[Fis] A new discussion session

Pedro C. Marijuán pedroc.marijuan at gmail.com
Thu Dec 1 14:02:51 CET 2022

Dear Sheri, Lou, and all discussants,

It is a pity that this excellent discussion has taken place in 
complicated academic weeks, as it has been caught in a sort of 
"punctuated equilibrium" of longer stasis than activities in our 
evolutionary list. Well, I have a couple of very brief comments:

First, emphasizing that one of the references in Youri's last messages 
should be obligated reading for biologically interested parties:  
"Sensing the world and its dangers: An evolutionary perspective in
neuroimmunology." By Aurora Krauset al. In, eLife 2021;10:e66706. DOI: 
https://urldefense.com/v3/__https://doi.org/10.7554/eLife.66706__;!!D9dNQwwGXtA!SqizL3x3CcntbhLaIdrhBHmGMi7btD5ZwhfvU15L4xIxjE3QCOJv6ua8XvelEf-PtASzBqEnHi_-s40a8WSen8bu1LAR$ . In this vein, I will follow with 
the argument that the multicellular self is a composite, an association 
with a microbial consortium that probably was the big evolutionary cause 
to create a defense system of such a great complexity.  The innate 
immune system would represent the evolutionary learning about those 
dangers, with scores of different components and pattern recognition 

And second, about the adaptive immune system, it is where the ongoing 
mostly formal discussion would apply (can we agree with that?). Then, it 
seems that the core of this adaptive immune branch is the Major 
Histocompatibility Complex molecule (MHC). This MHC molecules of two 
major classes are highly complex (polygenic and polymorphic) and they 
are in charge of presenting to lymphocyte T cells the protein fragments 
churned out from the proteosomes inside cells (fragments of variable 
lenght: 8-10 amino acids residues for Class 1, mostly "self",  and 13-18 
amino acids residues for Class 2, mostly "non self"). Then, the thymus 
is in charge of deactivating the T cells loaded with self stuff. My 
point is that the defense in front of the non-self is based on _indirect 
products of protein translation_. This causes me some uneasiness, as 
protein translation (see Youri's presentation months ago) introduces a 
layer of extra complexity, not to speak the processing via proteosomes. 
Further, with just 10 or 12 amino acids can we faithfully ascertain 
algorithmic non-self provenance??

Well, Sheri is far more acknowledged with all this stuff. And perhaps 
Lou can say something about the formal distinguishability of 10-12 aa.

