Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their (...) syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the nonrepetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs. (shrink)

This article compares three models for conceptualizing the political and ethical challenges of contemporary genetics, genomics, and postgenomics. The three analytical approaches are referred to as the state-politics model, the biopolitical model, and the infopolitical model. Each of these models is valuable for different purposes. But comparing these models in terms of their influence in contemporary discussions, the first is by far the dominant approach, the second is gaining in importance, and the third is almost entirely neglected. The widespread neglect (...) of the infopolitical dimensions of genetic sciences focused by the third model is puzzling in light of the fact that genetics, genomics, and postgenomics are all pre-eminent information sciences. The infopolitical model thus aims to bring into clearer view the specific political and ethical problems engendered by this informational nature of the genetic sciences. This model offers a way of understanding how ethically-salient and politically-fraught conceptual assumptions can be embedded in informational architectures such as algorithms and the formats (or data structures) upon which they rely. (shrink)

Using the two cases of the Icelandic Health Sector Database and Russian initiatives in biobanking, the article criticizes the view of narratives and imaginaries as a sufficient and unproblematic means of shaping public understanding of genetics and justifying population-wide projects. Narrative representations of national biobanking engage particular imaginaries that are not bound by the universal normative framework of human rights, promote affective thinking, distract the public from recognizing and discussing tangible ethical and socioeconomic issues, and harm trust in science and (...) technology. In the Icelandic case, the presentation of the project in association with national imaginaries concealed its market identity and could lead to the commodification of biodata. In the Russian case, framing in terms of "genetic sovereignty" and "civilizational code" offers pretexts for state securitization. Adherence to normative framework of human rights and public discussion of genetics in an argumentative and factual mode can counter these trends. (shrink)

The idea that development is the expression of information accumulated during evolution and that heredity is the transmission of this information is surprisingly hard to cash out in strict, scientific terms. This paper seeks to do so using the sense of information introduced by Francis Crick in his sequence hypothesis and central dogma of molecular biology. It focuses on Crick's idea of precise determination. This is analysed using an information-theoretic measure of causal specificity. This allows us to reconstruct some of (...) Crick's claims about information in transcription and translation. Crick's approach to information has natural extensions to non-coding regions of DNA, to epigenetic marks, and to the genetic or environmental upstream causes of those epigenetic marks. Epigenetic information cannot be reduced to genetic information. The existence of biological information in epigenetic and exogenetic factors is relevant to evolution as well as to development. (shrink)

Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural (...) genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing. (shrink)

The concepts of the origin of the genetic code and the definitions of life changed dramatically after the RNA world hypothesis. Main narratives in molecular biology and genetics such as the “central dogma,” “one gene one protein” and “non-coding DNA is junk” were falsified meanwhile. RNA moved from the transition intermediate molecule into centre stage. Additionally the abundance of empirical data concerning nonrandom genetic change operators such as the variety of mobile genetic elements, persistent viruses and (...) defectives do not fit with the dominant narrative of error replication events (mutations) as being the main driving forces creating genetic novelty and diversity. The reductionistic and mechanistic views on physico-chemical properties of the genetic code are no longer convincing as appropriate descriptions of the abundance of non-random genetic content operators which are active in natural genetic engineering and natural genome editing. (shrink)

Within the framework of historical epistemology (G. Canguilhem, M. Foucault, L. Loison) the key concepts of a scientific discipline are considered as historically and culturally contingtent, that is, predetermined by outside factors rather than by the internal logic of the development of science. A fundamental attempt to demonstrate the contingency of the concept of “genetic information” was made in 2000 by Lily Kay, who argues that there was an “epistemic rupture” between this concept and the previous biological discourse of (...) “specificity”. As I. A. Kuzin has recently demonstrated, this work is essential not only for the history of biology, but also for the methodology of history of science and for modern biology as well. This paper contains a critical approach to both works. The sociocultural (externalist) conceptualizations of the history of biology contain serious difficulties and contradictions that internalism can successfully cope with. Being an explanans, “discourse” is not able to explain the key features of the history of deciphering the genetic code. “Discourse”, “concept” and “metaphor” of information are confused; two separated phases of the deciphering the code are separated groundlessly as “formal” and “material” stages; the transition from syntactic aspect of information to semantic one (from the “cipher” metaphor to the “code” metaphor) is at least problematic. The internalist approach preserves the idea of the contingency of the concept of information (in the form of methodological contingency instead of historical and cultural one), and at the same time incorporates it into the internal development of genetics and molecular biology. (shrink)

How does the genetic code navigate through the mind-boggling list of alternatives? This brief article gives a clue.

Manfred Eigen extended Erwin Schroedinger’s concept of “life is physics and chemistry” through the introduction of information theory and cybernetic systems theory into “life is physics and chemistry and information.” Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language.However, the basics of scientific knowledge changed dramatically within the (...) second half of the 20th century.Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. (shrink)

Recent advances in neuroscience lead to a wider realm for philosophy to include the science of the Darwinian-evolved computational brain, our inner world producing organ, a non-recursive super- Turing machine combining 100B synapsing-neuron DNA-computers based on the genetic code. The whole system is a logos machine offering a world map for global context, essential for our intentional grasp of opportunities. We start from the observable contrast between the chaotic universe vs. our orderly inner world, the noumenal cosmos. So (...) far, philosophy has been rehearsing our thoughts, our human-internal world, a grand painting of the outer world, how we comprehend subjectively our experience, worked up by the logos machine, but now we seek a wider horizon, how humans understand the world thanks to Darwinian evolution to adapt in response to the metaphysical gap, the chasm between the human animal and its environment, shaping the organism so it can deal with its variable world. This new horizon embraces global context coded in neural structures that support the noumenal cosmos, our inner mental world, for us as denizens of the outer environment. Kant’s inner and outer senses are fundamental ingredients of scientific philosophy. Several sections devoted to Heidegger, his lizard debunked, but his version of the metaphysical gap & his doctrine of the logos praised. Rorty and others of the behaviorist school discussed also. (shrink)

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined (...) by natural laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer sciencebased formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language. (shrink)

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and non-coding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts (...) and compel a re-examination. In this review we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioural motifs of cooperative RNA consortia. In addition to molecular biological perspectives this may lead to a better understanding of genetic code evolution and dynamics. (shrink)

