topic mainly because of other threads where a computer scientist says "DNA is just like a computer language, I have proved this about computer languages therefore evolution is false". This is a classic strawman, DNA is not just like other languages so anything you prove about other languages may not say anything about DNA. To pre-empt brad, if I may be so bold, the DNA language is an artificial human construct existing as an emergent property of the natural world filtered through the human conciousness.


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 Message 20 by AnswersInGenitals, posted 12-29-2006 2:16 AM AnswersInGenitals has responded

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AnswersInGenitals
Member
Posts: 509
Joined: 07-20-2006


Message 22 of 26 (372762)
12-29-2006 12:37 PM
Reply to: Message 21 by alexcj
12-29-2006 6:22 AM


Re: Useful analogy, but just an analogy.
To pre-empt brad

I know Brad McF. I have read Brad McF posts. And you, Sir, are no Brad McF. I understand everything you say in your post. In fact, I agree with everything you say.


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Fosdick 
Suspended Member (Idle past 3611 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 23 of 26 (372771)
12-29-2006 1:03 PM
Reply to: Message 14 by 12345
12-28-2006 5:26 PM


Re: Useful analogy, but just an analogy.
12345 re:

An example of where the DNA code can be thought of as more of an anologue rather than digital code is in transcription factor binding sites. Here the "code" is bound based on its "shape". The binding protein can recognise varients of the sequence and will bind more or less strongly and so will activate/deactivate transciption depending on the concentration of the transcription factor.

I think you are saying that a stereochemical pathway exists for genetic messages from DNA to proetins, allowing all the structural information to be communicated by way of mechanical bonding. I would agree. Why do you suppose the structural information in that message cannot travel backwards from the protein to the gene? Irreversible mechanics?

—Hoot Mon


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Fosdick 
Suspended Member (Idle past 3611 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 24 of 26 (372775)
12-29-2006 1:24 PM
Reply to: Message 15 by AnswersInGenitals
12-28-2006 6:43 PM


Re: Genetic "language" and syntax
AnswersInGenitals, re:

I have to disagree with Maynard Smith & Eörs Szathmáry, although I do so with trepidation since i have an almost reverential respect for these two. One of the fastest growing and most important fields in molecular biology and genetics is called bio-informatics. One of the major thrusts of this field is to use a set of very high power computer programs to scan through DNA codes and do exactly what Maynard Smith & Eörs Szathmáry say cannot be done: derive by logical reasoning the genetic content of that code, the gene interactions, and to some extent the structure of the encoded proteins of the DNA sequence. This is possible precisely because the DNA code does have a fairly rigorous syntax and a lot of the current work in genetics is devoted to deciphering that syntax.

This debate over genetic "language" seems heavily dependent on term definitions. Language, code, analog, digital, logic, meaning, syntax, etc. need commonly agreed-upon defintions. Syntax to one person may not be syntax to another. I think Maynard Smith & Szathmáry are following Noam Chomsky's agruments about language and syntax. In biology, language has a braod meaning. Bees, for example, are said to have a language to communicate all sorts of socially important infromation. But do bees communicate with syntax? Maybe so, maybe not.

—Hoot Mon


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ringo
Member
Posts: 16362
From: frozen wasteland
Joined: 03-23-2005
Member Rating: 3.4


Message 25 of 26 (372964)
12-30-2006 9:34 AM
Reply to: Message 23 by Fosdick
12-29-2006 1:03 PM


Re: Useful analogy, but just an analogy.
Hoot Mon writes:

I think you are saying that a stereochemical pathway exists for genetic messages from DNA to proetins, allowing all the structural information to be communicated by way of mechanical bonding. I would agree.

Hmm... I was under the impression that you were disagreeing in a couple of other threads. Thanks for the acknowledgement. :)

Why do you suppose the structural information in that message cannot travel backwards from the protein to the gene? Irreversible mechanics?

Is there a problem with a mechanical process being irreversible?


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This message is a reply to:
 Message 23 by Fosdick, posted 12-29-2006 1:03 PM Fosdick has responded

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Fosdick 
Suspended Member (Idle past 3611 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 26 of 26 (372980)
12-30-2006 11:22 AM
Reply to: Message 25 by ringo
12-30-2006 9:34 AM


Re: Useful analogy, but just an analogy.
Ringo, re:

Hoot Mon writes:
I think you are saying that a stereochemical pathway exists for genetic messages from DNA to proetins, allowing all the structural information to be communicated by way of mechanical bonding. I would agree.

Hmm... I was under the impression that you were disagreeing in a couple of other threads. Thanks for the acknowledgement.

Yes, I was, but I've had a change of heart. The issue of syntax has taken its toll on me. I tried hard to maintain my argument that a genetic language defies all known principles of chemistry and physics. I have to agree with you that stereochemical mechanical bonding is firmly in place through the DNA-to-protein information pathway, even if the digital codons are quite unlike the amino acids they select. But I still don't have a clue as to how such a system of genetic codification originated. Natural selection certainly played a big part, but how? (I came to this forum to get my head kicked into shape on the issue of digital genes in a world chemical analogs . Your hard-nose mechanics have help me to revise my argument. Thanks.)

Why do you suppose the structural information in that message cannot travel backwards from the protein to the gene? Irreversible mechanics?

Is there a problem with a mechanical process being irreversible?

No, not really. As AZPaul3 has asserted, NS counts for a lot in the formation of a genetic coding system. My problem is that I don't know how NS did its job on those genes. There are not very many good hypotheses to consider.

—Hoot Mon


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