My reaction to Jerry's below:
Jerry's system of thought appears to be similar to reductionism in
biology. Reductionism in biology is the view that what is most important /
fundamental is what is inside -- and then further inside again, looking
always for what something is made of. Biologists usually stop reducing
when they reach macromolecules, thereby holding to genetic reductionism.
Jerry apparently wishes to go further yet, into molecular species and
atomic kinds. This, I think, is the basic difference between he and I.
For me, reality is irreducibly multiscaled -- as in [ etc.[biome
[population [organism [cell [macromoleule [etc. ]]]]]], with no level being
more fundamental than any other. One consequence of this is that no gene
is possible without a cell, and that is not possible without some
macroscopic scaffolding (syncitium, organism, etc.), and that is not
possible without still higher level supporting systems. The reality is BOTH
bottom-up AND top-down. In this scenario, thermodynamics has pride of
place because the entire system depends upon energy usage to keep it going,
and it seems there is as well fairly good reason to think that the whole
structure has the particular forms it has as a result of maximizing overall
entropy production. (Note that this statement excludes the potential
entropy that might be derived by destroying the system as well. The entropy
production in question is that produeced BY the system upon external
available energies. )
Now, turning to Jerry's questions:
>JLRC Stan - the focus on Pattee's arguments about initial conditions in
>not particularly meaningful for bionetwork theory.� (If you have
>counter-examples to this statement, I would be pleased to hear them.)
SS: My statement is more the point that I do not see how bionetwork
theory (to the extent that I have been able to fathom its very abstract
conceptualizations) has any meaning for understanding biology.
What does it mean to initialize a bionetwork?� Is any other initialization
outside of evolution possible?� (Sporulation is a special case that
requires a special discussion.)� �Such expressions as "constructed initial
and boundary conditions", which are based in real numbers and
thermodynamics,�do not describe the conditions internal to a cell.
SS: So, is the cell not a material system? Its inside is no whit
different than the inside of a biome as far as my viewpoint is concerned.
There is nothing magical about it. If we can "initialize" a biome, then we
an initialize a cell. Or does Jerry suppose that even a biome cannot have
initial and boundary conditions? Actually initial conditions really are
artificial, and refer to experimental setups only. Boundary condition,
however, are natural constraints. If there is something, then it
necessarily exists someWHERE.
�JLRC: Such properties are intrinsic to the concept of a bionetwork for a
living system. �In particular, Stan, given that the logic of proto numbers
is fundamentally different from the logic of the real numbers, I do not see
how these concepts are relevant� to�bionetworks. Perhaps you have some
ideas on how you might transform this hypothetical bio-logic into the logic
of the proto numbers?
SS: I'm afraid I need a primer on "proto-numbers". Below
they seem to
approximate integers, so I will continue on that premise. From that point
of view, I do not see any urgency to transforming "bio-logic" into integer
form. In my view integers, because they are crisp, are artificial human
constructions, with doubtful relevance to the actual world. And what is
bio-logic? For me biology's logic, like that of any material system, is:
build -> burn -> rebuild -> etc. If I was to be (again) a little boy with
blocks, I would stack them up, knock them down, and so on. In doing this,
a biologist would see ATP -> ADP -> ATP, etc., etc.
>JLRC: SS writes:philosophically MATTER is delayed energy, stickiness and
>delay, obstruction to the flow of energy.�
>JLRC:I think you are reversing the concepts of source and consequence.
>Only because of the concreteness of matter do we�have some understanding
>of energy as a mathematical abstraction.
SS: I agree that operationally we needed (to be and see) objects in
order to infer energy, but, as a natural philosopher, I am not an
operationalist.
>JLRC In particular, the proto numbers of the individual species of matter
>are the sources of our concept of real numbers in the sense of self -
>reference. The concept of energy is a generic concept, not a concept of
>species, a continuous variable, not a discrete variable. Bionetworks are
>composed of particular molecular species, mathematical graphs so that one
>must find a logical path from such a view of matter to a particular
>species.