Popular culture continues fuelling public imagination with things, human and non-human, that we might beco-me or confront. Besides robots, other significant tropes in popular fiction that generated images include non-human humans and cyborgs, wired into his-torically varying sociocultural realities. Robots and artificial intelligence are re-defining the natural order and its hierar-chical structure. This is not surprising, as natural order is always in flux, shaped by new scientific discoveries, especially the reading of the genetic code, that reveal and redefine (...) relationships between life forms. However, for the first time, a new, artificial, species is being introduced into the existing diagrams, and, for the first time, it appears to hybridise the anthro-pocentric natural world order. (shrink)

This paper examines the notion of the biopolitical body from the standpoint of Foucault’s logic of the security mechanism and the history he tells of vaccine technology. It then investigates how the increasing importance of the genetic code for determining the meaning and limits of the human in the field of 20th century cell biology has been a cause for ongoing transformation in the practices that currently extend vaccine research and development. I argue that these transformations mark the (...) emergence of a new kind of medical subject – the stabilized and infinitely reproducible human cell line – and that the practices and markets exploiting this new form of organism have had a destabilizing effect on the very biopolitical structures that engendered them and, in fact, mark a new way of conceiving the possibilities of cellular life. I call these new ways of organizing power that intervene in the logic of the security measure by mediating the relationship between populations and persons the microbiopolitical. (shrink)

This essay moves along broad lines from molecular biology to evolutionary biology and ecology to theology. Its objectives are to: 1) present some recent scientific findings in the emerging field of epigenetics that indicate that it is “the genome in context,” not genes per se, that are important in biological development and evolution; 2) show that this weakens the gene-centric neo-Darwinist explanation of evolution which, in fact, shares a certain preformationist orientation with intelligent design theory; 3) argue that the evidence (...) against a gene-centric view in no way negates Darwin’s central idea of “descent with modification”; 4) argue that an embrace of the evolutionary story, with all of its contingency and apparent lack of directionality, is not only consistent with Christianity, but actually resonates with the notion of the self-emptying love of God in Jesus Christ; and finally 5) suggest that we are called through an ecological imperative to embrace our evolutionary story, to listen to our “genetic coding,” and to reclaim our grounding as a species in the natural world. Corrigendum (published in later issue of journal): There was an error in the paragraph describing the mode of action of the small temporally-expressed RNAs (stRNAs) lin-4 and let-7 from Caenorhabditis elegans. Instead of reading "These two stRNAs act by binding to the tails of their target messenger RNAs (mRNAs); this results in destruction of the target and an overall drop in the level of production of protein from agouti mRNA" [note that agouti mRNA is not a target of these stRNAs], the sentence should have read, "These two stRNAs act by binding to the tails of target messenger RNAs (mRNAs); this leads to inhibition of translation of the mRNAs into protein and a consequent drop in the levels of the corresponding target protein.". (shrink)

● Any given placement (e.g. Sun in Taurus; Mars in Capricorn; Mercury in the third house) is necessarily common to tens of thousands of people. Saturn in the ninth house, for example, will not behave the same or produce the same effects in the twenty or one hundred charts in which we find it there. In each case Saturn will behave in accordance with the rest of the astrographic/chart composition (as if we stayed in the same hotel in different epochs (...) or different people contracted the same disease; our stay will be different each time, according to the epoch, and each person’s symptoms will too, be different, according to their individual biochemistry; not to mention that each chart or astrography, like each genetic code or sequence, is unrepeatable). Certainly, “no planet can produce, on its own, what only the combined or concerted action of all can” (BUSTAMANTE, 2023, SPICA magazine, pp. 93-111). Hence the synergistic nature of the interpretative exercise (i.e., the whole is greater than all its parts). The fundamental component of the mathematical expression of the interpretive exercise is: astrological triangulation, the functional denomination for what we know as synthesis (WEISS, 1946; LEO, 1983, HAND, 1981). In order to demonstrate its usefulness, as well as the convenience of its mathematical expression, we have chosen two individuals (JEFFREY DAHMER, STEVEN SPIELBERG) whose astrographies do not—according to the community—explain their lives. The rest of the astrographies correspond to those of serial killers JOHN WAYNE GACY, DAVID CARPENTER, and TED BUNDY. ● We explain, by means of algebraic notations, the synthesis and the functional values that make up the synthesis. ● We take the Moon and Neptune as relevant bodies for the purpose of diagnosing or studying endocrine or neurohormonal issues, and Mars, Pluto, and Saturn as relevant planets for the purpose of inferring violence or sinister behaviour, upon the case, and quadratures or oppositions—and conjunctions—between Venus and the Moon, the Moon and Neptune, and the Sun or Venus and Neptune or Uranus as indicators of neurohormonal disorders and/or sexual deviance (APA definition) . ● We consider quadratures (90º) or oppositions (180º)—and conjunctions—between Mercury or the Moon and Saturn, or between Mars or the Moon and Saturn, Uranus, Neptune, and/or Pluto as powerful indications of violence or mental disorders, upon the case. ● We have also regarded Sagittarius as a sign as expansive and abundant as its ruler, Jupiter, according to the best of its characterisations (or as an exceptionally swift and wild sign, according to other characterisations), and the fifth region of a natal chart as one closely related to fortune in a broad sense (material and immaterial). ● Because we advocate the idea that orbs should be predicated of the planet (size, speed), not the aspect itself, the gas giants (Jupiter, Saturn, Uranus, and Neptune) and the Sun have been granted up to 10º of orb (or 12º, in the case of broad influence ). We understand aspectual relationships as angular relationships held between two or more celestial bodies placed in signs with at least one property in common (according to our molecular theory of the ecliptic, compatible with the optical theory of the aspects from the Hellenistic tradition). (shrink)

Natural genome editing from a biocommunicative perspective is the competent agent-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements, and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism. Natural genome editing integrates both natural editing of genetic code and epigenetic marking that determines genetic reading patterns. As agents that edit genetic code and epigenetically mark genomic structures, viral and subviral agents have been (...) suggested because they may be evolutionarily older than cellular life. This hypothesis that viruses and viral-like agents edit genetic code is developed according to three well investigated examples that represent key evolutionary inventions in which non-lytic viral swarms act symbiotically in a persistent lifestyle within cellular host genomes: origin of eukaryotic nucleus, adaptive immunity, placental mammals. Additionally an abundance of various RNA elements cooperate in a variety of steps and substeps as regulatory and catalytic units with multiple competencies to act on the genetic code. Most of these RNA agents such as transposons, retroposons and small non-coding RNAs act consortially and are remnants of persistent viral infections that now act as co-opted adaptations in cellular key processes. (shrink)

