Abstract The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical (...) data than did the original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century. (shrink)

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and (...) genome innovations as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know (...) it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA-networks andRNA-communication can interconnect these levels.With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (shrink)

In searching for life in extraterrestrial space, it is essential to act based on an unequivocal definition of life. In the twentieth century, life was defined as cells that self-replicate, metabolize, and are open for mutations, without which genetic information would remain unchangeable, and evolution would be impossible. Current definitions of life derive from statistical mechanics, physics, and chemistry of the twentieth century in which life is considered to function machine like, ignoring a central role of communication. Recent (...) observations show that context-dependent meaningful communication and network formation (and control) are central to all life forms. Evolutionary relevant new nucleotide sequences now appear to have originated from social agents such as viruses, their parasitic relatives, and related RNA networks, not from errors. By applying the known features of natural languages and communication, a new twenty-first century definition of life can be reached in which communicative interactions are central to all processes of life. A new definition of life must integrate the current empirical knowledge about interactions between cells, viruses, and RNA networks to provide a better explanatory power than the twentieth century narrative. (shrink)

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)

Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally (...) forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses. (shrink)

Current research on the origin of DNA and RNA, viruses, and mobile genetic elements prompts a re-evaluation of the origin and nature of genetic material as the driving force behind evolutionary novelty. While scholars used to think that novel features resulted from random genetic mutations of an individual’s specific genome, today we recognize the important role that acquired viruses and mobile genetic elements have played in introducing evolutionary novelty within the genomes of species. Viral infections and (...) subviral RNAs can enter the host genome and persist as genetic regulatory networks. Persistent viral infections are also important to understand the split between great apes and humans. Nearly all mammals and nonhuman primates rely on olfaction, i.e., chemoreception as the basis of the sense of smell for social recognition, group membership, and the coordination of organized social life. Humans, however, evolved other means to establish social bonding, because several infection waves by endogenous retroviruses caused a loss of odor receptors in human ancestors. The human independence from olfaction for social recognition was in turn one driver of the rather abrupt human transition to dependence on visual information, gesture production, and facial recognition that are at the roots of language-based communication. (shrink)

Biological evolution and technological innovation, while differing in many respects, also share common features. In particular, implementation of a new technology in the market is analogous to the spreading of a new genetic trait in a population. Technological innovation may occur either through the accumulation of quantitative changes, as in the development of the ocean clipper, or it may be initiated by a new combination of features or subsystems, as in the case of steamships. Other examples (...) of the latter type are electric networks that combine the generation, distribution, and use of electricity, and containerized transportation that combines standardized containers, logistics, and ships. Biological evolution proceeds, phenotypically, in many small steps, but at the genetic level novel features may arise not only through the accumulation of many small, common mutational changes, but also when distinct, relatively rare genetic changes are followed by many further mutations. In particular, capabilities of biologically modern man may have been initiated, perhaps some 150 000 years ago, by one or few accidental but distinct combinations of modules and subroutines of gene regulation which are involved in the generation of the neural network in the cerebral cortex. It is even conceivable that it was one primary genetic event that initiated the evolution of biologically modern man, introducing some novel but subtle feature of connectivity into the cerebral cortex which allowed for meta-levels of abstraction and upgraded modes of information processing. This may have set the stage for the evolution of integrated but diverse higher capabilities such as structured language, symbolic thought, strategic thought, and cognition based empathy. (shrink)

The metamorphosis from larvae to adult butterflies has represented the “mystery” of life since the ancient Greeks. How could we explain the various steps of development from caterpillars to the most beautiful butterflies? A mystery preva lent in the twentieth century concerned the storage of the complete genetic informa tion of an organism in the DNA of its every cell. How and why do so many different cell types develop throughout the lives of organisms at the right time and (...) place? With the rise of epigenetics, the “fog” of mystery is starting to clear. We now know that the genetic storage medium in every living cell acquires an incredible plasticity through certain markings on the genetic text, linking the inheritable information with the contextuality of the real lifeworld of each organism. This means that the concrete living organism influences during development the various stages of gene expression, transcription, translation, immunity, and DNA repair actively and leads to various phenotypic outcomes without altering the DNA storage medium. More surprisingly, such variations of developmental phenotypes were found capable of successfully adapting to changing environmental circumstances. Better adapted organisms may lead to reprogramming in the epigenetic states which may reach an inheritable status for many generations or even become a fixed part of the genetic identity of the species. This is how evolution learns. (shrink)

