Forwarding for Stan:
Begin forwarded message:
> From: "Stanley N. Salthe" <ssalthe@binghamton.edu>
> Date: November 12, 2006 3:00:59 PM PST
> To: Richard Emery <rmemery@earthlink.net>
> Subject: Re: [Fis] genetics: the most outstanding problem, (un)SOLVED?
>
> 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 Sun Nov 12 23:45:39 2006
