Reverse Engineering the Genetic Code

The post is a slightly edited version of a submission I recently made for Challenge prize competion. I didn’t win it but he submission provides a reasonable and short overview of my project.

 

genetic code image

Reverse Engineering the Genetic Code

understanding the universal technology platform of Nature

Executive Summary

My proposed platform technology for advancing the life sciences is none other than the genetic code itself. Even though all life forms evolve over time the universal language that codes them remains virtually unchanged over billions of years. If one wants to find a fundamental platform for exploring and explaining life, the answer is already there in this universal language of Nature. The Central Dogma of biochemistry infers that the genetic code is a mere transcription language. My project challenges the dogma with the central claim that the four letters of the genetic code express logico-geometric, spacetime-like semantics. In fact, the four letters (A,T,G,C} express timelike, lightlike, spacelike, and singular-like semantics respectively. A central aim is to reverse engineer the code from first principles. In so doing, the code becomes the operational calculus for explaining the organisational principles of life.

The broad idea is not new and was envisaged by Leibniz over three centuries ago. In a famous passage, he sketched out his dream of developing a geometric algebra without number based on only a few letters that would simply and non-abstractly explain the form of the natural things of Nature. One could say that Leibniz anticipated the genetic code. However, his vision went much further than that. He claimed that the resulting algebra would have logico-geometric semantics and so his vision becomes quite revolutionary. Even more revolutionary still, he claimed that the same geometric algebra would explain, not just the animate, but also the inanimate. We now know that the organising generic material of biological organisms is distinct from the functional material of the organism. In the inanimate case of an “organism” like our universe, there appears to be no observable distinction between organising substance and the organised. Thus, if Leibniz’s vision is valid for the inanimate, then the elementary particles of Particle Physics should be directly and simply explained in terms of the four-letter algebra of the genetic code—now playing the role of a truly universal generic code. For inanimates like our universe, the organising material and the organised are the same stuff.

My project involves making Leibniz’s vision tractable in developing his Analysis Situs geometry without number in order to provide the logico-geometric semantics of the genetic code. My ideas have rapidly matured over the past year resulting in the publication of one book and the drafts of four long papers on the subject. The third “Leibniz paper” is the most pivotal. The rough draft of the fourth paper shows how the same genetic code organisation predicts the Standard Model of Particle Physics and even surpassing it. Because of its non-empirical nature, my Leibniz style methodology can predict not only the explicitly measurable particles but also the implicit, which may be impossible to observe empirically.

The Big Picture

This project takes a leaf from nature and provides a bilateral approach to science. There are two takes on Nature, requiring two “hemispheres” of knowledge. I refer to present day sciences as left side sciences. Left side sciences specialise in explaining the a posteriori in terms of the a priori. The empirical sciences harvest data and develop compatible theories to predict future outcomes. Axiomatic mathematics works deductively from a priori axioms to prove a posterior theorems.

The alternative right side approach, exemplified by the Stoics, concentrates on studying the world in between the a priori and the a posteriori, the world that exists now¾relative to the organism in question. For the Stoics, only corporeal bodies with extension exist. Only what exists can act upon and be acted upon. Thus, the Stoic perspective is that objective reality is sandwiched between the a priori and the a posteriori. The perspective is comparable to Leibniz, albeit more materialist.

Objective reality of an organism is anchored in the immediacy of its Nowness. I call machines based upon this principle Now Machines. I claim that all animates and inanimates are based on the Now Machine principle. The underlying principle is that the organism must not be subject to any extrinsic a priori principle. Borrowing a term from Computer Science, I call the principle First Classness (FC). The dominating principle of Now Machines is the non-violation of FC. The logic involved is similar to the Liar Paradox construct that Gödel used to prove that (left side) mathematics is incomplete. In right side mathematics, it becomes the organisational, self-justifying principle of Now Machines.

The mathematics of corporeal bodies acting and being acted upon leads to a particular kind of geometry with direct historic roots to Leibniz. As succinctly explained by Hongbo Li:

Co-inventor of calculus, the great mathematician G. Leibniz, once dreamed of having a geometric calculus dealing directly with geometric objects rather than with sequences of numbers. His dream is to have an algebra that is so close to geometry that every expression in it has a clear geometric meaning of being either a geometric object or a geometric relation between geometric objects, that the algebraic manipulations among the expressions, such as addition, subtraction, multiplication and division, correspond to geometric transformations. Such an algebra, if exists, is rightly called geometric algebra, and its elements called geometric numbers. (Li, 2008)

Li together with David Hestenes and other exponents claim that Geometric Algebra (GA) is the universal language of mathematics and science and so realises Leibniz’s dream. I consider their claim premature as it ignores two vital aspects of Leibniz’s vision. The claim ignores the truly universal genetic code of Nature “based only on a few letters.” In addition, although GA is not based on coordinates, it is still relies on ordinary numbers under the hood. Such a number scheme imposes absolute extrinsic ordering relationships from outside the system and so violates FC. I propose a solution founded on the ancient construct of ontological gender. The pure feminine gender entity is considered to have an attribute, albeit undetermined. The pure masculine gender type is that attribute as an entity in its own right. Thus two entities, the feminine has an attribute, the masculine is that attribute. The feminine corresponds to pure geometric extension, the masculine to geometric singularity. These are the two building blocks of Now Machines. With gender, the genetic code letters {A,T,G,C} can be expressed by the four binary genders {MF,FF,FM,MM}. Viewed from outside the system, genders are indistinguishable and so appear to be in superposition opening the way to Quantum Mechanics interpretations. Like Doctor Who’s Tardis on TV, a Now Machine appears bigger on the highly tuned and coded inside than the amorphous mass of superposition seen from the outside. The algebra of gender can replace the algebra of ordered numbers to provide a true “geometry without number.” The gendered version of GA articulates the dynamic geometric semantics of the genetic code and provides the final realisation of Leibniz’s dream.

Impact

New Science: Nature abounds with bilateral structures and asymmetries that remain unexplained by present day science. For example, why are all biologically produced L-amino acids left handed? In the inanimate realm, why are there no right-handed neutrinos? In order to address these kinds of question, a new kind of science is necessary. Not only must science explain bilateralism in Nature, but also the science must itself take on a bilateral epistemological architecture. Like the biological brain, science must develop two distinct but complementary takes on reality. In modern times, there has only been one “left side” science. This project unearths the complementary “right side.”

Overcoming Barriers: Nature herself has technological differences but no ontological barriers. The new right side science I propose unifies the science of the inanimate with the animate. “Life is everywhere,” so to speak.

Public Impact: Left side science got off the ground with Leibniz and Newton’s discovery of calculus, the ultimate public impact of which is incalculable. Right side science starts with the discovery of how the genetic code harbours the geometric calculus and semantics of life systems ranging from the animate to the inanimate. The public impact would surely be comparable.

Science Deficits: Psychologists have discovered that a patient with only a fully functional left-brain may exhibit bizarre behaviour like only eating food on the right side of the plate. They call it hemineglect. I claim that left side mathematics also suffers the same “cognitive deficit. The phenomenon can be traced to left side geometry, which only needs timelike and spacelike lines to work. In other words, the geometry only uses the two-letter alphabet {A,G}. It only fires on two cylinders! The right side geometry is based on the genetic code letters {A,T,G,C} and so, like its right side hemisphere biological counterpart, is cognizant of both sides of a bilateral world. Thus in some cases better instrument technology in left side science will be pointless because of the hemineglect blind spot of left side mathematics—and the mathematician will never know.

Both right side science and its right brain counterpart suffer a different kind of deficit. They are mute. However, although communication to outside the system is impossible, the right side can communicate with itself. That is what the universal language of Nature is for.

Novelty

Present orthodoxy sees living organisms as results of evolution. Thus, man is the product of millions of years of genetic accidents. He is a genetic freak. The alternative right side science view is that the very essence of life is present from the very beginning. As foreseen by Leibniz, there is a universal algebra articulating the same life essence shared by all beings, ranging from the neutrino, the quark, the amoeba, through to man. In this context, man emerges from a universal principle, a much more noble scenario than being a genetic freak.

Some novel points:

  • Science should be bilateral like the two brain hemispheres.
  • Everything from the ground up can be explained in terms of gender
  • The letters{A,T,G,C} of the genetic code correspond to the binary genders {MF,FF,FM,MM}
  • The organisational principle of life is based on a form of the Liars Paradox
  • Leibniz was right on the money. The Stoics also had the right mind set.

Risk and Challenges

If this kind of science were to be fundamentally intractable, as many claim, then the project would be doomed to failure. After many decades of effort, my four draft papers demonstrate tractability and hence remove that risk.