What is reality? How do we know? Answers to these fundamental questions of ontology and epistemology, based on Mahatma Gandhi's "experiments with truth", are: reality is nonviolent (in the sense of not-inconsistent), and nonviolence (in the sense of respecting-meaning) is the only means of knowing (Gandhi, 1940). Be that as it may, science is what we think of when we think of reality and knowing. How does Gandhi's nonviolence, discovered in his spiritual quest for Truth, relate to the scientific pursuit (...) of truth? Here we show that Gandhian nonviolent knowing of nonviolent reality is an abstraction of both individual knowing (looking, reasoning) and collective scientific knowing (measurements, calculations). Specifically, Gandhi's truth-through-nonviolence is a law-like summation of the methods of physics ("do not disturb" of measurements) and of mathematics ("do not tear" of calculations) that are used to know. Moreover, physics (with its lawful behaviour of bodies) and biology (in preserving the meaning of genetic code) do affirm that the defining attribute of reality is nonviolence. In light of these correspondences, the Mahatma's derivation of a universal method of knowing (nonviolence of preserving-structure) from a universal truth (nonviolence of consistent-becoming) constitutes a science-supported general theory of reality and knowing. (shrink)

Despite the Nazi horrors, in 1953 the new eugenics was founded, when Watson and Crick postulated the double helix of DNA as the basis of chemical heredity. In 1961, scientists have deciphered the genetic code of DNA, laying the groundwork for code manipulation and the potential building of new life forms. After thirty years from the discovery of the DNA structure, the experimenters began to carry out the first clinical studies of human somatic cell therapy. The practice (...) of prenatal genetic tests identifies genes or unwanted genetic markers. Parents can choose to continue pregnancy or give up the fetus. Once the preimplantation genetic diagnosis occurs, potential parents can choose to use in vitro fertilization and then test early embryonic cells to identify embryos with genes they prefer or avoid. Because of concerns about eugenics, genetic counseling is based on a "non-directive" policy to ensure respect for reproductive autonomy. The argument for this counseling service is that we should balance parental autonomy with child's autonomy in the future. Specialists have not yet given a clear answer to the question of whether these practices should be considered eugenic practices, or if they are moral practices. DOI: 10.13140/RG.2.2.28777.95849. (shrink)

When this article was first planned, writing was going to be exclusively about two things - the origin of life and human evolution. But it turned out to be out of the question for the author to restrict himself to these biological and anthropological topics. A proper understanding of them required answering questions like “What is the nature of the universe – the home of life – and how did it originate?”, “How can time travel be removed from fantasy and (...) science fiction, to be made scientific and practical?”, and “How can the proposed young age of genus Homo be made to actually be reasonable – when simply stating it would be solid ground for instant rejection and dismissal?” The result is that the article also talks about subjects like Artificial Intelligence, General Relativity, and cosmology. -/- From where did life originate? God? Evolution? Panspermia? If the tendency of humans and scientists to regard undiscovered science as pseudoscience can be overcome, Einstein gave another alternative to consider when he introduced General Relativity. Time isn’t linear – progressing in a straight line from past to present to future. That assumption ignores Relativity which states that space AND TIME are curved. Where did life and the genetic code come from? Can the answer build AI? -/- The first question can be answered by the section of this article titled SETI, Evolution, and Time which says life (possibly multicellular and intelligent) and the genetic code came from humans acquiring knowledge of these things over the centuries, then applying that knowledge – via terraforming, accumulation of raw materials like amino acids and nucleic acids, genetic engineering - to a time in the past when life didn’t exist. From that origin, life evolved through innumerable mutations and adaptations, with humans once again acquiring knowledge of it in cyclic (nonlinear) time. -/- The second question is answered by saying artificial intelligence (AI) as the product of life is only half of the equation. The other half refers to Relativity’s curved space-time and violation of the notion that time always travels from past to future. We have always lived in an artificially intelligent, non-probabilistic universe where everything in time and space is connected into one thing by quantum entanglement – making the brain and genes products of binary-digit activity or artificial intelligence (life is not merely dependent on biology’s “lock and key” mechanisms but also possesses AI). -/- The earliest documented representative of the genus Homo is Homo habilis, which evolved around 2.8 million years ago. Scientists used to believe there was a straight line from H. habilis to us, Homo sapiens. This article will use the “advanced” waves loved by Physics Nobel laureate Richard Feynman, view the history of science through the lens of Conic Sections applied to Relativity’s curved space-time, and incorporate the necessity of so-called imaginary time * – popularized by Prof. Stephen Hawking. While the evolutionary proposals are more in agreement with this early straight line than with modern theories, Albert Einstein’s General Relativity is used to transform the straight line into a curved line, ultimately concluding that Homo habilis (H. habilis) originated only (and unbelievably, as far as today’s science and technology is concerned) ~250,000 years ago. Other branches and dead ends of Homo – e.g. Neanderthals – are the result of mutations and adaptations, with the resultant modifications to anatomy and physiology. The surprisingly young age of H. habilis allows nearly 200,000 years for habilis, or one of its descendants, to reach Australia … if this country’s indigenous Aboriginal population did, as claimed, reach this “island continent” 60,000 years ago. -/- * The ultraviolet catastrophe, also called the Rayleigh–Jeans catastrophe, is a failure of classical physics to predict observed phenomena: it can be shown that a blackbody - a hypothetical perfect absorber and radiator of energy - would release an infinite amount of energy, contradicting the principles of conservation of energy and indicating that a new model for the behaviour of blackbodies was needed. At the start of the 20th century, physicist Max Planck derived the correct solution by making some strange (for the time) assumptions. In particular, Planck assumed that electromagnetic radiation can only be emitted or absorbed in discrete packets, called quanta. Albert Einstein postulated that Planck's quanta were real physical particles (what we now call photons), not just a mathematical fiction. From there, Einstein developed his explanation of the photoelectric effect (when quanta or photons of light shine on certain metals, electrons are released and can form an electric current). So it appears entirely possible that another supposed mathematical trickery (imaginary time and the y-axis of Wick rotation) will find practical application in the future. -/- The article includes mathematical references to cosmology (spoiler alert – you’ll read about things like Vector-Tensor-Scalar Geometry, topology, the “eternal present”, Einstein’s Unified Field, the inverse-square law, and there being no Big Bang and no multiverse - but there will also be no equations). -/- The other subheadings in this essay are – -/- NONLINEAR TIME AND ELECTRICAL ENGINEERING (about a 2009 electrical engineering experiment at America’s Yale University, and cosmic wormholes) -/- BITS AND TOPOLOGY (base-2 maths aka Binary digiTS, Mobius strips, and figure-8 Klein bottles) -/- WICK ROTATION, CAUSALITY, AND UNITING TIME (do past, present and future co-exist in an “eternal present”?) -/- DIGITAL BRAIN, DIGITAL UNIVERSE (if the brain and the universe are ultimately composed of binary digits, we'll someday be able to do the same things with the brain and universe that we now do with computers) -/- PROPOSAL: HUMAN AND ANIMAL INSTINCTS ARE THE RESULT OF THE UNIVERSE BEING UNIFIED BY BINARY DIGITS (AND TOPOLOGY) (If everything in the universe is ultimately composed of electronic BITS, then the universe must possess Artificial Intelligence - some prefer the term Cosmic Consciousness) -/- INFORMATION THEORY CONQUERS A RED GIANT (preserving Earth by keeping the Sun near today’s level of activity forever). 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Total ontological unification of matter at all levels of reality as a whole, its “grasp” of its dialectical structure, space dimensionality and structure of the language of nature – “house of Being” [1], gives the opportunity to see the “place” and to understand the nature of information as a phenomenon of Ontological (structural) Memory (OntoMemory), the measure of being of the whole, “the soul of matter”, qualitative quantity of the absolute forms of existence of matter (absolute states). “Information” and “time” (...) are multivalent phenomena of Ontological Memory substantiating the essential unity of the world on the “horizontal” and “vertical”. Ontological constructing of dialectics of Logos self-motion, total unification of matter, “grasp” of the nature of information leads to the necessity of introducing a new unit of information showing the ideas of dialectical formation and generation of new structures and meanings, namely Delta-Logit (Δ-Logit), qualitative quantum-prototecton, fundamental organizing, absolute existential-extreme. The simplest mathematical symbol represents the dialectical microprocessor of the Nature. Ontological formula of John A. Wheeler «It from Bit» [2] is “grasped” as the first dialectic link in the chain of ontological formulas → “It from Δ-Logit” → “It from OntoMemory” → “It from Logos, Logos into It”. Ontological Memory - core, semantic attractor of the new conceptual structure of the world of the Information Age, which is based on Absolute generating structure («general framework structure»), the representant of onto-genetic code and algorithm of the Universe. (shrink)

