Re: Genetics as a Language System
- From: "Kleuskes & Moos" <kleuske@xxxxxxxxx>
- Date: 31 Oct 2005 11:23:49 -0800
Seanpit schreef:
> John Harshman wrote:
>
> > Please, can we stop referring to the
> > genome as "the genetic code" or
> > "genetic codes". There is a perfectly
> > good word for what you are talking
> > about, i.e., "the genome", and
> > "genetic code" has a perfectly good
> > meaning of its own. All you do is
> > confuse things.
>
> The genome is made up of coded information. These codes are indeed
> "genetic codes". They aren't "The Genetic Code", but they are genetic
> codes none-the-less. All of these codes are language systems, to
> include The Genetic Code.
>
> > > Isn't genetic information written
> > > in coded form just like any other
> > > symbolically represented language
> > > system? Different sequences of base
> > > pairs are decoded with the use of
> > > specific rules of grammar.
> >
> > It's stretching way too far to call
> > the mapping of codons to amino acids
> > "grammar". Grammar is what is supposed
> > to enable a language to represent
> > an infinite number of thoughts. All
> > this "grammar" can do is represent
> > 20 amino acids in linear strings. No
> > real grammar is anywhere near that
> > simple.
>
> Isn't it interesting that the Morse Code can only represent 26 letters
> of the alphabet and some punctuation and yet it can be used to express
> an infinite number of thoughts? Funny how the same thing is true of
> computer codes which only use a basis of two symbols to express an
> infinite number of thoughts as well. The genome uses four different
> bases to express an infinite number of protein-based systems and other
> non-protein based functions. Sure looks to me like they are all the
> same - no fundamental difference. They are all language systems.
*FORMAL* language systems, and besides, Morsecode is merely a
steganographic system in shich *SINGLE LETTERS* are translated to
sequences of dashes and dots. In itself, morsecode does *not* allow you
to express any thought, but serves merely as a coding system (formal
language" to describe individual characters, like ASCII. Computer-codes
are narrowly defined to translate sequences of bits into computer
instructions or data. By themselves these do not imply a working
program, as I have explained in the post answering your first one.
Just for clarity: a formal language does not equal (and is not even
simular
to) a human/natural language.
> See the following thread if you won't take my word for it:
http://groups.google.com/group/talk.origins/msg/30472e6f0b052a2d?dmode=source&hl=en
You grossly misrepresent the content of that post. This is the third
time, and I resent that.
> > Where is the similarity aside from
> > this labored comparison? What kind of
> > language has only 64 words and two
> > forms of punctuation? What does it
> > gain us to call the genetic code
> > a language, or proteins sentences?
>
> It's more like 64 codes which code for 20 different letters in
> particular sequences that can themselves be compared to words,
> sentences, paragraphs, etc.
There are no words, paragraphs or sentences in the formal language of
DNA/RNA. This is (again) a gross misrepresentation of the facts.
> Again, computer languages are built on just two letters.
In fact computer languages are built on many *more* letters, they
usually employ ASCII sequences which are tokenized and parsed. If you
do not know the very basics of computer programming, please refrain
from drawing any conclusions based on that.
> At least genetics is built upon a basis of 4 fundamental characters.
Which are couples into tokens (triplets) and parsed by the ribosome.
The language used therein is in fact much more simple than 'computer
lamguages'.
Your analogies, from my perspective, "slaan als een lul op een
drumstel", that is, make no sense at all. You groslly misrepresent the
meaning of the post you are referring to.
I resent that.
> > Where do you look this up?
>
> See the link listed above.
yes. tjat post is mine. It also states you ignore much of the problem
and draw conclusions not supported by any facts.
> > True, if you distort the meaning of
> > "meaningful" to be "beneficial". But
> > what are the rules of grammar that
> > let us tell whether a sequence is
> > "meaningful"?
>
> It has to make sense to the one reading it.
In this case the ribosome, which deals with a single triplet at a time.
It is important to note that no triplet exists which will break the
translation. Much in contrast to (for instance) the computer laguanges
you mention. The quality descibed is called /closure/, a property which
is crucial to mutating systems and which is absolutely lacking from
computer languages, the resulting object-code or any human language.
> You have to be able to put the information together in a informationally
> complex way that "works" in a logical integrated emergent way.
