Danko, lists,
(*1*) I finally completed reading Danko's amazing paper on "practopoiesis"
(or 'making actions'), his theory of the mind-body relation. I am not a
mind-body researcher, but my impression, as a theoretical cell biologist,
is that Danko's theory of mind may be close to truth. This impression is
based on my finding that practopoiesis can be viewed as a member of the
ur-category (see Figure 1 below) along with other fundamental semiotic
processes (see Figures 2 through 6), including self-organizing chemical
reactions, enzyme catalysis, and gene expression, all of which being
essential for practopoiesis (but only the last process was explicitly
mentioned in [1]). I tried to arrange these semiotic processes in the
order of increasing *complexity *(defined as the number of bits required
to describe a process completely) resulting in the following five-node
series:
*Chemical reactions -----> Enzyme catalysis -----> Gene expression ----->
Practopoiesis ------> Semiosis*
*Figure 1. *The five levels of semiosis, from *molecules* to *mind*, that
underlie the mind-body relation. Semiosis includes the macrosemiosis of
the Peircean semiotics and the microsemiosis investigated in biosemiotics
[2].
The symbol *A -----> B* in Figure 1 can be read in more than one ways
(i.e., has more than one meanings):
1) A is the *necessary *(but *not sufficient*) condition for B.
2) A precedes B ontologically.
3) B is the emergent property of A; or B emerges from A.
4) B is *enabled* by A.
5) B is determined by A and the environmental condition.
6) "A ------>" symbolizes the combination of the system and
its environment, previously referred to as the "*systome*"
[3; see also Appendix II].
(*2*) The key point of this post is the suggestion that all the nodes in
Figure 1, including practopoiesis, embody (or are instantiations of) the
ur-category depicted in Figure 2 below. This diagram is in turn a
geometric representation of *ITR* (Irreducible Triadic Relation) that has
been found to apply to natural sciences, human sciences, and mathematics
[4]. The value of the parameters, A, B, C, f, g, and h, are determined by
the nature of the domain of the human knowledge to which the ITR
template/framework is applied.
f g
A ---------> C -----------> B
| ^
| |
|______________________|
h
Figure 2. *The Ur-Category.* A diagrammatic representation of the
ur-category, i.e., the category to which all categories belong. The*
commutativity condition *of the category theory is satisfied (which is
denoted as f x g = h), if the operation f followed by operation g leads to
the same result as operation h [5, 6]. The 3-node diagram satisfying the
commutativity condition is also called a “commutative triangle” in
category theory. The ur-category embodies the *Irreducible Triadic
Relation* (ITR) that is intrinsic to the definition of the sign given by
Peirce (see Figure 2). (Hence I think we can regard Peirce as the
originator of ITR.) So, the terms, *mathematical category*, *commutative
triangle*, *Peircean sign*, and *ITR* are more or less synonymous.
(*3)* It may be that one of the the simplest material processes that
embodies ITR is the Belousov-Zhabotinsky (BZ) reaction extensively studied
in chemistry since its discovery in Russia in the 1950's. In the
[PEIRCE-L] post dated 4/12/2015 and partially reproduced below, I suggested
the following identification of the components of the ITR in BZ
reaction. For
a more detailed explanation of the symbols appearing Figure 3, see *Appendix
I.*
f g
( A + B) -----------> (X + Y) -----------> (D + E)
| ^
| |
|_______________________________|
h
Figure 3. * Self-Organizing Chemical Reactions (SOCR).* The Brusselator as
a prototypical SOCR is a commutative triangle, embodies ITR and performs
semiosis at the molecular level. A, B = reactants; X, Y = transient
intermediates; C, D = products; f = production step, g = destruction step,
h = information flow (i.e., the molecular structures of E and E are
determined by those of A and B mediated by X and Y).
