[Fis] New Discussion on Complex Self-Other Interactions and Gödelization of Biology

[Karl Javorszky]

Dear Colleagues, dear Sheri,



What a pleasure to continue this enjoyable and fruitful discussion, and
with such high-level introduction to the present session!

Sheri’s expose deals with concepts which are deeply rooted in Nature. Her
context is that of an experimental biologist, not that of a theoretical
biologist. The concepts she uses are observed facts which were derived from
observations through microscopes, coming from empirical results.

*1.     **Let us use non-empirical concepts*

Approaching the subject of autoregulation in biologic processes has two
main ingredients: (a) that what is the collection of pixels constituting
the picture which we see thru the microscope, (b) the mental images the
observer creates from the factual picture.

Our main hypothesis is that we have less problems using the microscope than
we have problems using our perception and cognition. We already do see the
facts, only we do not recognize how the facts are related among each other.
We are in possession of the results of the experiments, what we do not have
is a general picture /principle/ which connects the results.

On this point Sheri’s opinion and mine agree.

*2.     **Let us put a pattern we recognize above the picture, better two
patterns *

Sheri proposes using Gödel numbers as a reference grid by means of which we
can superimpose a pattern on the picture. This is an idea of a genius.
Gödel numbers are descriptions of properties of *sequences, *and sequences
are observably a fundamental property of biology (in evolutionary, genetic,
physiologic, intellectual, psychologic, economic, etc. understandings). We
are on the right track.

On this point, one may suggest using alongside the mental tool of *sequential
*classification the mental tool of *commutative *classification when
regarding the picture of results which we want to make a sense of. It is
true that our heartbeat and respiratory processes are in a *sequence, *but
it is also true, that at any moment along the cycles of a pumping or
breathing period, the organism is in a *commutative *state which is
different to both its predecessor and to its successor states. During each
of the moments, the constituents of the organism are concurrently the case,
in a non-sequential relation among each other. The transversal
cross-section of time is as important as is important the longitudinal
interpretation of the same observation.

*3.     **Let us re-check our artefacts and biases, add a new reference
grid*

Before starting to interpret the results of an experiment, one needs to
re-check, which results are caused by artefacts of the setup of the
experiments and which blind spots of the observer result from his
assumptions about the experiment.

We stand before the task of interpreting a picture which is a combination
of contemporary and of sequenced symbols. We know, how to deal with
sequences: the Gödel numbers open the door.

We have, however, an inbuilt bias in our assumptions about the participants
of the experiment. Since the Sumerians, we are habituated to regarding the
logical objects we deal with to be multitudes of one basic unit of *1 (one)*.
This approach negates any inbuilt, immanent, axiomatic diversities among
the units we think the world (Nature) is being built up of.

We are presently not habituated to using a concept of units that are by
their nature, in an axiomatic fashion, diverse among each other.

The suggestion is to use an *etalon collection *of units that are each an
individual to generate a pattern-grid of commutative diversities we can
overlay the observed picture with, together with the sequence-based grid we
are already moving to bring into place.

*4.     **The interactions /interferences/ when using two grids are worth
looking deeper into*

The moment we first recognize an understandable principle, order, system,
pattern among the constituents of the picture is necessarily an
Aha!-experience. If it is a basic principle of Nature, it will be easily
understood. “Of course”, people will say.

The proposition is to merge the ultimate variant of the Gödel numbers, the
sequence *n! (oeis.org/A000142 <https://urldefense.com/v3/__http://oeis.org/A000142__;!!D9dNQwwGXtA!Qhb2noFWOoblISpMVvBhCs54MIIJv3OPVF-xKUjGnAo7ja75tytBcGffJ1gWXjP5tX6OOk_OR2KjfsnUxfO_fXefRpI$ >) *with the
ultimate variant of diversities in an assembly, *n?, (exp(ln(A000041)2). *The
slight inner incongruence within the Sumerian counting system (in the order
of magnitude of *10-94 %) *is the key to the manifold spectacles Nature
continues to astonish us with.

One can visualize the interdependencies on an *etalon collection *of
logical symbols. The etalon collection consists of pairs *(a,b) /a,b **≤
16, a **≤ b/ *of natural numbers.

