Re: i-culture and m-culture. Encoded information

Timothy Perper/Martha Cornog (
Mon, 9 Jun 1997 08:53:55 -0500

Message-Id: <>
Date: Mon, 9 Jun 1997 08:53:55 -0500
From: (Timothy Perper/Martha Cornog)
Subject: Re: i-culture and m-culture. Encoded information

>> My tendency is to agree with Mario, and say that the information viewpoint
>> unifies a broad set of phenomena, including physical, biological, and
>> cultural systems. We can argue with endless sophistry about the nature of
>> "matter", for example, whether a specific piece of matter "is" code (is DNA
>> in a test tube matter or code?), but the argument goes nowhere.
Hans-Cees Speel>
>I do not understand this, bnut would like to very much. Why does this
>argument go nowhere? Especially since you state below that biologists
>have found the concept extremely valuable ever since? Please

TP: I was suggesting that the concept of "genetic" information has proven
useful, but that a distinction between "code" and "matter" can involve
sophistry. Thus, as a material substance, DNA consists of nucleotides,
phosphodiester linkages, and deoxyribose molecules -- one view of the
Necker cube, if you like. Alternatively, one can view the *same* molecule
as instantiating information, in the sense that the sequence of nucleotides
(ATGC) along the linear backbone of the DNA carries information for
specifying the amino acid sequence of a peptide. In a test-tube, DNA does
nothing except sit there -- it has no activities beyond Brownian motion and
the like. But even so, the information is still present, because the DNA
can be used, for example, to transform recipient cells from one phenotype
to another. The most useful way of looking at these facts is to say that
the "coded information" in the DNA is expressed in one environment and not
in another. Arguing about what the DNA "is" in some metaphysical sense
doesn't get us very far. Instead, we ask what the DNA *does* in different
environments -- and that line of questioning proves fruitful because it
lets us investigate the role of the environment empirically.

>> However,
>> we obtain *substantive* knowledge about DNA when we understand that if
>> placed in a cell-free protein synthesizing system, the sequence of
>> nucleotides in the DNA is "translated" reproducibly into a a sequence of
>> amino acids. It was the astronomer-mathematician George Gamow, in 1954,
>> who first used the terms "information" and "coding" for these biological
>> process, and biologists have found the concepts extremely valuable ever
>> since.
> <snip>
>> Furthermore, if we speak of "information," then we can also talk about how
>> information is *organized*. Thus, we know that chromosomes represent
>> linear arrays of genes, and that when a given piece of DNA is read by the
>> cellular machinery it is read from point A down the strand to point B.
>> Thus, genetic information, as *information*, is organized linearly. By
>> contrast, computer programs contain loops, so that information is organized
>> in *topologically* more complex ways in a computer program. (No DNA
>> transcription enzyme that I know of reads downstream, then moves back
>> upstream, and then moves downstream again.)
>I do not agree I think. Computer programs are linearly also, but can
>be red in loops. But so is DNA. The simple view ( which I do not
>argue you use) that DNA is linear is very narrow.

TP: BY "linear," I meant only the the nucleotide sequence is linear --
.....ATTGCGCTAGCT... -- and that genes are organized one after the next in
linear order on a chromosome. I wasn't discussing how genes interact with
each other during embryogenesis, say.


> DNA can be seen as
>controlling the cell, but the cell also controls what DNA is
>expressed at what time, so the controlling goes both ways.
>In this sense DNA is not linear, because expression goes in loops as

TP: very true.

>So I take ther view that the organization in for instance chromosomes
>is important to unmderstand replication of chromosomes, but has
>little influence on how it is expressed. There is generally no
>difference between a gene on one chromosome and on another when it
>comes to expression.>
>So when is this 'organization' to be relevant? Only with replication
>I would say. (but enlighten me if I am wrong).

TP: The local structure of the chromosome is important for whether the
gene is expressed or not. Thus, if the chromatin (which means the DNA plus
chromosomal proteins) is tightly coiled, then the coiled-up genes won't be
transcribed. But if we ask what determines the amino acid sequence of the
protein encoded by a gene, then the answer is the nucleotide sequence

Unfortuntely, the word "organization" in a phrase like "the organization of
the genetic information" can refer to nucleotide sequence, to chromosome
structure (karyotype) or to local three-dimensional coiling of the DNA
strand into what is called "euchromatin" or "heterochromatin." I
apologize if I was using a piece of jargon without explaining it, and hope
that's at least a little bit clearer!

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