The challenge of developing the new mathematics required is quite daunting and I need help. One sub-project, possibly even Nobel Prize material, is to explain the so-called degeneracy of the genetic code at least in the biological realm. My approach is that each codon codes an elementary geometric form. According to my theory, the start codon ATG expresses the Lorentz semantics of Special Relativity where the codon is made up of a single timelike A, lightlike T, and spacelike G form. Such a composite geometric form can be considered homogeneous and so satisfy FC. Hence, no need for degeneracy. The only other non-degenerate codon is TGG. TGG codes the semantics of a de Sitter space, which has known General Relativity interpretations and is homogenous. I claim that, for homogeneity compliance, all other elementary forms must be appended with extra dimensions. Hence the degeneracy for all codons

 

References

Li, H., 2008. Invariant Algebras and Geometric Reasoning. Singapore: World Scientific Publishing.
Moore, D. J. H., 2012. The First Science and the Generic Code. Parmenidean Press. 450 Pages
Moore, D. J. H., 2013a. Now Machines
Moore, D. J. H., 2013b The Whole Thing is a (Now) Number
Moore, D. J. H., 2013d. Logic Driven Physics: How Nature’s genetic code predicts the Standard Model.
Moore, D. J. H., 2013. The Universal Geometric Algebra of Nature: Realising Leibniz’s Dream
Moore, D. J. H., 2013. Generic Model versus Standard Model Interactive Database. [Online Database Application]

   

What is Gender?

Aphrodite

There is no construct in science more fundamental than gender. The ancients knew this but the moderns have long since forgotten it.

This post will explore the epistemological and ontological potential of gender in providing a unifying foundation for science and mathematics. In this respect, the structure of the French language provides a first glimpse of the relationship between knowledge and gender. French tends to explain concepts in terms of oppositions, often expressed across opposing genders. For example, French for knowledge is the feminine term la connaissance. The natural corresponding opposition in French is the masculine le savoir. Someone with a lot of specialised connaissance or knowledge is a connasseur. The most extreme kind of connaisseur.is the legendary idiot savant, the one who can digest the contents of the Yellow Pages in one sitting. On the opposite side of the fence is the savant of the non-idiot kind. The most gifted savant of all time was the equally legendary Socrates who had no reliable knowledge whatsoever as expressed in his Confession of Ignorance. However, he knew that fact with absolute certainty, a mark of the true savant. It is quite ironic that the Socratic Confession of Ignorance provides the key principle in developing algebra capable of integrating pure ignorance with pure certitude in a tractable manner, as we shall see.

Including axiomatic mathematics, all of the traditional modern day sciences are of the ordinary, common sense, analytic, fact-based, “connaissance” style of scholarship. These sciences are all well known as deductionist, abstract, atomist, and dualist. Employing the metaphor of the biological brain, we will refer to these sciences as instances of the left side scientific paradigm. The position we take in this paper is that left side paradigm is totally unsuited to provide a foundational science. Any unifying foundational science must be based on savoir, not connaissance. The savoir kind of scholarship we refer to as right side science. Our first task will be to explain the central role of gender in right side science.

Different natural languages implement gender in various grammatical ways. For example, Tagalog of the Philippines is remarkable for its complete absence of grammatical gender Even personal pronouns are neuter and so do not explicitly expose the sexual gender of the respondent. At the other end of spectrum is Jingulu, an Aboriginal language of Australia that has four genders. It is also interesting to note that Jingulu, like other Aboriginal languages, does not categorically distinguish nouns from adjectives, they all collapse into a broader category of nominals. In this paper we introduce the study of a code like language where even the categorical distinction between nominal and verb. and any other grammatical category, all such distinctions evaporate. The syntax becomes so generic that it virtually disappears. We call this language the generic code. We propose this language as the calculus for right side science. All natural languages are left side languages. There is only one right side language, the generic code. We will show how the semantics of this generic code can be reverse engineered from generic principles. With great trepidation, we also claim that this reverse engineered language provides the semantic foundations of the biological genetic code. In other words, the genetic code is an instance of a totally universal, generic code. This generic code is not subject to evolution. It must be in place right from the very beginnings of whatever might start to begin. We will show that the most salient feature of this generic cum genetic code is that, like Jingulu, the language is based on four genders.
Before attempting to tackle the problem of developing a generic language, we must look at the generic problem domain in which it is to operate. Generic language is to provide the calculus for a generic science. What is the nature of such a science?
Continue reading “What is Gender?”

Syllogistic Logic

Traditional sciences and mathematics is very “left brained” – abstract, dualist, empirical, atomist, and rely on a rhetorical form of reasoning. In antiquity, the Epicureans priveledged that form of thought. The Stoics favoured a non-dualist, non-atomist, dialectical form of reasoning. When it comes to Aristotle, such a dichotomy is not at all clear cut. As well as being the greatest philosopher of all time, Aristotle was also the greatest fence sitter of all time. With him, our neat dichotomy between left side and right side thinking meets a blank. This man had a foot firmly placed on both sides. Nowhere is this more apparent than with his categorical logic and in particular his square of oppositions. In this section, without going into too much detail, we summarise the aspects that immediately concern our project.


Figure 1 The four kind of terms. The Scholastics later labelled them with four letters.

The Four Terms and the Left Side

Aristotle’s syllogistic term logic was half modern and half ancient. We will suspend judgment on which was the better half. The modern half is exhibited in two ways: it relies on abstraction and is involved with propositions expressible in natural language. The abstraction can be seen in the use of the existential qualifier “All.” “All men” for example, means every man. By referring to “all men” or every man, one is referring to an abstraction, a generalisation. As the Stoics pointed out, abstractions and generalisations do not exist as real entities. In addition to abstraction, there is the fact that the logical representation of these syllogisms can be covered by Venn diagrams as shown below. The terms can be said to have “Venn Diagram” semantics.

Both of these aspects, the abstract and static nature of the logic, are characteristics of left side thinking. By default, left side thinking has become synonymous with the modern.

The Four Terms and the Right Side

However, what is not modern in Aristotle’s logic is that his infrastructure of the four kinds of terms is not determined by a set of axioms, but rather by a pair of oppositions and the opposition between these oppositions. This is exactly the approach we have been using to construct our semiotic squares in other sections of the blog. Firstly, obtain a pair of oppositions. Employ one opposition to define a left-right dichotomy and the other opposition for the front back structure.


Figure 2 Venn diagrams for the four terms of Aristotle

In Aristotle’s case, the left-right dichotomy is a strict logical opposition between the affirmative form and the negative. The second opposition is between the universal and the particular. Both these oppositions must be true dichotomies in order to construct a non-trivial semiotic square. This is a technical point, but a very important one and will be discussed later when considering Aristotle’s square of oppositions. It turns out that there can be certain cases where an opposition is not a true dichotomy. This can occur when the subject of a term has no existential import. In other words, when dealing with empty sets such as “All centaurs.”


Figure 3 The semiotic square for the four terms of Aristotle’s Syllogistic logic. The square is formed from two oppositions, the negative/affirmative, and the universal/particular.

Term Logic

During the middle ages, the scholastics labelled the four kinds of terms with the four letters A, I, O, and E. Syllogisms consist of three propositions, a major, a minor, and a conclusion. Each syllogism could thus be labelled by a triplet of letters taken from the four-letter AIOE alphabet. This fascinated the Scholastics and, many years ago, entertained the author’s curiosity for some time. The reason for the author’s interest was that such a system did have some resemblance to the triadic structure of codons in the genetic code. With a bit of effort, one can make some kind of rapprochement between the AIOE alphabet of the scholastics and the genetic-cum-generic AUGC alphabet, but the effort is probably not justified, as there are richer pickings elsewhere, notably in Stoic logic.

The genetic codon structure only has 64 combinations. What we have ignored for the Aristotle’s syllogism is the detail of how the three propositions in each syllogism hook together. We have ignored the fact that there are four different figures of the syllogism. Thus, taking into account the four figures, instead of 64 possible syllogisms there will be 256. Only nineteen of these syllogisms are regarded as leading to a valid conclusion.

Aristotle’s syllogistic logic provides a logical tool that is applicable to the contingent world. Unlike modern logic, it also brings with it some nontrivial semiotic infrastructure, the square of oppositions.

The Square of Oppositions

Aristotle described how the four kinds of terms could be placed in a square illustrating the various oppositions between them. He then went about characterising each kind of opposition, although the subalterns were not mentioned explicitly. The oppositions between universal statements are contraries. Contraries have the property that both cannot be true together. One may be true and the other false. It is also possible that both can be false together. On the other hand, subcontraries involve oppositions between particulars. In this case, both cannot be false together.


Figure 4 (a) The modern logic version of the oppositions. (b) Aristotle’s square of oppositions.

The Modern Square of Oppositions

Of great interest to us is an opposition at a higher level altogether, the opposition between Aristotle’s syllogistic structures and modern logic. The dramatic difference between the two approaches was clearly illustrated by George Boole, in what has become the modern version of the Square of Oppositions.

Modern logic differs from the ancient logic by simply replacing the universal with the general, in other words with the abstract. This can be achieved by using labels and the logic becomes symbolic logic. Thus, the term ‘All men’ is replaced by the abstract version ‘All X’. The thing gets replaced by a label and introduces different semantics. One could say that the semantics go out the window and are left trivialised. The label becomes simply a placeholder and as such, like any placeholder, may be empty. The logicians explain this as relaxing the requirement of existential import. From a classical mathematics perspective, the generalisation introduced by modern logic is to allow sets to be empty. This allows modern logic to talk about things that are known not to exist, a characterising feature of abstraction.

Once the reasoning becomes abstract, the logical difference between yellow centaurs and canaries evaporates. Not only that, but all the oppositions except the contradictories have also evaporated. For example, both sides of the contraries opposition ‘All centaurs are yellow’ and ‘No centaur is yellow’ are true. The contraries opposition has evaporated.

