BioSystems 204 (2021) 104395

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BioSystems
journal homepage: http://www.elsevier.com/locate/biosystems

Mathematics in biological reality: The emergence of natural computation in

living systems
Abir U. Igamberdiev a, *, Joseph E. Brenner b, c
a
Department of Biology, Memorial University of Newfoundland, St. John’s, NL, A1B 3X9, Canada
b
International Center for the Philosophy of Information, Xi’an Jiaotong University, Xi’an, 710049, China
c
Chemin Du College 1, 1865, Les Diablerets, Switzerland

A R T I C L E I N F O A B S T R A C T

Keywords: Mathematics is a powerful tool to express the computable part of the reality of the physical world. For living
Biological evolution systems, mathematical relations emerge internally as an abstracting capacity in the course of development and
Biological code adaptation to the external world. All living systems possess internal coding structures which represent their
Complexification
embedded description. They are anticipatory in the sense that the embedded description generates deterministic
Computation
Epistemic cut
model of their behavior. If the model does not provide a correct result, they can evolve through the acquisition of
Hypercycle new statements inside the embedded description that overcome limitations of the existing model. The newly
Internal measurement generated statements acquire meaning in and from the changing environment. The growth of complexity, being a
Relational biology consequence of the internal active adaptation to externality performed by the systems, increases the amount of
Univalent foundations external work and generates the observed patterns of spatiotemporal structures of evolving systems. In living
systems, the symbolic memory constraints are dynamic processes in themselves, co-evolving with the other
components of biological systems. Separation of the symbolic memory and the dynamic laws (defined as the
epistemic cut), required for self-replication of biological systems, forms the basis for their onto-epistemic relation
to reality. In this regard, living systems possess their own internal abstracting capacity and invent mathematics.
The digital structure of the genetic code is a manifestation of this mathematics.

1. Introduction. Mathematics and reality far as they are certain, they do not speak about reality. Einstein (1956)
also noted: “Physics is essentially an intuitive and concrete science.
1.1. The operational reality of mathematical concepts Mathematics is only a means for expressing the laws that govern
phenomena”.
Since Pythagoras and Plato, mathematical concepts and structures The operational notion of the world external to the observer and of
are frequently treated as separate ideal essences not associated with its cognitive acquisition via external activity nevertheless opens a pos­
changing actual reality. The formal language of mathematics is suitable sibility of counting as an epistemic process. The origin of mathematics in
for the description of the part of the world that is computable but it is human society coincides with and has evolved with the recognition of
rather not suitable for common communication. On the contrary, the the reflexive capacity of a human consciousness that operates with dy­
language of art (e.g. poetry) is non-formalized and appropriate for the namic oppositions, developing dualism. The resulting variety greatly ex­
description of meaning in the real world. Both are derived from the basic ceeds the fundamental binary choices described in the model of reflexive
structure of human language, one by reducing the field of meanings to consciousness introduced by Lefebvre (1982). This capacity, established
symbols and the other by expanding it through metaphors and other on the basis of referral of the subject (self) to its symbolic image, ac­
means. Ordinary human communication always goes beyond mathe­ quires the potential to rationally describe the external world through the
matics, and the link between the mathematical and the physical world structure of human language. It also reveals computable principles in the
cannot be computably described within the frameworks of mathematics relation to externality and becomes a premise of the origin of counting
and formal logic. As once Albert Einstein (1921) mentioned, as far as and later mathematics (Igamberdiev, 2017). The origin of computability
theories of mathematics speak about reality, they are not certain, and as arises from the model of regulation of both actuality and potentiality

* Corresponding author.
E-mail addresses: [email protected] (A.U. Igamberdiev), [email protected] (J.E. Brenner).

https://doi.org/10.1016/j.biosystems.2021.104395
Received 7 October 2020; Received in revised form 19 February 2021; Accepted 22 February 2021
Available online 25 February 2021
0303-2647/© 2021 Elsevier B.V. All rights reserved.
A.U. Igamberdiev and J.E. Brenner BioSystems 204 (2021) 104395