*5.     **Needs learning to understand but is worth the effort*

The overlaid interpretational grid resulting from using *both sequential
and commutative symbols together *is by its nature a mother of all hybrids
between sudokus and Rubik’s cube. One absolutely needs computers to handle
the translation tables among *certainty *and *place, amount, time, how
different to, how similar to, what contemporaneous with, how predictable,
how many, etc. *What is worse, one must unfortunately learn something new.
One needs to self-educate about *matter in transit*. Like it is necessary
to solve an example sudoku and do the twists with the cube for
understanding the underlying principle, it is unavoidable that one
actually, in fact conducts a self-educating experiment. Please take say 10
books and order them on your table on author-subject. Now watch the steps
being done while you reorder the books onto subject-author. It will in all
probability come the moment that there are more than two books engaged in a
sequence-cycle of place changes: The reorder also includes such cases,
where the place of an object remains the same or two books are directly
changing place with each other. These we see as special cases and talk here
about the self-organizing of three or more objects into cycles during
reorders. This is a completely new logical category, that of goods being in
transit, as members of cycles. The idea of transit as such, the twin idea
to things as such, comes to mind. Logistics is that part of economy which
has by necessity broken first a way into formal logic. The necessity is
given by biology being a description of processes that happen both along
time and across time. Elements of a cycle have both *sequential and
commutative *properties, like merchandise in transit in an economy. The
constraints and imperatives of shipments have similarities across all
trades and seasons and have diversities by the inner diversity among trades
and seasons. We call attention to the principle caused by *patterns
observable on transit as such of things as such*. By the Sumerian
tradition, we do not possess different and diverse things as such, which we
could observe being in transit, much less in transit as such. This huge
blind spot needs to be willingly and conscientiously corrected. You need to
reorder some books on a table to gain the insight that this state of world
actually exists.

The existence of cycles must be incorporated into the personal repertoire,
experienced in the form of an exercise one has gone through. The category
of things being disconnected from their previous place and not yet having
arrived at the target place is a category of its own. It has its own rules.
The rules are as simple as *a+b=c *in principle, but for our neurological
limitations can only be put to useful practice by using the medium of
computers. To understand the idea, one needs to pay attention to details
while reordering a small collection of whatever from being sorted first on
property A and then sorted on property B. The details of the mechanism of
reorders are but a detail in our cultural tradition of today but what we
see today as a detail has a fundamental importance. Because cycles are so
much a part of our life, and because handling cycles overwhelms our
neurological abilities, the subject of cycles has not been dealt with by
those generations which had no computers. Cycles are too much usual and too
much complex, therefore cycles had not entered scientific discourse sooner.
They are of a fundamental importance.

Thank you, Sheri that you introduce a system of mental concepts, the Gödel
numbers, that overlays the picture of observed results. Let me join your
approach and offer you a second system of mental concepts, the cycles of
the etalon collection of variants of *a+b=c*, to concurrently overlay the
picture of the observed results with.

For more details, please see https://urldefense.com/v3/__https://www.preprints__;!!D9dNQwwGXtA!Qhb2noFWOoblISpMVvBhCs54MIIJv3OPVF-xKUjGnAo7ja75tytBcGffJ1gWXjP5tX6OOk_OR2KjfsnUxfO_Ys8x40E$ 
.org/manuscript/202209.0373/v1. The manuscript has been slightly improved
since, but the general ideas are there. Good luck with your research, I
believe that you are on the right path, and I hope to be able to contribute
to your work with supporting numeric evidence.

Karl



Am Di., 1. Nov. 2022 um 07:34 Uhr schrieb Francesco Rizzo <
13francesco.rizzo en gmail.com>:

>   Caro Sheri,
> con i miei commenti telegrafici e propedeutici ho cercato di porre le
> premesse per introdurre nella discussione
> quella che tu chiami      Godelization of Biology
>
> dal punto di vista dell'economia quantistica
> basata proprio sull'indeterminazione o indecidibilità di  Godel,   perchè
> a mio giudizio  qualunque altra economia bisogna buttarla alle
> ortiche. Altrimenti il mondo dell'uomo e della natura continuerà ad essere
> distrutto. Preciso inoltre che la quantistica economica è nata prima della
> quantistica biologica. Comunque, grazie lo stesso.
> Francesco.
> Dear Sheri, with my telegraphic and preparatory comments I have tried to
> lay the foundations for introducing into the discussion what you call
> Godelization of Biology
> from the point of view of quantum economics, based precisely on Godel's
> uncertainty or undecidability, because in my opinion any other economy must
> be thrown away. Otherwise the world of man and nature will continue to be
> destroyed. I also specify that economic quantum was born before biological
> quantum. Anyway, thanks anyway, Francesco.
>
>
> Il giorno mar 1 nov 2022 alle ore 07:32 Francesco Rizzo <
> 13francesco.rizzo en gmail.com> ha scritto:
>
>> Caro Sheri,
>> con i miei commenti telegrafici e propedeutici ho cercato di porre le
>> premesse per introdurre nella discussione
>> quella che tu chiami      Godelization of Biology
>>
>> dal punto di vista dell'economia quantistica
>> basata proprio sull'indeterminazione o indecidibilità di  Godel,   perchè
>> a mio giudizio  qualunque altra economia bisogna buttarla alle
>> ortiche. Altrimenti il mondo dell'uomo e della natura continuerà ad
>> essere distrutto. Preciso inoltre che la quantistica economica è nata prima
>> della quantistica biologica. Comunque, grazie lo stesso.
>> Francesco.
>> Dear Sheri, with my telegraphic and preparatory comments I have tried to
>> lay the foundations for introducing into the discussion what you call
>> Godelization of Biology
>> from the point of view of quantum economics, based precisely on Godel's
>> uncertainty or undecidability, because in my opinion any other economy must
>> be thrown away. Otherwise the world of man and nature will continue to be
>> destroyed. I also specify that economic quantum was born before biological
>> quantum. Anyway, thanks anyway, Francesco.
>>
>>
>> ---------- Forwarded message ---------
>> Da: Markose, Sheri <scher en essex.ac.uk>
>> Date: lun 31 ott 2022 alle ore 18:47
>> Subject: RE: [Fis] New Discussion on Complex Self-Other Interactions and
>> Gödelization of Biology
>> To: Francesco Rizzo <13francesco.rizzo en gmail.com>
>>
>>
>> Hello Francesco -  I am not familiar with Quantum Economics and so may
>> have little to say in that regard.
>>
>>
>>
>> You can put your comment in the discussion trail about how Quantum
>> Physics/Economics deals with self-non self.
>>
>>
>>
>> Many thanks
>>
>>
>>
>> Sheri
>>
>>
>>
>> *From:* Francesco Rizzo <13francesco.rizzo en gmail.com>
>> *Sent:* 31 October 2022 16:59
>> *To:* Markose, Sheri <scher en essex.ac.uk>
>> *Subject:* Re: [Fis] New Discussion on Complex Self-Other Interactions
>> and Gödelization of Biology
>>
>>
>>
>> Dear Sheri, Did my messages reach you or not?
>>
>> Francis
>>
>> caro Sheri, Ti sono arrivati o no i miei messaggi?
>>
>> Francesco
>>
>>
>>
>> Il giorno gio 27 ott 2022 alle ore 07:57 Francesco Rizzo <
>> 13francesco.rizzo en gmail.com> ha scritto:
>>
>> Dear Sheri, I would like to send you again the email I wrote you and
>> strangely you did not receive. Thanks Francesco
>>
>>
>>
>> Caro Sheri,
>>
>> mi permetto d'inviarti nuovamente l'email che Ti ho scritto e stranamente
>> non hai ricevuto.
>>
>> grazie.
>>
>> Francesco
>>
>>
>>
>> Dear Pedro,Louis and Sheri,
>>
>> as an economist who invented the concept of the good-money in 1975, I am
>> very much context of the topic that will be discussed in the session that
>> is about to begin, because the distinction between self and non-self is
>> typical of physics or of (my) quantum economics. In fact, between being a
>> living cat or a dying cat (probabilistic, non-deterministic is analogous:
>> to being a commodity (material) and being a sign or coin (immaterial);
>> between being production eing speculation; between being price and being
>> value; etc. In short, everything is the opposite of everything.
>>
>> A warm greeting.
>>
>> Francesco Rizzo, ore 18.29, 21 ottobre 2022.
>>
>>
>>
>> Dear Pedro, Louis and Sheri,
>>
>> da economista che ha inventato nel 1975 il concetto del bene-moneta, sono
>> molto contesto del tema che si discuterà nella sessione che sta per
>> iniziare, perché la distinzione tra sé e non sé è tipica della fisica o
>> della (mia)economia quantistica. Difatti tra l’essere gatto che vive o il
>> gatto che muore (probabilistico, non deterministico è analogo: all’essere