Figure 4 (a) shows the resulting modern logic version of the square of oppositions. The square has virtually collapsed and only the contradictories and the subcontraries survive. We have deliberately drawn the modern version on the left side relative to Aristotle’s square to illustrate that this is the left side variant of logic. The other variant is Aristotle’s seed for the right side version. The left side involves abstract, symbolic logic. The right side in the diagram represents Aristotle’s version of elementary generic logical structure. In practice, the modern symbolic logic approach boils down to a simple bipolar nominalism where the basic opposition is between two particulars, I and O. The letters A and E act as pure label signifiers for the I and O respectively, acting as the signified. The contradictory oppositions A-O and E-I model the relationships between signifier and signified. In essence, the system becomes a simple two letter system labelled by A and E. Thus, although we have not shown that modern day logicians only use half a brain, we are starting to see that they reason using only half of Nature’s alphabet.

 

 

 

The Alternative to Abstract Thinking : the Generic

Continuing from the previous post Is There an Alternative to Abstraction?
Having taken in Hegel’s little gem of wisdom we are now able to answer the question, “What does a radio shock jock and a theoretical physicist have in common?” The answer, of course is – abstraction.
However, this doesn’t answer the question as to the alternative to abstraction. Our Western universities have become abstraction factories. Is there an alternative product? The purpose of this book is to present the natural sibling to abstraction. I call it the generic. Instead of thinking abstractly, think generically. However, what is the generic?  Equally, what is abstraction for that matter?
Two Fundamental Questions
Our aim is to move towards a formal knowledge of knowledge. There are two kinds of knowledge. On one side, there is what we call left side knowledge, which is dependent on a priori information. On the other hand, right side knowledge expounds on what can be known, without any a priori information. Each kind of knowledge answers a different question. Thus, two very precise questions characterise each of the two sciences. We can simplify much of philosophical and scientific tussling over different answers if we recognise that there are two different questions behind the scene. The questions are in a natural opposition and antonymic symmetry with each other.
The domain of discourse for each question is totally disjoint. The questions are so distinct that they can be imagined as being “orthogonal” to each other. The first question, suitably schematically simplified, was posed by Kant in the Critique of Pure Reason:

Q1.

What knowledge can be achieved without reliance on any experimental  evidence whatsoever?

The answer would fall under the rubric of metaphysics. This question is familiar to all modern philosophers but is still waiting to be answered.
To some, like Karl Popper, the question is summarily dismissed. The problem posed by Kant is “not only insoluble but also misconceived.” (Popper, 1963) The problem was insoluble as we all know from Hume that there is no such thing as certain knowledge of universal truths. The only possibility was knowledge gleaned from observation of singular or particular instances. The inescapable truth is clearly “that all theoretical knowledge was uncertain.”
According to Popper, the problem was misconceived because Kant, even though he mentioned it, was not talking about metaphysics, but was really talking about what he didn’t mention; notably the pure natural science that had burst on the scene in his day, the science embodied in Newton’s gravitational theory. Newton’s theory has since been shown not to be the infallible exercise in pure reason that so impressed eighteenth century thinkers like Kant, but rather “no more than a marvellous conjecture, an astonishingly good approximation.” With the passage of time, Newton comes crashing down to earth and brings Kant’s question down with him. This demonstrates Kant’s misconception.
Popper concludes his demolition by replacing Kant’s bold question with his own languid alternative. “His question, we now know, or believe we know, should have been: ‘How are successful conjectures possible?’”
In this book, in order to arrive at a refutation, we actually go much further than Popper by bringing in some modern arguments to prove more convincingly that Q1 is insoluble. This is accomplished by showing that it is out of bounds of all formal mathematical reasoning.
To answer Q1 no axioms are allowed. Not only are operators of all sorts dispensed with – the commutative, the non-commutative, the associative, the non associative, even operator composition is declared a no go area. Traditional mathematics simply becomes non-operational in this zone. This is the domain where nothing can be said to proceed or succeed anything else.
In the business world, there is nothing more enticing to the entrepreneur than the accepted wisdom that something simply cannot be done. The proposition becomes even more enticing when learned abstract thinkers like Popper claim to have proven that it cannot be done.
Kant’s question Q1 viciously casts us into this apparently hopeless ultimate state of undetermined chaotic ignornace, However, by Popper arguing the futility of the enterprisse, the question becomes so well defined that surely there must be an answer. After all, it is only when the prisoner is actually placed in the confines of the four concrete walls of his cell can he really start plotting his way out. You cannot escape until you are locked up. Kant built the prison, Popper slams shut the door and rams home the bolt. It’s time to get out of this hell hole.
Once Q1 is clearly shown to be absolutely mathematically insoluble beyond any shadow of a doubt, we are then in possession of our first truth arrived at from pure reason alone. This is achieved without recourse to any experimental evidence whatsoever. We thus arrive at our first negative fact. We could call it a neg fact. The exercise then becomes one of building metaphysics out of neg facts in some way. This is obviously not an exercise in formal mathematics but an exercise in another genus of formalisation. We call it formal anti-mathematics. This and the remarkable results flowing from anti-mathematics eventually leads to code; a kind of “DNA of the Cosmos” so to speak. This is the principle theoretical contribution of this work and clearly the most enigmatic.
We now come to the second question, diametrically opposed to the first. It reads:

Q2.

What knowledge can be achieved with only reliance on experimental evidence?

The question is very brief and needs to be expanded somewhat in order to convey the intent. What kind of knowledge can be achieved under the assumption that only what is measured is real and only what is real is that which is being measured? What knowledge can be obtained by totally excluding counter factual reasoning?  Stated this way the answer to the question is probably already apparent as will be seen below. The implication is that the moon only exists if you are looking at it. What kind of knowledge can imply that?
In the first question the only discernable real was that discerned by all embracing pure reason – the Parmenidean real, the big picture. Q1 addresses the uppermost confines of the top down reality bucket barrel. On the other hand. this second question, Q2 imposes the opposite sense of what is real. It demands the ferociously materialist atomism and absolutist one to one nominalism that only the Epicureans ever had the audacity to contemplate to the fullest degree. To each sensation there is something, to each something a sensation. There is nothing else. For the Epicureans, this was the way the world ticks. For modern science, it becomes a particular scientific methodological paradigm. It’s the way the world ticks from a particular viewpoint. It’s the view from the bottom up. What kind of knowledge can be achieved within the confines of such a dogmatic straight jacket?
In this case the answer historically came before the question was ever seriously posed. The ancient answer was the physics of the Epicureans complete with their deterministic atoms moving along Bertrand Russel like causal lines but armed with an occasional, unpredictable, and at that time, indiscernible “swerve.” The modern answer is in the form of quantum mechanics, Heisenburg’s uncertainty principle, and in particular the classical Copenhagen interpretation of quantum mechanics.
The Epicurean ontological straightjacket implicit in Q1 limits the knowledge quest downwards to the minute, indivisible “Epicurean atoms” of reality: the elementary subatomic particles of modern physics. The only difference is that the atoms of Epicurus we assumed ot have extent. Modern physics is more radical in this regard. The elementary particles have no extent whatsoever. They are assumed to be point like. Such particles have nothing in the their interior. They simply don’t even have an interior. If there is something in the interior, your particle is not elementary. You haven’t reached rock bottom of the reality bucket.
The brutal minimalism of QM is succinctly expressed in Dirac’s razor principle.

Dirac’s razor

Quantum mechanics can only answer questions regarding the outcome of possible experiments. Any other questions, philosophical or otherwise, lie beyond the realms of physics.
This is the declaration that QM is a philosophical desert. QM declares that it is fundamentally a philosophical, metaphysical, epistemological, ontological, theological, spiritual vacuum. This is not a weakness, it is strength. It is this that gives it its rigour and even its vigour.

The Entanglement Problem

A situation arises in QM that there can exist minute particle systems which are non-localised. Consider the case of a pair of entangled photons produced by a photon splitting in two. Pairs of such photons can be produced in experiments. The polarisation of one entangled photon will be the opposite to that of the other. According to QM the actual polarisation for each photon would be indeterminate until the polarisation of one of the photons was actually measured. The measurement performed on one particle would flip its polarisation to say horizontal or vertical. According to QM, the polarisation of the other photon will instantly become the opposite polarity irrespective of how far away it is.
Einstein didn’t like the indeterminacy aspects of QM – “God doesn’t throw dice” but it was this “spooky action at a distance” that really bothered him. In the famous EPR paper, written with Podolsky and Rosen, he argued his case. QM conflicted totally with the classical view of physical reality that Einstein adhered to. According to his view a theory must allow for the simultaneous existence of “elements of reality” which are independent of measurement. The EPR paper gave a very concise and lucid definition of elements of reality:
If, without in any way disturbing a system, we can predict with certainty (i.e., with probability equal to unity) the value of a physical quantity, then there exists an element of physical reality corresponding to this physical quantity.
The EPR paper then put forward a thought experiment that revealed a paradox in the QM theory of entangled particles. The EPR paper argued that each of the “entangled” photons would possess their own element of reality and have their polarisations determined at the time of the pair’s  creation, not at the time when one of them was measured. The measurement of  the polarity of one wouldn’t affect that of the other as its polarisation had already been determined and couldn’t be altered by any “spooky action at a distance,” as predicted by QM.
Basically the EPR paper argued for what is sometimes called “local realism”. The two fundamental principles are that there exist elements of physical reality or “hidden variables” and that this realism be local. The locality principle demands that theory must adhere to the principles of relativity (causes cannot propagate faster than the speed of light). Thus the measurement on one member of an entangled pair of particles should not effect any measurement carried on the other member.
The simplified argument is that either the locality principle and with it the special theory of relativity was violated or the elementary particles harboured internal “hidden variables.” In the first case relativity theory is proved wrong. Alternatively in the second case there are aspects of reality not accounted for by QM. QM is not proved wrong but is proved “incomplete.”
With the passage of time thanks to the ingenious theorem of J. S. Bell and the experiments devised by A. Aspect et al and others, it has been demonstrated that the EPR paper’s proposed construct of local hidden variables could not possibly explain particle entanglement. This left the possibility that QM entanglement explanation would violate relativity theory. However, that is not a problem either as there is no determinate causal relationship between the particle pairs. The process cannot possibly be exploited for signalling and thus does not violate relativity theory.