(*4*) The example of ITR that follows the non-enzymic BZ reaction in
complexity is suggested to be the enzyme-catalyzed chemical reaction [7]:
f
g
Amino Acid Sequence --------> *Conforms* ---------> Catalysis
|
^
|
|
|____________________________________|
h
Figure 4. * Enzyme **Catalysis* as semiosis. f = protein folding; g =
generalized Franck-Condon principle (GFCP) [7];
h = information flow (supported by the free energy dissipation
accompanying Steps f and g). *Conformons* are defined as the mechanically
strained conformations of proteins that possess both mechanical energy and
genetic information to drive enzymic catalysis [8].
(*5*) As I already discussed on these lists in recent months, gene
expression can also be thought to exhibit ITR:
f g
DNA/RNA ----------> Proteins -----------> Chemical Waves
|
^
|
|
|_____________________________________|
h
Figure 5. *Gene expression* as semiosis. f = transcription/translation; g
= catalysis;
h = genetic constraint, genetic information flow. The
molecular agents in *proteins* that are responsible for catalysis are
suggested to be *conformons* [8].
(*6*) I see the ITR-connection between Danko's 'practopoiesis' detailed in
[1] and Peircean 'semiosis' as schematically represented in Figures 6 and
7:
f
g
Neuroanatomy ------------> Neural network -------------->
Neural Activity
(Long-term memory) (Working memory)
(Behavior)
|
^
|
|
|______________________________________________|
h
Figure 6. *Practopoiesis* as semiosis. f = memory recall; g = anapoiesis; h
= genetic constraint, genetic information flow.
f
g
Object ---------> Representamen ----------->
Interpretant
(1ns, 2ns, 3ns) (1ns, 2ns, 3ns)
(1ns, 2ns, 3ns)
|
^
|
|
|_______________________________________|
h
Figure 7. *Semiosis *(also called the Peircean sign) as a commutative
triangle and a member of the ur-category. f = sign production; g = sign
interpretation; h = information flow, or grounding, or meaning of the sign.
Each of the 3 nodes can exist in one of the 3 modes of being, thus giving
rise to the Peirce's 9 basic signs, i.e., qualisign, icon, rheme, sinsign
index, dicisign, legisign, symbol, and argument,
If the ITR-connection between practopoiesis and semiosis turns out to be
valid as claimed in Figures 6 and 7, this would suggest that the three
metaphysical categories of 1ns, 2ns , and 3ns would apply to all of the
individual nodes in Figure 6, which seems to partially support Dankos'
conclusion that
" . . . The three levels of organization do not correspond to these three
aspects of our consciousness. Actually, it seems that all three categories
should be assigned to the same level of organization, and this would be the
middle level, which I named anapoiesis."
(*7*) As Danko pointed out in [1], *anapoiesis* (see Step g in Figure 6)
bridges two time domains -- relatively *slow* process of forming neural
networks and very *fast* neural firing activities constituting behavior. I
considered a similar problem in 2012 [7] and came to the conclusion, based
on the Generalized Franck-Condon Principle imported from quatum
mechanincs. that
such kinetically disparate processes can be coupled if and only if the slow
process precedes the fast one.
(*8*) Danko's *anapoiesis* reminds me of the well-known linguistic
principle, the *principle of rule-governed creativity (PRGC) *[10, 11].
PRGC captures the property of a language which enables native speakers to
construct an indefinitely large number of sentences out of a finite number
of elements and to understand them even when encountering for the first
time. According to the cell language theory [11], PRGC operates in living
systems ranging from DNA (d) to RNA (r), proteins (p), metabolic network
(m), cells (c), organs (o) and
whole animals (a), leading to the coining of the terms d-, r-, p-, m-, c-,
o- and a-creatons, where *creatons *are defined as the physicochemical
systems capable of instantiating PRGC.
(*9*) If we define the physicochemical systems implementing practopoiesis
as 'practopoiesis-executing agent' or 'practopoietons' for brevity (as
already suggested on these list a while ago), anapoiesis would be an
essential component process performed by *practopoietons.
Practopoietons *would
in turn be 'isomorphic' with *creatons *as defined in the cell language
theory [12].
(*10*) In conclusion, I would heartily agree with Danko that
"Peirce's philosophy (at least a part of it) may even get some sort of a
foundation in hard sciences, which would be amazing."