>> merce (materiale) e l’essere segno o moneta (immateriale); tra l’essere
>> produzione e l’essere speculazione, tra l’essere prezzo e l’essere valore;
>> etc. Insomma. Tutto e il contrario di tutto
>>
>> Un caro saluto augurale.
>>
>> Francesco Rizzo, ore 18.40, 21ottobre 2022.
>>
>>
>>
>> Il giorno gio 27 ott 2022 alle ore 00:43 Markose, Sheri <
>> scher en essex.ac.uk> ha scritto:
>>
>> Hello Francesco -  I do not believe I received an email from your on 21
>> October.
>>
>>
>>
>> I tried to Goggle your work but could not find it – so I’m unable to
>> comment.
>>
>>
>>
>> Best Regards
>>
>>
>>
>> Sheri
>>
>>
>>
>> *From:* Francesco Rizzo <13francesco.rizzo en gmail.com>
>> *Sent:* 26 October 2022 15:31
>> *To:* Markose, Sheri <scher en essex.ac.uk>
>> *Subject:* Re: [Fis] New Discussion on Complex Self-Other Interactions
>> and Gödelization of Biology
>>
>>
>>
>> *CAUTION:* This email was sent from outside the University of Essex.
>> Please do not click any links or open any attachments unless you recognise
>> and trust the sender. If you are unsure whether the content of the email is
>> safe or have any other queries, please contact the IT Helpdesk.
>>
>> Dear Sheri,
>> last October 21 I sent you an email revealing that I am as happy with
>> your being an economist as I am. On October 25, you stated, among much
>> more: Discussion points and areas in which I would like collaborators and
>> from which I can learn since in my daily work I am an economist. I expected
>> you to dwell on the relationship between genomic biology and the genetic
>> economy underlying physics or quantum reality: a problem that I have
>> modestly dealt with at least in the last twenty years of my research. Why
>> didn't you do it? Anyway thanks.
>>
>> Francis
>>
>> Caro Sheri,
>>
>> il 21 ottobre scorso Ti ho mandato un’email rivelandomi contento del tuo
>> essere economista come lo sono io. Il 25 ottobre Tu hai affermato, tra
>> tanto altro: Spunti di discussione e aree in cui vorrei collaboratori e
>> da cui posso imparare visto che nel mio lavoro quotidiano sono un
>> economista (Points for discussion and areas where I would like
>> collaborators and those I can learn from as in my day job I’m an economis).
>> Mi aspettavo che Tu ti soffermarsi sul rapporto che passa tra la biologia
>> genomica e l’economia genetica sottese dalla fisica o realtà quantistica:
>> problematica di cui mi sono modestamente occupato almeno negli ultimi
>> vent’anni della mia ricerca. Perché non l’hai fatto? Comunque, grazie.
>>
>> Cari saluti Francesco
>>
>>
>>
>>
>>
>> Il giorno mar 25 ott 2022 alle ore 20:43 Markose, Sheri <
>> scher en essex.ac.uk> ha scritto:
>>
>> Dear Colleagues -  I look forward to your valuable comments.
>>
>>
>>
>> *G*ö*delian Self-Referential Genomic Information Processing: Complex
>> Self-Other Interactions and Novelty Production*
>>
>>
>>
>> *Overview for Foundations of Information Science Discussion – *
>>
>> *Sheri Markose         25-10-2022*
>>
>>    1. *Background *
>>
>> Complexity, evolvability, novelty production and ‘thinking outside the
>> box’ in biology and humans have for most part relied on models of
>> randomness or on statistical white noise error terms.
>>
>>                   The digitization of inheritable information in the
>> genome encoded in a near universal alphabet  (A,T,C,G/U) has been called
>> the ‘algorithmic takeover of biology’ by Walker and Davis (2013).  The
>> Faustian pact at the genesis of life colourfully portrayed by Freeman
>> Dyson  as ‘ the takeover of a replicative digital virus of an analogue
>> metabolism’ accords with the perspective of Forterre, Zimmer, Villareal,
>> Koonin and others.  This underpins the remarkable fact that in nature
>> only life and biology as we know it and the artifacts of genomic
>> intelligence (GI) thereof are explicitly code based digital systems.
>>
>>                      Genomic intelligence is a concept introduced in Markose
>> (2021)
>> <https://urldefense.com/v3/__https:/doi.org/10.3390/e23040405__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqV3O-kDY$>
>> specifically to characterize the Gödelization of code-based information
>> processing in genomic systems with the distinctive self-referential
>> conditions of Gödel Incompleteness results that appear to have been
>> acquired for complexification over the course of evolution of multicellular
>> eukaryote life, Markose (2022)
>> <https://urldefense.com/v3/__https:/doi.org/10.1016/j.biosystems.2022.104718__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqPn2Rp5k$>.
>> To explain the latter in contrast to the relative stasis of prokaryotes,
>> which has remain unchanged since inception, Barbieri (2012
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib10__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqdTKw3lg$>
>> ; 2018)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib13__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq0lIhVMs$>,for