Total ontological unification of matter at all levels of reality as a whole, its “grasp” of its dialectical structure, space dimensionality and structure of the language of nature – “house of Being” [1], gives the opportunity to see the “place” and to understand the nature of information as a phenomenon of Ontological Memory, the measure of being of the whole, “the soul of matter”, qualitative quality of the absolute forms of existence of matter (absolute states). “Information” and “time” are multivalent (...) phenomena of Ontological Memory (OntoMemory) substantiating the essential unity of the world on the “horizontal” and “vertical”. Ontological constructing of dialectics of Logos self-motion, total unification of matter, “grasp” of the nature of information leads to the necessity of introducing a new unit of information showing the ideas of dialectical formation and generation of new structures and meanings, namely Delta-Logit (Δ-Logit), qualitative quantum-prototecton, fundamental organizing, absolute existential-extreme. The simplest mathematical symbol represents the dialectical microprocessor of the Nature. Ontological formula of John A. Wheeler «It from Bit» [2] is “grasped” as the first dialectic link in the chain of ontological formulas → “It from Δ-Logit” → “It from OntoMemory” → “It from Logos, Logos into It”. Ontological Memory - core, the attractor of the new conceptual structure of the world of the information age, which is based on Absolute generating structure, the representant of onto-genetic code of the Universe. (shrink)

Many philosophers are skeptical about the scientific value of the concept of biological information. However, several have recently proposed a more positive view of ascribing information as an exercise in scientific modeling. I argue for an alternative role: guiding empirical data collection for the sake of theorizing about the evolution of semantics. I clarify and expand on Bergstrom and Rosvall’s suggestion of taking a “diagnostic” approach that defines biological information operationally as a procedure for collecting empirical cases. The more recent (...) modeling-based accounts still perpetuate a theory-centric view of scientific concepts, which motivated philosophers’ misplaced skepticism in the first place. (shrink)

Information Theory, Evolution and The Origin ofLife: The Origin and Evolution of Life as a Digital Message: How Life Resembles a Computer, Second Edition. Hu- bert P. Yockey, 2005, Cambridge University Press, Cambridge: 400 pages, index; hardcover, US $60.00; ISBN: 0-521-80293-8. The reason that there are principles of biology that cannot be derived from the laws of physics and chemistry lies simply in the fact that the genetic information content of the genome for constructing even the simplest organisms is (...) much larger than the information content of these laws. Yockey in his previous book (1992, 335) In this new book, Information Theory, Evolution and The Origin ofLife, Hubert Yockey points out that the digital, segregated, and linear character of the genetic information system has a fundamental significance. If inheritance would blend and not segregate, Darwinian evolution would not occur. If inheritance would be analog, instead of digital, evolution would be also impossible, because it would be impossible to remove the effect of noise. In this way, life is guided by information, and so information is a central concept in molecular biology. The author presents a picture of how the main concepts of the genetic code were developed. He was able to show that despite Francis Crick's belief that the Central Dogma is only a hypothesis, the Central Dogma of Francis Crick is a mathematical consequence of the redundant nature of the genetic code. The redundancy arises from the fact that the DNA and mRNA alphabet is formed by triplets of 4 nucleotides, and so the number of letters (triplets) is 64, whereas the proteome alphabet has only 20 letters (20 amino acids), and so the translation from the larger alphabet to the smaller one is necessarily redundant. Except for Tryptohan and Methionine, all amino acids are coded by more than one triplet, therefore, it is undecidable which source code letter was actually sent from mRNA. This proof has a corollary telling that there are no such mathematical constraints for protein-protein communication. With this clarification, Yockey contributes to diminishing the widespread confusion related to such a central concept like the Central Dogma. Thus the Central Dogma prohibits the origin of life "proteins first." Proteins can not be generated by "self-organization." Understanding this property of the Central Dogma will have a serious impact on research on the origin of life. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (...) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...) the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