Popper on Quantum mechanics

We have used Karl Popper as a point of reference for the first of our reality barrel questions, the one stemming from Kant. He dismissed the question outright with scant regard to any possible answer. For symmetry we should consider the other side of the reality barrel where we found an already existing answer in want of a suitable question. We provide the question but what would Popper think of the answer? The answer was in the form of a twentieth century science called quantum mechanics. Would Popper in fact agree that quantum mechanics was a proper science? As is well known Popper had great difficulty accepting many of the tenants of QM. For a start, QM would have to abide by his falsifiable criterion in order to be acceptable as a science. This allows provisionally valid propositions to be deemed scientific provided that there existed the potentiality for the propositions to be proven false. To Popper, all that was admissibly scientific was uniquely constructed from such potentially falsifiable propositions.
If one takes the long view at what Popper is saying here, one can easily get the impression that Popper is more concerned in fighting political dogmatism on the campus, than engaging in real science. He was more intent on arguing that what was inherently anti dogmatic was inherently scientific. But was hard core science itself inherently hard core non dogmatic?
This question takes on great importance when we consider quantum mechanics, the most fundamental and deepest of the empirical physical sciences. The difference between quantum mechanics and all other empirical sciences is not expressed in the details of the subject matter addressed, but in the fact that it is the only pure empirical science. Being purely empirical, methodologically pushes its subject down to the very bottom reaches of reality. It means that quantum mechanics is the only empirical science which tolerates absolutely no “elements of reality” which exist independently of the actual act of measurement.  In order to achieve this goal it must dig down to the bare, nude essentials of reality.
It is the only such science. To put it another way, quantum mechanics is dogmatically empirical. To put it even more bluntly, quantum mechanics is empericism as an absolute dogma. This dogmatism is most clearly expressed with its Epicurean like dogma of the one to one relationship between the sensation and the real. Quantum mechanics theory of the real is that only what is measured is real. This science, located at the very bottom of the bucket of reality, where is nothing is deemed below, expresses itself in empirical tautologies. The measured and the real are two sides of the one thing. As such, this most reliable, accurate, and most dogmatic of the empirical sciences is inherently unfalsifiable at its core.
All the same, Popper stuck to his guns and had no alternative but to reject some of the essential tenants of quantum mechanics as being, in his terms, “unscientific”. In so doing, he ignored one of the two most fundamental questions one can ask concerning knowledge of reality. In the case of Q2, the knowledge is not only true, but measurably so. After all the Copenhagen dogma declares only that which is measured is real. What is real is only that which is measured.
This has lead to a tautology, an implicit “analytic judgment”. Kant would have found that fascinating. Moreover, this fundamental tautology appears not on the transcendental side of the equation but on the empirical. Even more fascinating is that this fundamental construct defines the pure empirical itself. The pure empirical is, well…, purely empirical. Such is the fundamental nature of quantum mechanics as declared in the Copenhagen interpretation.

Is There a Fundamental Level?

There are two takes on reality. There are tow fundamental questions Q1 and Q2 that express the fundamental opposition between the two fundamental perspectives on reality. The fundmanetl opposition reveals itself in many ways. An important consideration concerns whether ther is a fundamantal level of reality.
Is there a fundamental level? Jonathan Schaffer asks the question and summarises the fundamentalist response. “The fundamentalist starts with (a) a hierarchical picture of nature as stratified into levels, adds (b) an assumption that there is a bottom level which is fundamental, and winds up, often enough, with (c) an ontological attitude according to which the entities of the fundamental level are primarily real, while any remaining contingent entities are at best derivative, if real at all.” He lists the physicalist, epiphenomenalist and atomist variants on the theme. Finding plausible the hierachial view of nature in (a) as being compatible with the discoveries of science, Schaffer homes in on (b) as the problem area, which he remarks has been almost entirely neglected. Concerning the primacy of what is real, the fate of (c) is linked to (b) as a reasonable but not inevitable conclusion.
And so is there a fundamental, bottom of the bucket, level in Reality?
In our preceding discussion of quantum mechanics we argued, with scarcely camouflaged glee, for a dogmatic interpretation of the science findings which would seem to place us firmly in Schaffer‘s camp of fundamentalists. We were advocating the bottom of the reality bucket theory. On the face of it we supported without reservation all three tenants of the fundamentalist argument. At the risk of seeming, or even blatantly being, excessively schematic we identified the ontological approach of quantum mechanics as smacking of pure Epicureanism, a natural logical set of conclusions resulting from a pure unadulterated atomistic,
uncompromisingly blunt materialism and one to one nominalism evolving down from Democritus, a thinker not particularly notable for his subtlety and dexterity of thought, At least Aristotle didn’t seem to be very impressed., advocating at one time that Democritus’s books should all be burnt. These Epicurians, and by implication the author, certainly seem to resemble Schaffer’s bottom feeding fundamentalists.
But the Epicurians should not be treated too harshly. They were, after all, primarily engaged in a peaceful quest for happiness in this life. They had identified perhaps the greatest obstacle to leading a happy life, notably fear of the gods and the accompanying troublesome predisposition towards deep, contemplative ways of thinking. An anti-metaphysical, anti-philosophizing, theologically bland, and some would say, anti-thinking creed called Epicureanism was the result. Few would have predicted that this creed would one day serve as the ontological stalwart of the successful and accurate modern sciences of today. Modern physics can even mathematically describe, at least probabalistically, the dynamics of Epicure’s mysterious micro-physicalist “swerve”. Strong on empirical scientific prediction and mathematical accuracy on one side, a self declared philosophical, ontological desert on the other. It aims to describe it all but can explain nothing. It’s as they say in the classics, you can’t have everything. At least not at the same time.
We return to the question. Is there a bottom fundamental level? We have answered in the affirmative. In so doing we have sided with a kind of metaphysic which, as Schaffer points out, is not particularly palatable for the more reasonable and civilised of people. Painfully it appears that we have excluded ourselves from such a community. Self declared metaphysical pariahs, we must face the dire consequences of our apparently foolhardy prise de position.
However, as we have argued throughout this work, there are two takes on reality, not just one. Hence we have assented to the proposition that there is a fundamental layer. This corresponds to the left side science take on the world, the simple, rather simplistic, abstract, naïvely realistic view of the world.
The right side science take on reality has a different vocation to its uncivilised and rather uncouth partner in crime. Right side science must not merely be content with describing the qualities that a thing has, it must explain what a thing is.
From a historical perspective, we argue that the ancient exponents of the left side take on reality were the Epicureans. In our sometimes desperate attempt to gain some traction for a right side science, we have singled out the Epicurean’s nemesis, the Stoics.
Of immediate concerns to our current discussion is the Stoic view on whether or not there is a fundamental level. The general view amongst the Stoics was that there was no bottom fundamental level. In some way reality was infinitely divisible, at no matter what level. This was also a position held by Leibnitz who made pains to add the nuance of being infinitely divided rather than infinitely divisible.
As for the Stoics, Chrysippus is credited with saying:
A key contribution of this work is to indicate how this genetic code is in fact a generic code applicable to anything. In the appendix the approach is applied to show how the generic code applies to particle physics.
As to answering the two fundamental questions Q1 and Q2, we can claim to have dealt with Q2, but the enigmatic Kantian question Q1 still remains to be answered. Nevertheless, we are starting to see what needs to be done. Rather flippantly we can say that all we have to do is to revamp ancient Stoic physics and logic and make it scientific. Let’s hope that we don’t die trying. So many have.

A later post is more to the point in answering this question,
see The Shape of Knowledge
See also What is Gender?

Chrysippus and Stoic Logic

The Stoic Five Undemonstratables

There are two kinds of logic, logic with infrastructure and logic that can be carried out with the bare brain, the terra nullus logic. We first consider the bare brained version. This variety of logic is virtually infrastructure free. The logic is abstract and makes extensive use of symbols that do not mean anything. It is often referred to as symbolic logic. At the base of symbolic logic is the propositional calculus and its second order extension, the predicate calculus. The other kind of reasoning requiring infrastructure will be a terra plenus logic. In accordance with our two-hemisphere brain metaphor we refer to terra nullus logic as left side logic and terra plenus Stoic style logic as right side.

