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Back to the ancients to find the future of science

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]

   

Shariing
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