Re: [Fis] Summing up: New Year Lecture

[tozziarturo]

Dear Karl, 

your words are so intriguing, that I will shamelessy quote them (and you, of 
course!), in my next papers.  I like very much your concept of sequential as 
well as commutative symbols in a biological context.  

Concerning your very interesting issue of the possible working principle that 
elucidates the interaction between sequences and mixtures, I have a (shameless, 
of course!) idea of mine:  http://vixra.org/abs/1801.0117


Again, thanks a lot for your very nice comment. 

And hallo to Pedro, who, it seems absourd, has to leave.  With his enthusiasm, 
he is surely younger that the most of my patients!  ...and I an a 
pediatrician...


 

 

> Il 2 febbraio 2018 alle 13.08 Karl Javorszky  ha 
> scritto:
> 
> Dear Arturo,
> 
>  
> 
> thank you for your forceful presentation of contemporary thoughts on 
> theoretical biology, specifically the problem of what the term “genetic 
> identity” in actual fact means.
> 
>  
> 
> Your handyman offers you tools which support that what you say. You say: 
> “ … Here we ask: what does “matching description” mean? Has it something to 
> do with “identity”? Going through different formulations of the principle of 
> identity, we describe diverse possible meanings of the term “matching 
> description”. …”
> 
> A very simple solution is to enumerate each and all of the variants of 
> whatever can have a description. Then we switch to a different describing 
> system and again describe all variants of whatever can have a description. 
> This is like making an inventory of the contents of one’s office: once with 
> regard to the things’ colour, once to their size. To each description we 
> attach a natural number. The inventory number of the red coffee cup on the 
> table will be probably different in the inventory list based on things’ 
> colour, to the inventory number of the same cup in the inventory list 
> according to size. The next step is to look for rules that allow matching the 
> two inventory numbers. Then we have “matching descriptions”.
> 
> In genetics, the combinatorial problem becomes quite evident. We 
> enumerate along time and we enumerate across time, too. We count the 
> sequential place of the elements of the DNA, and match this sequence to the 
> contemporary composition that is the living organism. Life happens in the 
> moment, across the temporal line, while the rules of assemblage and 
> maintenance are registered in a sequential form, along the temporal line.
> 
> We overcome the difficulty by employing as symbols for a general method 
> of enumeration the sequential number of the element within its cycle during 
> reorders. These symbols are as well sequential as well commutative. Symbols 
> that are both commutative and sequential are the basis for counting 
> consistently.
> 
> The picture becomes rather entertaining, as one finds that Nature uses a 
> clever little accounting trick. If one deals with a dozen or so cycles of 
> about 6 elements each, one can switch between how many, when, where and what 
> almost at one’s wishes. The working principle of the numeric connector 
> between enumerating across and along a sequence is explained 
> inhttp://www.oeis.org/A242615 . As said before, if we look at 66 elements all 
> at the same time (in a commutative fashion), what remains to be predicted, is 
> where specific combinations of symbols are to be expected. If we see 11 
> sequenced groups of 6 elements each, we can predict when, where and what will 
> be existing (contemporary).
> 
> The interaction between sequences and mixtures is a real, disruptive 
> game-changer. One has to re-learn all the basics of arithmetic. The positive 
> side is, that after having understood which basic rounding errors one has 
> learnt at elementary school, unlearning these and instead learning to use a 
> stricter concept of consistently counting, during this process of 
> self-education one will have found the answers to the questions you so 
> eloquently present.
> 
> PS.:  
> 
> 1) J Theor Biol 2000 Aug 21; 205(4):663-6 Interaction between sequences 
> and mixtures
> 
> 2) The lecture series: Learn to Count in Twelve Easy Steps was given in 
> FIS in 2013
> 
>
> 
> 
> 
> 2018-02-01 17:54 GMT+01:00  mailto:tozziart...@libero.it >:
> 
> > > 
> > Dear Karl and Pedro, 
> > 
> > A unifying principle underlies the organization of physical and 
> > biological systems. It relates to a well-known topological theorem which 
> > succinctly states that an activity on a planar circumference projects to 
> > two activities with “matching description” into a sphere. Here we ask: what 
> > does “matching description” mean? Has it something to do with “identity”? 
> > Going through different formulations of the principle of identity, we 
> > describe diverse possible meanings of the term “matching description”. We 
> > demonstrate that the concepts of “sameness”, “equality”

Re: [Fis] Summing up: New Year Lecture

[Karl Javorszky]

Dear Arturo,



thank you for your forceful presentation of contemporary thoughts on
theoretical biology, specifically the problem of what the term “genetic
identity” in actual fact means.



Your handyman offers you tools which support that what you say. You say: “
… Here we ask: what does “matching description” mean? Has it something to
do with “identity”? Going through different formulations of the principle
of identity, we describe diverse possible meanings of the term “matching
description”. …”

A very simple solution is to enumerate each and all of the variants of
whatever can have a description. Then we switch to a different describing
system and again describe all variants of whatever can have a description.
This is like making an inventory of the contents of one’s office: once with
regard to the things’ colour, once to their size. To each description we
attach a natural number. The inventory number of the red coffee cup on the
table will be probably different in the inventory list based on things’
colour, to the inventory number of the same cup in the inventory list
according to size. The next step is to look for rules that allow matching
the two inventory numbers. Then we have “matching descriptions”.

In genetics, the combinatorial problem becomes quite evident. We enumerate
*along* time and we enumerate *across* time, too. We count the *sequential
place* of the elements of the DNA, and match this *sequence *to the
*contemporary
composition* that is the living organism. Life happens *in the moment,
across the temporal line*, while the rules of assemblage and maintenance
are registered in a *sequential form, along the temporal line. *

We overcome the difficulty by employing as symbols for a general method of
enumeration the sequential number of the element within its cycle during
reorders. These symbols are *as well sequential as well commutative.*
Symbols that are both commutative and sequential are the basis for counting
consistently.