which becomes more powerful with the development of reflexive advantage for natural science of being unlimited by the properties of any
structure of human self. Operational regulation is achieved at this level particular process, but shares parts of all processes. Isolation and
as a noumenal reality and the concepts of computability and ‘dissection’ of ontolons is no more possible than of any other cognitive
non-computability evolve in parallel. process objects, but it is no more imaginary than a point of the complex
plane. These units can be related to the types in the concept of univalent
1.2. The relation of mathematics to the physical world foundations (Voevodsky, 1998, see below) but with a reference to their
operation in the actual world that includes the external reality.
Mathematics is thus a reflection of the real world that can be trans­
formed into a computable principle of its actualizations and potentiali­ 2. Logic in Reality and the foundations of mathematics
zations. Mathematics is a powerful tool for computing some
actualizations themselves, while the cognitive mathematical entities are 2.1. Logic and process in reality
separable from the actual reality. Mathematics also contains many for­
mulations that are not actualized in the real world. The most striking is The major contribution by Lupasco to a restructuring of logic was a
the dimensionality of space which is unlimited in mathematics but is view of phenomena in terms of processes instantiating dynamically
realized in physics as a perceived three-dimensional space. In modern different degrees of actuality and potentiality. Its fundamental postulate
physical theories, 3-D space is supplemented by additional compacted is that every real complex process is accompanied, logically and func­
dimensions whose number appears to be also limited. As far as the tionally, by its opposite or contradiction – Principle of Dynamic Oppo­
obvious curvature of space is concerned, in its relation to objects, there sition (PDO). The antagonistic dualities of our world can be formalized
is no basis for a particular mathematical value of it. The existence of as a structural, logical, and metaphysical principle of opposition or
metrics, according to the basic ideas of Riemann (1868), can be contradiction instantiated in complex higher-level phenomena. The
explained by the external physical forces of connection that operate fundamental postulate of Logic in Reality (LIR) is that all energetic
in/on space. These forces of connection, as suggested by Riemann, are phenomena alternate between degrees of actualization and of potenti­
related to the discreteness of space, and form its actual observed struc­ alization of themselves and their opposites or ‘contradictions’ but
ture. ‘Crystallizations’ of energy in the form of static objects and dy­ without either going to the absolute limits of 0% or 100%. The point
namic flows determine the characteristics of their spatial and temporal traversed at which a logical element and its opposite are equally actu­
environment and its evolution. Mathematics itself cannot establish the alized and potentialized is one of maximum interaction from which new
basis of the values of the fundamental constants in physics, which can be entities can emerge. It is designated by Lupasco as a ‘T’-state, T for
substantiated, say, as Diogenes proved the existence of movement by included middle or third (Tiers-inclus). It is thus itself the opposite of the
walking. As Einstein noted, “God does not care about our mathematical principle of the excluded middle in standard bivalent propositional
difficulties, he integrates empirically” (Infeld, 1949). In other words, the logic.
Nature establishes the limits of real processes that shape the physical The calculus of standard logics has its major role in the construction
world in a manner of Diogenes. of proofs of theorems. One of the major differences between Logic in
Kant (1747) analyzed the problem of dimensionality of space in Reality and standard semantic logic is that since its theorems do not
“Thoughts on the true estimation of living forces” (1747). Physical forces act refer to the truth of propositions, there are no proofs of a propositional
according to the inverse square law in three-dimensional space and thus kind. For a truth to be grounded is not for a binary relation to obtain
potentiality is actualized in a usually consistent manner (De Bianchi and between a proposition and a truth-maker; a grounding relation consists
Wells, 2015). In such space, it is possible to define energy as a countable in the existence of sub-sentential thought/world relations and the fact
representation of the potential for realizing a process measured as work. that the object instantiates the property in question. Proofs are not
Only in real space can processes take place operating in an apparent time primarily a matter of true and false, but of coherent indication. There are
that separates contradictory statements and generates dynamic opposi­ no proofs in LIR, and also no syllogisms nor standard principle of logical
tions (Igamberdiev, 2007). The explanation of three-dimensionality consequence. In a sense, our study is always a search for a dynamic
given by Kant depends on the assumptions of consistency and seman­ logical connectedness than for logical consequence, if one is seeking to
tic truth that beg the question of the origin of the dynamic oppositions it explain the relation between A and B.
describes. Our world exhibits Mathematics in Reality, not as a noumenal The dialectical Logic in Reality of Lupasco (Brenner, 2008) has not
description of the phenomenal world via actualization of the potentiality yet been accepted as a framework for the foundations of mathematics
of the Ding-an-sich, but as a consequence of our own reality as subjects because of the difficulty in visualizing and comprehending its key
able to cognize the various movements of the world and then become Principle of Dynamic Opposition as well as the operation of other
capable of transforming them into an epistemic Ding-für-uns. principles on which reality is established. This difficulty is particularly
significant for the interpretation of mathematics because of the
1.3. The principle of dynamic opposition, non-separability, ontolon explanatory problems associated with the application of computational
principles. Here we will discuss the interpretation of the complex plane
We use the expression “dynamic opposition” as a way of referring to based on Logic in Reality. The relation of complex numbers to the
real processes and their changes. In the next Section 2, we will show how duality of potential and actual realities was assumed in earlier philo­
a principle of dynamic opposition (PDO) underlies and orders all real sophical systems, in particular, by the Russian religious philosopher
phenomena, and we will see how it operates in knowledge, from logic Pavel Florensky (1882–1937) in his book Imaginaries in Geometry
and science to philosophy and in real systems from physics to biology. (Florensky, 1922). For recent developments of understanding of the
The grounding of the PDO in physics implies that the default relation­ relation of complex numbers to reality see the book of Nahin (2010).
ship between the elements in opposition is that they are never totally For people trained in classical logic, it is difficult to see implication
separate or separable in real, complex and changing systems. We will itself as a process; implication is a simple connective like and, or, and
give the examples of the operation of the PDO and of non-separability in equality. Material implication, or just implication, is another name for
different domains and see the operation of non-separability most clearly the material conditional if > then, both applying only to propositional
in the discussion of biosystems (living systems) in Section 5. The unit of logical proofs and rules of logical inference or their mathematical
reality that we can define as “ontolon” (Brenner and Igamberdiev, 2021) equivalents. (In Boolean algebra, True and False are assigned the values
holds dynamic oppositions within its spatiotemporal configuration and of 0 and 1.) As shown by Lupasco, however, it is useful to look at
represents a single embodiment of change, or a bundle of the concurrent implication, as well as the other logical operators as a real processes,
changes, which a real system undergoes and induces. It has the involving the energetic changes which accompany cognition, processes

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themselves capable of degrees of actualization and potentialization, and function of the graph is to facilitate visualization of a process in which
of being the source of emergence. the evolution of the actuality and potentiality of identity and diversity
cannot be separated from that of the process as a whole. Eventually, an
2.2. Potentialization and actualization animation would be required to capture the dual evolution in time.
We started with an attempt to describe information in the complex 2-
As noted, the evolution of a real interactive process involves the D plane. Does our ‘3-D’ picture, that is, the representation of a move­
(predominantly) actualized component becoming (predominantly) ment between identity and diversity apply to information? It certainly
potentialized. Since the value of actuality is the reciprocal of the value of would seem to apply to theories of information, whose proponents seek
potentiality, the new value resulting from evolution of a process can be to achieve some degree of unification or are content with an apparent
represented as (ai, b). In the simplest case, the line between the two unending series of different theories. We conclude that at each stage of
points has a slope of 45◦ . The values of a and b can vary between 0 and 1, complexification of our graphical picture, the real nature of change in
corresponding to different values of interaction between the elements, general becomes more apparent. We would call our representations
and to a required property of non-standard probabilities. However, the ‘living graphs’ but the trope has been overworked. We now will move
degree of interaction between the real elements is zero to all intents and backwards (or forwards?) toward the original graph. It has become, with
purposes in many processes. Without going into detail here, a limiting the four axes x, y, z and w, a four-dimensional hyperspace, even if only 2-
case is a standard process without an imaginary component, for D spaces or 3-D volumes of it are ‘active’ at any time.
example, a pendulum. Mathematics, as formulated by Pythagoras and ‘bracketed’ since
The values of the actuality and potentiality of opposing or contra­ then from perceived reality, as discussed above, thus has fundamental
dictional process elements have been defined, in Logic in Reality, as theoretical gaps in its construction. These flaws are substantial; they
never going to the abstract limits of zero and 1. Accordingly, a graph of cannot be overcome within the construction and require referral to a
the evolution of a process in two dimensions will not pass through the reality that is external to the epistemic reality of mathematics itself. The
origin, the point [0,0], nor intersect either of the two axes. Only the principles of constructive mathematics were one attempt to improve the
upper-right quadrant will be occupied. On the other hand, many phys­ foundations of mathematics. In our view, however, further structural
ical processes can and in fact have been described by equations to the substantiations are required to bridge the gap with reality. Voevodsky
solutions to which can take on zero and negative as well as imaginary was indeed fond of the idea to bridge the aforementioned gap (Rodin,
values. If real numbers are assigned to an x axis and the imaginaries to a 2021), and his concept of univalent foundations outlines a new approach
y axis, the upper-left quadrant defines the negative real and positive in which mathematics can be viewed operationally as a human activity
imaginaries, the lower-left quadrant the negative real and negative included in the dynamic processes of reality (Grayson, 2018). We sug­
imaginaries, and the lower-right quadrant positive real and negative gest that it will be possible to incorporate some of the principles first
imaginary values. explored in constructivist mathematics and in its univalent foundations
We conclude that a single graphical representation of both kinds of in a new fundamental concept based on Logic in Reality. This will pro­
processes is possible by moving to three dimensions, adding a z axis for vide a new understanding of the operational nature of mathematics and
the imaginaries of LIR kind. Here, we have two intersecting complex substantiates its explanatory power. In this framework, the basic foun­
planes. Values are defined by a triple [a, bi, ci], as noted. For all classical dations of mathematics can be reconsidered with a reference to their
physical processes which can take on zero or negative as well as standard operation in the external world. This resolves some of the problems
imaginary values, c is always zero. However, all quadrants in the x, y associated with the application of Logic in Reality to real systems,
plane can be occupied. For complex processes following the LIR logic, b bringing it closer to a synthesis, which includes mathematics (Brenner,
is always zero and the sole quadrant occupied is the upper-right in the x, 2018; Brenner and Igamberdiev, 2019, 2021).
z plane.
3. Mathematics in reality: overcoming Mathematical Platonism
2.3. Logical structures unfolding in nature in the 20th century