>> instance, has resorted to Code Biology and Codeopoiesis, viz. biotic code
>> based explanations to complement  the more popular thermodynamic
>> explanations of self-organization and autopoiesis
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/topics/mathematics/autopoiesis__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqDFaksjk$>.
>> Igamberdiev (2021)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib59__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqIQhnjCw$> gives
>> general principles, but no concrete evidence, for why “living systems
>> during evolution continuously realize the proof of Gödel's theorems
>> (1931).”
>>
>>                    Significantly, while debunking the idea that the
>> primary source of evolutionary changes arise from random
>> transcription/replication errors, the epochal discovery by Nobel
>> Laureate Barbara McClintock (1984)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib88__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqajIC2C4$>
>> of viral transposable elements that conduct cut-paste (transposons) and
>> copy-paste (retrotransposon) gives a code based explanation  for genomic
>> evolvability, brain plasticity and novel phenotype primarily in
>> eukaryotes.  This underscores the truism that primarily only software can
>> change software and also that viral hacking by such internal and external
>> biotic malware is the Achilles heel of genomic digital systems.
>>
>>    1. *Unpacking the Evidence* *for **Gödelization of Biology*
>>
>>                         While operations on encoded information fall
>> under the purview of Computation Theory and Recursion Function Theory (
>> *RFT*), till recently there was no evidence for how this and Gödel's
>> theorems apply to biology.  Markose (2022
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib61__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq6qlj9z0$>)
>> unpacks the recent breakthroughs here.
>>
>>                      Gödelization of information processing starts,
>> firstly, with unique identifiers or Gödel numbers for digital entities well
>> known in the digital economy and taking the form of bio-peptide unique
>> identifiers including ‘zip codes’ in organisms as discovered in the Nobel
>> prize winning work of Blobel (2009). It appears all signalling in bio-ICT
>> relies on peptide identifiers from transcription factors to neuron-neuron
>> links.
>>
>>                      Two other distinctive Gödelian features found in
>> genomic intelligence, using epithets from Hofstadter (1999) are
>> self-reference (*Self-Ref*) or the online machine execution involving
>> the Diagonal operator and offline virtual self-representation (*Self-Rep*)
>> of the former.  The breakthrough on the significance of these staples of
>> *RFT* found in textbooks such as Rogers (1967) and Cutland (1980),
>> starts with the insight from Gershenfeld (2012
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib48__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqGSrl56A$>
>> , 2017
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib49__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqpGCiPPQ$> Chapter
>> 3 p. 109) as to what the self-referential/Diagonal operator means for
>> biology, where a program *g *builds machine *f *to run *g *(typically
>> denoted as *fg(g)*). Gershenfeld (2012
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib48__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqGSrl56A$>)
>> says what 21 century digital fabrication is trying to achieve is something
>> biology solved 3.7 billion years ago with the self-assembly programs
>> associated with the ribosome and other transcriptase machinery involved in
>> gene expression for the morphology, somatic identity and regulatory control
>> of the organism.
>>
>>                       Despite the central role assigned to self-reference
>> for the sentient self in advanced organisms (Gardenfors  2003
>> <https://urldefense.com/v3/__https:/scholar.google.se/citations?view_op=view_citation&hl=sv&user=ZW8RWdAAAAAJ&citation_for_view=ZW8RWdAAAAAJ:Y0pCki6q_DkC__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqclXIy_8$>,
>> Northoff et. al, 2006
>> <https://urldefense.com/v3/__https:/doi.org/10.1016/j.neuroimage.2005.12.002__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqKaUbmro$>
>> , Newen (2018)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib94__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqkgZx_Ng$>
>> , Miller et.al., 2018
>> <https://urldefense.com/v3/__https:/doi.org/10.1016/j.pbiomolbio.2018.10.002__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqM9CMK80$>
>> , etc) only Tsuda (2014)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib114__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqPf630Ss$>
>>  and Markose (2017, 2021,2022) have noted how the evolutionary