What is interesting about the Stoic logic developed by Chrysippus is that it can be interpreted as a left side symbolic logic as well as a right side logic, all decked out with dialectical infrastructure. Thus, Chrysippus’ logic has both a terra nullus as well as a terra plenus interpretation.

The kernel of the logic is articulated in the form of the “five undemonstratables”. The undemonstratables can be stated as five three step syllogisms as follows (Chénique, 1974):

1 Conditional

If one has the first quality one has the second
one has the first
thus, one has the second

2 Contraposition of the conditional

If one has the first quality one has the second
one has not the second
thus, one has not the first

3 Incompatibility

One has not at the same time both the first and the second quality
one has the first
thus, one has not the second

4. ‘OR exclusive’ or alternative

One has either the first quality or the second quality
One has the first
hence, one has not the second

5. ‘OR non-exclusive’ or disjunction

One has either the first quality or the second quality
one has not the second
Hence, one has the first

All of these syllogisms can be interpreted from the symbolic logic perspective of propositional calculus. As such, it can be said that Chrysippus was the first to discover the propositional calculus. In addition, the first and second syllogisms can be interpreted as definitions of modus ponens and modus tollens respectively. This is all familiar ground for traditional logic.

The third syllogism deals with the incompatibly paradigm. In the propositional calculus context, this corresponds to the Sheffer stroke. In this context, the syllogism loses its explicit temporal nature and flattens down to the simple formula:

NOT (a AND b) is true

Note that the “at the same time” part of the formula has been dropped. Traditional modern logic has no notion of time. To entertain a notion of time, one needs a brain. The brain of the logician does not count, because that is not a formal part of the logic. Modern logic has no such infrastructure. It has virtually no infrastructure at all. Brainless, this is truly the logic of the terra nullus.

Building the Logical Brain

Logic combined with integrated cognitive structure goes from being logical to being ontological. In other words, it starts to become a science of being. Integral to a science of being is the science of the generic subject. The formal presence of the generic subject in the science provides a fundamental point of reference. All propositions become relative, relative to the subject. As we have said before, the subject, any subject, is the centre of the Cosmos. This means that you are located at the centre of the universe. Since you could be anybody located anyewhere, the centre of the can be literaly anywhaere. This identity of the generic centre of the universe and the individual centre of the universe is a most important principle. (In my book to appear, I show that any spatial reality with this property is equivalent to the Special Theory of Relativity. It is not verycomplicated)

As we have seen, the generic subject is endowed with a particular brain architecture. First, the impersonal, undetermined subject is based on a left-right dichotomy, with the subject on one side and its kingdom of objects on the other. The usual polarity convention is right and left sides respectively, but this does not have to be the case.

The above paragraph has a certain apparently outrageous dimension. It is probably enough to make some readers choke on their crumpet. However, it just takes time to become comfortable with the generic viewpoint. The situation can get untenable when we move on to the next paragraph. Written in italics in an effort to ease the reader’s pain, it reads something like this:

The brain architecture of the personal subject, in addition to the left right dichotomy of the impersonal, has a front back determination with the polarity, subject in front and kingdom in the back. These left right, and front back determinations can be explained in terms of gender, where the singular Oneness of the subject corresponds with the masculine and the non-singular wild card Otherness corresponds to the feminine. The configuration at this stage is that of a square divided into four quarters. Reading from left to right, starting from the front, the quarters are gender typed MF, MM, FF and FM respectively. Any subject whatsoever will have this configuration.

Perhaps one redeeming point is that we are not the only ones to have ever argued along these lines. Apparently, the ancients, going back thousands of years, have passed by here many times before. One thing to keep in mind is that we have not yet distinguished between the form of the world and the cognitive structure needed to comprehend it. Our basic thesis on this matter is that:

  1. The form of the world and the cognitive structure are different,
  2. The form of the world and the cognitive structure are indistinguishable.

This constitutes the basis of generic science and is why it is only necessary to study cognitive structures. Just put yourself into the position of that electron over there, the one that’s peering at you. It is a subject just like you. It might surprise you to know that, in this context, it has a cognitive structure indistinguishable from yours.

In the final analysis, the two points above apply perfectly to the two basic building blocks of generic science. These were the pure feminine entity and the pure masculine entity. They are both different whilst being indistinguishable. The masculine, in this sense, is the ultimate embryonic cognitive structure; the feminine corresponds to the ultimate embryonic world.

Bridging Laws of Consciousness

David Chalmers characterised what he called the Hard Problem (Chalmers, 1995) as the problem of explaining the relationship between a physical account of reality and conscious experience. As he saw it, solving this Hard Problem required determining the “bridging laws” that related physical reality and conscious experience.

The “bridging laws” solution to the consciousness question is a natural response of traditional left side scientific thinking. Such thinking is naturally dualistic where dichotomies abound between Mind and Body, the abstract and the real, and in this case, between the realms of the physical and the conscious. The solution to the problem seems like after the fall: How do you put Humpty Dumpty back together again? How do you bridge the broken? Chalmers is looking for an abstract solution to a problem that is a direct consequence of abstract thinking itself. Explaining abstractly how to bridge the abstract with the real is definitely a very Hard Problem, reserved only for the most courageous of abstract thinkers. For the less courageous, an alternative approach is to avoid abstraction and think generically.

From the monist right side viewpoint of the generic, there is never any need for a bridge as nothing was ever broken apart in the first case. At the ontological foundations of the generic, the very first spark of consciousness stirs with the pure unqualified feminine that has the pure attribute of Oneness. The masculine entity is this attribute. The embryonic physical unites with embryonic consciousness: One has an attribute; the other is this attribute. The bridging here is more like how some of the Hindus describe it, as a coital embrace. This couple have no need for a prosthesis, bridging or otherwise.

According to our embryonic Generic Science based on the generic algebra of gender, any being is coded and organised through this generic code. In the case of the biological, the generic code becomes the genetic code. The four-letter code is really based on binary valued gender. Any life form is coded in this gender algebra and organised through it. The original gender construct of the masculine and feminine now becomes a massive complex entwinement of gendered entities. The overall coherence and survival of the organism absolutely depends on maintenance of the coherence of the gender typing that runs throughout every nook and cranny of the organism. If there is failure of coherence then no bridging Band-Aid will ever bring this organism back into consciousness. The organism would be well and truly dead by now.

When viewing the healthy gender typed organism from the perspective of a third party, everything appears to be in ambiguous and chaotic superposition. Gender states are dynamic and something like quantum states, except that they are relative to each other and the organism, not absolute. Unlike quantum states, the subject sees its states quite differently from any third party. Viewed from the perspective of the organism, these states are in coherence with its own being and articulate its being. There must be no ambiguity whatsoever in gender typing.

We propose that the formal mechanism of gender regulation can be articulated in the form of Chrysippus’ third undemonstratable, that of incompatibility.The premise of the syllogism states:

One has not at the same time both the first and the second quality.

In the context of the generic coded organism, this becomes

One has not at the same time both the masculine and the feminine gender.

It is by the implementation and maintenance of this principle that any living being maintains its Self. This solution demands a dynamically gendered system with a global mechanism for the maintenance of gender coherence.

For a cosmological system, the mechanism is that of pure rational coherence, including the non-violation of the causality principle. As a science, it will present as a much more generic version of present day relativity theories. The geometric aspect of the mathematics (or anti-mathematics) will however need a substantial overhaul. In fact, a new geometry is needed. It will be a more generic version of what is now called geometric algebra.

In biological systems, the genetic code, although material, is a different substance from the proteins it codes. In the realm of pure physics, the code and the substance entities are possibly the one and the same. However, the same generic principle is at work in any realm.

Chrysippus and The Square of Oppositions

Chrysippus’ remarkable logical system can be naively interpreted as a simple left side version of the propositional calculus. There the incompatibility paradigm can play a pivotal role as the key operator from which all other logical constructs can be constructed.

The incompatibility paradigm, as Clark Kent, steps into the phone box and remerges as a virtual superman, ready to bring order and life into a chaotic world. Dumb left side logic transforms into the right side logic of the generic.

Having situated one of Chrysippus’ five paradigms into the generic scheme of things, we now have four left. There is no mystery where these fit in. The diagram below shows how they fit together to form a new kind of square of oppositions. Moreover, each of the four undemonstratables fits in snugly with our gender typing. This naturally leads to associating each of the four syllogisms with the corresponding four letters of the generic-cum-genetic code based on the AUGC alphabet. This is quite important, as the four letters now take on more semantic baggage than that of being a mere transcription language.

It is not clear how much of this was known to Chrysippus. Nevertheless, he does follow in the footsteps of Aristotle and his Organon. Here we have our version of Chrysippus’ Logos, the forerunner to the semantic cracking of the genetic code.
Chrysippus and the reconstructed Stoic square of oppositions
Figure 30 Author’s Reconstitution of Chrysippus’ Square of Oppositions.

Chrysippus and Ground Zero

By Ground Zero, we mean the centre of the Cosmos. Ground Zero has a certain shape, the shape of the entity located at the centre of the Cosmos. As we know, this entity is none other than any subject whatsoever that takes the pain to reflect on its particular spot in the universe. Without fail, this subject, like any other subject, sees itself as being located at the aforesaid location, notably the centre of the Cosmos, the centre of its Cosmos, at least.