As emphasized by (Nicolescu, 1985), Lupasco’s system supports an 3.1. The operational interpretation of mathematics
isomorphism in the structure of processes at inorganic, biological,
cognitive, and social levels of reality. The methodology of the applicable The operational nature of mathematics was developed in the 20th
logic involves identifying the logical elements of the processes which are Century and codified in the logical approaches of intuitionism and
in fact opposing one another and from which a third element may constructivism. It resulted in an understanding that the power of
emerge at a higher level. One example is the residual positive or nega­ mathematics is in the process of real computation, which also determines
tive charge on an amino acid that determines its possibilities for the computational limits of reality itself. The operational power of
non-covalent bonding and the secondary structure of proteins which mathematics is realized if and only if it refers to reality. The basic
includes it. The question is now whether the graphical representation of operational aspect can be analyzed by applying the Zermelo-Fraenkel
the degrees of actuality and potentiality of those elements, and their Axiom of Choice, considered the most basic foundational axiom un­
evolution of those degrees toward an opposite one, adds to our analysis derlying the whole construction of mathematics. The Axiom of Choice is
of complex processes. Once the concept is understood, our answer would logically independent from the remaining Zermelo-Fraenkel axioms. It
be no unless the further parameter at the core of the Lupasco logic, refers to a function f for any set A that includes in its domain every non-
Identity and Diversity, is taken into account. empty subset of A and selects (chooses) exactly one element from each
It is therefore necessary to add additional two real variables to our subset. The Axiom of Choice itself cannot substantiate the operational
picture which we represent by the additional real values d and e, plotted nature of mathematics, but it became the basis for discussing the oper­
on a new axis w. This converts the x, z complex plane to a three- ational principles in the foundations of mathematics and, in particular, it
dimensional complex graph. In words, we state that any point in the stimulated Lupasco (1947) in his development of Logic in Reality (LIR)
3D graph [a, ci, d, e] is characterized, in addition to its degree of actu­ for describing the processes taking place in the physical, biological and
ality and potentiality, by a similar reciprocal degree of identity and di­ social domains of reality.
versity which evolves concurrently but independently of the first In 1951, Lupasco suggested, although not fully developed, a project
property. The trajectory of a real process, involving the movements (see Lupasco, 1973), for a contradictorial set theory, based on the
between a and ci, and between d and e, will be a two-dimensional sur­ principle of dynamic oppositions (PDO) and the logic of the included
face, which may be plane or curved, in a three-dimensional space. The middle. He showed that the Axiom of Choice, which he considered a

