DNA to represent proteins
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Evgenii Rudnyi
Nov 10, 2012, 7:40:49 AM11/10/12
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Recently I have read Bas C Van Fraassen Scientific Representation:
Paradoxes of Perspective where a representation is defined as
p. 21 “Z uses X to depict Y as F”
Does it make sense to say “Z uses” when Z is not a human being? For
example, what is a meaning of a sentence “a robot uses X to depict Y as F“?
Below I will present some sense for the statement that a DNA is a
representation of proteins. I will go along arguments of Marcello
Barbieri expressed in
Barbieri, M. (2007). Is the cell a semiotic system? In: Introduction to
Biosemiotics: The New Biological Synthesis. Eds.: M. Barbieri, Springer:
179-208.
http://www.springerlink.com/content/n0143kh20946g050/
Well, if a cell could be considered as a semiotic system then it should
be also possible to find a representation of a protein in the DNA. First
it is worthy to be mentioned that according to Barbieri
“Genes and proteins, in short, are assembled by molecular robots on the
basis of outside instructions. They are manufactured molecules, as
different from ordinary molecules as artificial objects are from natural
ones. Indeed, if we accept the commonsense view that molecules are
natural when their structure is determined from within, and artificial
when it is determined from without, then genes and proteins can truly be
referred to as artificial molecules, as artifacts made by molecular
machines. This in turn implies that all biological objects are
artifacts, and we arrive at the general conclusion that life is
artifact-making.”
This means that in principle the result should concern robots as well.
In our case, it is easy to identify X, Y, and F in the definition of a
representation:
“Z uses a gene in DNA to depict a protein as a primary sequence“.
What is left is to find out a meaning of “Z uses” in respect to a
biological cell. This could be, according to Barbieri, a codemaker:
“Protein synthesis arose therefore from the integration of two different
processes, and the final machine was a
code-and-template-dependent-peptide-maker, or, more simply, a codemaker.
The second Major Transition of the history of life (Maynard Smith and
Szathmáry, 1995) is generally described as the origin of proteins, but
it would be more accurate to say that it was the origin of codemaking,
or the origin of codemakers, the first molecular machines that
discovered molecular coding and started populating the Earth with
codified proteins.”
“It is an experimental fact, at any rate, that every cell contains a
system of RNAs and ribonucleoproteins that makes proteins according to
the rules of a code, and that can be described therefore as a
“code-and-template-dependent-protein-maker”, i.e. as a “codemaker”. That
is the third party that makes of every living cell a trinity of
genotype, phenotype and ribotype. The genotype is the seat of heredity,
the phenotype is the seat of metabolism and the ribotype is the seat of
the genetic code, the codemaker of the cell.”
In my understanding, a codemaker then is a collection of molecules (a
molecular machine) that produces a protein from a DNA. Now similar to
the logic in Barbieri’s paper one can write
“A codemaker uses a gene in DNA to depict a protein as a primary sequence“.
The sentence is complete now. For me however the question remains if
such a sentence has a meaning. Let me quote Barbieri again:
‘The sequence of a gene and the sequence of a protein, in conclusion,
may look like “objective” properties of these molecules, but they are
not. They are “codemaker-dependent” entities because they do not exist
without a codemaking process, and because they would be different if the
codemaker had a different conformation. The sequences of genes and
proteins, in short, have the essential characteristics that define signs
and meanings, and we can say therefore that they “are” organic signs and
organic meanings.
More precisely, we can say that “an organic sign is the sequence used by
a codemaker in a coding process”, and that “an organic meaning is the
sequence produced by a codemaker in a coding process”. All we need to
keep in mind is that signs and meanings are mental entities when the
codemaker is the mind, but they are organic entities when the codemaker
is made of organic molecules.’
It well might be that we can employ “depict” in such a sense but in my
view not without remaining strain.
Evgenii
--
http://blog.rudnyi.ru/2012/11/dna-to-represent-proteins.html
Paradoxes of Perspective where a representation is defined as
p. 21 “Z uses X to depict Y as F”
Does it make sense to say “Z uses” when Z is not a human being? For
example, what is a meaning of a sentence “a robot uses X to depict Y as F“?
Below I will present some sense for the statement that a DNA is a
representation of proteins. I will go along arguments of Marcello
Barbieri expressed in
Barbieri, M. (2007). Is the cell a semiotic system? In: Introduction to
Biosemiotics: The New Biological Synthesis. Eds.: M. Barbieri, Springer:
179-208.
http://www.springerlink.com/content/n0143kh20946g050/
Well, if a cell could be considered as a semiotic system then it should
be also possible to find a representation of a protein in the DNA. First
it is worthy to be mentioned that according to Barbieri
“Genes and proteins, in short, are assembled by molecular robots on the
basis of outside instructions. They are manufactured molecules, as
different from ordinary molecules as artificial objects are from natural
ones. Indeed, if we accept the commonsense view that molecules are
natural when their structure is determined from within, and artificial
when it is determined from without, then genes and proteins can truly be
referred to as artificial molecules, as artifacts made by molecular
machines. This in turn implies that all biological objects are
artifacts, and we arrive at the general conclusion that life is
artifact-making.”
This means that in principle the result should concern robots as well.
In our case, it is easy to identify X, Y, and F in the definition of a
representation:
“Z uses a gene in DNA to depict a protein as a primary sequence“.
What is left is to find out a meaning of “Z uses” in respect to a
biological cell. This could be, according to Barbieri, a codemaker:
“Protein synthesis arose therefore from the integration of two different
processes, and the final machine was a
code-and-template-dependent-peptide-maker, or, more simply, a codemaker.
The second Major Transition of the history of life (Maynard Smith and
Szathmáry, 1995) is generally described as the origin of proteins, but
it would be more accurate to say that it was the origin of codemaking,
or the origin of codemakers, the first molecular machines that
discovered molecular coding and started populating the Earth with
codified proteins.”
“It is an experimental fact, at any rate, that every cell contains a
system of RNAs and ribonucleoproteins that makes proteins according to
the rules of a code, and that can be described therefore as a
“code-and-template-dependent-protein-maker”, i.e. as a “codemaker”. That
is the third party that makes of every living cell a trinity of
genotype, phenotype and ribotype. The genotype is the seat of heredity,
the phenotype is the seat of metabolism and the ribotype is the seat of
the genetic code, the codemaker of the cell.”
In my understanding, a codemaker then is a collection of molecules (a
molecular machine) that produces a protein from a DNA. Now similar to
the logic in Barbieri’s paper one can write
“A codemaker uses a gene in DNA to depict a protein as a primary sequence“.
The sentence is complete now. For me however the question remains if
such a sentence has a meaning. Let me quote Barbieri again:
‘The sequence of a gene and the sequence of a protein, in conclusion,
may look like “objective” properties of these molecules, but they are
not. They are “codemaker-dependent” entities because they do not exist
without a codemaking process, and because they would be different if the
codemaker had a different conformation. The sequences of genes and
proteins, in short, have the essential characteristics that define signs
and meanings, and we can say therefore that they “are” organic signs and
organic meanings.
More precisely, we can say that “an organic sign is the sequence used by
a codemaker in a coding process”, and that “an organic meaning is the
sequence produced by a codemaker in a coding process”. All we need to
keep in mind is that signs and meanings are mental entities when the
codemaker is the mind, but they are organic entities when the codemaker
is made of organic molecules.’
It well might be that we can employ “depict” in such a sense but in my
view not without remaining strain.
Evgenii
--
http://blog.rudnyi.ru/2012/11/dna-to-represent-proteins.html
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