With all the best.
Sung
____________________________________________
Sungchul Ji, Ph.D.
Associate Professor of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
Piscataway, N.J. 08855
732-445-4701
www.conformon.net
*References:*
[1] Nikolic, Danko (2015). Practopoiesis: Or How life fosters a mind. *J.
theoret. Biol.* *373*:40-61.
[2] Ji, S. (2001). Isomorphism between Cell and Human Languages: Micro-
and Macrosemiotics. *in:* *Semiotics 2000: “Sebeok’s Century”, *S.
Simpkins, J. Deely (eds.), Legas, Ottawa, pp. 357-374.
[3] Ji, S. (2013). Systome as the complementary union of system and
environment. [biosemiotics:4003] dated December 2, 2013.
[4] Burgin, M. (2010). Theory of Information: *Fundamentality,
Diversity and Unification. * World Scientific, New Jersey.
[5] Brown, R. and Porter, T. (2006). Category Theory: an abstract
setting for analogy and comparison
<http://pages.bangor.ac.uk/~mas010/Analogy-and-Comparison.pdf>. In: *What
is Category Theory?* Advanced Studies in Mathematics and Logic, Polimetrica
Publisher, Italy, 2006, pp. 257-274. PDF at
http://pages.bangor.ac.uk/~mas010/Analogy-and-Comparison.pdf.
[6] Spivak, D. I. (2013). Category Theory for Scientists. PDF at
http://math.mit.edu/~dspivak/CT4S.pdf.
[7] Ji, S. (2012). Ji, S. (2012). The Kinetics of Ligand-Protein
Interactions: The“Pre-fit” Mechanism
<http://www.conformon.net/?attachment_id=983>Based on the Generalized
Franck-Condon Principle. In: Molecular Theory of the Living Cell:
Concepts, Molecular Mechanisms, and Biomedical Applications. Springer, New
York. Pp. 209-214. PDF at http://www.conformon.net under Publications >
Book Chapters..
[8] Ji, S. (2000). Free energy and Information Contents of C*onformons*
in proteins and DNA. *BioSystems* *54: *107-130.
[9] Ji, S. (2012). Micro-Macro Coupling in the Human Body, in *Molecular
Theory of the Living Cell: concepts, Molecular Mechanisms, and Biomedical
Applications. * Springer, New York, pp. 554-571. PDF at
http://www.conformon.net under Publicaitons > Book Chapters. (Please read
the indicated text, and do not download it, unless you do not mind other
related chapters of the book downloaded along with it.)
[10] Hockett, C. F. (1960). The origin of speech. *Sci. Am*. *203* (3):
89-96.
[11] Ji, S. (1997). Isomorphism between cell and human languages:
molecular biological, bioinformatics and linguistic implications.
*BioSystems* *44: *17-39.
[12] Ji, S. (2016). *The Cell Language Theory: From Molecules to Mind.
*Imperial College Press, London (to appear).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
*Appendix I *- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - -
Reproduced from [PEIRCE-L] dated 4/14/2015.
"In this category-theoretical sense, all self-organizing chemical reactions
(exemplified by the Belousov-Zhabotinsky reaction which can be modeled by
the Brusselator) can be said to exhibit "thought" and has "mind" if they
are "irreducibly triadic", which seems to be the case (see below).
(4) The Brusselator is probably the simplest theoretical model of chemical
reactions that can self-organize. See the video at
http://en.wikipedia.org/wiki/Brusselator. (Prigogine once told me that the
key step in the Brusselator is the 'termolecular' step, 2X ---> 3 X.) It
has the following 4 chemical steps involving reactants, (A + B), products,
(D + E), and the transient intermediates, (X + Y) that interact obeying the
following rules or mechanisms:
A --------> X
2X + Y --------> 3X
B + X --------> Y + D
X --------> E
______________________________
A + B ----------> D + E
Figure 1. The Brussleator -- a theoretical model of self-organizing
chemical reactions, both organic and inorganic.
http://en.wikipedia.org/wiki/Brusselator.