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difficult problem for classical logic, was a natural illustration of such a Gödel established that logical systems of arithmetic could never contain
set theory. In this framework, each element of a set is a contradictory a valid proof of their own consistency, which led him to the formulation
duality, composed of an element and its anti-element, such that the of a set-theoretic Platonism in the foundations of mathematics, which
former expresses primarily an actualized identity and potentialized di­ strongly deviates from the classical Platonism. Brenner and Igamberdiev
versity (or non-identity) and the second the contradictory picture of (2019, 2021) philosophically analyzed Gödel’s concept, seeing it as a
diversity and identity. Since sets, as well as elements, must be accom­ model of the fundamental duality of the universe.
panied by their contradictories, the Logic in Reality (LIR) of Lupasco
(1947) and Brenner (2008) results in the existence of three related sets. 3.3. Intuitionistic logic and paracompleteness
One of these sets is the set M of Zermelo, in which the identity of the
elements is actualized and the diversity of the elements is potentialized. Intuitionism, as the 20th Century alternative to mathematical
Another one, of maximum contradiction (T-state) which forms sub-sets Platonism, did not refer mathematics to reality, but rather it referred it
whose elements are characterized by both identity and diversity – the set to the human mind and creativity. Intuitionism, contrary to Pythagoras,
P of Zermelo. The third set, which is exactly the set N – that of choice, in considers numbers as merely mental entities which would not exist if
which diversity is actualized and identity potentialized. This is why it there were never any human minds to think about them. A development
can, and must, contain one element and one element only of each of the of intuitionism toward referring mathematics to reality instead of pure
sets in P (otherwise, if more than one, it would be equivalent to a partial subjective mind came with the formulation of constructivism that re­
actualization of identity). It is the principle of non-identity, absent in quires proofs to be “constructive” in nature. According to this view, the
classical logic, but here given its correct place in the scheme of things, existence of an object must be demonstrated in reality. The major logical
which makes possible this result. developments of the 20th Century involved the demonstration, by
Newton Da Costa (1974) and others, that rigorous logics could be con­
3.2. Ontologization of mathematics structed by rejecting the universal application of the 2nd and 3rd clas­
sical axioms. The logics in which the axiom of non-contradiction does
The positioning of mathematics in reality means overcoming the not apply but that of the excluded middle does are called paraconsistent;
Pythagorean paradigm often defined as Mathematical Platonism that in the opposite case, they are paracomplete. It is in this sense that
tends to restrict the domain of its application to epistemological entities. Jean-Yves Béziau (2005) described them as ‘duals’.
The problem is that this paradigm fits the internal meaning and structure The most significant example of a paracomplete logic is intuitionistic
of mathematics well, and the whole subject of mathematics was initially logic. Brouwer (1951), who is often considered as a founder of intui­
formulated and historically developed as the area of knowledge in the tionism, strongly objected the very idea that mathematics is based or
frames of this paradigm. The first substantial direction towards over­ should be based on some logical principles but itself provides a foun­
coming this paradigm was the formulation of geometry by Euclid who dation for logic. In particular, Brouwer (1951) had claimed that the law
placed mathematics into abstract spatiotemporal reality, while his par­ of the excluded middle is not applicable in mathematics, “once it has
allel postulate (Euclid’s fifth postulate) placed geometry into observed been recognized to be an autonomous interior constructional activity
spatiotemporal reality. This movement, however, did not go beyond the which, although it can be applied to an exterior world, neither in its
mathematical Platonism, as Euclid in his “Elements” did not provide any origin nor in its methods depends on an exterior world”. He rejected the
philosophical commentary concerning the “reality” of mathematical classical way of thinking about infinite sets and proposed an alternative.
objects. The Euclid-style Greek mathematics still allow for different Arend Heyting (1956) reconstructed Brouwer’s concepts of spread and
philosophical interpretations including the Platonic one. species, which (together) provide an intuitionsitic counterpart to clas­
The foundations of the scientific revolution in Europe in the 17th sical (infinite) sets, and developed the intuitionistic logic, which helped
century were substantiated by Descartes who built the bridge between him to make the Brouwerian concepts more transparent. He thus opened
algebra and geometry, which later led to the discovery of infinitesimal a possibility of the application to mathematics of a multi-valued logic,
calculus and analysis. The Cartesian coordinate system as a cornerstone and rejected the concept of truth as a relationship between language and
of analytical geometry was a further breakthrough in placing mathe­ an extra-linguistic reality. However, there is no indication in his work of
matic in reality and led to the formulation of the classical physics. The a basis or need for applying such principles outside mathematics. He did
later development faced certain difficulties in the formulation of ap­ not, apparently, formulate or show the necessity of a law of the included
proaches to the ontologization of mathematics. The two programs of the middle of the dialectical logic of Lupasco (1947). Intuitionistic formu­
foundations of mathematics in the 20th Century (Hilbert’s formalism lations contain idealized distinctions and processes that apply only
and Frege’s logicism) were rather Pythagorean. The third (intuitionism) within mathematics. As the law of non-contradiction is maintained,
was anti-Pythagorean but it did not develop into a sufficiently powerful however, as shown by Graham Priest (1995, 2001) and others, intui­
framework for replacing the most fundamental Pythagorean and Pla­ tionistic logic remains closely related (congruent) to classical logic.
tonic principles. Another aspect of interest, however, relates to the concept of intui­
The foundational crisis of mathematics of the early 20th Century (in tion as such. Brouwer’s concept of the non-mathematical aspects of
German Grundlagenkrise der Mathematik) was the most important event intuitionism, apart from the rejection of the excluded middle, has a
in the search for the proper foundations of mathematics. The dichotomy philosophical kinship with the idea of a logical status of both intuition
of mathematics from reality was seen to be clearly reflected in its in­ and knowledge (Largeault, 1993). Paracompleteness implies a funda­
ternal paradoxes. In the formalist approach, David Hilbert grounded mental incompleteness in a logical system. Neither of two elements is
mathematics on a logical system supported by metamathematical considered true by itself, and new concepts must be introduced to close
means. This was opposed by the intuitionist school of L.E.J. Brouwer the gap between them. We consider this a form of an included middle
(1951) who rejected formalism as a meaningless game with symbols. and the applicable logic would seem to be the Logic in Reality (LIR)
Hilbert, in turn, insisted this game is not based on the arbitrary rules but formulated by Lupasco (1947) and developed by Brenner (2008). This
develops in the internal necessity of how our thinking proceeds. Logi­ logic is also paraconsistent, but in a new sense. All other paraconsistent
cism has some points in common with formalism but it is based on the logics are propositional, truth-functional logics, while LIR is a logic of
more explicitly formulated thesis that mathematics is an extension of real processes, states and events.
formal semantics and mathematical logic. Gottlob Frege, influenced by
Richard Dedekind, initiated this theory, which was further philosophi­ 3.4. Intuitionism as a part of the constructivist program
cally supported by Bertrand Russell and Alfred N. Whitehead in their
Principia Mathematica (Russell and Whitehead, 1910–1913). Later Kurt Intuitionism referring to the human mind represents only one part of