[ENGLISH] This article discusses the potential of synthetic biology to address fundamental questions in the philosophy of biology regarding the nature of life and biological functions. Synthetic biology aims to reduce living organisms to their simplest forms by identifying the minimal components of a cell and also to create novel life forms through genetic reprogramming, biobrick assembly, or novel proteins. However, the technical success of these endeavors does not guarantee their conceptual success in defining life. There is a lack (...) of consensus among researchers on how to define and classify the entities produced in the lab, whether they should be considered living or categorized differently. The criteria for minimal cells and minimal life are subject to arbitrary choices and varying interpretations. The concept of function, crucial to synthetic biology, is also difficult to define. The article highlights the need to consider the minimal set of functions that characterize life before determining the smallest genomes that code for those functions. The arbitrary nature of defining both life and function complicates the understanding and classification of these entities. The article suggests that the traditional dichotomy between the living and the non-living may no longer be valid and that the concept of life itself may not require precise scientific definition. As synthetic biology advances, the article emphasizes the importance of redefining or constructing new categories to encompass the expanding possibilities and creations in the field. The ability to create new life forms raises questions about recognition, identification, and ethical implications, requiring a conceptual and philosophical engagement beyond the technical achievements of synthetic biology. -/- [FRENCH] L'article aborde le potentiel de la biologie synthétique pour répondre à des questions fondamentales de la philosophie de la biologie concernant la nature de la vie et des fonctions biologiques. La biologie synthétique vise à réduire les organismes vivants à leurs formes les plus simples en identifiant les composants minimaux d'une cellule et à créer de nouvelles formes de vie grâce à la reprogrammation génétique, à l'assemblage de biobriques ou à des protéines nouvelles. Cependant, le succès technique de ces approches ne garantit pas leur réussite conceptuelle dans la définition de la vie. Il n'y a pas de consensus parmi les chercheurs sur la façon de définir et de classer les entités produites en laboratoire, qu'elles doivent être considérées comme vivantes ou catégorisées différemment. Les critères des cellules minimales et de la vie minimale sont soumis à des choix arbitraires et à des interprétations variables. La notion de fonction, essentielle en biologie synthétique, est également difficile à définir. L'article met en évidence la nécessité de prendre en compte l'ensemble minimal de fonctions qui caractérisent la vie avant de déterminer les plus petits génomes qui codent ces fonctions. La nature arbitraire de la définition de la vie et de la fonction complique la compréhension et la classification de ces entités. L'article suggère que la dichotomie traditionnelle entre le vivant et le non-vivant pourrait ne plus être valable et que le concept même de vie ne nécessite pas une définition scientifique précise. À mesure que la biologie synthétique progresse, l'article souligne l'importance de redéfinir ou de construire de nouvelles catégories pour englober les possibilités et créations croissantes dans le domaine. La capacité à créer de nouvelles formes de vie soulève des questions de reconnaissance, d'identification et d'implications éthiques, nécessitant une réflexion conceptuelle et philosophique au-delà des avancées techniques de la biologie synthétique. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...) the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism. Graphical Abstract. (shrink)

The co-evolutionary concept of three-modal stable evolutionary strategy of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path of human evolution are defined by descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctness) parameters simultaneously, that cannot be instrumental reduced to other ones. Resulting volume of both parameters define the vectors of biological, social, cultural and techno-rationalistic human evolution by two gear mechanism — genetic and cultural co-evolution and (...) techno-humanitarian balance. Explanatory model and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. Integral part of the model is evolutionary semantics (time-varying semantic code, the compliance of the biological, socio-cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). (shrink)

The precautionary principle in public decision making concerns situations where following an assessment of the available scientific information, there are reasonable grounds for concern for the possibility of adverse effects on the environment or human health, but scientific uncertainty persists. In such cases provisional risk management measures may be adopted, without having to wait until the reality and seriousness of those adverse effects become fully apparent. This is the definition of the precautionary principle as operationalized under EU law. The precautionary (...) principle is a deliberative principle. Its application involves deliberation on a range of normative dimensions which need to be taken into account while making the principle operational in the public policy context. Under EU law, any risk management measures to be adopted while implementing the precautionary principle, have to be proportionate to ensure the chosen high level of protection in the European Community. This articlewill illustrate the established practice concerning the release of genetically modified organisms into the environment and how the principle is implemented under hard law. The article also provides an outlook on what this may imply for the relative new case of nanotechnology and the use of precautionary principle within the context of soft law (use of codes of conduct). (shrink)

The co-evolutionary concept of tri-modal stable evolutionary strategy (SESH) of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path of human evolution are defined by descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctness) parameters simultaneously, that cannot be instrumental reduced to others ones. Resulting volume of both parameters define the vectors of human evolution by two gear mechanism ˗ genetic and cultural co-evolution and techno-humanitarian balance. Explanatory model (...) and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. The mechanism of influence of each module on the evolution of the two remaining modules of SESH a priori can be twofold: (1) informational co-evolution (direct selective pressure); (2) semantic co-evolution (time-varying semantic code, the compliance of the biological, socio- cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). More rapidly evolving autonomous element of the co-evolutionary pair becomes making sense factor for the partner. Semantic co-evolution is the discrete acquisition of adaptive significance of individual alleles by changing socio-cultural types, manifested as an increase in the genetic variability of populations of Homo sapiens, and domesticated species parallel to socio-culturogenesis. The socio- cultural landscape leads to drastically difference of direction in biological evolution of Atlantic and East-Slavic ethnicities/civilizations. (shrink)

