Stan,
Your nested solution to my query�What is biological life and where
did it come from?�seems reasonable at first blush. I'm good with
"(1)...begin with physical dynamics, which are continuous." But then
I get progressively more bothered by the notions of "entraining
chemical species" (2), "connected in historical accident" (3), and
"...functioning as a template" (4). While I also feel that something
like this could have happened, I still don't know HOW a digitally
"symbolic" (non-stereochemical) language arises to hold the necessary
code. At lot is left to conjecture. And why only one code with only
one chemical template? So I'm searching for possible principles,
alternative principles maybe, that allow for the distillation of
digital information from analogous bits of matter. (I do like your
argument #2, however..."discrete bits of matter participating in
digital relations.") But nests and hierarchies seem to get me only
part of the way; they appear to me to be biased toward analogs.
Regards, Richard
On Nov 12, 2006, at 3:00 PM, Stanley N. Salthe wrote:
> Replying to Richard (who I will rely on to place it in fis, where I am
> treated as SPAM) if he feels a reply is warranted. He said:
>
>> But how did those upstart crystalline micelles, containing
>> numerical/chemical relations, learn algebra well enough to enable the
>> emergence of a genetic code?� How did such a uniquely non-analogous
>> language for communicating pure digital information in biological
>> systems
>> come into existence?
>> Maybe this emergent property cannot be explained in hierarchical
>> terms
>> applying to a single universe.� Maybe the emergent property Jerry
>> speaks
>> of is evidence of another universe, a coincidental one, where
>> digits rule
>> and analogs are the exception. Yes, it's a wild idea.� But I don't
>> think
>> there is enough hierarchy in this pedestrian universe of ours to
>> get us
>> the principles we need to explain what biological life actually is
>> and
>> where it came from.
>
> (1) Well, we begin with physical dynamics, which are continuous
> (2) these entrain chemical species, which are discrete bits of matter.
> Being discrete bits of matter, they can participate in 'digital'
> relations
> -- A with B, with a certain intensity, which varies between pairs
> according
> to kind.
> (3) Biology appears when some chemical kinds that happened to become
> connected in an historical accident, found themselves rather
> tightly bound.
> As a more-than-microscopic association, these have preserved history.
> (4) Eventually one kind of these more-than-microscopic entities finds
> itself functioning as a template on which rather similar entities
> have a
> tendency to form. The historical moment this kind had preserved
> now can
> survive its passing, when it eventually breaks down.
>
> So, {interactions {between kinds {at given moments}}}.
>
> STAN
>
>
>
>
> ------------------------------------------
>> Jerry,
>> You wrote:
>>
>> Biological information emerges as flows of changes of chemical
>> relations -
>> metabolic dynamics.�
>>
>>
>> By what principle does this emergent property you describe�adopt a
>> specifically digital language to manage those analogously chemical
>> affairs
>> of biological systems?� To recognize such an emergent property I
>> would
>> have to agree to a few brave assumptions.� One would be that
>> biological
>> systems, comprising hierarchical atoms and molecules, are just
>> naturally
>> capable of writing their own operational programs.� That's a reach
>> for me,
>> because nothing is explained.� Even though I am aware that
>> organisms do
>> exactly that, there are no principles I know of to support it.�
>> HOW they
>> do it (not WHY they do it) is the key issue for me.� How do
>> analogs write
>> their own digital scripts?� One again, the only other time in natural
>> history that I know of this sort of thing happening was when human
>> analogs
>> wrote their own digitally symbolic language about 10,000 years ago.