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the constructivist program. In a broader sense, constructivism refers to Voevodsky, 1998; Grayson, 2018).
the reality in which human mind is only one of the aspects. The apparent Voevodsky called the invariance property of the mathematical lan­
limitations of constructive analysis, which many mathematicians asso­ guage univalence. Formal mathematical language, together with an
ciate solely with removing the principle of excluded middle, was axiom of univalence, fulfills the mathematician’s dream: a language for
compared by Hilbert to the prohibition of astronomers to use telescope. mathematics invariant under equivalence and thus freed from irrelevant
The rejection by many mathematicians of any mathematics not based on details, capable of merging the results of mathematicians taking
constructive methods led to the development of new approaches to its different but equivalent approaches. Following Voevodsky, the unity of
foundations. These incorporate the elements of the constructivist cognition and spatiotemporality needs to be incorporated not only in
approach but search for broader substantiation of the operational power philosophical thought but also into the foundations of mathematics, into
of mathematics. In rejecting the excluded middle, the intuitionist which Voevodsky also included geometry. When geometry is introduced
mathematicians and logicians did not go far enough in the direction of to the foundations of mathematics, the world can be shaped theoreti­
reality, since the principle of absolute non-contradiction was cally in a way that fits its inhabitability, which resembles the anthropic
maintained. principle in physics. The limits of geometry are associated with the
The progress of mathematics after the formulation of set theory limits of the computability of the particular world, and in the theory of
aimed at overcoming its limitations, and the invention of category the­ homotopic types developed by Voevodsky, the basic foundations of
ory by Eilenberg and MacLane (1945) led to the idea developed by F. mathematics can be verified computationally (Grayson, 2018). Voe­
William Lawvere (1963) that category theory can serve as a foundation vodsky in his three unpublished works initiated the program of appli­
of mathematics. The notion of category incorporates the unity of objects cation of his mathematical ideas in biology. In particular, he performed
and relational operators (functors, arrows) in their connection thus a retrospective reconstruction of the temporal historical processes, e.g.
introducing a process of epistemic interaction between mathematical of the change of population size in time, with or without using available
objects and their axiomatic foundations. The objects and arrows may be genetic data (Fimmel, 2021).
abstract entities of any kind, and the mathematical entities together with Voevodsky’s types in the above univalent foundations do not
their relationships provide the explanation for the interactive contin­ correspond exactly to anything in the foundations of set-theory, but they
uum appearing through the process of actualization. Further develop­ may be thought of as spaces, with equal types corresponding to homo­
ment of category theory resulted in elaboration of the idea of topos and topy equivalent spaces, and with equal elements of a type corresponding
the topos logic. The special type of category defined as a topos possesses to points of a space connected by a path. Univalent concepts were
its own internal logic (Goldblatt, 1979), which can be paraconsistent inspired both by the Platonic ideas of Hermann Grassmann and Georg
and include contradictory statements. The topoi with paraconsistent Cantor, and by “categorical” mathematics in the style of Alexander
internal logics have been constructed and studied (Estrada-González Grothendieck. Univalent foundations depart from the use of classical
2015). Although the attempts to accommodate paraconsistent logic in predicate logic as the underlying formal deduction system, replacing it
topos theory do not represent the mainstream categorical logic, the with a version of Martin-Löf type theory and thus represent a powerful
fundamental logical structure of a topos possesses its own logical cal­ operational interpretation of pure mathematics. The next step is to place
culus with potentially and actually existing elements, in which a certain mathematics itself in reality, which will be considered in the subsequent
set of points is stable in relation to topological reconstructions (Béziau, section.
2005; Andreas and Verdée, 2016). The development of topos logic
represents a significant breakthrough in positioning the foundations of 4. Living systems: the epistemic relation to reality
mathematics in relation to reality (Rodin, 2010, 2016), however the
limitations of category theory and topos logic are due to its incorpora­ 4.1. The problem of the origin of computation in reality
tion of the principles of truth-functionality based on standard categories.
The use of the process-based Logic in Reality (Lupasco, 1947; Brenner, Up to this point, the main paradox in our conception of mathematics
2008, see also Section 3) for substantiation of the foundations of the and its place in reality is to describe the origin of computation by
topos structures applied to living systems can be considered as a basis for computational means. It may be considered as an expression of the basic
understanding how intrinsically lower-level logical structures appear in paradox of our relation to the external world, which generates the dy­
the nature and unfold in the evolution of living systems. namic opposition of computable and non-computable aspects of reality
(see Conrad and Liberman, 1982).
3.5. Using univalent foundations of mathematics to place mathematics in The universality of mathematical laws can be explained by the fact
reality that the same limits of iteration and recursion (‘loops’) are formed in
different generally non-equivalent systems having internal constraints
Following the development of the ideas of mathematical foundations (Igamberdiev, 2008). Any internal choice exhibits a structure resulting
in the 20th Century and incorporating the principles that underline the from mixing the notion of indicating an element with the act of indi­
computational process, a new approach to foundations of mathematics cating a set consisting of elements (Igamberdiev, 2004). Closed loops of
was introduced by Vladimir Voevodsky (1966–2017). In his concept of causation in them appear as objective entities which can be mapped into
univalent foundations, all mathematical structures are built out of ob­ a single coherent space–time frame (Rosen, 1993). This assumes, of
jects called types. Generally, under the path induction (homotopical) course, that such a framework corresponds to reality. If so it can follow
interpretation of type theories, types are seen as spaces and terms of these that the fundamental parameters may correspond to a consistency of the
types are seen as points of those spaces. When types are seen as terms of spatiotemporal landscape formed through communication (Igamber­
other “big” types, each entity (type) can be considered as a mathemat­ diev, 2008). A physically embodied recursive loop has certain parame­
ical point, the points create topological spaces in which the definition of ters that correspond to its objective existence. These parameters include
distances is replaced by that of paths. The process from one point to a values that can be redundantly repeated in all loops that co-exist, cor­
next point is path induction, while homotopy is a continuous trans­ responding to a topological inevitability of actualization processes. We
formation of one path into another path. Voevodsky’s type theory is a observe ourselves as being embedded in the whole world simulated by
deductive system with suitable rules of inference and one of its goals was our internal computation. This world itself is internal and external to us
the automatization of mathematical proofs. The idea behind univalent at the same time and formal logic and mathematics appear in it as a
foundations is to make mathematical proofs built on univalent founda­ consequence of a self-identification process of the observers inhabiting it
tions computationally testable. In his paradigm, foundations of mathe­ (Dodig-Crnkovic, 2016).
matics can appear as computationally testable (for details see The origin of internal computation related to our conscious activity

