A mechanical Turing machine: blueprint for a biomolecular computer

The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence

This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.

Tracing a new path in the field of AI and robotics: mimicking human intelligence through chemistry. Part II: systems chemistry

Inspired by some traits of human intelligence, it is proposed that wetware approaches based on molecular, supramolecular, and systems chemistry can provide valuable models and tools for novel forms of robotics and AI, being constituted by soft matter and fluid states as the human nervous system and, more generally, life, is. Bottom-up mimicries of intelligence range from the molecular world to the multicellular level, i.e., from the Ångström (10 - 10 meters) to the micrometer scales (10 - 6 meters), and allows the development of unconventional chemical robotics. Whereas conventional robotics lets humans explore and colonise otherwise inaccessible environments, such as the deep oceanic abysses and other solar system planets, chemical robots will permit us to inspect and control the microscopic molecular and cellular worlds. This article suggests that systems made of properly chosen molecular compounds can implement all those modules that are the fundamental ingredients of every living being: sensory, processing, actuating, and metabolic networks. Autonomous chemical robotics will be within reach when such modules are compartmentalised and assembled. The design of a strongly intertwined web of chemical robots, with or without the involvement of living matter, will give rise to collective forms of intelligence that will probably reproduce, on a minimal scale, some sophisticated performances of the human intellect and will implement forms of "general AI." These remarkable achievements will require a productive interdisciplinary collaboration among chemists, biotechnologists, computer scientists, engineers, physicists, neuroscientists, cognitive scientists, and philosophers to be achieved. The principal purpose of this paper is to spark this revolutionary collaborative scientific endeavour.

Agency in evolution of biomolecular communication

Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an organized system of signs-a communicative agency-for creating and transmitting meaning. The emergence of agency, the capacity to act in a given context and generate end-directed behaviors, has baffled evolutionary biologists for centuries. Here, I explore its emergence with knowledge grounded in over two decades of evolutionary genomic and bioinformatic exploration. Biphasic processes of growth and diversification exist that generate hierarchy and modularity in biological systems at widely ranging time scales. Similarly, a biphasic process exists in communication that constructs a message before it can be transmitted for interpretation. Transmission dissipates matter-energy and information and involves computation. Agency emerges when molecular machinery generates hierarchical layers of vocabularies in an entangled communication network clustered around the universal Turing machine of the ribosome. Computations canalize biological systems to perform biological functions in a dissipative quest to structure long-lived occurrents. This occurs within the confines of a "triangle of persistence" that maximizes invariance with trade-offs between economy, flexibility, and robustness. Thus, learning from previous historical and circumstantial experiences unifies modules in a hierarchy that expands the agency of systems.

An RNA-Based Theory of Natural Universal Computation

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of universal computation, i.e., Turing-equivalent in scope. Generic finite-dimensional dynamical systems (which encompass most models of neural networks, intracellular signaling cascades, and gene regulatory networks) fall short of universal computation, but are assumed to be capable of explaining cognition and development. I present a class of models that bridge two concepts from distant fields: combinatory logic (or, equivalently, lambda calculus) and RNA molecular biology. A set of basic RNA editing rules can make it possible to compute any computable function with identical algorithmic complexity to that of Turing machines. The models do not assume extraordinarily complex molecular machinery or any processes that radically differ from what we already know to occur in cells. Distinct independent enzymes can mediate each of the rules and RNA molecules solve the problem of parenthesis matching through their secondary structure. In the most plausible of these models all of the editing rules can be implemented with merely cleavage and ligation operations at fixed positions relative to predefined motifs. This demonstrates that universal computation is well within the reach of molecular biology. It is therefore reasonable to assume that life has evolved - or possibly began with - a universal computer that yet remains to be discovered. The variety of seemingly unrelated computational problems across many scales can potentially be solved using the same RNA-based computation system. Experimental validation of this theory may immensely impact our understanding of memory, cognition, development, disease, evolution, and the early stages of life.