>> As Stan has said:
>>
>> Of course, the origin of the genetic system is arguably the
>> mostoutstanding problem facing natural science.��
>>
>>
>> �And you go on to say:
>>
>> Thus, if one wishes to develop a compelling argument about chemical
>> numbers and structures and genetic information,� one should start
>> with
>> relational algebras that keep track of changes of relations...�A
>> living
>> system is a society of associative relations among atomic numbers.��
>>
>>
>> If an emergent property truly emerges in nature I think it ought
>> to do so
>> on first principles.� Still, to argue that "biological
information
>> emerges
>> as flows of changes..." interests me. Seems a little like a DC
>> electrical
>> system�something new for me to worry about.� But how did those
>> upstart
>> crystalline micelles, containing numerical/chemical relations, learn
>> algebra well enough to enable the emergence of a genetic code?�
>> How did
>> such a uniquely non-analogous language for communicating pure digital
>> information in biological systems come into existence?
>> Maybe this emergent property cannot be explained in hierarchical
>> terms
>> applying to a single universe.� Maybe the emergent property Jerry
>> speaks
>> of is evidence of another universe, a coincidental one, where
>> digits rule
>> and analogs are the exception. Yes, it's a wild idea.� But I don't
>> think
>> there is enough hierarchy in this pedestrian universe of ours to
>> get us
>> the principles we need to explain what biological life actually is
>> and
>> where it came from.
>> Best regards, Richard
>> On Nov 11, 2006, at 8:19 AM, Jerry LR Chandler wrote:
>>
>>
>> (To the List: I am re-posting my message to Karl because the original
>> message was not distributed in it's totality; the arguments were
>> truncated.� Cheers� Jerry )
>> Karl:
>> I fear that I must once again disagree with your strong
>> conclusions about
>> the relations between mathematics and genetics.� I would urge you to
>> attempt to find exact correspondence relations between empirical
>> evidence
>> and your views of models based on numbers.
>> See my comments below.
>> Subject: [Fis] genetics: the most outstanding problem, SOLVED
>>
>> Dear Stan,
>> In your last posting, you said:� � SS:� Of course, the origin of the
>> genetic system is arguably the mostoutstanding problem facing natural
>> science.� It seems that, other than the(to me) unconvincing RNA World
>> idea, there is no compelling model of it.
>> The model that the RNA (together with the DNA) is a sequence and that
>> thegenetic mechanism copies the information from a sequence (the
>> dna/rna)
>> intoa nonsequenced assembly (the living organism) and from there
>> (by means
>> ofthe ovaries and the testes) back into a sequence is a quite
>> compellingmodel.
>> The term "information" has been shown in this chatroom to
mean the
>> cuts
>> thatsegregate, separate and distinguish summands;The term
>> "sequence" has
>> been defined by Peano;The term "nonsequenced /=commutative/
>> assembly" is
>> indeed hairy, as thereexists no definition for multidimensional
>> partitions, although this is whatit means;The term "copies"
means
>> a filter
>> restriction on a set of entries into adatabase (a restricted, in
>> optimal
>> case, bijective map between twoenumerations).
>>
>> I certainly will not support this view of the relationships among
>> numbers,
>> genetics and information.I find your post to be outside the scope
>> of the
>> standard theories of biochemistry and genetics.
>> Chemical information is grounded in the list of chemical elements
>> and the
>> relations among them.The terms "DNA" and "RNA"
etc, are chemical
>> names of
>> specific relationally rich bio-molecules.The information content of
>> chemical molecules must be expressed in terms of atomic numbers and
>> relations among the electrical particles (graphs).Biological
>> information
>> emerges as flows of changes of chemical relations - metabolic
>> dynamics.�
>> In general, chemical structures / information does support transitive
>> relations among the atomic numbers organized into graphs.��
>> Thus, if one wishes to develop a compelling argument about chemical
>> numbers and structures and genetic information,� one should start
>> with
>> relational algebras that keep track of changes of relations.��
>> Bijective maps are not a suitable basis for describing change of
>> chemical
>> relations and hence the flow on biological information.
>> Finally, if one wishes to describe a mathematics of biological
>> information, the suitable starting point is the fact that a single
>> position in a DNA sequence can control the fate of the entire
>> organism.� A
>> living system is a society of associative relations among atomic
>> numbers.�
>> Cheers
>> Jerry
>>
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Received on Mon Nov 20 23:10:26 2006
