Re: [Fis] genetics: the most outstanding problem, (un)SOLVED?
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, RichardOn 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, SOLVEDDear 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
Fwd: [Fis] genetics: the most outstanding problem, (un)SOLVED?
Forwarding for Stan:Begin forwarded message:From: "Stanley N. Salthe" [EMAIL PROTECTED]Date: November 12, 2006 3:00:59 PM PSTTo: Richard Emery [EMAIL PROTECTED]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 amtreated as SPAM) if he feels a reply is warranted. He said: But how did those upstart crystalline micelles, containingnumerical/chemical relations, learn algebra well enough to enable theemergence of a genetic code?Ý How did such a uniquely non-analogouslanguage for communicating pure digital information in biological systemscome into existence?Maybe this emergent property cannot be explained in hierarchical termsapplying to a single universe.Ý Maybe the emergent property Jerry speaksof is evidence of another universe, a coincidental one, where digits ruleand analogs are the exception. Yes, it's a wild idea.Ý But I don't thinkthere is enough hierarchy in this pedestrian universe of ours to get usthe principles we need to explain what biological life actually is andwhere 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 accordingto kind.(3) Biology appears when some chemical kinds that happened to becomeconnected 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 findsitself functioning as a template on which rather similar entities have atendency to form. The historical moment this kind had preserved now cansurvive 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.ÝBy what principle does this emergent property you describeÝadopt aspecifically digital language to manage those analogously chemical affairsof biological systems?Ý To recognize such an emergent property I wouldhave to agree to a few brave assumptions.Ý One would be that biologicalsystems, comprising hierarchical atoms and molecules, are just naturallycapable of writing their own operational programs.Ý That's a reach for me,because nothing is explained.Ý Even though I am aware that organisms doexactly that, there are no principles I know of to support it.Ý HOW theydo it (not WHY they do it) is the key issue for me.Ý How do analogs writetheir own digital scripts?Ý One again, the only other time in naturalhistory that I know of this sort of thing happening was when human analogswrote their own digitally symbolic language about 10,000 years ago.As Stan has said:Of course, the origin of the genetic system is arguably themostoutstanding problem facing natural science.ÝÝÝAnd you go on to say:Thus, if one wishes to develop a compelling argument about chemicalnumbers and structures and genetic information,Ý one should start withrelational algebras that keep track of changes of relations...ÝA livingsystem is a society of associative relations among atomic numbers.ÝÝIf an emergent property truly emerges in nature I think it ought to do soon first principles.Ý Still, to argue that "biological information emergesas flows of changes..." interests me. Seems a little like a DC electricalsystemósomething new for me to worry about.Ý But how did those upstartcrystalline micelles, containing numerical/chemical relations, learnalgebra well enough to enable the emergence of a genetic code?Ý How didsuch a uniquely non-analogous language for communicating pure digitalinformation in biological systems come into existence?Maybe this emergent property cannot be explained in hierarchical termsapplying to a single universe.Ý Maybe the emergent property Jerry speaksof is evidence of another universe, a coincidental one, where digits ruleand analogs are the exception. Yes, it's a wild idea.Ý But I don't thinkthere is enough hierarchy in this pedestrian universe of ours to get usthe principles we need to explain what biological life actually is andwhere it came from.Best regards, RichardOn Nov 11, 2006, at 8:19 AM, Jerry LR Chandler wrote:(To the List: I am re-posting my message to Karl because the originalmessage was not distributed in it's totality; the arguments weretruncated.Ý CheersÝ Jerry )Karl:I fear that I must once again disagree with your strong conclusions aboutthe relations between mathematics and genetics.Ý I would urge you toattempt to find exact correspondence relations between empirical evidenceand your views of models based on numbers.See my comments below.Subject: [Fis] genetics: the most outstanding problem, SOLVEDDear Stan,In your last posting, you sai
[Fis] genetics: the most outstanding problem, (un)SOLVED?
(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, SOLVEDDear 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. CheersJerry___ fis mailing list fis@listas.unizar.es http://webmail.unizar.es/mailman/listinfo/fis
[Fis] genetics: the most outstanding problem, (un)SOLVED?
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.From: "Karl Javorszky" [EMAIL PROTECTED] Date: November 7, 2006 10:04:13 AM EST To: "'Stanley N. Salthe \(by way of Pedro Marijuan[EMAIL PROTECTED]\)'" [EMAIL PROTECTED], fis@listas.unizar.es 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 most outstanding 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 the genetic mechanism copies the information from a sequence (the dna/rna) into a nonsequenced assembly (the living organism) and from there (by means of the ovaries and the testes) back into a sequence is a quite compelling model. The term "information" has been shown in this chatroom to mean the cuts that segregate, separate and distinguish summands; The term "sequence" has been defined by Peano; The term "nonsequenced /=commutative/assembly" is indeed hairy, as there exists no definition for multidimensional partitions, although this is what it means; The term "copies" means a filter restriction on a set of entries into a database (a restricted, in optimal case, bijective map between two enumerations). 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. CheersJerry___ fis mailing list fis@listas.unizar.es http://webmail.unizar.es/mailman/listinfo/fis