As for the shape of this entity, the generic subject, it has a left, a right side, also a front, and a back. This is the structure we have been referring to as the semiotic square. It is a structure that can be interpreted in many ways, as a blueprint for epistemological organisation of knowledge, for example.. The same semiotic structure might be taken as a good framework for brain architecture, but we will avoid that topic here.  There are also ontological, and of course many biological interpretations. On the biological front, this structure can be thought of as the structure of a whole, as coded by a chromosomal codon. Any biological organism is organised as an entity viewed as a whole from a myriad of points of views. To each codon, there corresponds a holistic point of view. The genetic cum generic code is the language that articulates the geometric algebra of this exhaustive but holistic view of the organism. Another interpretation of this highly generic semiotic square is that it offers a schematic for elementary cognitive structure.

So prodigiously generic is a structure that it can make the head spin. To top it off, we now have Chrysippus joining the fray. Now Chrysippus was conceded by the ancients to be the equal of Aristotle, so he cannot be dismissed as a lightweight. In above, we have organised four of his five fundamental syllogisms into a form that falls quite naturally into the elementary structure of the generic semiotic square. As can be seen, the premises of the first and the second hypothetical conjunctive syllogisms make one diagonal of the square and the two disjunctive forms mark out the other diagonal. It is becoming clear that we have here, a structure that resembles the Square of Oppositions of Aristotle. The Scholastics added the AEOI four lettered labelling to Aristotle’s system and spent over a millennium probing into its delights. Not to be outdone, we have added our lettering to our reconstructed version of the Chrysippus Square in the hope of preparing it for its reinvigorated role in the present millennium. Suffering from a lack of creativity, we have borrowed the RNA version of the biologist’s genetic code. Why invent when you can steal, is our motto. It took the author a little while to get the right fit, but he is reasonably confident that his allocation of the CAUG lettering is spot on. He would be very miffed if this was not the case.

Chrysippus and the Grand Unification

The ancient Stoics have been the historic mentors for the material presented in this work. They developed the most successful and diverse form of monistic philosophy that the Western world has ever seen. Zeno provided the intuitive and informal core elements of the doctrine. Chrysippus logic marked the first tentative steps towards the formalisation of a unifying science. The full significance of Chrysippus’ contribution has been little understood by the moderns, blinded as they are by the achievements of the current day sciences. Despite these achievements, the present day sciences are lacking in any kind of cohesive unifying discipline. The unifying science pioneered by the Stoics, will provide such a unification.

Of critical importance is to learn how to reason in a different way from what is customarily taught in modern schools and universities. The moderns only have a partial grasp on rationality. Modern science and mathematics only understand the notion of the true and the false. What lacks, is the understanding of truth. However, the very mention of this word, truth, can seem off putting. After all, probably more people have been burned at the stake because of an allegedly incorrect understanding of truth, than for any other reason. However, buried amongst the historic debris of lost causes lurks indeed the rusted hulk of truth.

Nevertheless, as any philosopher knows well, truth of this kind must be self-justifying. For many, such as Karl Popper, the notion of a self-justifying truth is synonymous with the blind faith of religious zealots and doctrinaire extremists, something anathema to science. Popper is content with the kind of knowledge where each proposition is forever condemned to the judgment that it might be false. Even worse, at the same time the proposition must accommodate the stark reality that this judgment might indeed be true. Then again, it might not. Modern scientists are a brave lot.

Sidenote:

Popper did eventually nuance his views on this matter in the light of the self-justifying biological organism notion. In so doing he implicitly admits that the biological organism is obsessed with self-justifying its continual existence in the world. As such, biological organisms seem to have ontologically more in common with the logic of religious zealots and political fanatics, than with the cool, dry head of the analytic philosopher.

The stark truth about truth is that it must be relative and never absolute. Only in this way can it become an absolute truth. In other words, it becomes an absolute truth relative to itself. This is the essence of monistic philosophy: It is the rationality of the self-justifying Self. Relative to this subject, there is only one truth.

We have already made inroads into the science of the subject. Unlike the analytic rhetorical type reasoning of analytic philosophy, the reasoning of this right side, monist philosophy, is expressed in terms of oppositions and oppositions between oppositions. It is in this way that the reasoning becomes a relativistic form of reasoning. Rather than rhetorical, it becomes dialectical. The nuts and bolts of the reasoning deals with the dialect of two entities, one which has and the other that is. These entities differ by gender, the first corresponding to the feminine gender, the second to the masculine. The dialectic of to have and to be, constitues the core essence of the monistic, right side form of reasoning.

This is the dialectic of the subject minimally conscious of itself. It leads to a particular kind of knowledge. It leads to the generic truth that reality, viewed from any particular perspective, is the reality viewed from the point of view of the generic subject, the any subject whatsoever kind of subject,

The elementary form that arose from our investigations was the semiotic square. This structure arose from the opposition between what the subject is and what the subject is not, that is to say, what it has. This opposition was formalised in terms of the gender construct. This leads to the four distinct parts of the square being gender typed MF, FF, FM and MM.

This very generic quadruple structure is highly lacking in determination. The edifice is so undetermined that it is not even clear whether it corresponds to the semiotic structure of knowledge of the world, or the structure of the world itself. Is this epistemology or is it physics? Is this the structure of Mind or is it the structure of Body? Is it the structure of a generic language or that of a generic world?

Finding an answer to these kinds of questions is key. It is here that we find the great enigma of this science. Unlike the analytical thinkers who want to understand the relationship between Mind and Body in terms analogous to that between horse and cart, the synthetic monist thinker must take a different tack. The horse will not be separated from the cart, but treated as an organic whole. One cannot have one without the other. We came across the very essence of the monist solution in the form of the gender construct. Rather than plucking attributes from a predefined definitional framework or harvested from empirical measurements, we constructed the one single fundamental attribute from which stem all other attributes of our science. This was the attribute possessed by the pure feminine entity. The attribute, an entity in its own right, was the masculine entity. These two entities are different. They differ by gender. However, they are absolutely indistinguishable. Two entities are distinguishable if they have different attributes. Here there might be two entities, but there is only one attribute between them: two entities; one has an attribute, the other is the attribute.

This gender construct provides the generic formula for all of the science that follows. The dialectic of the masculine and the feminine provides the generic base for all other seemingly dyadic structures such as the popular Mind-Body duality of the analytic philosophers. The relationship between the pure feminine and masculine is a generic form of the same relationship between Mind and Body.

Not everyone will agree with this assertion. Certainly, an analytic philosopher or anyone reasoning from a Cartesian viewpoint would take the abstract road, abstractly arguing that Body is like a machine and Mind is an intelligence that drives the machine. The two are linked together by some kind of “bridging laws” perhaps. There is no dialectic here, as the notion of a bodiless mind and mindless body, is considered quite respectable. They can conceivably go their separate ways: put the brain in the bottle and the brain dead body on life support, should do the trick.

Such a surgical separation is impossible for an organism constructed from the gender construct. The organism is constructed according to a four-lettered code. According to our gender calculus version of this code, each letter is made up of one of the four binary gender typings, MF, FF, FM and MM. On the face of it, the organism might be just a highly complex assemblage of hydrocarbon-based compounds. However, from an organisational point of view, it is a seething mass of intertwined, gendered entities. It is this gender typing of content and form of the organism that ensures systemic coherence. It is in this way that the One can be constructed from the inseparable and indistinguishable Two.

The Stoics saw this dynamic systemic organisation of the organism in terms of the tensions and tenos of a fifth kind of substance they called pneuma.

The pneuma is in constant motion. It is a process into itself, and from itself. The inward process produces unity and substance, the outward process dimensions and qualities. The pneuma is a disposition (hexis) in process. As a disposition, the pneuma holds the cosmos together, and accounts for the cohesions of each individual entity. The pneuma is the cause of the entity being qualified: for the bodies are bound together by these. [Chrysippus views on the pneuma (Reesor, 1989)]

The coherence, the very being of an organism, is synonymous with it maintaining Oneness. The mechanism for achieving and maintaining Oneness is through the establishment and maintenance of gender typing. The organism must know, without a shadow of doubt, what it has and has not and what it is and is not in all cases. These are the key determinants of consciousness. In addition, the determinations are purely relative. They are purely subject-ive. This, one must admit, is truly a beautiful, self-referring system.

Beautiful indeed, but how does it work? With profound beauty, one would expect an accompanying simplicity, a profound but simple principle. Seeing that everything involved in this kind of self-organising organism is relativistic, there should be some fundamental relativistic principle at play. In the traditional sciences of our day, the only relativistic principle known is in physics. There is no known equivalent in biology. In physics, we see relativity theory expressed as demanding that the laws of physics remain invariant from one reference frame to another. Perhaps more pointedly, as shown by Zeeman, the principle of relativity is intimately bound up with the non-violation of the causality principle. It is here that one can grasp the simplicity and elegance of the theory. System coherence demands the coherence of causality. The claim of generic science is that this is not enough. A much more demanding form of relativity is we call generic relativity.