5
A.U. Igamberdiev and J.E. Brenner BioSystems 204 (2021) 104395

can be explained on the basis of self-reflection as suggested by Lefebvre topological, and their use in biological and social sciences continues the
(1992). When the reflexive process builds “the image of the self in the conceptual paradigm of Spinoza to conceptualizing the world (Zim­
image of the self”, which we call “a Double Homunculus” (Sawa and mermann, 2010).
Igamberdiev, 2016) a dialogue process between the two agents becomes The categorial approach to living systems and their behavior estab­
possible which includes both exchange of information and observation lished a relation between semiosis in cognition/communication and
of external objects. The Double Homunculus model has substantial po­ standard logic. It aimed at describing the complete complex network of
tential for describing interactions of communicating agents in the social biological and social interactions, as well as a model for the recursive
environment and their ability to perceive and transform the outside operations necessary for the acquisition of knowledge. The mathemati­
world as well as generate entire social systems of different types cally grounded conceptualization of science in topos theory thus
(Igamberdiev and Brenner, 2020). Further, it was shown that two attempted to establish a methodological bridge between philosophy,
conscious agents estimating their own reflection in the opposite ways via logic and science and even the development of an ethical system that
generation of the two-valued versus many-valued logic become incor­ could clarify the grounds of social behavior. Nevertheless, this approach
porated in the evolving process of perpetual relational transformation was only partly successful since it bracketed too many of the actual
(Sawa and Igamberdiev, 2017). The structure of formal logic itself process aspects of living and cognitive systems. While Rosen’s initial
emerges as a universal tool for understanding and description of reality concept has a disjunction with the approach based on energy (classi­
via intercommunication of reflexive subjects. It takes place in time and cally, force), the internal measurement concept of Matsuno and Gunji
space and results in the fractal features that appear in the course of returns back to physics and establishes the relation of topological en­
spatiotemporal unfolding (Sawa and Igamberdiev, 2021). The descrip­ tailments in the foundation of living systems with the basic physically-
tion of the generation of logic and of the appearance of counting by grounded energetic processes. Further development is needed to incor­
means of logic itself assumes that we need to apply a special type of logic porate these processes in the fundamental theory explaining life as a
of process (such as LIR) that avoids the proofs of a propositional kind but process unfolding on the basis of its internal logic underlying the bio­
introduces the coherent indications in a search for a dynamic logical logical organization.
connectedness (Lupasco, 1947; Brenner, 2008). This logic will not have
a deterministic power in the sense of strictly defined formal logics but it 4.3. The biological code
provides an important tool for our understanding of the origin and
establishment of the principles of the informational exchange and The principles underlying relational biology do, however, have suf­
mathematical operation and application. ficient power to substantiate the existence of a biological code. Ac­
While the suggested models aim to describe the origin of the infor­ cording to Stent (1971), Aristotle was the first to formulate in
mational transfer between conscious objects, mathematics itself appears philosophical terms the concept that resembles our understanding of
already in non-conscious living systems having the internal digital coding in living systems, which was not recognized until the invention of
description within them, which is realized in the appearance of the genetics. In his tractate De Anima, Book II, Aristotle introduced the
digital code having its own internal logic (Igamberdiev, 2007). This fundamental triadic structure that underlies all phenomena related to
assumes that the problem of applicability of mathematics in biology is the internal activity of living systems. It includes 1) Matter (potential­
grounded in the fact that biology is not just about application of math­ ity); 2) Entelechy as knowledge, which is the first or pre-actualized ac­
ematics but about the building of mathematical relations in biological tuality; and 3) Entelechy as an exercise of knowledge, which is activity
systems. The “endo-observer” of the biological system operates with this of recognition or actualized actuality. This profound structure is related
mathematics and applies it in its internal activity. In the next section, we to the biological level of reality. It can be associated directly with genetic
will outline the approaches that help to understand biological reality as organization where Entelechy as knowledge corresponds to the
a process of perpetual generation of digital descriptions and their in­ embedded description, i.e. to genetic structures.
teractions in the realm of communicating and evolving living systems. The idea of code is seen as the main characteristics of living systems
(Barbieri, 2015) similarly to the reference frame in physics. Only after
4.2. Living systems perform mathematics the rediscovery of Mendel’s laws of inheritance, the idea of code was
firmly reinstated in biology. The idea of code is directly connected to
The basic problem of understanding living systems lies in the oper­ such main property of living system as the “closure to efficient causa­
ation of mathematics in biological reality, which can clarify the essence tion” (Rosen, 1991) which also refers back to Aristotle. The wholeness of
of living processes and their evolutionary transformations. The appli­ living organisms can thus be rationally described and logically analyzed.
cation of category theory and the concept of topos became an important It determines the characteristic features of biosystems, realized at the
step in formulation of the basic principles of theoretical biology in the level of the internal structure of an organism as well as at the level of
relational biology of Robert Rosen (1991). Liberman (1972) explicitly interactions between organisms. In Lupascian terms, one would say that
stated that living systems ‘perform’ mathematics. The concept of inter­ the whole is present also as potentiality, which in LIR is not limited to
nal measurement of Koichiro Matsuno (1995) and Yukio Gunji (1995) “matter”. The dynamic approach to code assumes that it should be read
introduced the notion of endo-observer, and Louie (2020) suggested the in the system by a processing device that was defined as a molecular
most abstract representation of living beings based not on their physical computer of the cell (Liberman, 1972; Vaintsvaig and Liberman, 1973).
and chemical structures but on the abstract entailments underlying the No natural code can code itself, as it needs certain agents that act on this
fundamental biological organization. Plamen Simeonov (2010) refor­ code that form a structure that decodes genetic statements. Genes
mulated relational biology as Integral Biomathics, which incorporates establish and determine the direction that the structural change of the
the basic principles of relational biology in the framework of an whole undergoes, independent of the prior dynamics of the whole.
expanded concept of theoretical biology. The process of natural calculation (see Dodig-Crnkovic, 2016) per­
Living systems can be modeled in part using category theory as if one formed in the processing of genetic information is based on multiple
were an epistemic ‘endo-observer’, with its own self-referential coding, searches of addressed molecular operations of informational molecules
operating on the model in an iterative recursive process. The output of (Liberman, 1972). The chemical structure of molecular operators is
the operation then appears as the development and evolution of the important only for the process of readout, while the information itself is
system, with any solution relative to that observer (Igamberdiev, 2007). independent from its carrier. In the physical reality of the cell, the digital
This methodology introduces the topological language in the episte­ genetic information receives its interpretation, and its material carriers
mological domain avoiding the concentration on the physical operation (nucleotides) exhibit their real physical properties, in particular in the
of the system. The most fundamental geometric relations are secondary, tertiary and quaternary DNA structures up to chromosomes

6
A.U. Igamberdiev and J.E. Brenner BioSystems 204 (2021) 104395

that possess the species-specific architecture (Igamberdiev and optimal fitness in their embedding and persisting in external space. This
Shklovskiy-Kordi, 2016). Life exists in the unique natural form of living principle of optimality is an evident basis for understanding space-time
cells operating according to the program written on DNA. It uses an generation by living organisms. We note that this is an exact repro­
internal process of calculation by means of the physical system with the duction of the statement by Lupasco (Brenner 2008) that objects do not
embedded mathematical operations to perform the strategy of ontoge­ ‘float’ in an external space-time but generate their own. Robert Rosen
netic and evolutionary adaptations that arise to the correctness of cal­ (1967) in his earlier book Optimality Principles in Biology showed how
culations performed by the molecular computer of the cell. The latter morphogenetic structures correspond to most optimal functional solu­
possesses not only the reading but indirectly also the writing capacity tions. In this regard, Rosen considered some empirical relations that
memorizing the new statements and loading them by meaning (Shapiro, govern evolution, growth, and the transformation of biological forms.
2016). He analyzed feedback control principles to explain optimality in
different, in particular related to morphogenesis, processes. In fact,
5. Computation, emergence and complexity living system is involved in a continuous internal measurement to
maintain its structure and optimally respond to the challenges of
5.1. The problem of endo-observer in biological systems environment.