The picture becomes rather entertaining, as one finds that Nature uses a
clever little accounting trick. If one deals with a dozen or so cycles of
about 6 elements each, one can switch between how many, when, where and
what almost at one’s wishes. The working principle of the numeric connector
between enumerating across and along a sequence is explained in
www.oeis.org/A242615. As said before, if we look at 66 elements all at the
same time (in a commutative fashion), what remains to be predicted, is
*where* specific combinations of symbols are to be expected. If we see 11
sequenced groups of 6 elements each, we can predict *when, where and what *will
be existing (contemporary).

The interaction between sequences and mixtures is a real, disruptive
game-changer. One has to re-learn all the basics of arithmetic. The
positive side is, that after having understood which basic rounding errors
one has learnt at elementary school, unlearning these and instead learning
to use a stricter concept of consistently counting, during this process of
self-education one will have found the answers to the questions you so
eloquently present.

PS.:

1) J Theor Biol 2000 Aug 21; 205(4):663-6 Interaction between sequences and
mixtures

2) The lecture series: Learn to Count in Twelve Easy Steps was given in FIS
in 2013




2018-02-01 17:54 GMT+01:00 :

> Dear Karl and Pedro,
>
> A unifying principle underlies the organization of physical and biological
> systems. It relates to a well-known topological theorem which succinctly
> states that an activity on a planar circumference projects to two
> activities with “matching description” into a sphere. Here we ask: what
> does “matching description” mean? Has it something to do with “identity”?
> Going through different formulations of the principle of identity, we
> describe diverse possible meanings of the term “matching description”. We
> demonstrate that the concepts of “sameness”, “equality”, “belonging
> together” stand for intertwined levels with mutual interactions. By showing
> that “matching” description is a very general and malleable concept, we
> provide a novel testable approach to “identity” that yields helpful
> insights into physical and biological matters. Indeed, we illustrate how a
> novel mathematical approach derived from the Borsuk-Ulam theorem, termed
> bio-BUT, might explain the astonishing biological “multiplicity from
> identity” of evolving living beings as well as their biochemical
> arrangements.
>
> https://www.sciencedirect.com/science/article/pii/S0079610717302055
>
>
>
> Il 1 febbraio 2018 alle 17.16 Karl Javorszky 
> ha scritto:
>
> Biodiversity and Cartography
>
>
>
> The excellent summary by Pedro of the session just past highlights several
> different areas of processes, which appear to be interrelated at least in
> some methodological ways. Pedro says in effect: “… systems such as
> circulatory, pulmonary, renal, brain, etc. …” appear to work in a
> comparable fashion, which has probably to do with fu

Re: [Fis] Summing up: New Year Lecture

[tozziarturo]

Dear Karl and Pedro, 

A unifying principle underlies the organization of physical and biological 
systems. It relates to a well-known topological theorem which succinctly states 
that an activity on a planar circumference projects to two activities with 
“matching description” into a sphere. Here we ask: what does “matching 
description” mean? Has it something to do with “identity”? Going through 
different formulations of the principle of identity, we describe diverse 
possible meanings of the term “matching description”. We demonstrate that the 
concepts of “sameness”, “equality”, “belonging together” stand for intertwined 
levels with mutual interactions. By showing that “matching” description is a 
very general and malleable concept, we provide a novel testable approach to 
“identity” that yields helpful insights into physical and biological matters. 
Indeed, we illustrate how a novel mathematical approach derived from the 
Borsuk-Ulam theorem, termed bio-BUT, might explain the astonishing biological 
“multiplicity from identity” of evolving living beings as well as their 
biochemical arrangements.

https://www.sciencedirect.com/science/article/pii/S0079610717302055



> Il 1 febbraio 2018 alle 17.16 Karl Javorszky  ha 
> scritto:
> 
> Biodiversity and Cartography
> 
>  
> 
> The excellent summary by Pedro of the session just past highlights 
> several different areas of processes, which appear to be interrelated at 
> least in some methodological ways. Pedro says in effect: “… systems such as 
> circulatory, pulmonary, renal, brain, etc. …” appear to work in a comparable 
> fashion, which has probably to do with fusing of two different spaces into 
> one common space.
> 
>  
> 
> Please allow me to propose a visualisation. We see a landscape with hills 
> and valleys. Some local biotopes have evolved, in which specific flora and 
> fauna are endemic, well adapted to their respective local circumstances. We 
> suspect that there are common traits present in the management of the diverse 
> habitats, with some obviously sustainable feedback loops – otherwise the area 
> would be barren. In this allegory, if one investigates the functions in 
> circulatory systems, one would be likened to someone investigating insect 
> life in a rainy forest in a division of our imagined landscape. A person 
> looking into the workings of the renal systems could be seen as a team 
> investigating the life of mammals in a savanna.
> 
>  
> 
> Among these field workers, a land surveyor tries to find someone who 
> would be interested in a new way to formalise the parameters of each and all 
> of the habitats, and tabulate every possible variety of anything that lives 
> in any of the habitats. This invention is way beyond the needs of any of the 
> field teams investigating the adaptations the fauna had to undergo due to the 
> properties of the flora, or partly the other way around. The teams have heard 
> about trigonometry and satellite positioning, but they are not involved with 
> the infrastructure of science. It would take a road building engineer to see 
> slopes and angles everywhere, and of that profession are the biologists not. 
> The teams could have heard about continual change, because they understand 
> that change is what life is all about, but they had never thought to be 
> possible to actually use measurable change tools like one uses a scalable 
> microscope.
> 
>  
> 
> Trigonometry would have remained a special pastime for scientists, had 
> not lenses, oculars and sextants been produced to the necessary degree of 
> mechanical precision. For the applications of trigonometry to become 
> ubiquitous in our everyday life, it was necessary to have achieved progress 
> in fine mechanics and precision measurement tools. The technology had to keep 
> step with the ideas. Both the ideas were present and the tools have become 
> available. The innovation could become integrated into the culture.
> 
>  
> 
> Presently, we try to understand the concept of information. In Pedro’s 
> words: “… two 3D projections are fused into a 4D one. The gain in information 
> is evident …”. The implication of Pedro’s thought is that sequences, 
> generally: order, are depositories of information, which gets – in a fashion 
> – released or actualised in the moment of the fusion of two spaces into a 
> common, third, space.
> 
> This state of affairs puts the problem with technology and ideas on its 
> head. We do have the technology to produce any kind of imaginable order and 
> disorder and to find such closed loops that are self-replicating. What we 
> lack presently is the understanding by the prospective users that they need 
> such a tool, and that such a tool is a) thinkable, b) designable, c) 
> realisable, d) working, e) useful.   
> 
>  
> 
> To give an example:
> 
> The two spaces Pedro refers to are well defined. They can be observed by 
> reordering exp