El 15/11/2022 a las 21:19, Markose, Sheri escribió:
> Dear Louis, dear Colleagues -
> Louis has given an excellent exposition of Gödel Numbering (g.n) (your 
> point number 2 on coding and semantics is giving me food for thought) 
> , giving example of prime factorization and also of Gödel Sentence as 
> one that states its own unprovability.  Unlike statements like  "this 
> is false", GS is not paradoxical and in a consistent system it is a 
> theorem with a constructive g.n. The latter in terms of the prime 
> factorization format, it is indeed a Hilbert 10 Diophantine equation 
> with no integer solutions.  A remarkable achievement in maths, 
> considering Gödel was only 23 years of age ....   But what has this 
> got to do with Biology and novelty production, the objectives of the 
> my FIS discussion ?
> In view of brevity and also urged by Pedro, I dropped a couple of 
> paragraphs in my FIS kick off submission as to why we need to exceed 
> Gödel (1931) and couch the Gödel Incompleteness Results and the Gödel 
> Sentence with a fuller understanding of algorithms as encoded 
> instructions and as machine executable codes, of the notion of 
> recursive enumeration (re) and re sets that was developed in the Emil 
> Post (1944).  I hope Louis Kauffman can comment on the the application 
> of the fuller Gödel-Turing -Post-Rogers framework mentioned in my FIS 
> note and in my papers cited there.
> 1. I have found the following statement by Joel Hamkins (  : 
> https://urldefense.com/v3/__http://jdh.hamkins.org/wp-content/uploads/A-review-of-several-fixed-point-theorems-1.pdf__;!!D9dNQwwGXtA!SqizL3x3CcntbhLaIdrhBHmGMi7btD5ZwhfvU15L4xIxjE3QCOJv6ua8XvelEf-PtASzBqEnHi_-s40a8WSenw8_avhB$  
> <https://urldefense.com/v3/__http://jdh.hamkins.org/wp-content/uploads/A-review-of-several-fixed-point-theorems-1.pdf__;!!D9dNQwwGXtA!SqizL3x3CcntbhLaIdrhBHmGMi7btD5ZwhfvU15L4xIxjE3QCOJv6ua8XvelEf-PtASzBqEnHi_-s40a8WSenw8_avhB$ > 
> ) useful as it makes an important observation that the original Gödel 
> (1931) framework permits an encodable proposition to make statements 
> about itself while Second Recursion Theorems (SRT) also called Fixed 
> Point Theorems  are needed “to construct programs/algorithms that 
> refer to themselves”.  The terms programs and algorithms will be used 
> interchangeably.
> I choose Rogers Fixed Point Theorem of (total) computable functions 
> starting with the staple I have already indicated Diag (g) (RHS of (8) 
> below) is what Neil Gerschenfeld  calls ribosomal self-assembly 
> machines in gene expression where the program /g builds the /machine 
> that runs g.
> II. The first requirement of a system to identify Fixed Points viz. 
> self-referential constructions of algorithms/programs is (8) viz to 
> identify  what function/algorithm has altered the Diag (g).
> When online gene expression takes place on RHS of (8), viz. these 
> programs have halt commands  and builds the somatic and phenotype 
> identity of vertebrates online, the offline record of this is made in 
> the Thymus that can not only represent the Thymic/immune self but also 
> concatenate changes thereof.
> I have suggested that the Adaptive Immune System and the Mirror Neuron 
> System have these structures in (8).  And the domain of self-halting 
> machines as in (8) are the Theorems of the system and a subset of Post 
> (1944) Creative Set.   The non-Theorems have codes say g^¬ which 
> cannot halt in a formal system that is consistent.  To my mind, the 
> embodiment via the physical self being self-assembled and an offline 
> record of this on LHS of (8) is what fuses syntax and semantics.
> II. Once, (8) is in place, the Adaptive immune system has to identify 
> novel negation software function /f^¬! /_of non-self antigens which is 
> an uncountable infinite possibilities. Hence the close to astronomic 
> search with V(D) J of  10 ^20 – 10 ^30 ) of non-self antigens that can 
> hijack the self- assembly machines as recorded  on RHS of (8).  Only 
> from knowledge of self can the hostile other, in the case of the AIS, 
> be identified.
> III.  Roger Fixed Point assures us that the indexes of the fixed point 
> for /f^¬! /_be generated. I have cced Guillame Bonfante who I think 
> was among the first (with coauthors, 2006) to suggest how SRT can be 
> used to identify computer viruses. But they do not use the full force 
> of Self-Ref and Self -Rep  and only implicitly use Post Creative and 
> Productive Sets. The index of the Godel Sentence for the fixed point 
> will endogenously lie outside of Post listable or recusively 
> enumerable set for Theorems and known non-Theorems.
> IV. From these Gödel Sentences produced in the immune-cognitive 
> systems, the explicit use of Post (1944) Theorems indicates how novel 
> antibodies cannot be produced in the absence of the Gödel Sentence 
> which allows a biotic element to self-report it is under attack.
> V. In conclusion, while it has become fashionable for some like 