>> development of *Self-Rep* mirror structures as in the Gödel
>> Meta-Representation Theorem (Rogers,1967) is necessary for biotic elements
>> to make statements about themselves, first having self-assembled
>> themselves.  This *offline* embodied *Self-Rep*, which contrasts with no
>> such structures in prokaryotes, was a paradigm shift in the Adaptive
>> Immune System (AIS) some 500 million years ago in the lineage of jawed
>> fish, called the Big Bang of Immunology, Janeway et. al (2005).  This
>> latterly appears as Mirror Neuron System (MNS) mostly in primate brains
>> first discovered by the Parma Group of neuroscientists.
>>
>>                    The *AIS* demonstrates virtual offline mirrored
>> self-representation (*Self-Rep*) in the MHC1 T cell receptors of ~85 %
>> of expressed genes viz. *halted *machine executions of genomic
>> self-assembly codes that determine the somatic and phenotype identity for
>> the organism.  As will be seen, these Self-Repped gene codes in the Thymus,
>> called the *Thymic Self * (Ramon and Faure, 2021
>> <https://urldefense.com/v3/__https:/www.frontiersin.org/articles/10.3389/fpsyt.2020.540676/full__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqRtkoQzk$>)
>> or ‘the science of self’ (Greenen, 2021
>> <https://urldefense.com/v3/__https:/link.springer.com/article/10.1007/s00281-020-00831-y__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq71KRW4U$>)
>> are primarily used to identify the hostile other, viz. negation function
>> operators of non-self antigens.  In turn, the Mirror Neuron System (*MNS*)
>> reuses codes of self-actions from the sensory-motor cortex for social
>> cognition and inference regarding conspecifics via virtual simulations in
>> the *MNS* (Fadiga et al. (1995)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib35__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqek3WNP4$>
>> ; Gallese et al. (1996)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib46__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqHLWVVsM$>
>> ; Rizzolatti et al. (1996)
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/science/article/pii/S0303264722001022*bib102__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqmxeFzqA$>).
>>
>>
>>                  It is conjectured that an identical *RFT* machinery is
>> involved in the self-other nexus in both the *AIS* and *MNS*.  The
>> graphics for *Self-Rep* Mirror Mapping in the *AIS* and *MNS* is given
>> in Figure 1 in Markose (2021)
>> <https://urldefense.com/v3/__https:/www.mdpi.com/1099-4300/23/4/405__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq8Rs91D0$>
>> .
>>
>>
>>
>>    1. *Detection of Non-Self Antigen in AIS: New Diversity-Selector
>>    Model and Gödel Sentence in Genomic Blockchain Distributed Ledger (BCDL) *
>>
>>                      The most significant of all breakthroughs here is
>> the one made by the game theorist Binmore (1987) who raised the ‘spectre of
>> Gödel (1931)’ in the form of Gödel’s Liar who will negate or falsify what
>> can be computed/predicted. Binmore effectively mooted the adversarial
>> digital game which is co-extensive with life itself (Markose, 2017, 2021).
>> This constitutes the *fourth* condition of Gödel systems and involves an
>> adversarial agent in the form of a virus or a hacker whose actions cannot
>> be constrained in anyway.
>>
>>                 The Gödel Incompleteness result that generates the Gödel
>> Sentence permits a code qua biotic element to self-report  “I’m under
>> attack”, when it has been hacked/negated by a novel malware. This marks an
>> endogenous exit from listable sets, a necessary condition for novelty and
>> the production of novel antibodies, to avoid the irrational state of
>> logical inconsistency of formal systems (Smullyan,1961
>> <https://urldefense.com/v3/__https:/www.jstor.org/stable/j.ctt1b7x7ww__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqtrLoY_E$>).
>> The genomic Gödel Sentence in terms of 21 century nomenclature is a
>> *hash* that helps demonstrate endogenously that the outputs of expressed
>> genes have been maliciously altered. Note, that halting self-assembly gene
>> codes, *g* Î *G *that create the organism are theorems of the genomic
>> system theorems and is disjoint from known non-theorems or what the
>> immunologist Burnett (1958) famously called ‘forbidden codes’ if allowed to
>> run will ‘negate’ the theorems and cause harm.
>>
>>                 Indeed, how the *AIS* identifies novel software attacks
>> on own gene codes, *g* , by malware/parasite negating functions *fp*¬ !
>> , which belongs to an uncountable infinite set that cannot be mechanically
>> listed, is stupendous case of uber bio-cybersecurity.
>>
>>               The AIS implements ‘out of the box’ astronomic
>> anticipative search for novel non-self antigens necessary for novel