Re: [Fis] Summing up: New Year Lecture

[Karl Javorszky]

Biodiversity and Cartography



The excellent summary by Pedro of the session just past highlights several
different areas of processes, which appear to be interrelated at least in
some methodological ways. Pedro says in effect: “… systems such as
circulatory, pulmonary, renal, brain, etc. …” appear to work in a
comparable fashion, which has probably to do with fusing of two different
spaces into one common space.



Please allow me to propose a visualisation. We see a landscape with hills
and valleys. Some local biotopes have evolved, in which specific flora and
fauna are endemic, well adapted to their respective local circumstances. We
suspect that there are common traits present in the management of the
diverse habitats, with some obviously sustainable feedback loops –
otherwise the area would be barren. In this allegory, if one investigates
the functions in circulatory systems, one would be likened to someone
investigating insect life in a rainy forest in a division of our imagined
landscape. A person looking into the workings of the renal systems could be
seen as a team investigating the life of mammals in a savanna.



Among these field workers, a land surveyor tries to find someone who would
be interested in a new way to formalise the parameters of each and all of
the habitats, and tabulate every possible variety of anything that lives in
any of the habitats. This invention is way beyond the needs of any of the
field teams investigating the adaptations the fauna had to undergo due to
the properties of the flora, or partly the other way around. The teams have
heard about trigonometry and satellite positioning, but they are not
involved with the infrastructure of science. It would take a road building
engineer to see slopes and angles everywhere, and of that profession are
the biologists not. The teams could have heard about continual change,
because they understand that change is what life is all about, but they had
never thought to be possible to actually use measurable change tools like
one uses a scalable microscope.



Trigonometry would have remained a special pastime for scientists, had not
lenses, oculars and sextants been produced to the necessary degree of
mechanical precision. For the applications of trigonometry to become
ubiquitous in our everyday life, it was necessary to have achieved progress
in fine mechanics and precision measurement tools. The technology had to
keep step with the ideas. Both the ideas were present and the tools have
become available. The innovation could become integrated into the culture.



Presently, we try to understand the concept of information. In Pedro’s
words: “… two 3D projections are fused into a 4D one. The gain in
information is evident …”. The implication of Pedro’s thought is that
sequences, generally: order, are depositories of information, which gets –
in a fashion – released or actualised in the moment of the fusion of two
spaces into a common, third, space.

This state of affairs puts the problem with technology and ideas on its
head. We do have the technology to produce any kind of imaginable order and
disorder and to find such closed loops that are self-replicating. What we
lack presently is the understanding by the prospective users that they need
such a tool, and that such a tool is a) thinkable, b) designable, c)
realisable, d) working, e) useful.



To give an example:

The two spaces Pedro refers to are well defined. They can be observed by
reordering expressions of *a+b=c *on the properties *{a+b,a;b-2a,a;a-2b,b-2a
(A), a+b,b;b-2a,a-2b;a-2b,a (B)}*. Euclid spaces *(A) *and *(B)* merge
together into Newton space *(C), *of which the axes are *a+b, b-2a, a-2b.*
The axes of space *(C)* have each *two *sub-axes: this is the reason that 1
logical linear position can have 4 planar coordinate-pairs. (This was
narrated some two years ago in this FIS chatroom also, being Step Eight of
the lecture Learn to Count in Twelve Easy Steps. Otherwise see: Natural
Orders.)



May be suggestion be allowed that it would be more precise to talk of
merging (co-resonance) of planes rather than of merging of spaces. In a
logical sense, the space is generated by a continuous turn of 3 planes and
should not be assumed to have an independent, a-priori existence.



The land surveyor presents his compliments to the officials involved in
managing progress of society and may politely suggest, that some precision
tools have been fabricated, by which the results of the endoscopy of order
and information can be unwrapped, extricated and applied to manifold uses.






2018-01-30 14:06 GMT+01:00 Pedro C. Marijuan :

> Dear FISers,
>
> Apart from the very interesting critique by Sungchul, there is an
> intriguing comment I would like to make respect the new evolutionary views
> presented. I will risk to discuss on a topic, topology, too far from my
> usual fields. So I trust the benevolence of FIS readers.
>
> As far as we have been told, the germ line cells, the gametes, co

Re: [Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear FISers,

Apart from the very interesting critique by Sungchul, there is an 
intriguing comment I would like to make respect the new evolutionary 
views presented. I will risk to discuss on a topic, topology, too far 
from my usual fields. So I trust the benevolence of FIS readers.