Relational biology describes life as ontologically independent 5.2. Emergence

generic phenomenon (Rashevsky, 1954; Rosen, 1991). The generic
property of living systems can be analyzed as possessing self, which is Living beings are complex systems and their complexity is irreduc­
related to internal determination (Aristotle’s “di aytoy”) or “closure to ible to their elements as was realized early in philosophical thought.
efficient causation” (Rosen, 1991). Life corresponds to a certain relation Complexification in the course of individual development is a mostly
between constituent elements, and its physical structure can possibly be ordered process taking place in the natural world that needs a specific
substitutable, i.e. the material substrate of living structures could be framework for its description and analysis. The development of a
different. In the system closed to efficient causation, the internal concept for explanation of the emergence of new actualizations is a
determinant, defined by Lefebvre (2016) as “eidos-navigator”, ulti­ difficult philosophical problem. A principle that is beyond the standard
mately appears. A living system has at least one point of determination principles operating in the physical world was introduced in biology as
by the eidos-navigator, so any living body has a point referred to its the principle of natural selection. This principle, which was formulated
“self” in which its movement is not determined physically. This move­ by Darwin but arises to Lucretius and earlier to Empedocles, has been
ment unfolds into a structure that reflects the internal choice that is viewed from Darwin’s time as the most fundamental principle in
uniquely possible for living systems. In the advanced social systems, biology. It was generalized in the mathematical concepts describing
eidos-navigator becomes attributed to the global conceptual structures evolution, and then was applied to the origin of life as the formation of
that represent initially religious and later philosophical and other hypercycles (Eigen and Schuster, 1979). It still dominates as the basis of
fundamental reflections. explanation in biology today. The application of this principle to
For understanding the nature of living beings, the problem of a self non-living matter was initially abandoned until it was applied in cos­
internally determining their activity, has to be analyzed in detail. The mology as a ‘natural selection’ of universes (Smolin, 1997). It always
“self” is characterized by a spontaneous activity, which appears as a non- seems straightforward to use this principle as the basis of a final
computable decision attributable to the living system that introduces explanation of everything that is observed in the Universe including
computation into the real world. An apparent “unreasonable ineffec­ actualization in quantum measurement. However, we need to keep in
tiveness” of mathematics in theoretical biology (Borovik, 2021) refers to mind the limitation of this principle for the explanation of real, that is,
this essential non-computability of the action that introduces compu­ both inseparable actual and potential existence, and realize its philo­
tation in living systems. In fact, its description requires non-trivial sophical deficiency despite the apparent transparency of such explana­
mathematical approaches partially realized in the frames of relational tions. In the changing world, i.e. in Reality, there is no fixed
biology by Rashevsky (1954), Rosen (1991) and Louie (2020), and used “environment” in which the actual is selected, and this diminishes its
in the works of Gunji (1995) for the analysis of the dynamics initiated by role as a “frame of reference”, not only in biology. If space-time were
endo-observer. Schrödinger (1944) was the first to suggest that the na­ absolute in the Newtonian sense, such a principle could work, but in our
ture of the self is quantum mechanical and should be placed beyond relational Universe its applicability is limited.
quantum reduction. It corresponds to the internal quantum state (IQS, the In physics, the objective of a principle of “natural selection” is to
term introduced by Igamberdiev, 2004, 2007) that is the potentiality bring out or emphasize the final cause for observability, i.e. to replace
that directs possible actualizations, is delocalized and pre-programs the the unfounded anthropic principle, which refers to the fundamental
a priori forms of space and time, generating the spatiotemporal frame in constants in our universe being of the right size to permit life. The
which the world is observed. principle in biology is based on the concept of the survival of the fittest,
When there is no “active” observer concerned, the modeling of which is also teleonomic in the Aristotelian sense. This principle can be
space–time results in Newtonian geometry with a single unitary viewed in a more general paradigm as the consequence of spatio­
Euclidean coordinate system. When we consider the observer “actively” temporality generated by the multiplicity of actualizations and poten­
measuring space–time by signals with finite velocity, we arrive at Ein­ tializations in reality. It, however, cannot directly explain
stein’s relational space–time but one in which all coordinate systems are complexification and the necessity of evolutionary growth unless it is
equal. When the effect of measurement is taken into account, we come to viewed as a consequence of the more general principle of dynamic op­
the choice (generation) of coordinate system and its consequent trans­ position (PDO) and the actualizations and potentializations resulting
formation toward a stable (or homeostatic) state as an attractor. This from it.
generates various structures whose generation can be described by the While open-endedness is the main presumption of the generative
non-Euclidean geometry. For biological systems, we introduce a virtual nature of biological evolution (Pattee, 1993, 2001), the notion of gen­
notion of an endo-observer realizing the internal measurement and erativity can be viewed as a concept antithetical to computation
establishing space-time relations (Igamberdiev, 2018). (Igamberdiev and Shklovskiy-Kordi, 2016). In order to save its decid­
When we consider an individual living system embedded in physical ability, computation must halt in the end. The idea of natural selection
space–time, we assume that the spatiotemporal structure of the living seems to resolve this opposition by attributing generativity to casual
system itself should have certain optimality parameters that allow co­ mistakes in computational programs, which occasionally can be gener­
ordination of systems’ processes inside this structure and result in ative. How a casual mistake is internalized in biological system to

7
A.U. Igamberdiev and J.E. Brenner BioSystems 204 (2021) 104395

become generative is apparently left beyond the framework of the conscious beings (Sawa and Igamberdiev, 2016, 2017, 2021). They are
concept of natural selection. When we consider genetic program as a able to count and perform operations with external objects, while in
case of natural computation, we have to assume that there is a direct biological systems mathematics is applied internally in the absence of
isomorphism between computer programs and mathematical proofs the reflexive capacity manifesting consciousness.
(Curry–Howard isomorphism) (Boniolo et al., 2015). The transitions Besides its error-correcting cybernetic controls, a living system
from one molecular structure to another appear as mathematical proofs contains anticipatory mechanisms to pre-empt possible errors, as dis­
and the propositions as interpretation types. To establish the corre­ cussed by Rosen (1991) and others. These controls are realized through
spondence between proofs and propositions, second-order logical the agency of a predictive model, converting present information into
schemes are applied. While first-order calculus quantifies the variables predicted future consequences. These are ipso facto essentially potential
that range over individuals, second-order calculus also quantifies over and we propose that their evolution of the corresponding mechanisms
sets. Second order logic represents the functional relation as a domain of follows the rules of LIR. Rosen’s theory formulates the basic structure of
discourse, so a predicate acquires the property of universal quantifier living systems. Other approaches include Eigen’s theory of hypercycles
(corresponding to the Platonic eidos). The logics of third and higher (Eigen and Schuster, 1979) and the autopoietic theory of Maturana
orders quantify over sets of sets and their semantics are more complex (2003) and Varela (1999). The latter have common features to Rosen’s
(Rossberg, 2004). model but remain less developed in relation to their formalizable and
In biology, the generative process is apparently strictly limited hence logical and ultimately computational value. Rosen’s (M, R) sys­
within the dual system of genes and proteins. However, in the system tem includes the operation which designates the system as a whole and
with an intermediate component (RNA), a huge flexibility appears and acts as a generator of the complete enclosed (for the efficient causation)
its evolution can take place as a complex language game, in which RNA structure of such systems which remain open for the fluxes of matter and
becomes a part of the temporal component, mediating incomplete energy. There is no rigid algorithm to apply as this operation has its own
identification and increasing the plasticity between genes and their ambiguity. When it is applied, the ambiguity becomes frozen and in­
realized functions. Liberman (1972, 1989) defined the primary role of ternal computation is possible. This is basically a recognition of the
RNA in operation of the molecular readout device and its evolution. real-life phenomenon that dynamic systems can and do slow down and
Even the role of accidental choice is increased significantly in the system even stop, before restarting. Living systems having the (M,R) structure
that includes the set of RNA molecules having enormous combinatorial not only can be modeled, which assumes a possibility of applying
capacities (Witzany, 2016). Therefore, the RNA pool can be considered mathematics to them, but also they generate internal models and
as a realizer of a powerful combinatorial field, which provides for the perform the equivalent of mathematical computations by themselves.
selection of pragmatically valid realizations. This can be modeled by the Rosen’s understanding of organizational invariance is similar to a
infinite combinatorics, which is considered a powerful tool in theoret­ Gödelian encoding of statements about the system, applied to biological
ical biology (Shelah and Strüngmann, 2021). The induction of genericity systems. The parameter representing organizational invariance is
emerges via the combinatorial pool when the incomplete information equivalent to an agent establishing the set of Gödel numbers generated
forms the set of forcing conditions that move the system to a new level within the system. The whole biological system as an entity which can
and open a possibility of the generation of new coding systems. be defined as “ontolon” in our terms (Brenner and Igamberdiev, 2021)
The presence of the combinatorial pool of RNA expands the central can be viewed as consisting of: (a) Metabolism—sets and relations; (b)
dogma of molecular biology to a more generative scheme that resembles Replacement—relations on relations; and (c) Organizational invari­
the main structure of Rosen’s concept of (M,R)-systems (Igamberdiev ance—Gödel statements about the sets actually in place and their dy­
and Shklovskiy-Kordi, 2016). The RNA pool thus denotes a powerful namic relations. It is important to note that Gödel statements are not sets
source of generativity via its capacity for recombination, which repre­ or relations; they are meta-mathematical statements with the dual
sents the mechanism driving evolutionary adaptation. In other words, function of both sets and relations. Logic in Reality is the first metalo­
the pool of different types of RNA appears as a materialized T-state gical system in which such statements can be embedded and given a real
(included middle) in the Lupascian ontology that underlies generativity interpretation.
and provides the highest possible capacity for potentializations and Thus, the triadic structure of life includes sets, relations, and meta-
actualizations. The logic of Lupasco thus substantiates a relational mathematical as well as metalogical statements (encoded within the
evolution in which the increase of complexity corresponds to the in­ system) that are as real and as causally efficient as any physical element
crease of combinatorial power and ultimately leads to the increase in of the system. Translation of these statements into the system occurs via
energy of transformation that results in the increased external work a sophisticated ‘machinery’ of transcription, translation and recombi­
performed by evolving organisms which was first noted by Ervin Bauer nation, e.g., splicing events, which occurs within the advanced and
(1935) in his book “Theoretical Biology”. expanding “middle state” of combinatorial events. We remind the reader
that any such event is a consequence of the operation of the real dualities
5.3. Complexity or polarities in chemical and biological systems appearing as dynamic
oppositions, and the movement within them between potentiality and
Complexity appears to be a relational property, not of the system but actuality and vice versa, and the process of emergence of complex new
of its observation, and relational complexity implies also relational en­ entities which this makes possible.
tropy (Rosen, 1991). To describe the fundamental structure of a living
system, Rosen introduced the concept of (M, R) system where M refers to 5.4. The epistemic cut and living processes
metabolism and R – to repair (or replacement as in subsequent in­
terpretations). The system is internally closed because metabolism uses The concept of an epistemic cut was originally formulated by von
its own components for replacement and is dependent on the external Neumann in his demonstration that the function of measurement of
influx of matter and energy only as a material, but not efficient, cause. some physical variable is irreducible to the dynamics of the measuring
The level of complexity corresponding to (M, R) systems is homologous device (Pattee, 2001). The logic here is related to the necessary sepa­
to a self-maintained internal model and has advanced generational (or ration of symbolic memory and the dynamic laws required for the
“generic” in Rosen’s terms) properties. The organization of living system self-replication of a biological system. It has been considered as a special
is an example how the internal logic generates the topological structure case of a general epistemic problem: how to bridge the separation be­
and the abstracting capacity of the system (Matsuno, 2014). At the very tween the observer and the observed, the controller and the controlled,
high level of complexity, double homunculus structures appear having the subject and the object.
an internal reflexive model of themselves and corresponding to An epistemic cut appears in a view of dynamical laws which requires