Viruses and related infectious genetic parasites are the most abundant biological agents on this planet. They invade all cellular organisms, are key agents in the generation of adaptive and innate immune systems, and drive nearly all regulatory processes within living cells.

Abstract: Early detection of breast cancer plays a pivotal role in improving patient prognosis and reducing mortality rates. Recent technological advancements have significantly enhanced the accuracy and effectiveness of breast cancer screening methods. This paper explores the latest innovations in early detection, including the evolution of digital mammography, the impact of 3D mammography (tomosynthesis), and the use of advanced imaging techniques such as molecular imaging and MRI. Furthermore, the integration of artificial intelligence (AI) in diagnostic tools is (...) discussed, highlighting how machine learning algorithms are refining imaging analyses and reducing diagnostic errors. Advances in genetic screening, liquid biopsies, and biomarkers are also examined, showcasing their potential in identifying high-risk individuals and enabling personalized treatment plans. This paper provides insights into the future of breast cancer detection, outlining both the opportunities and challenges that lie ahead in adopting these innovative technologies to improve patient outcomes. (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)

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)

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)

Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies (...) to many other types of formal networks and weakens the emergentist claim attached to bio-molecular networks, and by extension to living systems. (shrink)

Universal Basic Income (UBI) has been proposed as a potential way in which welfare states could be made more responsive to the ever-shifting evolutionary challenges of institutional adaptation in a dynamic environment. It has been proposed as a tool of “real freedom” (Van Parijs) and as a tool of making the welfare state more efficient. (Friedman) From the point of view of complexity theory and evolutionary economics, I argue that only a welfare state model that is “polycentrically” (Polanyi, Hayek) organized (...) as an evolving network of distributed decision-making can respond to the challenges of complexity in an adaptively efficient manner. UBI has the theoretical possibility to facilitate flexible, bottom-up innovation, since a) it embodies the “rule of law” principles of generality, nondiscrimination, simplicity, and transparency, and b) it grants people widespread freedom to experiment, innovate, and deviate from established practices and norms; but whether it can be made to work as intended depends on a number of variables in its design. I situate my research in the contemporary UBI debate around automation and technological development, which I interpret creatively through the lens of contemporary evolutionary political economy. I advance a syncretic model of institutional design based upon the shared insights of the Santa Fe, Neo-Hayekian, and Neo-Schumpeterian schools of evolutionary economics that, following Adam Thierer and Michael Munger, I call the framework of Permissionless Innovation (PI). Under the PI framework, which is a development of the tradition of evolutionary liberalism (Hume, Smith, Mandeville, Mill, Hayek, Polanyi, Schumpeter, Hodgson), individuals are granted the default right to innovate without having to ask for permission, and the right to basic income, which they can use to support their right to innovate, mutate, and experiment. This framework is a liberal framework to the extent it relies on widespread human freedom as a means of fostering innovation and social learning. And it is an evolutionary framework to the extent that it seeks to facilitate evolutionary socioeconomic processes for the sake of social progress and welfare advancement. I proceed to show, through an analysis of how innovation operates in both the economy and the cultural domain, that UBI can be used as an important cornerstone of an evolutionary liberal model of “ecostructural” governance that treats the socioeconomic order as an ecological garden of spontaneous growths, adaptations, and innovations. I call this the Permissionless Innovation Universal Basic Income (PIUBI) framework. In it, the right to innovate, deviate, and mutate is upheld as the “gold standard” of institutional design whereby individuals are granted widespread freedoms combined with the provision of UBI and other innovation-fostering (carefully bound) services and regulations. In the coming decades, UBI may even enable poor people to take better advantage of Human Enhancement Technologies (HETs) and other experimental innovations. Such a framework is compatible with a fast pace of evolutionary development, but the regulatory model accompanying such a framework must be capable of responding to evolutionary lock-ins, maladaptive innovations, self-destructive behaviour on the part of UBI recipients, and the management of catastrophic and existential risks. In the end, I will have shown that the PIUBI framework can be justified as a plausible default institutional mechanism for responding to radical uncertainty, but it needs to be experimentally adapted to changing circumstances with the help of various situation-specific, polycentric, multi-level, approaches. (shrink)

Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead (...) of time the ”niches” which constitute the boundary conditions on selec- tion. More generally, by the mathematical unprestatability of the ”phase space”, no laws of mo- tion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound concep- tual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of symmetries as invariant preserving transformations will allow us to under- stand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of ”enablement”. Life lives in a web of enablement and radical emergence. This will restrict causal analyses to differential cases. Mutations or other causal differ- ences will allow us to stress that ”non conservation princi- ples” are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as sym- metries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to ”extended criticality” as a conceptual frame for a better understanding of the living state of matter. (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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The study of cultural evolution has taken on an increasingly interdisciplinary and diverse approach in explicating phenomena of cultural transmission and adoptions. Inspired by this computational movement, this study uses Bayesian networks analysis, combining both the frequentist and the Hamiltonian Markov chain Monte Carlo (MCMC) approach, to investigate the highly representative elements in the cultural evolution of a Vietnamese city’s architecture in the early 20th century. With a focus on the façade design of 68 old houses (...) in Hanoi’s Old Quarter (based on 78 data lines extracted from 248 photos), the study argues that it is plausible to look at the aesthetics, architecture, and designs of the house façade to find traces of cultural evolution in Vietnam, which went through more than six decades of French colonization and centuries of sociocultural influence from China. The in-depth technical analysis, though refuting the presumed model on the probabilistic dependency among the variables, yields several results, the most notable of which is the strong influence of Buddhism over the decorations of the house façade. Particularly, in the top 5 networks with the best Bayesian Information Criterion (BIC) scores and p<0.05, the variable for decorations (DC) always has a direct probabilistic dependency on the variable B for Buddhism. The paper then checks the robustness of these models using Hamiltonian MCMC method and find the posterior distributions of the models’ coefficients all satisfy the technical requirement. Finally, this study suggests integrating Bayesian statistics in the social sciences in general and for the study of cultural evolution and architectural transformation in particular. (shrink)

Heyes’ book is an essential addition to the literature on human uniqueness. Her main claim is that the key human cognitive capacities are products of cultural rather than genetic evolution. Among these distinctively human capacities are causal understanding, episodic memory, imitation, mindreading, and normative thinking. According to Heyes, they emerged not by genetic mutation but by innovations in cognitive development. She calls these mechanisms ‘cognitive gadgets.’ This is perhaps one of the best and most comprehensive views (...) of human cognitive evolution advanced in recent years. (shrink)

This article investigates the profound mysteries of consciousness and the afterlife, topics that have captivated humanity for centuries. Despite extensive scientific inquiry, the existence of an afterlife remains unverified, and the nature of consciousness poses significant challenges. This research presents innovative hypotheses through thought experiments grounded in empirical evidence and robust theoretical frameworks. It examines the complexities of consciousness, its intricate relationship with the brain, and advocates for interdisciplinary approaches that integrate physics, psychology, and philosophy. The study boldly posits the (...) likelihood of continuous consciousness post-death, arguing that existing evidence lends substantial support to this notion. Furthermore, it explores the practical implications of these insights, suggesting that understanding these phenomena could enhance human well-being and foster a more harmonious society. In essence, this article embarks on a quest to illuminate age-old questions surrounding consciousness and the afterlife. By employing novel methodologies, it seeks to offer fresh perspectives that may transform our understanding of existence and inspire positive advancements at both individual and societal levels. (shrink)

Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory could translate (...) empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology. (shrink)

Abstract: Early detection of breast cancer is vital for improving patient outcomes and reducing mortality rates. Technological advancements have significantly enhanced the accuracy and efficiency of screening methods. This paper explores recent innovations in early detection, focusing on the evolution of digital mammography, the benefits of 3D mammography (tomosynthesis), and the application of advanced imaging techniques such as molecular imaging and MRI. It also examines the role of artificial intelligence (AI) in diagnostic tools, showing how machine learning (...) algorithms are improving imaging analysis and reducing diagnostic errors. Furthermore, the paper discusses advancements in genetic screening, liquid biopsies, and biomarkers, emphasizing their potential in identifying high-risk individuals and supporting personalized treatment plans. The paper provides a forward-looking perspective on the future of breast cancer detection, addressing both the opportunities and challenges associated with the adoption of these cutting-edge technologies to improve patient outcomes. (shrink)

A growing number of linguistic attempts to explain how languages change use cultural-evolutionary models involving selection or drift. Developmental constraints and biases, which take center stage in evolutionary developmental biology or evo-devo, seem to be absent within this framework, even though linguistics is home to numerous notions of constraint. In this paper, we show how these evo-devo concepts could be applied to linguistic change and why they should. This requires some conceptual groundwork, due to important differences between linguistic and biotic (...) evolution. In biological evolution, development generates the organism's variable traits on which selection and drift act. In linguistic evolution by analogy, we say development generates the linguistic variants on which selection and drift can act. “Linguistic development” then picks out how individual speakers produce and comprehend language. It involves much more than just learning. Using this broad notion of development, we distinguish between different types of bias that could operate in the processes of linguistic innovation and transmission, which correspond to genetic mutation and biological reproduction, respectively. Having thus sharpened our conceptual toolbox, we then reanalyze two well-documented cases of linguistic change and show that, in both these cases, linguists have only considered Neo-Darwinian evolutionary explanations, falsely deploying an exclusive disjunction of selection and drift. We show that there is at least a third relevant alternative in these examples, namely developmental constraint or bias in the sense we explicate here. (shrink)

A network of gene regulation organized in a hierarchical and combinatorial manner is crucially involved in the development of the neural network, and has to be considered one of the main substrates of genetic change in its evolution. Though qualitative features may emerge by way of the accumulation of rather unspecific quantitative changes, it is reasonable to assume that at least in some cases specific combinations of regulatory parts of the genome initiated new directions of evolution, leading (...) to novel capabilities of the brain. These notions are applied, in this paper, to the evolution of the capability of cognition-based human empa­thy. It is suggested that it has evolved as a secondary effect of the evolution of strategic thought. Development of strategies depends on abstract representations of one’s own pos­sible future states in one’s own brain to allow assessment of their emotional desirability, but also on the representation and emotional evaluation of possible states of others, allowing anticipation of their behaviour. This is best achieved if representations of others are con­nected to one’s own emotional centres in a manner similar to self-representations. For this reason, the evolution of the human brain is assumed to have established representations with such linkages. No group selection is involved, because the quality of strategic thought affects the fitness of the individual. A secondary effect of this linkage is that both the actual states and the future perspectives of others elicit vicarious emotions, which may contribute to the motivations of altruistic behaviour. (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)