As far as we have been told, the germ line cells, the gametes, contain 
each one a DNA algorithmic "hemi-description" of the future 
multicellular ensemble organism. When fertilization occurs, the two 
different hemi-descriptions are put together in a unique, complete DNA 
algorithm. Then, paying attention to the BUT (Borsuk Ulam Theorem) 
insights presented in this list by Tozzi and Peters, we might interpret 
that two 3D projections are fused into a 4D one. The gain in information 
is evident, and it is this gain what makes possible the construction of 
the multicellular ensemble. That 4D structures and dynamics are present 
in the multicellular may be evidenced by the fractality of most of that 
construction (systems such as circulatory, pulmonary, renal, brain, 
etc.). Actually the presence of 4D dynamics in cerebral information 
processing has been repeatedly highlighted by different authors. Now, 
what John Torday argues, is that an essential mission of the 
multicellular construct becomes the gathering of adaptive epigenetic 
marks editing the 3D hemi-descriptions, so that the future ensemble may 
be better adapted to its environment...


In the extent to which the above has any cogency, there emerges a new 
disciplinary front to check the enigmatic continuation of the 
gamete/zigote/organism along the eons of life.


Best--Pedro


El 24/01/2018 a las 15:33, JOHN TORDAY escribió:
Dear FIS colleagues, Pedro has pointed out some rookie errors in my 
post. You can find my paper "From cholesterol to consciousness" at 
https://www.ncbi.nlm.nih.gov/pubmed/28830682. Hopefully you have 
access to the paper without having to buy it. If you don't please 
email me at jtor...@ucla.edu  and i will send 
you a copy. As for addressing consciousness at the cellular/molecular 
level, I understand that the mental health professionals have a 
problem with consciousness beyond the brain/mind. But I consider that 
anthropocentric. Just like every other aspect of our physiology, 
consciousness is the endogenization of environmental factors. In the 
case of consciousness it is the vertical integration of calcium fluxes 
for all of the cells of the organism. All organisms are conscious of 
their surroundings to one degree or another. And self-reference is, in 
my opinion, a result of the Singularity/Big Bang, so it would apply to 
all organisms, unicellular and multicellular alike. I refer to the 
experiments of Helmut Plattner, exposing paramecia to glucose. When 
the paramecium homes in on the sugar its 'nervous system' of calcium 
flux lights up just like the neurons in our brains. And as to the 
extrapolation from individual consciousness to cosmology based on the 
homologies between Quantum Mechanics and Evolutionary Biology, I see 
that as a means of fully understanding the significance of 
consciousness as the connection between the animate and inanimate as 
one continuous Singularity. It is only in that way that the true 
nature of Nature can be fully understood. As for smaller increments, 
the work of Daniel Fels on electromagnetic communication between cells 
may hold the answer 
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793142/).


Best, John

On Wed, Jan 24, 2018 at 5:41 AM, Pedro C. Marijuan 
mailto:pcmarijuan.i...@aragon.es>> wrote:


Dear John and FIS colleagues,

It was nice hearing your response. For technical reasons of the
server, _attachments are unwelcome_ (and often directly rejected).
Send please a web address where interested people can download
your document. Also, it is better if you send directly your
response to FIS list (_*fis@listas.unizar.es
*_). About your content, I see a
couple of problems introducing "consciousness" at the
cellular/molecular level. For this term has a very definite
meaning in the /ad hoc/ research that is taken place during last
decades. Conflating it with basic cellular processes may not be
necessary, given that other terms (more realistic ones?) are
available. For instance, I referred to self-referential cognition.
In any case, I agree that classical autopoiesis  falls too short
of what is needed... Besides, about the cosmological relationship
with fundamental physics, is it a convenient step? Does it
introduce a premature closure in the bio-informational thinking
process?

Best--Pedro


El 22/01/2018 a las 16:02, JOHN TORDAY escribió:

Dear FISers, I greatly appreciate Pedro's comments regarding my
New Year Lecture. I fully agree with his comment " That life's
physiology is based on the conjunction of a few principles:
neguentropy, 

Re: [Fis] Summing up: New Year Lecture

[Sungchul Ji]

Hi John, Pedro, and FISers


(1) I agree with John that there must exist a set of the principles, laws or 
concepts that apply universally, from molecules to cells to human brains to the 
cosmos.  But the millions dollar question is what are these  principles, laws 
and concepts?


(2)  I disagree that "chemiosmosis" of P. Mitchell is one of the principles 
underlying life's physiology.  I will delineate the reasons for my objecting 
the concept of chemiosmosis being a fundamental mechanism of energy 
transduction in living cells in a later post.  I recently discussed this topic 
in Section 3.3.3 in [1] entitled "Deconstructing the Chemiosmotic Model"


(3) I disagree that "negentropy", also called "negative entropy", is a 
fundamental concept in biology or physics.  I critiqued this concept in Section 
3.3.3 in [2].  To make a long story sort,  there are two meanings to the term 
"negentropy", one violating the Third Law of thermodynamics and the other not 
(see Table 1 below).


Table 1.  The dual meanings of the term “negentropy”



Negentropy

Negative Entropy
   (-S)

   Negative Entropy Change
   (- ΔS)

Third Law of thermodynamics

   is violated

 is not violated



(4)  The Second Law of thermodynamics when applied to an isolated system (i.e., 
a system that does not exchange energy nor matter with its environment) states 
that the entropy of the system increases with time or that the thermodynamic 
driving force of an isolated system is the increase in entropy:



ΔS = S_final - S_initial > 0.   
  (I)



But many scientists do not realize that Inequality (I) holds only for isolated 
systems and not for non-isolated systems such as living organisms (which are 
open systems, i.e., systems that exchange both energy and matter with their 
environment) or physical systems, e.g., refrigerators that are closed (i.e., 
exchange energy but not matter with their environment).


