# Re: [Fis] Summing up: New Year Lecture

```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 <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”, “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 <karl.javors...@gmail.com>
> 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 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 <pcmarijuan.i...@aragon.es>:
>
> 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 <
> 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
> you send directly your response to FIS list (*fis@listas.unizar.es
> 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)
> 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 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 (&
> -------------------------------------------------
>
> _______________________________________________ Fis mailing list
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>
>
>
> --
> -------------------------------------------------
> 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 (&
> -------------------------------------------------
>
> _______________________________________________
> Fis mailing
> listFis@listas.unizar.eshttp://listas.unizar.es/cgi-bin/mailman/listinfo/fis
>
>
>
> --
> -------------------------------------------------
> 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 (&
> -------------------------------------------------
>
>
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>
> _______________________________________________
> Fis mailing list
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>
>
> *Arturo Tozzi*
>
> AA Professor Physics, University North Texas
>
> Pediatrician ASL Na2Nord, Italy
>
> Comput Intell Lab, University Manitoba
>
> http://arturotozzi.webnode.it/
>
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