Genomic Intelligence as Über Bio-Cybersecurity: The Gödel Sentence in Immuno-Cognitive Systems

This paper gives formal foundations and evidence from gene science in the post Barbara McClintock era that the Gödel Sentence, far from being an esoteric construction in mathematical logic, is ubiquitous in genomic intelligence that evolved with multi-cellular life. Conditions uniquely found in the Adaptive Immune System (AIS) and Mirror Neuron System (MNS), termed the genomic immuno-cognitive system, coincide with three building blocks in computation theory of Gödel, Turing and Post (G-T-P). (i) Biotic elements have unique digital identifiers with gene codes executing 3D self-assembly for morphology and regulation of the organism using the recursive operation of Self-Ref (Self-Reference) with the other being a self-referential projection of self. (ii) A parallel offline simulation meta/mirror environment in 1–1 relation to online machine executions of self-codes gives G-T-P Self-Rep (Self-Representation). (iii) This permits a digital biotic entity to self-report that it is under attack by a biotic malware or non-self antigen in the format of the Gödel sentence, resulting in the “smarts” for contextual novelty production. The proposed unitary G-T-P recursive machinery in AIS and in MNS for social cognition yields a new explanation that the Interferon Gamma factor, known for friend-foe identification in AIS, is also integral to social behaviors. New G-T-P bio-informatics of AIS and novel anti-body production is given with interesting testable implications for COVID-19 pathology.

Nonhuman rationality: a predictive coding perspective

How can we rethink 'rationality' in the wake of animal and artificial intelligence studies? Can nonhuman systems be rational in any nontrivial sense? In this paper, we propose that all organisms, under certain circumstances, exhibit rationality to a diverse degree and aspect in the sense of the standard picture (SP): Their inferential processes conform to logic and probability rules. We first show that according to Calvo and Friston (J R Soc Interface 14(131):20170096, 2017) and Orlandi (2018), all biological systems must embody a top-down process (active inference) to minimize free energy. Next, based on Maddy's (Second philosophy, Oxford University Press, Oxford, 2007; The logical must: Wittgenstein on logic, Oxford University Press, Oxford, 2014) analysis, we argue that this inferential process conforms to logic and probability rules; thus, it satisfies the SP, which explains the rudimentary logic and arithmetic (e.g., categorizing and numbering) found among pigeons and mice. We also hold that the mammalian brain is only one among many ways of implementing rationality. Finally, we discuss data from microorganisms to support this view.

Is Research on "Synthetic Cells" Moving to the Next Level?

"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?

Enzyme-based logic gates and circuits-analytical applications and interfacing with electronics

The paper is an overview of enzyme-based logic gates and their short circuits, with specific examples of Boolean AND and OR gates, and concatenated logic gates composed of multi-step enzyme-biocatalyzed reactions. Noise formation in the biocatalytic reactions and its decrease by adding a "filter" system, converting convex to sigmoid response function, are discussed. Despite the fact that the enzyme-based logic gates are primarily considered as components of future biomolecular computing systems, their biosensing applications are promising for immediate practical use. Analytical use of the enzyme logic systems in biomedical and forensic applications is discussed and exemplified with the logic analysis of biomarkers of various injuries, e.g., liver injury, and with analysis of biomarkers characteristic of different ethnicity found in blood samples on a crime scene. Interfacing of enzyme logic systems with modified electrodes and semiconductor devices is discussed, giving particular attention to the interfaces functionalized with signal-responsive materials. Future perspectives in the design of the biomolecular logic systems and their applications are discussed in the conclusion. Graphical Abstract Various applications and signal-transduction methods are reviewed for enzyme-based logic systems.

Antibiotics and evolution: food for thought

The role of secondary metabolites in effecting and modulating reactions during early biochemical evolution has been largely unappreciated. It is possible that low molecular weight effectors were gradually replaced by polypeptides as polymerizing reactions became more complex, but retained some ability to interact with original receptor sites. Indeed, by reviewing the era of antibiotics in this light we can begin to reconcile the ancient and contemporary activities of these molecules. The corollary being that secondary metabolites participate in a vast array of interactions in nature and investigating their intended receptors will be revealing in both pharmacological and evolutionary terms.

Nature versus design: synthetic biology or how to build a biological non-machine

We suggest that progress in synthetic biology will be achieved by abandoning the bio-machine paradigm and by using an alliance between engineering and evolution as a guiding tool.

Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.