(5) For biological systems under constant pressure (P) and temperature (T), the 
driving force behind all spontaneous physicochemical changes occurring in them 
(e.g., respiration, morphogenesis) is a decrease in Gibbs free energy (ΔG) , 
which is a function of both energy and entropy:

   ΔG = ΔE + PΔV - TΔS  
(II)


As you can see here,  ΔG can be negative (thus driving all spontaneous living 
processes) without any negative entropy change (or negentropy), since ΔG <0 as 
long as (ΔE + PΔV) < - TΔS, regardless of whether ΔS is negative or positive.   
This demonstrates that negentropy cannot serve as a fundamental focces for 
life's physiology.


(6)








References:

[1] Ji, S. (2018).  "The Cell Language Theory: Connecting Mind and Matter", 
World Scientific Publishing, New Jersey.

[2] Ji, S. (2012). The Third Law of Thermodynamics and “Schroedinger’s 
Paradox”<http://www.conformon.net/?attachment_id=1033>.  In:Molecular Theory of 
the Living Cell: Concepts, Molecular Mechanisms, and Biomedical Applications.  
Springer, New York.  pp. 12-15.  PDF at 
http://www.conformon.net/wp-content/uploads/2014/03/Schroedinger_paradox.pdf


From: Fis  on behalf of JOHN TORDAY 

Sent: Wednesday, January 24, 2018 9:33 AM
To: fis@listas.unizar.es
Subject: Re: [Fis] Summing up: New Year Lecture

Dear FIS colleagues, Pedro has pointed out some rookie errors in my post. You 
can find my paper "From cholesterol to consciousness" at 
https://www.ncbi.nlm.nih.gov/pubmed/28830682<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F28830682&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C9f589c1cbb2849cc703708d563379424%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636524012734836141&sdata=UqJTwNJJ3%2B7mLi8d1co0TQ7V%2FyWFlrk7eRX3w217tSQ%3D&reserved=0>.
 Hopefully you have access to the paper without having to buy it. If you don't 
please 
email<http://7769domain.com/Ad/GoIEx2/?token=eUdrQTFmaHMwNEgweUZVY0UvNnNXOUozTEpmWlNNcnh1czlxT0xGS2xReW93SkpzNXNvNVZ1UCtsYVZEZy8xNDZsdkJMYWlVN1JlR1hEL29DYzB2blVYVmJITG1jUkRaNjR0N0xMbnd0SDNFQXF1OTlSNFhJQldrVnZGVDRldlY0V0pjRk5CaUc4MjRSWDRGcll5aHFZYm5nWXpxL0NJRlpDbmtvVk9Bb05FPQ2>
 me at jtor...@ucla.edu<mailto:jtor...@ucla.edu> and i will send you a copy. As 
for addressing consciousness at the cellular/molecular level, I understand that 
the mental 
health<http://7769domain.com/Ad/GoIEx2/?token=RURoMlVLRFhYRytKQUovU21uTjVyMlExUVA0eEoyK29icGtYMENQa1BIazUxMlJZR2hTY05iVXN6UnB4TEsyZEFweC80T2lLRmxYQThOMGlCVkI1S21RaVdOMUlnMmFVOVZRMGVBTVVoYlRPTXBTVEFxa0RGTGhFcDZCZlZxU2JhcnJaaWJtMFJESWRZYlRWUUFqZGZKc2ZFTWhuZVBKc05BQ1BIbEgxL25LK3Z0M2ZwaFNreTk1clN4aEZ

Re: [Fis] Summing up: New Year Lecture

[JOHN TORDAY]

Dear FIS colleagues, Pedro has pointed out some rookie errors in my post.
You can find my paper "From cholesterol to consciousness" at
https://www.ncbi.nlm.nih.gov/pubmed/28830682. Hopefully you have access to
the paper without having to buy it. If you don't please email me at
jtor...@ucla.edu and i will send you a copy. As for addressing
consciousness at the cellular/molecular level, I understand that the mental
health professionals have a problem with consciousness beyond the
brain/mind. But I consider that anthropocentric. Just like every other
aspect of our physiology, consciousness is the endogenization of
environmental factors. In the case of consciousness it is the vertical
integration of calcium fluxes for all of the cells of the organism. All
organisms are conscious of their surroundings to one degree or another. And
self-reference is, in my opinion, a result of the Singularity/Big Bang, so
it would apply to all organisms, unicellular and multicellular alike. I
refer to the experiments of Helmut Plattner, exposing paramecia to glucose.
When the paramecium homes in on the sugar its 'nervous system' of calcium
flux lights up just like the neurons in our brains. And as to the
extrapolation from individual consciousness to cosmology based on the
homologies between Quantum Mechanics and Evolutionary Biology, I see that
as a means of fully understanding the significance of consciousness as the
connection between the animate and inanimate as one continuous Singularity.
It is only in that way that the true nature of Nature can be fully
understood. As for smaller increments, the work of Daniel Fels on
electromagnetic communication between cells may hold the answer (
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793142/).