SS: Again, I fail to see why we would wish, in biology, to priviledge
discreteness. This discreteness of 'species of matter' is something that I
think needs to be shown to be critical for biology. That is not apparent
to me.
>SS:In contrast, NUMBER concerns the size of distinct collections of matter
>-- most primitively, just: one, some, many.�
>JLRC:By starting with the abstraction of size, you miss the point.Proto
>numbers stand in exact correspondence with the integers of everyday
>ordinary language.
SS: I thought your discourse is all about abstraction! Is there
anything more abstract than number?
>SS:Finally, IDENTITY is based in the uniqueness of configurations of
matter.�
>JLRC:In the first part of your answer, you deploy real numbers to invoke
>energy as a source. In the comment on identity, you invoke the proto
>number concept of identity as a species.(In the real numbers, identity is
>associated with the operations of addition and multiplication.)
SS: I fail to see that identity / uniqueness is necessarily associated
with integral numbers. In my view, identity is holistic. I know my
friend's face from front, side, back, in shadow or in light, in sillouette,
and from any other perspective one wishs to present it (hopefully, not
hanging upside down).
>SS:But suppose we were to take seriously a switch from integers to real
>numbers in describing elements.� Are you willing to assert that an
>elementwould show itself as, e,g.,13.00000000000...000...infinity?��
>JLRC:As noted above, the proto numbers are precursors of real numbers.��As
>such, they correspond exactly with the natural language integers,
>1,2,3,... N, where N is a 'small' number, the list of chemical elements is
>finite..
SS: But the number of kinds of biological species is not, nor is the
number of possible individuals in a biological population. (Actually, I am
among a small number of structuralists in biology, who note that the number
of possible, e.g., faces, is not unlimited, and that the same model is used
again and again, regardless of genetic connection. However, historical
contingeny always inteferes in the construction of faces and produces
unlimited kinds of variants upon a given model -- none are identical.)
>JLRC: Proto numbers are monomials.When you
>write,�13.00000000000...000...infinity?, you presuppose that the proto
>numbers are polynomials and that the concept of extension as used in the
>real numbers applies to proto numbers.� Both presuppositions fail in proto
>numbers.��
>
>SS:Even if you would opt for that, where IS any individual of this element
>at this moment?
>JLRC:��Again, you invoke a property of real numbers and the physical
>tradition when you ask about where IS an element at this moment. For
>bionetworks, the self-referential property of the proto number system
>renders such language as artificial.
Well, which tradition in mathematics is "artificial" seems
to me a
vexed question, hardly settled. We need tools to deal with Nature. These
tools are our constructs, nothing more. Their use is optional.
>The self-referential character of� proto numbers / DNA / bionetworks is
>sufficient to conduct biological function.
Well, if you lose contact with ATP, you will decline into entropic
dissolution.
>If you wish to invoke the concept of a common spatial axis for locating
>matter, then the location will be expressed in terms of real numbers
>(using such concepts as center of gravity and linear vector spaces), not
>proto numbers and illations based on informed relationships.
>Stan:� It seems to me that you ought to try your hand at explaining the
>optical isomer problem and the wine fermentation problem in terms of your
>entropic digestion of nature.
SS: I will try the fermentation problem. The energy use
potentials
of actual systems are limited. VERY few machines utilize available energy
completely. Almost always there is some non-heat residual matter left over
(which I have recently argued should be taken to be 'entropic'). The
yeasts can only do so much. The dissipation (in two senses!) is taken a
step further in someone's brain.
STAN
>JLRC ***The logic of the proto numbers is a simple logic using integers
>and ratios of integers. This logic differs from the usual abstraction in
>that it is grounded in the chemical elements, in calculations that are
>extendable to molecules of unbounded size, not the abstractions related to
>continuity.
_______________________________________________
fis mailing list
fis@listas.unizar.es
http://webmail.unizar.es/mailman/listinfo/fis
Received on Sat Dec 24 23:26:49 2005