As a sort of intellectual provocation and as a lateral thinking strategy for creativity, this chapter seeks to determine what the study of the dynamics of biodiversity can offer linguists. In recent years, the analogical equation "language = biological species" has become more widespread as a metaphorical source for conceptual renovation, and, at the same time, as a justification for the defense of language diversity. Language diversity would be protected in a way similar to the mobilization that has taken place (...) to protect endangered species. Nevertheless, one must be careful when uncritically transferring conceptualizations and theoretical frameworks from one field to another, since obviously, these two phenomena are quite different in the real world. The dialogue with bioecologists starts by asking about the formation of diversity, i.e., about specialization. Here, one can observe the similarity between the processes of linguistic and genetic fragmentation, in the sense that both phenomena have a (socio)geographical basis for dispersion and consequently, for the loss of their original compact nature and their intercommunication. The self-organizing and creative properties of human beings favor the development of specific varieties for each subset, varieties that continue to evolve constantly, through the unceasing "languaging" of humanity. Regarding the continuity of species or languages, one can also observe the decisive role of intragroup relations. The staying power of linguistic varieties will increase in direct proportion to the intensity of the relationship among the components of the subset. On the other hand, if exotic elements are introduced, especially if these elements are aggressive in nature, the alteration of the ecological niche may turn out to be fatal for the continuity of the previously existing forms. This suggests to us the need to make an in-depth study of what the minimal contextual conditions would be so that a set linguistic group could be assured a sustainable continuity within a framework of linguistic contact. What type of minimum (socio-)ecological niche would a language have to have if we wished to ensure its habitual reproduction? A proposal is made here to explore the ideas of "exclusive functions" and "non-hierarchical functional distribution" for codes in situations where there is high contact and a danger of disuse. As regards change, this phenomenon is seen as an inherent element in the tendency of life to create new developments, which may or not be accompanied by an adaptation to changing environmental conditions. It is pointed out that, similar to what happens in biology, much of linguistic innovation stems from a systemically reorganized mixture of solutions from different codes. An important research question would be, however, to determine why some of these innovations disappear and others survive and extend throughout the community. The big question mark, as Mufwene points out, is, then how to manage to understand how "the evolution of language proceeds by naturally selecting from among the competing alternatives available through the idiolects of individual speakers". Extinction, whether it be of languages or of species, is caused in most cases "by a combination of demographic processes and environmental changes", as Brown points out. Thus, the environment plays a fundamental role in the direction of evolution, since the "the survival of the fittest is, in actuality, the survival of those who fit into the context (Allen and Hoekstra)". This allows us to see the great degree of importance of political-economic contexts in the case of languages. In the same way, migratory movements are also one of the major variables determining the extinction of biodiversity and language diversity. Species and habitat form the basic unit of existence, and this is the major point of departure for understanding the problem of the preservation and recovery of species or languages. Given the increase in the degree of linguistic contact, the continuity of language diversity depends on determining, as exactly as possible, as Prigogine, the physicist, would say, what precise conditions of imbalance may prove to be stable. The great challenge is not so much avoiding contact but managing it. And "restorative ecology" can also be of help to us here. Being able to reach sustainable solutions for language diversity implies a profound knowledge of the dynamics for determining the ways in which language is used in contact situations. The general conclusion is that linguistics is still terminologically and conceptually ill prepared to deal with the dynamic character of human languages. The world and our objects must be conceived of as elements in a state of flux, as changing systems in an unstable equilibrium. With respect to language policy, it would be necessary to make an effort to manage to establish some general principles regarding the linguistic organization of the human species that would make it possible for local linguistic diversity and communication on a planetary scale, which must necessarily take place, to be compatible with each other. To succeed, it will be necessary to continue promoting an autonomous socio-ecological perspective devoted to the comprehension of language phenomena. Such a perspective would be based on a paradigm of complexity, and would, at the same time, place human beings at the center of its theoretical underpinnings. (shrink)

The monograph is an English, expanded and revised version of the book Cheshko, V. T., Ivanitskaya, L.V., & Glazko, V.I. (2018). Anthropocene. Philosophy of Biotechnology. Moscow, Course. The manuscript was completed by me on November 15, 2019. It is a study devoted to the development of the concept of a stable evolutionary human strategy as a unique phenomenon of global evolution. The name “An Evolutionary Metaphysics (Cheshko, 2012; Glazko et al., 2016). With equal rights, this study could be entitled “Biotechnology (...) as a result and factor of the evolutionary processˮ. The choice in favor of used “The Evolutionary Metaphysics of Human Enhancement Technologiesˮ was made in accordance with the basic principle of modern post-academician and human-sized science, a classic example of which is biotechnology. The “Metaphysics of Evolution” and “Evolutionary Metaphysics” concepts are used in several ways in modern philosophical discourse. In any case, the values contain a logical or associative reference to the teleological nature of the evolutionary process (Hull, 1967, 1989; Apel, 1995; Faye, 2016; Dupre, 2017; Rose, 2018, etc). In our study, the “evolutionary metaphysics” serves to denote the thesis of the rationalization and technologization of global evolution and anthropogenesis, in particular. At the same time, the postulate of an open future remains relevant in relation to the results of the evolutionary process. The theory of evolution of complex, including the humans system and algorithm for its constructing are а synthesis of evolutionary epistemology, philosophical anthropology and concrete scientific empirical basis in modern science. ln other words, natural philosophy is regaining the status bar element theoretical science in the era of technology-driven evolution. The co-evolutionary concept of 3-modal stable evolutionary strategy of Homo sapiens is developed. The concept based оn the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path of human evolution are defined bу descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctness) parameters simultaneously, that cannot bе instrumental reduced to others ones. Resulting volume of both parameters define the vectors of blological, social, cultural and techno-rationalistic human evolution Ьу two gear mechanism genetic and cultural co-evolution and techno-humanitarian balance. The resultant each of them сап estimated Ьу the ratio of socio-psychological predispositions of humanization / dehumanization in mentality. Explanatory model and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. Integral part of the model is evolutionary semantics (time-varying semantic code, the compliance of the blological, socio-cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). It is seem necessary to make three clarifications. First, logical construct, “evolutionary metaphysics” contains an internal contradiction, because it unites two alternative explanatory models. “Metaphysics”, as a subject, implies deducibility of the process from the initial general abstract principle, and, consequently, the outcome of the development of the object is uniquely determined by the initial conditions. Predicate, “evolutionary”, means stochastic mechanism of realizing the same principle by memorizing and replicating random choices in all variants of the post-Darwin paradigm. In philosophy, random choice corresponds to the category of “free will” of a reasonable agent. In evolutionary theory, the same phenomenon is reflected in the concept of “covariant replication”. Authors will attempt to synthesize both of these models in a single transdisciplinary theoretical framework. Secondly, the interpretation of the term “evolutionary (adaptive) strategyˮ is different from the classical definition. The difference is that the adaptive strategy in this context is equivalent to the survival, i.e. it includes the adaptation to the environment and the transformation (construction) of the medium in accordance with the objectives of survival. To emphasize this difference authors used verbal construction “adaptiveˮ (rather than “evolutionaryˮ) strategy as more adequate. In all other cases, the two terms may be regarded as synonymous. Thirdly, the initial two essays of this series were published in one book in 2012. Their main goal was the development of the logically consistent methodological concept of stable adaptive (evolutionary) strategy of hominines and the argumentation of its heuristic possibilities as a transdisciplinary scientific paradigm of modern anthropology. The task was to demonstrate the possibilities of the SESH concept in describing and explaining the evolutionary prospects for the interaction of social organization and technology (techno-humanitarian balance) and the associated biological and cultural mechanisms of the genesis of religion (gene-cultural co-evolution). In other words, it was related to the sphere of cultural and philosophical anthropology, i.e. to the axiological component of any theoretical constructions describing the behavior of self-organizing systems with human participation. In contrast, the present work is an attempt to introduce this concept into the sphere of biological anthropology and, consequently, its main goal is to demonstrate the possibility of verification of its main provisions by means of procedures developed by natural science, i.e. refers to the descriptive component of the same theoretical constructions. The result of this in the future should be methods for assessing, calculating and predicting the risk of loss of biological and cultural identity of a person, associated with a permanent and continuously deepening process of development of science and technology. (shrink)