Best, John

On Wed, Jan 24, 2018 at 5:41 AM, Pedro C. Marijuan <
pcmarijuan.i...@aragon.es> wrote:

> Dear John and FIS colleagues,
>
> It was nice hearing your response. For technical reasons of the server, 
> *attachments
> are unwelcome* (and often directly rejected). Send please a web address
> where interested people can download your document. Also, it is better if
> you send directly your response to FIS list (*fis@listas.unizar.es
> *). About your content, I see a couple of problems
> introducing "consciousness" at the cellular/molecular level. For this term
> has a very definite meaning in the *ad hoc* research that is taken place
> during last decades. Conflating it with basic cellular processes may not be
> necessary, given that other terms (more realistic ones?) are available. For
> instance, I referred to self-referential cognition. In any case, I agree
> that classical autopoiesis  falls too short of what is needed... Besides,
> about the cosmological relationship with fundamental physics, is it a
> convenient step? Does it introduce a premature closure in the
> bio-informational thinking process?
>
> Best--Pedro
>
>
> El 22/01/2018 a las 16:02, JOHN TORDAY escribió:
>
> Dear FISers, I greatly appreciate Pedro's comments regarding my New Year
> Lecture. I fully agree with his comment " That life's physiology is based
> on the conjunction of a few principles: neguentropy, chemiosmosis, and
> homeostasis-homeorhesis" applies to non-living states too. I did not intend
> to make that statement exclusive, and if it sounded like that Pedro's
> clarification is important. In fact have just published a paper entitled
> "Quantum Mechanics Predicts Evolutionary Biology" which is predicated on
> the hypothesis that self-referential self-organization is the result of
> the Singularity/Big Bang, Newton's Third Law of Thermodynamics that every
> action has an equal and opposite reaction. That idea would apply to both
> evolutionary biology and to balanced chemical reactions alike. As for the
> question of the emergence of self-referential consciousness 'right at the
> beginning', I am in favor of that concept, as I have expressed it in a
> recent paper, entitled "From Cholesterol to Consciousness" (see attached)
> so I look forward to reading your comments about that idea as well, since
> it has the potential to fully integrate physics and biology in my humble
> opinion.
>
> On Mon, Jan 22, 2018 at 4:01 AM, Pedro C. Marijuan <
> pcmarijuan.i...@aragon.es> wrote:
>
>> Dear FISers,
>>
>> Going to the extreme, I think this year opening lecture can be summarized
>> in three contentious points.
>>
>> 1. That life's physiology is based on the conjunction of a few
>> principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.
>>
>> 2. That communication (cell signaling) is an essential factor in the
>> multicellular evolution towards complexity.
>>
>> 3. That epigenetic inheritance and the obligate recursion to the
>> unicellular state become the basis of a new evolutionary theory.
>>
>> I disagree with point 1, as I think some nonliving states could also be
>> characterized by those principles (eg, chemical cycles/hypercycles in
>> marine vents, and other outcomes derived from "energy f

Re: [Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear John and FIS colleagues,

It was nice hearing your response. For technical reasons of the server, 
_attachments are unwelcome_ (and often directly rejected). Send please a 
web address where interested people can download your document. Also, it 
is better if you send directly your response to FIS list 
(_*fis@listas.unizar.es*_). About your content, I see a couple of 
problems introducing "consciousness" at the cellular/molecular level. 
For this term has a very definite meaning in the /ad hoc/ research that 
is taken place during last decades. Conflating it with basic cellular 
processes may not be necessary, given that other terms (more realistic 
ones?) are available. For instance, I referred to self-referential 
cognition. In any case, I agree that classical autopoiesis  falls too 
short of what is needed... Besides, about the cosmological relationship 
with fundamental physics, is it a convenient step? Does it introduce a 
premature closure in the bio-informational thinking process?


Best--Pedro

El 22/01/2018 a las 16:02, JOHN TORDAY escribió:
Dear FISers, I greatly appreciate Pedro's comments regarding my New 
Year Lecture. I fully agree with his comment " That life's physiology 
is based on the conjunction of a few principles: neguentropy, 
chemiosmosis, and homeostasis-homeorhesis" applies to non-living 
states too. I did not intend to make that statement exclusive, and if 
it sounded like that Pedro's clarification is important. In fact have 
just published a paper entitled "Quantum Mechanics Predicts 
Evolutionary Biology" which is predicated on the hypothesis that 
self-referential self-organization is the result of 
the Singularity/Big Bang, Newton's Third Law of Thermodynamics that 
every action has an equal and opposite reaction. That idea would apply 
to both evolutionary biology and to balanced chemical reactions alike. 
As for the question of the emergence of self-referential consciousness 
'right at the beginning', I am in favor of that concept, as I have 
expressed it in a recent paper, entitled "From Cholesterol to 
Consciousness" (see attached) so I look forward to reading your 
comments about that idea as well, since it has the potential to fully 
integrate physics and biology in my humble opinion.


On Mon, Jan 22, 2018 at 4:01 AM, Pedro C. Marijuan 
mailto:pcmarijuan.i...@aragon.es>> wrote:


Dear FISers,

Going to the extreme, I think this year opening lecture can be
summarized in three contentious points.

1. That life's physiology is based on the conjunction of a few
principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.

2. That communication (cell signaling) is an essential factor in
the multicellular evolution towards complexity.

3. That epigenetic inheritance and the obligate recursion to the
unicellular state become the basis of a new evolutionary theory.

I disagree with point 1, as I think some nonliving states could
also be characterized by those principles (eg, chemical
cycles/hypercycles in marine vents, and other outcomes derived
from "energy flows"); besides, some previous "info stuff" has to
be in place. Then I completely agree with point 2, for signaling
is not just another characteristic of the cell, it is "the"
eukaryotic trait par excellence.  And I am curious on how point 3
could be further substantiated... In this respect I recommend the
two papers that Bill sent to the list a few weeks ago. Do we need
to postulate the emergence of a form of "self-referential
cognition" right at the beginning?
Perhaps!