If the work presented in this book is to be more than the usual exposition of inconclusive philosophical prose, then we should be able to advance an equally simple and elegant formulation concerning the essence of generic relativity, the cornerstone of the generic science we are trying to develop. Fortunately, we do not have to look very far. The principle is located at Ground Zero and there is no one who knew this spot in the Cosmos better than Chrysippus, the Stoic logician par excellence. Ground Zero is the location of the Logos, the reasoning faculty of any subject whatsoever. The form of the Logos can be understood in terms of the dialectic of having and being, a form expressed by the semiotic square. Chrysippus provided the logical framework of the Logos semiotic square in the form of four of his five undemonstratables. We have resurrected this structure as an alternative to Aristotle’s Square of Oppositions, discussed previously. We have named this the Chrysippus’ Square of Oppositions. The fit between this structure and the four undemonstratables is comfortable and reasonably self-evident. The structure effectively provides an additional logical impetus to the thrust of our argument. The four undemonstratables provide a logical dimension to the interpretation of the four-element theory and the corresponding four letters.

Absolute Incompatibility

Five undemonstratables minus four leaves one. The missing syllogism is the third undemonstrable, the incompatibility syllogism: One cannot have one quality and the other at the same time. We now come to the fundamental tenet of generic science. It is founded on the premise that there is nothing more incompatible in this world than the masculine and the feminine. This premise does have some intuitive appeal and so we will stick with it. This is not a bad idea, as it appears that the whole cosmos hinges on the concept. It is the incompatibility principle that holds not only the cosmos together, but any being whatsoever that exists.

In the case of biological organisms, the concept should be relatively easy to grasp. A stumbling block might be in accepting that the genetic code is more than a mere transcription language. One should keep in mind that curiously, and apparently accidently, the code became a convention adopted by all living organisms since the year dot; without exception. Accidents do happen, but this accident does seem a little bigger than most. Life might be subject to evolution, but the language of life seems absolutely impervious to change. The gamble of Nature seemed to have hit the jackpot absolutely spot on, right from the start.

The reader may rest with that interesting accident hypothesis or move on to considering that the code may be based on a generic semantic and ontological structure. According to our take on the question, this structure is based on the dialectics of being and its naturally orthogonal counterpart, that of having. This can be formalised in terms of the gender construct and leads to a four-letter code based on the four possible binary combinations of the two genders. It is generally accepted that all biological processes are coded by the genetic code, what we claim to be the generic code. Moreover, in multi-celled creature, the same code is repeated for each cell. We say that this code expresses a relative typing on all aspects of the organism. At the very ground roots level, the typing is in terms of complex combinations of gender typing. We claim that the organism relies on this form of organisation in order to arrive at knowledge and consciousness of itself. It is via this absolutely relativistic gender typing that the entity knows what pertains to it or what does not. This is the most elementary and most essential feature of life.

Moreover, the basic health of the organism will be placed in peril if this typing mechanism starts breaking down. The cohesion of the system demands the constant maintenance of the integrity of gender typing through the organism. The Stoic picture of a pneuma permeating every aspect of the organism is very helpful. The pneuma is constantly attracting and repelling, constantly maintaining the equilibrium of the organism.

The Stoics claim that there are two primary principles working through the pneuma: the active principle and the passive principle. This terminology is also helpful, as long as we recognise that the active and passive ultimately refer to the masculine and feminine, in a particular configuration. For example, we refer to the feminine as active by the mixed gender term FM.

The masculine as active becomes MM and so on for the passive MF and FF variants.

Maintenance of the integrity of gender typing throughout the organism is paramount. Since the system is changing and reacting to its environment, this integrity must be synchronised. This brings us back to the key logical ingredient that guarantees such coherence: the coherence principle.

The Gender Coherence Principle

The organisational coherence of an organism is regulated through gender typing. The maintenance of organisational coherence is synonymous with maintaining the integrity of gender coherence. This can best be expressed in the form of Chrysippus’ third undemonstratable, the incompatibility syllogism. The premise can be restated in the form:

In no single moment can an entity be both masculine and feminine at the same time.

We will call this the gender coherence principle, the fundamental organisational principle of Nature.

Note in passing that an entity can have multiple gender typing. However, it cannot have two different gender typings at the same time. This raises interesting question regarding the degeneracy of the genetic code. Take the amino acid asparagine, for example. It can be coded by the bases either AAU or AUC. In gender terms, this translates to the gender typing MFMFFF or MFMFMM. According to the gender coherence principle, such an entity has two possible “quantum” gender states. At any time, it can be functioning as either MFMFFF or MFMFMM, but not both at the same time. Remember that gender typing at any instant of time is not absolute and cannot be measured deterministically by a third party. Gender typing is relativistic and dynamic and in coherence with the organism so typed.

Note that the so-called superposition of states addressed by quantum mechanics disappears if they are considered to be more like relativistic gender states. Any observer that deterministically tries to measure a relativistic gender state of an organism will encounter superposition. For the organism in question, there is no superposition whatsoever. Relative to its integrity system, the gender coherence principle demands that the very opposite apply at each and any instant.

As for the organism, in the life sciences the organism might be a cat on a slab in the lab. For the physicist, the organism might be a much smaller or much larger creature. However, it is still an organism based on the same generic organisational principles.

Physics Interpretation

In an appendix attached to this work, elementary particle physics will be interpreted from a generic point of view. This leads to elementary entities like quarks and leptons being gender typed in terms of codons reminiscent of biology. In this way, any being in nature codes itself in terms of the generic code based on gender typing. This includes the cosmos itself, as a dynamic self-organising being.

In traditional relativity theory, one can discern an elementary organisational coherence that can be stated in a form comparable to the gender coherence principle. In this case, it becomes the principle of causal integrity. The principle states the dialectic of cause and effect:

The cause event is always antecedent to the effect event.

This is the most fundamental organisational principle known to traditional physics. The law must not be violated in any context (i.e., in any reference frame) and so demands a system that obeys Einstein’s Special and General Theory of Relativity.

One can see that the form of Einstein’s relativity has a certain resemblance to the generic form expressed, not as a causality coherence, but as gender coherence. There is also a fundamental difference. Einstein’s relativity demands coherence across time: causes must precede effects in time. In other words, Einstein’s relativity is diachronic in nature. In contrast, the generic version of relativity demands coherence at the same time. In other words generic relativity is synchronic in nature and, up until now, has been totally ignored in physics.

Computer Science Interpretation

It is important to keep in mind at all times when dealing with the generic that it is not an abstract science. Generic science is capable of formalism but not as an abstraction, which is necessarily dualist. Generic science is monist and non-abstract. Some effort is required to become accustomed to this totally different paradigm. Interpreting some of the concepts in a Computer Science setting can help, in this regard. Unlike axiomatic abstract mathematics, Computer Science is a constructive science and naturally synthetic in nature. The science also enjoys a natural tendency towards monism in the sense that the theory of code can be expressed in code.

Generic science is a discipline, which has for its vocation the task of articulating the structure and organisational principle of any living being. The science is naturally constructionist. This raises the question of how to construct an organism based on generic science principles. Such an organism would have to be based on gender typing and be organised on the gender coherence principle. In addition, the whole system must not violate the principle of First Classness. Is this possible?

This is a silly question as our very own presence on this globe is at least some kind of feasibility proof of the concept, a living proof in fact.

What we wish to do in this section is to provide a very simple example of how Computer Science, unknowingly, has already started to go down the path of Generic Science. Our example is the very computer itself, the Von Neumann computer.

Before Von Neumann, there already existed programmable calculating devices. However, they all had one thing in common. They were based on an absolute dichotomy between data and program. For example, the program might be hard wired into the device and the data fed in via paper tape. If we want to put some gender typing into the mix, we could say that the program was masculine stuff and the data feminine. With this arrangement, the gender coherence principle could be satisfied because at no time is any confusion possible between what was program stuff and what was data stuff. Data was always on the paper, and program in the machine. The only problem was that such a device violates First Classness.  First Classness is incompatible with such a blatant and absolute duality. First Classness cannot tolerate a world cut up into two, one made of paper and one made of the other stuff.

Von Neumann started the process of moving the calculating machine into the realm of a generically organised entity. He made two innovations. The first innovation was shared memory where there was no longer to be any absolute dichotomy between data stuff and program stuff. They were all loaded into shared memory in the same format as small chunks of information. Von Neumann was then faced with the problem of how the computer could tell the difference between program stuff and data stuff. It was here that Von Neumann decided to invoke his version of Chrysippus’ incompatibility principle. The principle was that:

No chunk of information in shared memory could be both data and program at the same time.

In order to implement this principle, he came up with his second innovation. It was called the Program Counter. The Program Counter is a pointer into the shared memory of the computer. The rule was that a program instruction was the chunk of memory pointed to by the Program Counter at a particular instance in time. All the rest of the chunks were considered data. Having executed that instruction, the Program Counter would be incremented to the next memory location, and that would then be considered a program chunk and no longer potential data. In the case of a JUMP instruction, the Program Counter would be moved to some other distant place in memory and the process continues. The computer was born.

Like practically every major advance in computer science, the Von Neumann’s computer was an exercise of eliminating violations in First Classness; in this case, eliminating the fixed dichotomy between data and program. Henceforth, the distinction became relative to the dynamically changing Program Counter. What was program and what was data depended on context.

However, such a device is far from freeing itself from violation of First Classness. The Program Counter itself becomes a rigid privileged memory location, totally estranged from the run of the mill information chunk in shared memory. That is yet another dichotomy to be eliminated by generic engineering principle. There is a long way to go.

