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

Pedro C. Marijuán pedroc.marijuan at gmail.com
Wed Oct 26 20:48:10 CEST 2022

Dear Sheri and FIS Colleagues,

Thanks a lot for your impressive text. The interpenetration of 
logic-computation and biology-immunology for the analysis of the 
"algorithmic" defense of self versus the non-self raises a number of 
relevant issues. I will refer to a few.
You briefly mention Barbieri's code biology & codepoieis on the 
complexification of eukaryotes vs. prokaryotes (my own take comes from 
Villarreal, "ex viruses omnia", enlarging McClintock on mobile 
elements). It is very interesting to discuss the new forms of 
vulnerability of the multicellulars precisely by those viral ancestries 
at the same time evolutionary associates & foes. The innate branch of 
the immune system probably already had predecessors in unicellular 
eukaryotes (there is an ancestral form of "protosynapse" between them 
that predates the immune and the neuronal synapses). The relationship 
between immune and nervous systems is so deep... you can be quite right 
searching for both self vs. non-self recognition-strategies in both of 
them. There is also the intriguing presence and tentative regulation of 
around 20 trillion bacteria (also fungi & viruses) of more than 2,000 
species into the gut microbiome. The way immune & neural enteric system 
intermingle in the sheparding of that "ecosystemic cattle" is amazing. 
Probably it could be another instance of mixed algorithmic strategy not 
far away from your own search scope.
Months ago, a leading researcher on ribosome 
structure/function/evolution lectured in this list--Youri Timsit. I 
wonder whether he has been around and read the present text, at least in 
the comment on ribosomes.
Going to Mirror System Neurons, my opinion is that other species apart 
from primates use it, see for instance domestic dogs' amazing mind 
reading capabilities. Perhaps in the very inner representations of self 
(sensory, motor, visceral, plus the different pain systems) you may find 
other instances of advanced self vs. non-self operatives.
And cancer? That means a dramatic breach of the self organization. The 
transformation of self into an invader non-self. We start to understand 
a little bit into the sets of mutations of the different cancer types. 
Whatever formal approaches will be of help.

Sorry that I cannot discuss on the suggestive formalisms you 
utilize--other FISers will do. At the time being these are my initial, 
mostly biological, comments.

Thanks again,

El 25/10/2022 a las 20:42, Markose, Sheri escribió:
> 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$>of 
> viral transposable elements that conduct cut-paste (transposons) and 
> copy-paste (retrotransposon) gives a code based explanation  for 
> genomic evolvability, brain plasticity and novel phenotype primarily 
> in eukaryotes. This underscores the truism that primarily only 
> software can change software and also that viral hacking by such 
> internal and external biotic malware is the Achilles heel of genomic 
> digital systems.
>  2. *Unpacking the Evidence**for **Gödelization of Biology***
>                         While operations on encoded information fall 
> under the purview of Computation Theory and Recursion Function Theory 
> (*RFT*), till recently there was no evidence for how this and Gödel's 
> theorems apply tobiology.  Markose (2022 
> <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0303264722001022*bib61__;Iw!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq6qlj9z0$>) 
> 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 Gödelianfeatures 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 /f//_g //(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$>). 
>                  It is conjectured that an identical *RFT* machinery 
> is involved in the self-other nexus in both the *AIS* and *MNS*.  The 
> graphics for *Self-Rep* Mirror Mapping in the *AIS* and *MNS* is given 
> in Figure 1 in Markose (2021) 
> <https://urldefense.com/v3/__https://www.mdpi.com/1099-4300/23/4/405__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSq8Rs91D0$>.
>  3. *Detection of Non-Self Antigen in AIS: N**ew 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 /f_p /^¬ ! , 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 10^20 
>  – 10^30  that exceed the pre-scripted germline genome size many times 
> over.
>  The Rogers (1967) fixed point indexes for yet to happen /f_p /^¬ ! 
> 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 /f_p /^¬ ! 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 {/f_p /^¬ , /g_n / 
> } denoted by /g^¬ /. When the attack by /f_p /^¬ !   takes place in 
> real time in the periphery involving the said pair {/f_p /^¬ , /g_n / 
> }, 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$> 
> experiment on rats, could lead to loss of immune capabilities as well 
> as their sociability.  Note, the Markose *RFT* machinery for the 
> self-other nexus is a different explanation to the evo-devo one given 
> by Kipnis et.al.
> *#4*Finally, it is a matter of incredulity that over 90 years have 
> passed since Gödel (1931) for evidence  to be found that the staples 
> of *Self-Ref* and *Self-Rep* and the Gödel Sentence are ubiquitous in 
> Biology.  A number of factors can be adduced. Even those who espouse 
> that code-based operations are relevant in cognition such as in the 
> Computational Theory of Mind never mention *Self-Ref* and *Self-Rep*, 
> let alone that the Gödel Sentence is like a /hash /which permits a 
> software document to endogenously self-report it has been hacked.  
> There is a strong anti-machine view which overlooks the encoded basis 
> of the genome and biology and claims that biology is a non-digital 
> natural process that is creative in some vitalistic way.
> *References *
> *#Blog on University of Essex Website: /How we became smart – a 
> journey of discovery through the world of game theory and genomic 
> intelligence/ 
> https://urldefense.com/v3/__https://www.essex.ac.uk/blog/posts/2021/10/26/how-we-became-smart__;!!D9dNQwwGXtA!VjWwIkL60bibt959O3m6EV26nqXTKieshoXQHxU79whq7T-NQL_EcMrWjLFpM1IfqAtiSZZuqeZNDwqrzlTo2kfEPIh5$   
> <https://urldefense.com/v3/__https://www.essex.ac.uk/blog/posts/2021/10/26/how-we-became-smart__;!!D9dNQwwGXtA!RRmmHQCs_Cav9UXiPz27dODNI-Kke3ky-PhpVLOvgOETwB-s3hTK7egkhJHf5AFKr0UuxLxzixSqVgSsoLo$> 
> *
> *
> #*Markose, S.M, 2022, Complexification of eukaryote phenotype: 
> Adaptive immuno-cognitive systems as unique Gödelian blockchain 
> distributed ledger, Biosystems, ISSN: 0303-2647, Vol: 220, 
> https://urldefense.com/v3/__https://doi.org/10.1016/j.biosystems.2022.104718__;!!D9dNQwwGXtA!VjWwIkL60bibt959O3m6EV26nqXTKieshoXQHxU79whq7T-NQL_EcMrWjLFpM1IfqAtiSZZuqeZNDwqrzlTo2q0q-ZPi$   
> <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
> 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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