>> anti-body production and cognition in humans manifests unbounded
>> proteanism for novel extended phenotypes, Dawkins (1987), in the form of
>> artifacts outside of ourselves.  This facility found only in the *AIS*
>> relying on the Recombination Activator genes (*RAG* 1 and 2) and in the
>> human brain for neural receptor diversity runs into orders of magnitude of
>> 1020 – 1030 that exceed the pre-scripted germline genome size many times
>> over.
>>
>>                 The Rogers (1967) fixed point indexes for yet to happen
>> *fp*¬ ! attacks by the non-self antigens are generated in the *AIS*  in
>> most ingenious fashion: a large number of codes/indexes purported to be of
>> different *fp*¬ ! on each *self-repped* * g *are generated in the T-Cell
>> Receptors. This is the most spectacular case of predictive coding. Suppose
>> that the g.n for the specific tuple {* fp*¬ , *gn* } denoted by *g¬*.
>> When the attack by *fp*¬ !  takes place in real time in the periphery
>> involving the said pair {* fp*¬ , *gn* }, the experientially driven
>> peripheral MHC1 receptor must record this and if this ‘syncs’ with the one
>> that was speculatively generated in the thymic MHC1 receptors, two parts of
>> the fixed point come together to construct a genomic Gödel Sentence.
>>
>>                This molecular genomic diversity-selector model follows a
>> unique self-referential blockchain distributed ledger that is different, in
>> terms of the self-referential design, from man-made *BCDLs* first
>> invented circa 2009.  The genomic *BCDL *manifests secure digital and
>> decentralized record keeping where no internal or external bio-malware can
>> compromise the immutability of the life’s building blocks and no novel
>> blocks can be added that is not consistent with extant blocks.
>>
>>                     There are no doubt macroscopic environmental and
>> population level pressures of the Neo-Darwinian style natural selection
>> arising from conspecific or multi-species competition for survival in terms
>> of those which reproduce more and those which die out. There is growing
>> evidence that at level of bio-digital smart controls of the eukaryote
>> genome and homeostasis, selective pressures are based on the principles of
>> a unique self-referential *BCDL*
>>
>>                     In conclusion, genomic intelligence in vertebrates
>> that has reached its apogee in humans is highly empathic as the
>> conspecific/other is the projection of self; greatly Machiavellian having
>> co-evolved with adversarial viral agents; geared toward unbounded
>> proteanism from the get-go starting with transposon based diversity of
>> *RAG* genes in the immune system and stringently self-regulated by a
>> *BCD*L driven by the principle of autonomy of the life of the organism
>> and an agenda to be hack-free.
>>
>>
>>
>> *Points for discussion and areas where I would like collaborators and
>> those I can learn from as in my day job I’m an economist *
>>
>> *#1* I fully concur with the latter part of Miller/Torday (2018)
>> <https://urldefense.com/v3/__https:/doi.org/10.1016/j.pbiomolbio.2018.10.002__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqM9CMK80$>
>> statement :
>>
>> “As self-referential cognition is demonstrated by all living organisms,
>> life can be equated with the sustenance of cellular homeostasis
>> <https://urldefense.com/v3/__https:/www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/homeostasis__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq8F9h1Jc$> in
>> the continuous defence of 'self'.” However, Miller/Torday do not use any
>> of the code based *RFT* Gödel style *Self-Ref* mirror structures for
>> genomic information processing.
>>
>>                 No doubt prokaryote CRISPR based identification of
>> non-self antigens is highly sophisticated and so are the innate immune
>> system strategies which primarily entail analog defences of setting up
>> barriers, toxicity, raising temperature by inflammation and ingestion by
>> phagocytes. Prokaryotes distinctively do not have the mirror * Self-Rep *offline
>> structures of self as in the Rogers (1967) *RFT* fixed point theorems
>> which permit bio-molecules to self-report changes to their own codes.  My
>> take on homeostasis in eukaryotes post jawed fish is that bio software data
>> security and hence the autonomy of self was taken to the next level: the
>> design of how codes can self-report they have been changed by bio malware
>> by utilizing hashes like the Gödel Sentence.
>>
>>                 It will be interesting to compare the bacteria-phage arms
>> race in prokaryotes with the one in the *AIS* antibody production
>> outlined above. I have reached out to John Mattick and Silvia Sanchez Ramon
>> on these issues.
>>
>>
>>
>> *#2.*  In Markose (2021) I indicate that the generation of genomic Gödel
>> Sentences for detection of novel the non-self antigen is necessary for