All the best--Pedro



El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest,
all of  which have all been occasioned by John Torday's profound
insights about the nature of evolutionary development in light of
the importance of cell-cell signaling and molecular biology. 
From the comments, it is clear that there is a strong impulse to

seek a means of integrating the role of symbiogenesis, viruses
and mobile elements, multilevel selection, niche construction,
genomic plasticity into a common narrative with an informational
perspective at its foundation.
In the spirit of that line of discussion, I am offering two
links that discuss evolution as an biologic information
management system. Some of this work shares direct commonality
with John's, since he and I are frequent collaborators.

http://www.mdpi.com/2079-7737/5/2/21/htm


https://www.sciencedirect.com/science/article/pii/S007961071730233X


Both of these articles can be considered as complementary to
Pedro's very fine article, 'How prokaryotes ‘encode’ their
environment: Systemic tools for organizing the information flo

Re: [Fis] Summing up: New Year Lecture--J.Torday

[Pedro C. Marijuan]

 Mensaje reenviado 

Asunto: Re: [Fis] Summing up: New Year Lecture
Fecha:  Mon, 22 Jan 2018 07:02:42 -0800
De: JOHN TORDAY 
Para:   Pedro C. Marijuan 



Dear FISers, I greatly appreciate Pedro's comments regarding my New Year 
Lecture. I fully agree with his comment " That life's physiology is 
based on the conjunction of a few principles: neguentropy, chemiosmosis, 
and homeostasis-homeorhesis" applies to non-living states too. I did not 
intend to make that statement exclusive, and if it sounded like that 
Pedro's clarification is important. In fact have just published a paper 
entitled "Quantum Mechanics Predicts Evolutionary Biology" which is 
predicated on the hypothesis that self-referential self-organization is 
the result of the Singularity/Big Bang, Newton's Third Law of 
Thermodynamics that every action has an equal and opposite reaction. 
That idea would apply to both evolutionary biology and to balanced 
chemical reactions alike. As for the question of the emergence of 
self-referential consciousness 'right at the beginning', I am in favor 
of that concept, as I have expressed it in a recent paper, entitled 
"From Cholesterol to Consciousness" (see attached) so I look forward to 
reading your comments about that idea as well, since it has the 
potential to fully integrate physics and biology in my humble opinion.



On Mon, Jan 22, 2018 at 4:01 AM, Pedro C. Marijuan 
mailto:pcmarijuan.i...@aragon.es>> wrote:


   Dear FISers,

   Going to the extreme, I think this year opening lecture can be
   summarized in three contentious points.

   1. That life's physiology is based on the conjunction of a few
   principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.

   2. That communication (cell signaling) is an essential factor in the
   multicellular evolution towards complexity.

   3. That epigenetic inheritance and the obligate recursion to the
   unicellular state become the basis of a new evolutionary theory.

   I disagree with point 1, as I think some nonliving states could also
   be characterized by those principles (eg, chemical
   cycles/hypercycles in marine vents, and other outcomes derived from
   "energy flows"); besides, some previous "info stuff" has to be in
   place. Then I completely agree with point 2, for signaling is not
   just another characteristic of the cell, it is "the" eukaryotic
   trait par excellence.  And I am curious on how point 3 could be
   further substantiated... In this respect I recommend the two papers
   that Bill sent to the list a few weeks ago. Do we need to postulate
   the emergence of a form of "self-referential cognition" right at the
   beginning?
   Perhaps!

   All the best--Pedro



   El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest,
all of  which have all been occasioned by John Torday's profound
insights about the nature of evolutionary development in light of
the importance of cell-cell signaling and molecular biology.  From
the comments, it is clear that there is a strong impulse to seek a
means of integrating the role of symbiogenesis, viruses and mobile
elements, multilevel selection, niche construction, genomic
plasticity into a common narrative with an informational
perspective at its foundation.
In the spirit of that line of discussion, I am offering two
links that discuss evolution as an biologic information management
system. Some of this work shares direct commonality with John's,
since he and I are frequent collaborators.

http://www.mdpi.com/2079-7737/5/2/21/htm
<http://www.mdpi.com/2079-7737/5/2/21/htm>

https://www.sciencedirect.com/science/article/pii/S007961071730233X
<https://www.sciencedirect.com/science/article/pii/S007961071730233X>

Both of these articles can be considered as complementary to
Pedro's very fine article, 'How prokaryotes ‘encode’ their
environment: Systemic tools for organizing the information flow',
which is in BioSystems.

I am grateful to John for inviting me to participate in the forum
and to Pedro for encouraging me to share these manuscripts.

Best regards,
Bill

William B. Miller, Jr., M.D.
602-463-5236 
wbmill...@cox.net <mailto:wbmill...@cox.net>


   -- 
   -

   Pedro C. Marijuán
   Grupo de Bioinformación / Bioinformation Group
   Instituto Aragonés de Ciencias de la Salud
   Centro de Investigación Biomédica de Aragón (CIBA)
   Avda. San Juan Bosco, 13, planta 0
   50009 Zaragoza, Spain
   Tfno.+34 976 71 3526   (& 6818)
   pcmarijuan.i...@aragon.es <mailto:pcmarijuan.i...@aragon.es>
   http://sites.google.com/site/pedrocmarijuan/
   <

Re: [Fis] Summing up: New Year Lecture

[tozziarturo]

Dear FiSers, 

gamechanging?  Look at here: 

https://www.ncbi.nlm.nih.gov/pubmed/29310692


Ciao!