The Von Neumann computer needed a few further innovations in order to become operational. However, not many other innovations were needed. Add a stack, interrupts, and a few input/output ports and that is about it.

The Semiotic Logic of Chrysippus

Before reaching an understanding of our reconstruction of the Chrysippus semiotic square, we need to know a bit about semiotics, or at least, our version of it. We provide here a summary of our approach.

The author’s first acquaintance with the semiotic square came from following the courses of Greimas back in Paris, many years ago. The term “semiotic square” is nowadays generally associated with his name. The big weakness in the Greimas approach was his failure to come to terms with the subject. His semiotics is sans sujet. We will sketch out here a more fundamental approach to semiotics and the semiotic square that does include the subject.

To begin with, there are two kinds of semiotics, one associated with Ferdinand de Saussure (dyadic, arbitrariness of the sign etc.) and one associated with Charles Sanders Peirce (triadic). In our view, the approach of de Saussure is not semiotics, but General Linguistics. Like Greimas, the approach of de Saussure is sans sujet. If there is a subject, it is part of the Spectacle, not the Spectator. It is merely what Hegel referred to as the empirical ego. In this perspective, the de Saussure approach is like that of the traditional sciences and mathematics. All of these sciences are sans sujet. We call all of these traditional science left side sciences. Left side sciences claim to be objective, which is another way of saying that they only concerned with a reality of objects where any reference to the subject has been excluded. They are all sans sujet. As such, these sciences look at the world from a very specific point of view. This point of view has been described as the “view from nowhere” or the “God’s eye view”. This is a general characteristic of science sans sujet. It is a general characteristic of all the sciences and mathematics of today.

The other possible scientific paradigm goes in the opposite direction. It demands that the subject is always present. In other words, if there is a spectacle there must also be an accompanying spectator. You cannot have one without the other. We call the science based on this paradigm, right side science. The right side science becomes, in fact, the dialectic of the Spectator and the Spectacle, the Subject and its kingdom.

Unlike the many left side sciences, there is only one right side science. This is because its focus is on the science of the subject and this is quite different to the science of objects. It is the science of the Self. For a Stoic logician like Chrysippus, it is the science of the Logos. This generic entity, the Self, the Logos, the Ego, has a generic form. This form can be worked out from pure reason.

Now Charles Sanders Peirce was more inclined to the right side paradigm, but he did not make much headway. He also despised the Stoics, which did not help. Thus, we have to start from scratch. Starting from scratch means that we start with a subject and its kingdom. Alternatively, we start with a kingdom and its subject, the same thing. Both spectator and spectacle must be present in the same moment.

This is where we have to put our thinking caps on. The relationship between the Subject and its Other is a very particular kind of relationship. They each determine one another. The Hindus sometimes see this as a coital relationship. The subject corresponds to the masculine. The mysterious other is the feminine where gender gets interpreted as sex, poetic licence oblige. The Stoics saw the relationship as that between the Active Principle and the Passive Principle. Vedanta philosophy often refers to the Active principle as the Principle of Individualization, the Spiritual Principle, or simply the masculine principle. We have here the building block for right side science. It is getting a bit steamy, so here is one way to arrive at a dispassionate view. It involves the gender construct.
Semiotic square personal and impersonal subject
Figure 31 The generic semiotic square is constructed from the feminine masculine opposition applied to itself.

The main role of the subject in this right side science is that it does provide a determined point of view. As such, it is a pure singularity. What is non-subject is non-singularity. This can be formalised with the concept of gender. The gender concept is very ancient, in both the West and the East. First, there is the unqualified substance totally devoid of any determined specificity. Such an entity is typed as the pure feminine. One might say that the pure feminine is devoid of specificity and so has no attribute. This is not the case. It is only devoid of a determined specificity. It has an undetermined specificity. That is its attribute. This attribute, using the argument of First Classness, must be an entity in its own right. (Note that the Stoics always claimed that the property of an entity is an entity in its own right). This attribute entity will be said to be of masculine gender. Two entities; one has an attribute, the other is the attribute. The first entity corresponds to the feminine, the second to the masculine. These two entities provide the building blocks for the right side science paradigm.

The first thing to construct is the semiotic square. One way of understanding this square is as the architecture of a whole. Totality can only be understood from a determining point of view of the subject. Instead of comprehending the totality in any moment, which is impossible, it is understood as a whole. A whole is totality looked at from a particular point view. There are as many wholes as there are points of view. This requires that the subject must be present in the whole. Right side science always understands things in terms of wholes.

Thus, the semiotic square, as a generic understanding of a whole, is a map of the subjects conscious understanding of the whole, any whole. The first moment of understanding is “Wow, here I am, this is me and the rest is not me.” We thus draw a square, cut it down the middle and adopt the convention that the right side corresponds to subject and the left side to what is not subject. The right side is masculine typed and the left side is feminine typed.

However, the subject in this particular configuration is not you or I. It represents the impersonal subject. In fact, it is this subject that corresponds to the “view from nowhere”, the “God’s eyes view” of the traditional sciences. These sciences, in their quest for objectivity, remove all reference to subject from consideration. They even remove this impersonal subject from consideration, as they have no need for it. They demand a godless science, a pure science sans sujet. Thus, the semiotic square for the left side sciences is the same as for the right side science, except that the right side is blacked out. Left side sciences thus suffer from a symptom well known to the psychiatrist. It is called hemi-neglect. Right side science knows about the left side, left side science wings it alone, content with half a brain, so to speak. Curiously, in passing, the human brain exhibits exactly this same bi-lateral specialisation. The right hemisphere does not exhibit hemi-neglect and sees a whole world. Only the left side exhibits hemi-neglect.

This is now where left side and right side science part company. Not content with just the presence of the impersonal subject, right side science must find a way of introducing a more determined subject, the personal subject. This is constructed by applying the first feminine-masculine opposition to itself, an opposition of two oppositions. It might sound complicated but is easily visualised with the semiotic square. The second opposition is orthogonal to the first and so instead of a left-right dichotomy, the dichotomy is front-back. We use the convention of masculine in front, feminine at the back. It appears that we are not the only ones to adopt this polarity convention.

The end result is that we end up with a square shaped kind of placeholder for dealing with knowledge. The first kind of knowledge involves an elementary consciousness of self, a knowledge of what is and what is not. This is expressed logically in our reconstruction of the Chrysippus square. For the moment, note that the four parts of the semiotic square have been binary typed with gender. For example, the left front part is typed as MF. This reads that, from the impersonal subject perspective, it is typed as feminine. From the personal subject perspective, it is typed as masculine. Thus, the first letter in the binary gender typing is that of the personal subject, the second letter is that of the impersonal.

The semiotic square is a placeholder, the architecture of the generic mind, so to speak. The semiotic square is static and unique, for the purposes of the science. You only need one brain, it can be said.

In addition to the placeholder, there are values relative to it. These values are mobile. There are the four kinds of elementary substance that can be binary typed by the four binary gender types. The binary typed substance corresponds to MF, FF, FM and MM. The ancients called them air, earth, water and fire respectively.

We now come to the semiotic square constructed with four of the Chrysippus undemonstratables. Note that one diagonal is constructed from the conjunctive syllogisms. These are known to logicians as Modus Ponens and Modus Tollens. The other diagonal is constructed from the two forms of the disjunctive. The diagram can be gender typed by matching the is copula with the masculine and the is not with the feminine, as shown. This matches perfectly with the semiotic square gendering shown above.

What is interesting is that the logic of Chrysippus has introduced yet another dimension into the semiotics, a vertical axis. The square becomes the “Chrysippus cube”! We have used the convention of the implication arrows in the diagram going left to right to signal the upwards direction, and the downwards for the right to left. Talking intuitively, this indicates that the top two entities have an “upward flow” and the bottom two entries have a “downward flow”.

One should note that the gender coding of the top two elements correspond to the “elements” of air and fire. These are the “light” elements, being predominantly masculine and less substantial than the feminine bottom two elements of earth and water. Such reasoning is not very rigorous, as we are not talking about the same kind of elements as in the left side, traditional science. The logic of Chrysippus however adds a different complexion to the matter.

These principles must have been part of core Stoic teaching, as Marcus Aurelius wrote in Meditations.

Your aerial part and all the fiery parts which are mingled in you, though by nature they have an upward tendency, still in obedience to the disposition of the universe they are overpowered here in the compound mass. And also the whole of the earthy part in you and the watery, though their tendency is downward,

The Stoics claimed that theirs was a unifying science that integrated logic, physics, and morality. Some people are attracted to Stoic values whilst thinking that their science has been completely eclipsed by the modern day sciences. However, how antiquated is the science of antiquity? Consider the following.

In our diagram, we have added in the four letters CAUG matching up with the gender typings MM, MF, FF and FM respectively. This is part of another story in this book. These are the four letters of what we call the generic code. We have taken them from the RNA version of the genetic code. The genetic code is a standard code that codes all living beings, without exception. This is an established fact. The generic code is impervious to evolution and has remained unchanged since the year dot. By extending the notion of the living to that of the universe, itself considered as living by the Stoics, this same code takes on a generic vocation. In this book, we explore its application to understanding elementary particle physics from a new angle (see Appendix). We use the generic code to code quarks and leptons. These claims may test our short-term credibility. However, in the longer term that is the way it will pan out once we have properly digested this new science, a science with such ancient roots.