The theory of evolution of complex, including the humans system and algorithm for its constructing are a synthesis of evolutionary epistemology, philosophical anthropology and concrete scientific empirical basis in modern science,. In other words, natural philosophy is regaining the status bar element theoretical science in the era of technology-driven evolution. The co-evolutionary concept of 3-modal stable evolutionary strategy of Homo sapiens is developed. The concept based on the principle of evolutionary complementarity of anthropogenesis: value of evolutionary risk and evolutionary path (...) of human evolution are defined by descriptive (evolutionary efficiency) and creative-teleological (evolutionary correctly) parameters simultaneously, that cannot be instrumental reduced to others ones. Resulting volume of both parameters define the vectors of biological, social, cultural and techno-rationalistic human evolution by two gear mechanism ˗ genetic and cultural co-evolution and techno-humanitarian balance. The resultant each of them can estimated by the ratio of socio-psychological predispositions of humanization/dehumanization in mentality. Explanatory model and methodology of evaluation of creatively teleological evolutionary risk component of NBIC technological complex is proposed. Integral part of the model is evolutionary semantics (time-varying semantic code, the compliance of the biological, socio-cultural and techno-rationalist adaptive modules of human stable evolutionary strategy). (shrink)

We often hear how scientists have discovered that a certain human trait – or a trait of another type of organism – is innate, genetic, heritable, inherited, naturally selected etc. All these claims have something in common: they all declare a trait to have significant organism internal (for instance genetic) causes that are present in the organism at its birth. I call claims like these “nativist claims”. Nativist claims are important. They shape our overall understanding of what we (...) are, what we can do and what is good for us. They also impact our practical decision making. For instance, we know that certain types of genes increase the risk of certain diseases, and increasingly this has an effect on healthcare practices. Many people believe that in the matter of children’s education we should consider the fact that many cognitive abilities are highly heritable. Associations between genetics and aggressive behavior have been taken to be alleviating circumstances in criminal sentencing. It is therefore important to correctly understand the content and implications of nativist claims. In this doctoral thesis I analyze, by philosophical means, the content of different kinds of nativist claim. What does it mean that some psychological tendency is innate? What does it mean that intelligence is 50% heritable? How (if at all) do genes come to carry information about the traits of an organism – they are nothing like the information carriers familiar to us, such as newspapers, e-mails, secret codes, and audio files. This thesis emphasizes two things. Firstly, I demonstrate, that in different scientific contexts these words ('innate', 'genetically caused' etc.) can mean very different things. Therefore, the implications of a given nativist claim in one scientific context can be remarkably different from another nativist claim’s implications in some other scientific context. Secondly, I explain how the development of innate, heritable and genetically caused traits can be determined in different and often unexpected ways by our environment and experiences. I demonstrate that the content of a concept that is considered innate by cognitive scientists can be determined by what the organism that possesses the concept has experienced. I also show that even a trait which is 100% heritable can at the same time be a socially constructed trait. (shrink)

Applying mild methods of preparation, part of the ribosomes of rabbit reticulocytes are found in aggregates (later called polyribosomes) of up to six ribosomal units. Upon treatment with RNA-ase, they desintegrate into single ribosomes. The fast-sedimenting aggregates are found to be more active in protein synthesis in terms of incorporation of radioactive amino acids, whereas the single ribosomes are more receptive to stimulation by the artificial messenger RNA poly-U. The findings indicate that the linkage of ribosomes into aggregates is due (...) to the messenger RNA. They support a tape-reading mechanism of protein synthesis whereby growth of the peptide chain is accompanied by shifting the active site of the ribosome from one coding group of nucleotides of the messenger RNA to the next. (shrink)

According to the predictive coding theory of cognition , brains are predictive machines that use perception and action to minimize prediction error, i.e. the discrepancy between bottom–up, externally-generated sensory signals and top–down, internally-generated sensory predictions. Many consider PCT to have an explanatory scope that is unparalleled in contemporary cognitive science and see in it a framework that could potentially provide us with a unified account of cognition. It is also commonly assumed that PCT is a representational theory of sorts, in (...) the sense that it postulates that our cognitive contact with the world is mediated by internal representations. However, the exact sense in which PCT is representational remains unclear; neither is it clear that it deserves such status—that is, whether it really invokes structures that are truly and nontrivially representational in nature. In the present article, I argue that the representational pretensions of PCT are completely justified. This is because the theory postulates cognitive structures—namely action-guiding, detachable, structural models that afford representational error detection—that play genuinely representational functions within the cognitive system. (shrink)

Genetically engineered (GE) insects, such as the GE OX513A Aedes aegypti mosquitoes, have been designed to suppress their wild-type populations so as to reduce the transmission of vector-borne diseases in humans. Apart from the ecological and epidemiological uncertainties associated with this approach, such biotechnological approaches may be used by individual governments or the global community of nations to avoid addressing the underlying structural, systemic causes of those infections... We discuss here key ethical questions raised by the use of GE mosquitoes, (...) with the aim of fostering discussion between the public, researchers, policy makers, healthcare organizations, and regulatory agencies at the local, national, and international levels. We affect that goal by outlining a procedural approach to decision-making about the use of the “biotechnology” that goes beyond “community engagement.” The protocol we advocate for entails informed deliberations and decision-making at the community level. It is designed to ensure that the voices of the marginalized and vulnerable groups that would be disproportionately affected by the decision are heard during the community-wide discussions. Moreover, we make the case that the values embedded in the risk assessment should be identified so that the community can make an informed decision about the use of GE insects. In addition, we advocate for the involvement of a variety of actors whose responsibility would be to ensure that the community has the opportunity to make an informed decision based on deliberations about the use of the “biotechnology.”. (shrink)