Thi is easily achieved when using a language which has closure. Any
sequence of triplets result in a polypeptide. There is no way to break
the translation process by inserting some codon. The worst that can
happen is that the resulting polypeptide is not functional, the usual
consequence is a polypeptide that functions differently.
You once more ignore the fact that the formal language in DNA has a
very limited scope and that much of the actual functionality is
determined by many different systems, as I allreay pointed out in the
post you now quote.
I resent that.
> If the reading apparatus of the cell didn't know how to read its own genetic
> sequences "correctly", the cell would rapidly disintigrate.
Fortunately, there are no codons that would result in the ribosome not
producing a polypeptide. Again, the formal language described by DNA
has /closure/, much in contrast to the object-code your computer
employs, which is very fragile.
> > It would seem that you have
> > shifted analogies massively
> > here without noticing. From grammar
> > being the genetic code, you now must
> > have the rules of grammar include
> > all the interactions among proteins
> > and the environment that determine w
> > hether a given sequence is
> > selectively advantageous or not.
> > Your "grammar" is now natural selection.
>
> Natural selection is a big part of the "reading for useful content"
> process. The "grammar" must make sense in the "context" of nature or
> the surrounding environment.
The formal language described is explicitly context INDEPENDENT. and
has nothing to do with the "surrounding environment". It merely codes
for sequences of aminoacids. How these function in the environment, is
irrelevant.
> The informaiton being read must make sense to the audience.
The audience, in this case, being the ribosome. Any triplet can be
interpreted, so no matter how much mutations occur, a polypeptide will
always be the result.
How this polypeptide eventually interacts with it's environment, is not
determined bty the DNA itself. There are many other mechanisms at work,
which have *ZILCH*, *NIENTE*, *NADA* to do with the formal language
described.
As I stated in the post you now gleefully refer to, you are ignoring
(out of ignorance or malice) many othere layers of functonality.
> And, for the genome in particular, the audience
> is the environment in which the genome is supposed to function
> "successfully"- as defined by competative survival.
Bullshit. The only "audience" is the ribosome. There are many other
factors which wil determine expression of genes, regulation of genes,
enzyme activity, signal substances (Sonic Hedgehog, once again).
> If what the cell "reads" doesn't make sense in light of the surrounding
> environment, that cell and its genome will die out of the gene pool.
Bullshit. First of, the cell reads nothing. Ribosomes do. They will
produce a sequence of aminoacids, which may (if the DNA sequence has
mutated) have a completely different function.
> It is nature that decides whether or not something "makes sense" in this
> language system.
Nope. It is the ribosome, and any sequence of triplets will result in
*some* polypeptide. Wether or not this sequence of aminoacids has any
function at all, or a very different function if the genome was
mutated, is quite another matter.
You consistently employ oversimplifications and misrepresent my
argument.
I resent that.
>
> > > Exactly the same thing is true of all
> > > language systems. They all work,
> > > fundamentally, the very same way.
> > > They are the same. Genetics is a
> > > language system(s).
> >
> > Repeating a claim doesn't
> > make it true or convincing.
>
> There are others, besides myself, who find this concept very
> convincing. Mainstream papers have been written on this.
Carefully avoiding, however, the gross misrepresentations and
oversimplifications your argument relies on. The guys that wrote the
papers (to which I provided the references) know better than that and
actually *have* an understanding of the *very* limited scope of this
formal language.
> Perhaps you
> are just incapable of finding it "convincing" because I'm the one
> saying it?
Perhaps he knows by gut feeling your argument is utterly misleading?
> But, if someone else said exactly the same thing, it would
> suddenly make much more sense to you? Go figure . . .
If anyone in the realm of formal language theory made claims like
yours, no one would take him/her seriously.
> The same thing happened to Richard Forrest. I can explain how genetics
> really is a language system all day long and he will never be
> convinced.
Once again, you misrepresent the facts. I explained how genes are a
formal language system. Even in the title of this post, you make the
grave error of conflating *formal* language systems with languages.
> But, someone else comes along and says exactly the same
> thing, and suddenly it makes sense to him? What does that say about
> ones ability to think for one's self?
Once the fact has been established and backed up by publications and
fact, they are convinced. However it wasn't you that convinced them.
So that last paragraph is a blunt lie. Yu have not understood a word I
said, nor did you address any of the objections I made against your
claims.
I resent that.
.
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