I suggest that the Brusselator, Figture 1, can be mapped onto the
ur-category, Figure 2, as shown in Figure 3. Mathematically speaking,
Figure 1 and Figure 3 are isomorphic (i.e., embody similar regualarites or
principles).
f g
A ----------> B ----------> C
| ^
| |
|_____________________|
h
Figure 2. The ur-category, a high-level category to which all lower-level
categories belong (see the emails attached).
f g
( A+B) -----------> (X+Y) -----------> (D+E)
| ^
| |
|_____________________________|
h
Figure 3. The Brusselator as a semiosic process and hence a member of the
ur-category. f = production step, g = destruction step, h = information
flow (i.e., the structures of E and E are determined by those of A and B
mediated by X and Y).
(5) Since the Brusselator and all its token self-organizing chemical
reactions are capable of semiosis (i.e., "undergoing irreducibly triadic
process") as shown above, it would be logical to conclude that all
self-organizing chemical reactions are associated with "thoughts" or
"minds" of their own. This does not mean that all chemical reactions can be
considered to have thoughts, since not all chemical reactions undergo
irreducibly triadic processes, just as not all utterances from human mouth
can carry information."
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - *Appendix
II* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
[biosemiotics:4003] SYSTOME as the complementary union of SYSTEM and
ENVIRONMENT
Inbox
x
Sungchul Ji <[email protected]>
[image: Attachments]12/2/13
to biosemiotics
Sep 28 (5 days ago)
Hi,
The terms ‘system’ and ‘environment’ have been widely used in many fields
of natural, engineering, and social sciences for over a half century.
Most discussions on systems, e.g., 'systems biology', ‘systems
physiology’, etc. tend to focus on the structure and workings of a system
and its components rather than on the systems' environment and its effects
on the system .
A paradigm example of system-biased approach to science is provided by
the protein folding experiment of Anfinsen carried out in the 1950’s
focuses on the changes in the conformational structure of a protein,
ribonuclease A. His experiments viewed this enzyme as a system and
downplayed the role of the environment of the protein on its
conformations. To be more specific, when he denatured ribonuclease
molecules by adding 2-mercaptoethanol (2ME) and urea and are allowed the
denatured protein to refold under two different environmental conditions,
i.e., A (removing urea before 2ME) and B (removing 2ME before urea), the
enzyme refolds into native the conformation under the condition of A but
not B.
(
http://sandwalk.blogspot.com/2007/02/anfinsen-experiment-in-protein-folding.html
).
Thus, it is logical to conclude that
“The Anfinsen dogma is upheld when the refolding (1201-1)
experiment is performed under the experimental
condition A and disproved when it is carried out
under the experimental condition of B.”
In other words,
“The Anfinsen dogma can be experimentally proven or (1201-2)
disproven, depending on which of the two possible
environmental conditions of the experiment is chosen.”
One corollary of Statements (1201-1) and (1201-2) is that
“The native folding of proteins is determined not (1201-3)
only by the amino acid sequence of the protein but
also by the environmental condition under which
proteins fold.”
The concept of the “environment” of a system is synonymous with the term
“boundary condition” of a system. There are two kinds of boundary
conditions – “stationary boundary condition (SBC)” and “moving boundary
condition (MBC)”. A boundary condition of a system can “move” or
“change” in space, in time, or in both space and time. An example of a
system with a boundary condition (this combination may be conveniently
referred to as a ‘systome’; see below) that moves is the combination of a
surfer who maintains his/her upright position and moving waves (see the
picture attached). Another example of the ‘systome’ with MBC is the
beating heart (see http://vimeo.com/8321006) where the muscle cells are
the system and the blood vessels and nerves providing oxygen and
electrical impulses to muscle cells constitute the boundaries that are
constantly in periodic motion.