>> novel antibody production is a testable hypothesis. Those who died of Covid
>> 19 were found not to be capable of antibody production and instead were
>> subjected by a cytokine storm brought about by the analog defences of
>> toxicity and inflammation of the innate immune system.
>>
>>
>>
>> *# 3* A common *Self-Rep* mirror *RFT* machinery for self-other
>> recognition in the *AIS *and social cognition following from the Mirror
>> Neuron Systems in primates has been conjectured. Similar conjectures have
>> been made at least since Irun Cohen, but without any *RFT* to guide the
>> discussions.  Figure 1 in Markose (2021)
>> <https://urldefense.com/v3/__https:/www.mdpi.com/1099-4300/23/4/405__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq8Rs91D0$>
>> shows how a knock-out of the circuitry for self’s updates on non-self
>> activity vis-à-vis self (the RHS entry in the *offline* *Self-Rep* s(g,g)
>> operator ) known to be controlled by interferon gamma as in Jonathan
>> Kipnis Group 2016
>> <https://urldefense.com/v3/__https:/www.nature.com/articles/nature18626__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqF1KRYvk$>
>> experiment on rats, could lead to loss of immune capabilities as well as
>> their sociability.  Note, the Markose *RFT* machinery for the self-other
>> nexus is a different explanation to the evo-devo one given by Kipnis
>> et.al
>> <https://urldefense.com/v3/__https://linkprotect.cudasvc.com/url?a=http*3a*2f*2fet.al&c=E,1,oLd773HrF_aCgtWnjI-egqgTBJBabXHBEhV_ASbCNjvrs4fCH3rQ9HZWFf4XPIsUL1rA6xRIDZ7O_CJrgQlkYYqyuPsjYY-mHKhFJwzmD9dv7a0,&typo=1__;JSUl!!D9dNQwwGXtA!XF-jXURnDCu4ySaj7hcIkH2-vybbuRWRO4lFebwlJtWqb_yaJyG3xcmfo0bBA9bpK7tF6Rg2cBF4_HycxJRtt7-wMMmv$>.
>>
>>
>>
>>
>> *#4* Finally, it is a matter of incredulity that over 90 years have
>> passed since Gödel (1931) for evidence  to be found that the staples of
>> *Self-Ref* and *Self-Rep* and the Gödel Sentence are ubiquitous in
>> Biology.  A number of factors can be adduced. Even those who espouse that
>> code-based operations are relevant in cognition such as in the
>> Computational Theory of Mind never mention *Self-Ref* and *Self-Rep*,
>> let alone that the Gödel Sentence is like a * hash *which permits a
>> software document to endogenously self-report it has been hacked.  There is
>> a strong anti-machine view which overlooks the encoded basis of the genome
>> and biology and claims that biology is a non-digital natural process that
>> is creative in some vitalistic way.
>>
>>
>>
>> *References *
>>
>> *#Blog on University of Essex Website: How we became smart – a journey of
>> discovery through the world of game theory and genomic intelligence
>> https://urldefense.com/v3/__https://www.essex.ac.uk/blog/posts/2021/10/26/how-we-became-smart__;!!D9dNQwwGXtA!Qhb2noFWOoblISpMVvBhCs54MIIJv3OPVF-xKUjGnAo7ja75tytBcGffJ1gWXjP5tX6OOk_OR2KjfsnUxfO_yEgvzvM$ 
>> <https://urldefense.com/v3/__https:/www.essex.ac.uk/blog/posts/2021/10/26/how-we-became-smart__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqVgSsoLo$>
>> *
>>
>>
>> * #*Markose, S.M, 2022, Complexification of eukaryote phenotype:
>> Adaptive immuno-cognitive systems as unique Gödelian blockchain distributed
>> ledger, Biosystems, ISSN: 0303-2647, Vol: 220,
>> https://urldefense.com/v3/__https://doi.org/10.1016/j.biosystems.2022.104718__;!!D9dNQwwGXtA!Qhb2noFWOoblISpMVvBhCs54MIIJv3OPVF-xKUjGnAo7ja75tytBcGffJ1gWXjP5tX6OOk_OR2KjfsnUxfO_kzn3Rdw$ 
>> <https://urldefense.com/v3/__https:/doi.org/10.1016/j.biosystems.2022.104718__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqPn2Rp5k$>
>>
>>
>> * #*Markose, S.M, 2021, “Genomic Intelligence as Über Bio-Cybersecurity:
>> The Gödel Sentence in Immuno-Cognitive Systems”
>> <https://urldefense.com/v3/__https:/doi.org/10.3390/e23040405__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqV3O-kDY$>
>> , *Entropy. *23(4), 405; ttps://doi.org/10.3390/e23040405
>> <https://urldefense.com/v3/__https://linkprotect.cudasvc.com/url?a=http*3a*2f*2fdoi.org*2f10.3390*2fe23040405&c=E,1,MYX9fzR-YZjn1Wl8_9SrWA1FvLGGNOQ3sacYwrqQHVf2V5YbetS_ZLgFWWwUBWe6apNDJXOrMFJ_BBhGgziGh3oqjelhyoVjt787woDDO_LZ4qckWicA0JJXh9M,&typo=1__;JSUlJSU!!D9dNQwwGXtA!XF-jXURnDCu4ySaj7hcIkH2-vybbuRWRO4lFebwlJtWqb_yaJyG3xcmfo0bBA9bpK7tF6Rg2cBF4_HycxJRtt_Nx6ZmH$>
>>
>>
>>
>> Markose, S.M, 2017, Complex type 4 structure changing dynamics of digital
>> agents: Nash equilibria or a game with arms race in innovations. *Journal
>> of Dynamics & Games*, 2017, 4 (3) : 255-284. doi: 10.3934/jdg.2017015
>> <https://urldefense.com/v3/__http:/dx.doi.org/10.3934/jdg.2017015__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqC_UOvRc$>
>>
>>
>>
>>
>>
>>
>> -------------------
>>
>> Professor Sheri Markose
>>
>> Economics Department
>>
>> University of Essex
>>
>> UK
>>
>> _______________________________________________
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