Re: Biological Phlogiston (Closure, and degreees of organization and taxonomy

Dear Pedro and All:

Thank you for the questions with regard the biochemical perspectives.
As you are aware, biochemistry has one foot in chemistry (particiularly
analytical methods) and one foot in biology (particularly efforts to
itentify chemical components of living systems and the rates of
biological processes). It is closely linked to both physiology and
genetics, as you well know.

One sharp distinction between biochemistry and biology is the analytical
methodology of biochemistry seeks to sustain the chemical principles of
conservation of mass and energy as well as the one-to-one correspondence
principle in causality relationships.
(It must be clearly stated that the one-to-one correspondence relations
are not widely used in biology or medicine - the notable exception being
in genetics via Mendel's Rules. see further explaination below.)

Thus, the taxonomy of biochemicals is the same as the taxonomy of
chemistry. We count up the atoms and the bonds and form a mathematical
graph which connects all the atoms and bonds in a systematic manner.
This "graph" conserves the one-to-one correspondence as a truth function
over the material content and is the primary linkage to all
thermodynamics functions, including the (much maligned) entropy
function.

With this as background, I turn to your questions with regard to
taxonomy, closure and function of biochemical constitutents of a living
organism.

Pedro C. Marijuan wrote:

I wrote:
> >If a connetion is to be made between physical particles and living
> >behaviors, then we must search for mapping functions which allow us to
> >relate the attributes of the various contributors to the game... In a well
> >>known case, we can look at the example of three
> >degrees of organization - subatomic particles, atoms and molecules. One
> >hundred and fifty years ago, we were uncertain about the character of
> >each of these degrees of organizations. Today, we assume that quantum
> >mechanical rules are adequate for many purposes - including calculating
> >the entropy content of good-sized molecules...

>
> Looking at the first paragraph, perhaps it looks rather close to the
> grandiose reductionist claims about biology...

I did not explain myself well:
The notion of 'degrees of organization' is a constructive notion and
does not have any simple relationship to reductionism. The example
means to show that:

1. particles can be composed into atoms and that
2. atoms can be composed into molecules.

I add to this list two further compositions:

3. Molecules can be composed into biopolymers (proteins, nucleic acids,
lipids, polysaccarides, and combinations of these.)
4. A cell is composed from particles, atoms, molecules, and biopolymers.

The operations connecting these compositions are ADDITIVE operations
which construct degrees of organization 1,2,3,4 and 5.
No DIVISIONAL operations are used in these compositions! (No
"reductionism")

>. In
> this regard I would like to hear your biochemical responses to these three
> questions which could be related to your tenets:
>
> 1- what are the fundamental molecular players of life?
>
The fundamental players are the set of molecules necessary and
sufficient for life.
For a pre-existing organism, these are the essential nutrients which
sustain life itself.

For physiological or functional purposes, a large set of molecules are
essential for normal function. In effect, it is the set of molecules
which the organism makes from the essential nutrients.

>From a logical perspective, the sufficiency for life does not come from
any one molecule.
>From a biochemical perspective, life is a cooperative, collaborative
effort, distributed over a large set of molecules. (Of course, DNA is
important - but DNA as a molecule is relatively inert and serves to
complement other molecular structures rather than generate new molecular
structures. The "power" of DNA comes from its influence on other
molecules as a source of potential, not its generative capacities per
se.)

I conjecture that biochemical functioning is a metaphor for social
system functioning. At it's essence, it is cooperative, collaborative
effort distributed over a large set of contributors. Sequences of
internal and external exchanges sustain the dynamics of the system as a
whole.

> 2- are their corresponding functions "picturable" from a quantum point of view?

Quantum rules relate to electrical charges of subatomic particles.
Since the compositional taxonomy starts with the three particles
(electrons, protons and neutrons), all further compositions of molecules
(including biopolymers) are based on quantum rules.
The literature contains 'pictures' of biomolecular structures as a
function of 'quantum rules'. Often, related pictures from 'molecular
mechanics' are given because the mathematics is more tractable.

More specifically, any structural change of molecules (such as burning
sugars for energy)
require changes in the chemical graphs and the one-to-one
correspondences. These chemical graph changes must be accounted for in
a precise one-to-one correspondence in the quantum calculations.

Note that you question and my answer span all five degrees of
organization!!

>
> 3- is life strictly related to such molecules--and only to them?

Yes and No - if you wish an answer based on experimental evidence.
All living systems depend on essential nutrients from the surrounding
"ecoment" to support themselves.
In sharp contrast to quantum systems, for which the equations are set-up
to identify a minimal energies to satisfy the objectives of the physical
and chemical observations, I am not aware of any assertions that living
systems seek minimal energy levels. A contrary rule exists - organisms
grow exponentially.

To cite Bergson: A living system climbs hills, inert matter does not.

>Does it
> make sense the claim that we may have "Artificial Life" built upon other
> (eg, silicon) molecular supports?

 I defer to others on this question.

(or instead of AL, put "artificial
> intelligence" or "Infophlogiston" for that matter). In another way, in what
> degree do you assume the bio-separability between "matterial support" and
> "logical form"?
>
The experiemntal evidence does not suggest a strict one-to-one
correspondence between materiality and a cell. Rather a cell (as as
well as mammals) have a wide range of adaptibility from this
perspective. Many genes may be deleted and the organism may still
function. This must be placed in contrast with Shannon information,
where a critical assumption is the stationarity of the statistical
distribution. Living organism are neither at equilibrium nor are they
stationary. Therefore, one can not assign truth functions on the basis
of one-to-one correspondences that are routinuely used in physics and
chemistry.
(As noted above, certain genetic functions can be treated as
one-to-one.)

> If you wish, an extra question further ascending in the bio realm could be
> the biochemical cellular tools which support the emergence of multicell
> organisms...

>From a philosophical prerspective, this question can be viewed as an
extension of cooperation and collaboration to a higher degree of
organization.
>

In your second message of March 12, you ask:
---snip---
May I come back to my awkward question a few days ago on the fundamental
molecular players of life? Perhaps you would agree with this
classification
of sorts:

1) WATER, 2) PROTEINACEOUS STUFF, 3) NUCLEIC ACID STUFF, 4)
PHOSPHOLIPIDS
and others.
---snip--
The introduction to this message addresses specifically why I would not
accept these terms as a suitable taxonomy.

--another snip--
After Szent Gyvrgyi so wonderful comments in the 604s and 704s, it seems
that no one talks any more about the properties and roles (including
info
ones) of water. But in biology, water would be like a parallel of the
VACUUM and its generative properties in quantum physics... of course,
including the possibility of playing compositional games-languages of
cells
within that (solvent) milieu.

are these views palatable to you?

-----snip--
This metaphor misses the taxonomical role of water in the chemistry of
life. Water furnishes a proton for many, many, many reactions in the
cell. It has a specific geometric structure. It is an active
participant in virtually all living processes but is not generative in
the sense that amino acids, carbohydrates, etc are generative of
biopolymers.

I hope the responses to your questions is not too technical for this
group. If anyone needs a translation to more general language, I will
be happy to attempt to clarify the meanings. I presume many will
disagree with some of the philosophies expressed. Your responses would
be of considerable interest to me... The challenge is to integrate many
views into a coherent whole.

Cheers to All
Jerry
Received on Sat Mar 14 01:09:51 1998