Thus, when what is observed is the result of the interaction between a
system and its environment, it would be useful to have a term that
combines the system and its environment. Since there seems to be no
English word for such an entity, to the best of my knowledge, I elected to
coin one: ‘ Systome’, a neologism derived from ‘system’ with a minimal
alteration:
‘Systome’ = System + Environment (1201-4)
The following characteristics of a systome come to mind:
“A systome is characterized by a set of internal (1201-5)
states, each with discrete (or quantized) enegy
levels.”
“Energy is defined as the systome’s ability (1201-6)
to do work, is in turn defined as the product
of force and displacement.”
“ Depending on the properties of the boundary (1201-7)
condition, the the energy of a systome can be
‘internal energy’, E, or Gibbs free energy,
G = E + PV - TS, where P is pressure, V is
volume, T is temperature and S is entropy.”
“ A systome can undergo ‘state transitions’ (1201-8)
from one energy level to another, leading to
experimentally observable changes or ‘observables’
of the systome, just as electronic transitions
in atoms lead to emission or absorption of photons. “
I suggest that all of the Statements (1201-5) through (1201-8) presuppose
the QUANTIZATION of ENERGY of a systome, without which no organization of
any kind is possible. Since biological systomes are ORGANIZED in space
and time, it would follow that their energies must be QUANTIZED, as
directly demonstrated by the fitting of biological data from many systomes
(e.g., proteins, enzymes, RNA metabolic network in cells, T-cell
receptors, and human breast cancer tissues) to the blackbody
radiation-like equation, BRE (see attached) -- the gold standard for the
existence of ENERGY QUANTIZATION in physics.
With all the best.
Sung
____________________________________________
Sungchul Ji, Ph.D.
Associate Professor of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
Piscataway, N.J. 08855
732-445-4701
www.conformon.net
On Mon, Sep 28, 2015 at 4:57 AM, Danko Nikolic <[email protected]
> wrote:
> Dear all,
>
> When I presented the list with the theory of practopoiesis and suggested
> that the three traverses can account for abductive reasoning, I also
> received a number of questions regarding Peirce's work to which I had no
> answers. The reason I had no answers was that I did not know much about
> work of Peirce other than abductive reasoning.
>
> Now, I would like to share with you that I have made a bit of a step
> forward. One of the questions (or suggestions) that I received was that
> perhaps the three levels of organization that I proposed (three traverses)
> correspond to the three Peirce's categories: Firstness, Secondness, and
> Thirdness.
>
> Meanwhile, I have learned more about Peirce and I think that the answer
> is: No. The three levels of organization do not correspond to these three
> aspects of our consciousness. Actually, it seems that all three categories
> should be assigned to the same level of organization, and this would be the
> middle level, which I named anapoiesis.
>
> I always thought that this middle level is the most interesting part of
> the theory, as it can produce a fascinatingly rich dynamics to explain
> consciousness. Now, it seems to me that 1ness, 2ness, and 3ness correspond
> very nicely to different aspects of its dynamics. So, it appears that this
> aspect of Pierce's work will be extremely helpful in the future in
> describing different aspects of adaptive processes in tri-traversal systems.
>
> Peirce's philosophy (at least a part of it) may even get some sort of a
> foundation in hard sciences, which would be amazing.
>
> I hope that someone finds this useful.
>
> Best,
>
> Danko
>
> --
>
> Prof. Dr. Danko Nikolic
>
>
> Web: http://www.danko-nikolic.com
>
> Mail address 1:
> Department of Neurophysiology
> Max Planck Institute for Brain Research
> Deutschordenstr. 46
> 60528 Frankfurt am Main
> GERMANY
>
> Mail address 2:
> Frankfurt Institute for Advanced Studies
> Wolfgang Goethe University
> Ruth-Moufang-Str. 1
> 60433 Frankfurt am Main
> GERMANY
>
> ----------------------------
> Office: (..49-69) 96769-736
> Lab: (..49-69) 96769-209
> Fax: (..49-69) 96769-327
> [email protected]
> ----------------------------
>
>
>
>
> -----------------------------
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> .
>
>
>
>
>
>
--
Sungchul Ji, Ph.D.
Associate Professor of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
Piscataway, N.J. 08855
732-445-4701
www.conformon.net
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