> Jurgen  Schmidhuber to claim that there can be endogenous self 
> improving recursive novelty (he calls them Gödel machines) , the Gödel 
> Logic says that the original theorems and self-codes are kept 
> unchanged/hack free and novelty is produced only in response to 
> adversarial attacks of self codes.  So the AIS story is somatic 
> hypermutation so that nothing in the genome changes.  As to how the 
> germline itself changes, needs more investigation, in Biosystems 
> paper, I suggest something very briefly.
> So thankyou all again for your in depth comments and interest.
> Best Regards
> Sheri
> -----Original Message-----
> From: Fis <fis-bounces at listas.unizar.es 
> <mailto:fis-bounces at listas.unizar.es>> On Behalf Of Louis Kauffman
> Sent: 08 November 2022 00:13
> To: "Pedro C. Marijuán" <pedroc.marijuan at gmail.com 
> <mailto:pedroc.marijuan at gmail.com>>
> Cc: fis <fis at listas.unizar.es <mailto:fis at listas.unizar.es>>
> Subject: Re: [Fis] A new discussion session
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> Dear Pedro,
> Here are some comments about Goedel numbering and coding.
> It is interesting to think about Goedel numbering in a biological context.
> Actually we are talking about how a given entity has semantics that 
> can vary from context to context.
> It is not simply a matter of assigning a code number. If g —> F is the 
> relation of a Goedel number g to a statement F, then we have two 
> contexts for F.
> 1. F as a well formed formula in a formal system S.
> 2. g as a number in either a number system for an observer of S or g 
> as a number in S, but g, as a representative for F can be regarded in 
> the system S with the meanings so assigned.
> Thus we have produced by the assignment of Goedel numbers a way for a 
> statement F to exist in the semantics of more than one context.
> This is the key to the references and self-references of the Goedelian 
> situations.
> Lets look at this more carefully. Recall that there is a formal system 
> S and that to every well formed formula in S, there is a code number g 
> = g(S). The code number can be produced in many ways.
> For example, one can assign different index numbers n(X) to each 
> distinct generating symbol in S. Then with an expression F regarded as 
> an ordered string of symbols, one can assign to F the product of the 
> prime numbers, in their standard order, with exponents the indices of 
> the sequence of characters that compose F. For example, g(~ x^2 = 2) = 
> 2^{n(~)} 3^{n(x)}5^{n(^)}7^{n(2)}11^{n(=)}13^{n(2)}. From such a code, 
> one can retrieve the original formula in a unique way.
> The system S is a logical system that is assumed to be able to handle 
> logic and basic number theory. Thus it is assumed that S can encode 
> the function g: WFFS(S) —> N where N denotes the natural numbers.
> And S can decode a number to find the corresponding expression as 
> well. It is assumed that S as a logical system, is consistent.
> With this backgound, let g —> F denote the condition that g = g(F). 
> Thus I write a reference g —> F for a mathematical discussion of S, to 
> indicate that g is the Goedel number of F.
> Now suppose that F(x) is a formula in S with a free variable x. Free 
> variables refer to numbers. Thus if I write x^2 = 4 then this 
> statement can be specialized to 2^2 = 4 with x =2 and the 
> specialization is true.
> Or I can write 3^2 = 4 and this is a false statement. Given F(x) and 
> some number n, I can make a new sentence F(n).
> Now suppose that
> g —> F(x).
> Then we can form F(g) and this new statement has a Goedel number. Let 
> #g denote the Goedel number of F(g).
> #g —> F(g).
> This # is a new function on Goedel numbers and also can be encoded in 
> the system S. I will abbreviate the encoding into S by writing #n for 
> appropriate numbers n handled by S.
> Then we can consider
> F(#x) and it has a Goedel number
> h —> F(#x)
> And we can shift that to
> #h —> F(#h).
> This is the key point.
> Now we have constructed a number #h so that F(#h) discusses its own 
> Goedel number.
> This construction allows the proof of the Goedel Incompleteness 
> Theorem via the sentence B(x) that states
> B(x) =  “The statement with Goedel number x is provable in S.” (This 
> can also be encoded in S.)
> We then construct
> h—> ~B(#x)
> and
> #h —> ~B(#h)
> and obtain the statement
> G= ~B(#h).
> G states the unprovability of the Goedel decoding of #h.
> But the Goedel decoding of #h is the statement G itself.
> Thus G states its own unprovability.
> Therefore, S being consistent, cannot prove G.
> By making these arguments we have have proved that G cannot be proved 
> by S.
> Thus we have shown that G is in fact true.
> We have shown that there are true statements in number theory 
> unprovable by system S..
> ##########################
> The above is a very concise summary of the proof of Goedel’s 
> Incompleteness Theorem, using Goedel number encoding.
> It is a very interesting question whether such encoding or such 