> Il 22 gennaio 2018 alle 13.01 "Pedro C. Marijuan"  
> ha scritto:
> 
> Dear FISers,
> 
> Going to the extreme, I think this year opening lecture can be summarized 
> in three contentious points.
> 
> 1. That life's physiology is based on the conjunction of a few 
> principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.
> 
> 2. That communication (cell signaling) is an essential factor in the 
> multicellular evolution towards complexity.
> 
> 3. That epigenetic inheritance and the obligate recursion to the 
> unicellular state become the basis of a new evolutionary theory.
> 
> I disagree with point 1, as I think some nonliving states could also be 
> characterized by those principles (eg, chemical cycles/hypercycles in marine 
> vents, and other outcomes derived from "energy flows"); besides, some 
> previous "info stuff" has to be in place. Then I completely agree with point 
> 2, for signaling is not just another characteristic of the cell, it is "the" 
> eukaryotic trait par excellence.  And I am curious on how point 3 could be 
> further substantiated... In this respect I recommend the two papers that Bill 
> sent to the list a few weeks ago. Do we need to postulate the emergence of a 
> form of "self-referential cognition" right at the beginning?
> Perhaps!
> 
> All the best--Pedro
> 
> 
>  
> El 09/01/2018 a las 19:05, Bill escribió:
> 
> > > Dear Pedro and Colleagues,
> > 
> > I have been following the thread of comments with great interest, 
> > all of  which have all been occasioned by John Torday's profound insights 
> > about the nature of evolutionary development in light of the importance of 
> > cell-cell signaling and molecular biology.  From the comments, it is clear 
> > that there is a strong impulse to seek a means of integrating the role of 
> > symbiogenesis, viruses and mobile elements, multilevel selection, niche 
> > construction, genomic plasticity into a common narrative with an 
> > informational perspective at its foundation.
> > In the spirit of that line of discussion, I am offering two 
> > links that discuss evolution as an biologic information management system. 
> > Some of this work shares direct commonality with John's, since he and I are 
> > frequent collaborators. 
> > 
> > http://www.mdpi.com/2079-7737/5/2/21/htm
> > 
> > https://www.sciencedirect.com/science/article/pii/S007961071730233X
> > 
> > Both of these articles can be considered as complementary to 
> > Pedro's very fine article, 'How prokaryotes ‘encode’ their environment: 
> > Systemic tools for organizing the information flow', which is in BioSystems.
> > 
> > I am grateful to John for inviting me to participate in the forum 
> > and to Pedro for encouraging me to share these manuscripts.
> > 
> > Best regards,
> > Bill
> > 
> > William B. Miller, Jr., M.D.
> > 602-463-5236
> > wbmill...@cox.net mailto:wbmill...@cox.net
> > 
> > > 
> -- 
> -
> Pedro C. Marijuán
> Grupo de Bioinformación / Bioinformation Group
> Instituto Aragonés de Ciencias de la Salud
> Centro de Investigación Biomédica de Aragón (CIBA)
> Avda. San Juan Bosco, 13, planta 0
> 50009 Zaragoza, Spain
> Tfno. +34 976 71 3526 (& 6818)
> pcmarijuan.i...@aragon.es mailto:pcmarijuan.i...@aragon.es
> http://sites.google.com/site/pedrocmarijuan/
> - 
> 


 

> ___
> Fis mailing list
> Fis@listas.unizar.es
> http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
> 


Arturo Tozzi

AA Professor Physics, University North Texas

Pediatrician ASL Na2Nord, Italy

Comput Intell Lab, University Manitoba

http://arturotozzi.webnode.it/ 
___
Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis

[Fis] Summing up: New Year Lecture

[Pedro C. Marijuan]

Dear FISers,

Going to the extreme, I think this year opening lecture can be 
summarized in three contentious points.


1. That life's physiology is based on the conjunction of a few 
principles: neguentropy, chemiosmosis, and homeostasis-homeorhesis.


2. That communication (cell signaling) is an essential factor in the 
multicellular evolution towards complexity.


3. That epigenetic inheritance and the obligate recursion to the 
unicellular state become the basis of a new evolutionary theory.


I disagree with point 1, as I think some nonliving states could also be 
characterized by those principles (eg, chemical cycles/hypercycles in 
marine vents, and other outcomes derived from "energy flows"); besides, 
some previous "info stuff" has to be in place. Then I completely agree 
with point 2, for signaling is not just another characteristic of the 
cell, it is "the" eukaryotic trait par excellence.  And I am curious on 
how point 3 could be further substantiated... In this respect I 
recommend the two papers that Bill sent to the list a few weeks ago. Do 
we need to postulate the emergence of a form of "self-referential 
cognition" right at the beginning?

Perhaps!

All the best--Pedro



El 09/01/2018 a las 19:05, Bill escribió:

Dear Pedro and Colleagues,

I have been following the thread of comments with great interest, all 
of  which have all been occasioned by John Torday's profound insights 
about the nature of evolutionary development in light of the 
importance of cell-cell signaling and molecular biology.  From the 
comments, it is clear that there is a strong impulse to seek a means 
of integrating the role of symbiogenesis, viruses and mobile elements, 
multilevel selection, niche construction, genomic plasticity into a 
common narrative with an informational perspective at its foundation.
In the spirit of that line of discussion, I am offering two links 
that discuss evolution as an biologic information management system. 
Some of this work shares direct commonality with John's, since he and 
I are frequent collaborators.


http://www.mdpi.com/2079-7737/5/2/21/htm

https://www.sciencedirect.com/science/article/pii/S007961071730233X

Both of these articles can be considered as complementary to Pedro's 
very fine article, 'How prokaryotes ‘encode’ their environment: 
Systemic tools for organizing the information flow', which is in 
BioSystems.


I am grateful to John for inviting me to participate in the forum and 
to Pedro for encouraging me to share these manuscripts.


Best regards,
Bill

William B. Miller, Jr., M.D.
602-463-5236
wbmill...@cox.net


--
-
Pedro C. Marijuán
Grupo de Bioinformación / Bioinformation Group
Instituto Aragonés de Ciencias de la Salud
Centro de Investigación Biomédica de Aragón (CIBA)
Avda. San Juan Bosco, 13, planta 0
50009 Zaragoza, Spain
Tfno. +34 976 71 3526 (& 6818)
pcmarijuan.i...@aragon.es
http://sites.google.com/site/pedrocmarijuan/
-

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Fis mailing list
Fis@listas.unizar.es
http://listas.unizar.es/cgi-bin/mailman/listinfo/fis