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A.U. Igamberdiev and J.E. Brenner BioSystems 204 (2021) 104395

that such laws and the initial conditions of a system are sharply sepa­ substantiate the emergence of consciousness based on the appearance of
rated, the initial conditions are capable of being measured, and mea­ new reflexive loops entailing externality.
surement and laws have no reciprocal influence. This intellectual During the origin and evolution of living systems, mathematics
distinction between initial conditions and laws allegedly has its origin emerges internally as a capacity for abstraction exhibiting itself in the
and embodiment in living organisms. In this conception, our perceptions course of development and adaptation to the external world. The in­
as well as our natural languages support a deterministic, either-or logical ternal coding structures which represent embedded descriptions of
syntax and a causal semantics that conform to a classical dynamics. This living systems manifest this natural mathematics. They generate deter­
happens to be true. We would say science is burdened with this concept ministic models of behavior being anticipatory in this sense, and can
of state-determined behavior as a modern form of Laplacean deter­ evolve due to the acquisition of new statements inside the embedded
minism, but it does not validate these considerations as the basis for a description that overcome limitations of the existing models. The newly
theory of biology in particular or reality in general. Such a view of generated statements are empowered by meanings in the changing
syntax and dynamics is suspect, since it fails in many areas in addition to environment. The growth of complexity, being a consequence of the
quantum mechanics. For example, natural language cannot be described internal active adaptation to externality performed by the systems, in­
even by categorial extensions of classical logic, in which a necessary creases the amount of actualized external work and generates the
operative concept of process is absent. observed patterns of spatiotemporal structures of evolving systems.
Non-integrable conditions, or constraints can be proposed for Separation of the symbolic memory and the dynamic laws (defined as
bridging the epistemic cut. One constraint states that, in order to provide epistemic cut), required for self-replication of biological systems, forms
configurational space for hereditary processes, there must be more de­ the basis for their epistemic relation to reality in us as sentient beings.
grees of freedom available for the description of the total system than for The emergence of social systems puts the self into relation to the
following its actual motion. As stated by Pattee (2001), since law-based external world in a way that the symbolic image of the self becomes
dynamics are based on energy, in addition to non-integrable memory recognized reflexively within the social system. This allows trans­
reading, memory storage requires alternative states of energy. Con­ formation of external objects into the tools of practical activity. The
straints are formally equivalent to laws, and the evolution of systems structure of the subject in which the external world is incorporated as a
depends on both. The complementarity of dynamic laws and the mea­ symbolic internal image makes possible the formulation of mathematics
surement function is irreducible, based on a demonstration by von as learned knowledge and the use of its power to perceive and deter­
Neumann that the contrary would lead to an infinite regress of mea­ ministically transform the outside world, while leaving ‘space’ for the
surement devices operating on the systems of systems plus measuring limited operation of processes that are partly non-deterministic as well.
devices and so on. However, Pattee makes the assumption that epistemic
irreducibility does not imply any ontological dualism and that it arises Declaration of competing interest
whenever a distinction must be made between a subject and an object, or
in semiotic terms, between a symbol and its referent. If the terms are The authors declare no conflicts of interest.
different, they cannot communicate or interact; if they are the same
there is no cut. The only possibility of a bridge is that they are the same Acknowledgment
and different, and for this to have meaning requires a Lupascian
framework, that is, one in which a categorial feature of non-separability The authors thank Andrei Rodin for his constructive comments that
predominates. helped to improve the manuscript.
The classical view of logical disjunction is of something is totally
different from something else. Is the epistemic cut, then, essentially
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