In this paper I present an argument in favour of a parental duty to use preimplantation genetic diagnosis (PGD). I argue that if embryos created in vitro were able to decide for themselves in a rational manner, they would sometimes choose PGD as a method of selection. Couples, therefore, should respect their hypothetical choices on a principle similar to that of patient autonomy. My thesis shows that no matter which moral doctrine couples subscribe to, they ought to conduct the (...) PGD procedure in the situations when it is impossible to implant all of the created embryos and if there is a significant risk for giving birth to a child with a serious condition. (shrink)

In this paper I argue that the extent to which a human trait is genetically caused can causally depend upon whether the trait is categorized within human genetics as genetically caused. This makes the kind genetically caused trait an interactive kind. I demonstrate that this thesis is both conceptually coherent and empirically plausible. I outline the core rationale of this thesis and demonstrate its conceptual coherence by drawing upon Waters’ (2007) analysis of genetic causation. I add empirical plausibility to (...) the thesis by describing a hypothetical but empirically plausible mechanism by which the fact that obesity is categorized as genetically caused within human genetics increases the extent to which obesity is in fact genetically caused. (shrink)

How we ought to diagnose, categorise and respond to spectrum disabilities such as autism and Attention Deficit/Hyperactivity Disorder (ADHD) is a topic of lively debate. The heterogeneity associated with ADHD and autism is described as falling on various continua of behavioural, neural, and genetic difference. These continua are varyingly described either as extending into the general population, or as being continua within a given disorder demarcation. Moreover, the interrelationships of these continua are likewise often vague and subject to diverse (...) interpretations. -/- In this paper, I explore geneticists' and self-advocates’ perspectives concerning autism and ADHD as continua. These diagnoses are overwhelmingly analysed as falling on a continuum or continua of underlying traits, which supports the notion of “the neurodiversity spectrum”, i.e., a broader swath of human neural and behavioural diversity on which some concentrations of different functioning are diagnosed. I offer a taxonomy of conceptions of the genetic, phenotypic, and endophenotypic dimensionality within and beyond these diagnostic categories, and suggest that the spectrum of neurodiversity is characteristically endophenotypic. (shrink)

The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less on community system traits (synergetic/organizational traits) that characterize transgenerational biological, ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of interacting populations, and for which the (...) individual members can belong to the same or to different species. Examples of communities include biofilms, ant colonies, symbiotic associations resulting in holobiont formation, and human societies. The proposed model of evolution at the level of communities revises classic theorizing on the major transitions in evolution by analyzing the interplay between community/social traits and individual traits, and how this brings forth ideas of top-down regulations of bottom-up evolutionary processes (collaboration of downward and upward causation). The work demonstrates that such interplay also includes reticulate interactions and reticulate causation. In this regard, we exemplify how community systems provide various non-genetic ‘scaffoldings’, ‘constraints’, and ‘affordances’ for individual and sociocultural evolutionary development. Such research complements prevailing models that focus on the vertical transmission of heritable information, from parent to offspring, with research that instead focusses on horizontal, oblique and even reverse information transmission, going from offspring to parent. We call this reversed information transfer the ‘offspring effect’ to contrast it from the ‘parental effect’. We argue that the proposed approach to inheritance is effective for modelling cumulative and distributed developmental process and for explaining the biological origins and evolution of language. (shrink)

Genetic engineering technologies are a subclass of the biotechnology family, and are concerned with the use of laboratory-based technologies to intervene with a given organism at the genetic level, i.e., the level of its DNA. This class of technologies could feasibly be used to treat diseases and disabilities, create disease-resistant crops, or even be used to enhance humans to make them more resistant to certain environmental conditions. However, both therapeutic and enhancement applications of genetic engineering raise serious (...) ethical concerns. This paper examines various objections to genetic engineering (as applied to humans) which have been raised in the literature, and presents a new way to frame these issues, and to look for solutions. Specifically, this paper frames genetic engineering technologies within the ‘design turn in applied ethics’ lens and thus situates these technologies as covarying with societal forces. The value sensitive design (VSD) approach to technology design is then appropriated as the conceptual framework in which genetic engineering technologies can be considered so that they can be designed for important human values. By doing so, this paper brings further nuance to the scholarship on genetic engineering technologies by discussing the sociotechnicity of genetic engineering systems rather than framing them as value-neutral tools that either support or constrain values based on how they are used. (shrink)

The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect (...) sense of genetic programs, if only we abandon the preconception that all computers have a von Neumann architecture. Instead, genetic programs instantiate the computational architecture of Post–Newell Production Systems. That is, genetic programs are unordered sets of conditional instructions, instructions that fire independently when their conditions are matched. For illustration I present a paradigm Production System that regulates the functioning of the well-known lac operon of E. coli. On close reflection it turns out that not only genes, but also proteins encode instructions. I propose, therefore, to rename genetic programs to biomolecular programs. Biomolecular and/or genetic programs, and the cellular computers than run them, are to be understood not as von Neumann computers, but as Post–Newell production systems. (shrink)

This paper outlines a critique of the use of the genetic variance–covariance matrix (G), one of the central concepts in the modern study of natural selection and evolution. Specifically, I argue that for both conceptual and empirical reasons, studies of G cannot be used to elucidate so-called constraints on natural selection, nor can they be employed to detect or to measure past selection in natural populations – contrary to what assumed by most practicing biologists. I suggest that the search (...) for a general solution to the difficult problem of identifying causal structures given observed correlation’s has led evolutionary quantitative geneticists to substitute statistical modeling for the more difficult, but much more valuable, job of teasing apart the many possible causes underlying the action of natural selection. Hence, the entire evolutionary quantitative genetics research program may be in need of a fundamental reconsideration of its goals and how they correspond to the array of mathematical and experimental techniques normally employed by its practitioners. (shrink)

In recent years, humans’ ability to selectively modify genes has increased dramatically as a result of the development of new, more efficient, and easier genetic modification technology. In this paper, we argue in favor of using this technology to improve the welfare of agricultural animals. We first argue that using animals genetically modified for improved welfare is preferable to the current status quo. Nevertheless, the strongest argument against pursuing gene editing for welfare is that there are alternative approaches to (...) addressing some of the challenges of modern agriculture that may offer ethical advantages over genetic modification; namely, a dramatic shift towards plant-based diets or the development of in vitro meat. Nevertheless, we provide reasons for thinking that despite these possible comparative disadvantages there are important reasons for continuing the pursuit of welfare improvements via genetic modification. (shrink)

In the past few decades, peer review has come to dominate virtually all professionally respectable academic and scientific publications. However, despite its near-universal acceptance, no code of conduct has been developed to which peer reviewers and their editors are encouraged to adhere. This paper proposes such a code of conduct.