Hi Jerry C,
I knew I shouldn’t have opened my big mouth… I don’t want to extend this conversation because as I understand the matter, the only good of comparing the structure of ammonia with triadicity is to show that it’s a bad comparison; that they are different and one should NOT compare them. But since I butted in, the answer to your question is that many genetic mutations don’t result in phenotypic changes. It’s true that there are paradigmatic examples where a clear phenotype results from a clearly defined genetic mutation; Progeria is a great example of this: http://www.pnas.org/content/106/49/20788.full With advent of gene knockout technology, one can systematically delete/mutate a gene of interest and examine what happens. So, wrt to CP 5.189, C (the phenotype that is observed) is expected to change if you modify A, where A is a system of interactions in which your gene product of interest is operating during ontogeny. So, C results from deduction of A. In that context of A, if there are other genes that compensate for the gene that has been modified, there will be no expected changes to the phenotype. The situation is complicated even more when you realize that even if there are no redundant genes, the system, itself (that is, the context in which gene products operate during ontogeny) may also compensate for the mutation (concept of variable expressivity). This is one reason why many knockout experiments result in disappointment and why forward screens are preferred, provided you know how to find the mutation. Because a phenotype is guaranteed because you've selected for it. This all presupposes that you know where to even look for the expected phenotype because the defect may be subtle, only temporary (system compensates) and therefore, missed. It’s very difficult to talk about this field even with all the information we currently have because it's HUGE, so to bring in a conversation about atoms is ridiculous. It’s not about our imagination not being able to grasp the complexity of nature but one of practicality. Talking about atoms and valences goes against the leading consideration of abduction, which is economy of money, time, thought and energy. The world is HUGE, too big to entertain every possible theory. “What need of reasoning was there? Is he not free to examine what theories he likes? The answer is that it is a question of economy. If he examines all the foolish theories he might imagine, he never will (short of a miracle) light upon the true one. Indeed, even with the most rational procedure, he never would do so, were there not an affinity between his ideas and nature’s ways.” Hth, Jerry R On Thu, Apr 7, 2016 at 11:20 PM, Jerry LR Chandler < [email protected]> wrote: > jerry: > > I do not understand your post. > > Can you clarify your meaning? > Hopefully in terms of of syllogisms or propositional functions or numeric > relations. > > Nevertheless I agree with with you our assertion that : > > Even talking of mutations in individual genes and consequences on > phenotype is problematic for many situations. > > perhaps the reality of nature is more perplex than your imagination allows > for. > > Cheers > > Jerry > > > > On Apr 7, 2016, at 10:35 PM, Jerry Rhee <[email protected]> wrote: > > Hi all, > > > Just a friendly public service announcement: > > > If your interest is in genotype/phenotype mapping (i.e., relation between > mutation and change in organism), talk of atoms, molecules and valences is > considered bizarre. > > > I say this as a biologist and because talk of such things is antithetical > to what’s expected of a good hypothesis (a good relation between C and A in > abduction). They’re too far apart. Even talking of mutations in > individual genes and consequences on phenotype is problematic for many > situations. > > > Best, > Jerry R > > On Thu, Apr 7, 2016 at 7:28 PM, Jerry LR Chandler < > [email protected]> wrote: > >> List, Kirsti: >> >> >> On Apr 7, 2016, at 3:15 AM, [email protected] wrote: >> >> But let me first ask you some questions, to help me formulate my answer. >> >> 1) You concentrate on chemical symbols. - How about chemical reactions? >> >> >> JLRC: My interest for several decades has been on the >> antecedent-consequent relation between a mutation and the change in an >> organism. How does it happen? >> Chemical symbols and chemical reactions (as biochemical processes) are >> necessary connections between the antecedent and the consequence. >> That being said, the pre-percept of all chemical symbols, today, is the >> chemical table of elements. All chemical processes, reactions, diffusion, >> bindings, transfers are expressed in terms of the components (nuclei and >> electrons) of the table of elements as ordinal and cardinal numbers. The >> chemical elements stand in strict one-to-one correspondence with the >> natural integers. This relationship gives closure on the relationship >> between matter and the sub-atomic components of matter (but not the >> sub-sub-atomic components of particle physics.) *The perplex number >> system suffers one form of physical closure under this constraint. Valence >> opens the closure by material addition of atoms to form molecules. * The >> logic of chemistry consists of propositional functions on atomic numbers >> with valence relations that creates new identities from atomic identities, >> constrained by physical laws. Thus, CSP’s logical doctrine of individuals. >> >> >> 2) Is geometry left out of the ways of posing the problem? >> >> >> Geometry enters into chemical thought secondarily as a consequence of >> arrangements of parts of the whole. The primary root of relations is the >> chemical table of elements and valences and other forms of interaction. >> That is, by secondary, I mean that one must have at least a pair of nodes >> to have a distance. >> And three nodes for an angle. The concept of a graph node pre-supposes >> chemical particles. >> >> Note that QM assumes that geometric relations exist among the parts of >> the whole of an atom and assign angles to relations to between orbitals on >> the basis of electrical relations between nuclei and electrons. Chemists >> measure angles between x-ray diffraction patterns and relate these to >> angles between atoms in crystals. At the material level of molecules the >> languages of chemistry, physics and mathematics use a common terminology >> but the meanings of the terms vary with the discipline. >> >> The diagrammatic logic of chemistry is COMPOSED from relations among >> ordinal and cardinal numbers as counts of electrons and nuclei. The >> diagrams can be interpreted by various physical measurements. >> >> In terms of handedness, note that the left and right hand forms have >> exactly the physical properties with respect to mass, electrical particles, >> bond structures and other physical attributes. The mirror images of the >> pair of optical isomers (handedness) is not predicted by physics laws per >> se. The specific arrangement discovered by Pastuer requires an arrangement >> of at least 5 separate and distinct “radicals” in a pattern such that the >> mirror images differ. (Today, the physical origin of optical rotation of >> polarized light is attributed to the rotation of the electrical field >> vector of a light ray by interaction with the five different “radicals”.) >> >> In short, the logic of physics and the logic of chemistry start with >> different pre-suppositions with regard to the nature of matter. Different >> symbolic antecedents results in different symbolic consequences. Hence, the >> different meta-languages of the two disciplines. In “Primary Logic”, M. >> Malatesta (1997), GraceWings, derives the distinctions in terms of the >> historical development of differences of logical notations. >> >> Cheers >> >> Jerry >> >> >> ----------------------------- >> PEIRCE-L subscribers: Click on "Reply List" or "Reply All" to REPLY ON >> PEIRCE-L to this message. PEIRCE-L posts should go to >> [email protected] . To UNSUBSCRIBE, send a message not to PEIRCE-L >> but to [email protected] with the line "UNSubscribe PEIRCE-L" in the >> BODY of the message. More at >> http://www.cspeirce.com/peirce-l/peirce-l.htm . >> >> >> >> >> >> > >
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