> multiple relationships to context occur in biology. Here are some remarks.
> 1. In biology is is NORMALLY the case that certain key structures have 
> multiple interpretations and uses in various contexts.
> The understanding of such multiple uses and the naming of them 
> requires an observer of the biology. Thus we see the action of a cell 
> membrane and we see the action of mitosis, and so on.
> 2. There are implicit encodings in biology such as the sequence codes 
> in DNA and RNA and their unfoldment. To what extent do they partake of 
> the properties of Goedel coding?
> 3. The use of the Goedel coding in the Incompleteness theorem depends 
> crucially on the relationship of syntax and semantic in the formal 
> system and in the mathematician’s interpretation of the workings of 
> that system. The Goedel argument depends upon the formal system S 
> being seen as a mathematical object that itself can be studied for its 
> properties and behavior.
> When we speak of the truth of G, we are speaking of our assessment of 
> the possible behaviour of S, given its consistency. We are reasoning 
> about S just as Euclid reasons about the structure of right triangle.
> 4. In examining biological structures we take a similar position and 
> reason about what we know about them. Sufficiently complex biological 
> structures can be seen as modeled by certain logical formal systems.
> And then Goedelian reasoning can be applied to them. This can even be 
> extended to ourselves. Suppose that I am modeled correctly in my 
> mathematical reasoning by a SINGLE CONSISTENT FORMAL SYSTEM S.
> Then “I” can apply the above proof of Goedel’s Therem to S and deduce 
> that G cannot be proven by S. Thus “I” have exceeded the capabilities 
> of S. Therefore it is erroneous to assume that my mathematical 
> reasoning is encapsulated by a single formal system S. If I am a 
> formal system, that system must be allowed to grow in time. Such 
> reasoning as this is subtle, but the semantics of the relationship of 
> mathematicians and the formal systems that they study is subtle and 
> when biology is brought in the whole matter becomes exceedingly 
> interesting.
> 5. We man not need numbers to have these kinds of relationships. And 
> example is the Smullyan Machine that prints sequences of symbols from 
> the alphabet {~,P,R} on a tape. Sequences that begin with P,~P,PR and 
> ~PR are regarded as meaningful, with the meanings:
> PX: X can be printed.
> ~PX: X cannot be printed.
> PRX: XX can be printed.
> ~PRX: XX cannot be printed.
> Here X is any string of the symbols {~,P,R}.
> Thus PR~~P means that XX can be printed where X = ~~P. Thus PR~~P 
> means that ~~P~~P can be printed.
> By printed we mean on one press of the button on the Machine, a string 
> of characters is printed.
> Then we have the
> Theorem. There are meaningful true strings that the Smullyan Machine 
> cannot print.
> This is a non-numerical analog of the Goedel Theorem. And the string 
> that cannot be printed is G = ~PR~PR.
> For you see that G is meaningful and since G = ~PRX, G says that XX 
> cannot be printed. But X = ~PR and XX = ~PR~PR = G. So G says that G 
> cannot be printed.
> If the machine were to print G, it would lie. And the machine does not 
> lie.
> Therefore G is unprintable.
> But this is what G says.
> So we have established the truth of G and proved the Theorem.
> 6. Examine this last paragraph 5. The Machine is like an organism with 
> a limitation. This limitation goes through the semantics of reference. 
> ~PRX refers to XX and so can refer to itself if we take X = ~PR. ~PX 
> refers to X and cannot refer to itself since it is longer than X. In 
> biological coding the DNA code is fundamentally smaller or equal to 
> the structure to which it refers.
> Thus the self-reproduction of the DNA is possible since DNA = W+C the 
> convention of the Watson and Crick strand and each of W and C can by 
> themselves engage in an action to encode, refer to, the other strand. 
> W can produce a copy of C in the form W+C and C can produce a copy of 
> W in the form W+C each by using the larger environment. Thus W+C 
> refers to itself, reproduces itself by a method of encoding quite 
> similar to the self reference of the Smullyan Machine.
> 7. Von Neuman devised a machine that can build itself. B is the von 
> Neuman machine and B.x —> X,x where x is the plan or blueprint or code 
> for and entity X. B builds X with given the blueprint x.
> Then we have B,b —> B,b where b is the blueprint for B. B builds 
> itself from its own blueprint. I hope you see the analogy with the 
> Goedel code.
> 8. I will stop here. The relationships with biology are very worth 
> discussing.
> Before stopping it is worth remarking that the Maturana Uribe Varela 
> autopoeisis is an example of a system arising into a form of 
> self-reference that has a lifetime due to the probabilisitic dynamics 
> of its process.
> Very best,
> Lou Kauffman
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