Function talk is a constant across different life sciences. From macro-evolution to genetics, functions are mentioned everywhere. For example, a limb’s function is to allow movement and RNA polymerases’ function is to transcribe DNA. Biochemistry is not immune from such a characterization; the biochemical world seems to be a chemical world embedded within biological processes. Specifically, biochemists commonly ascribe functions to biomolecules and classify them accordingly. This has been noticed in the recent philosophical literature on biochemical kinds. But while (...) a lot has been written on biological and psychological functions, little has been said explicitly about biochemical fuctions. Here, I explore functional attribution to biochemical molecules. I argue that if we accept this attribution, then biochemical functions are constituted by chemical dispositional properties that causally contribute to selected biological processes. In section 2, I discuss the controversy concerning the characterization of biochemical functions. In section 3, I consider whether a biological or a chemical under- standing of function can be applied to biochemical functions, illustrating the account with the example of vitamin B12. The result is that none of the theories on their own provides an adequate characterization. In section 4, I present an account of biochemical functions. In section 5, I assess this account taking into consideration common requirements for a theory of functions and an objection. (shrink)

The aspiration for volitional evolution, or human evolution directed by humans themselves,has increased in philosophical, scientific, technical, and commercial literature. The prospect of shaping the very being who is the consumer of all other innovations offers great commercial potential, one to which all other innovations would in effect be subservient. Actually an amalgam of projected technical/commercial developments, this prospective innovation has practical and ethical ramifications. However, because it is often discussed in a scientific way (specifically that of (...) evolutionary theory), it first calls for examination in terms of common scientific approaches to evolution. Yet, as evolutionary-theory controversies point up, evolution may be considered as neither a directed nor a directable process – a problem for the ontology of volitional evolution. One challenge for theories and programs aiming to implement the proposed innovation is then whether it is theoretically coherent. While I offer responses to the challenge in the form of objections, these in turn remain problematic. Two central issues of responsible innovation arise: (1) If this prospect were feasible, would it be responsible to implement it, and (2) if it is not even theoretically coherent, is it responsible for innovators, even this early-on, to keep promoting it as if it were? (shrink)

The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis (...) view was a prevailing orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change. (shrink)

The article entitled “Cultural evolution in Vietnam’s early 20th century: A Bayesian networks analysis of Hanoi Franco-Chinese house designs” investigates how diverse cultures and religious creeds influenced the architecture of Hanoi in the early 20th century.

Social network structure has been argued to shape the structure of languages, as well as affect the spread of innovations and the formation of conventions in the community. Specifically, theoretical and computational models of language change predict that sparsely connected communities develop more systematic languages, while tightly knit communities can maintain high levels of linguistic complexity and variability. However, the role of social network structure in the cultural evolution of languages has never been tested experimentally. Here, we present results (...) from a behavioral group communication study, in which we examined the formation of new languages created in the lab by micro‐societies that varied in their network structure. We contrasted three types of social networks: fully connected, small‐world, and scale‐free. We examined the artificial languages created by these different networks with respect to their linguistic structure, communicative success, stability, and convergence. Results did not reveal any effect of network structure for any measure, with all languages becoming similarly more systematic, more accurate, more stable, and more shared over time. At the same time, small‐world networks showed the greatest variation in their convergence, stabilization, and emerging structure patterns, indicating that network structure can influence the community's susceptibility to random linguistic changes (i.e., drift). (shrink)

Upon separation of the protein from the nucleic acid component of tobacco mosaic virus by phenol, using a fast and gentle procedure, the nucleic acid is infective in assays on tobacco leaves. A series of qualitative and quantitative control experiments demonstrates that the biological activity cannot depend on residual proteins in the preparation, but is a property of isolated nucleic acid which is thus the genetic material of the virus.

Aspects of human symbolic evolution are studied by scholars active in a variety of fields and disciplines in the life and the behavioral sciences as well as the scientific-philosophical, sociological, anthropological, and linguistic sciences. These fields and disciplines all take on an evolutionary approach to the study of human symbolism, but scholars disagree in their theoretical and methodological attitudes. Theoretically, symbolism is defined differentially as knowledge, behavior, cognition, culture, language, or social group living. Methodologically, the diverse symbolic evolution (...) sciences establish their teachings upon diverging evolutionary biological schools and paradigms. This chapter reviews past and current research fields in human symbolic evolution for how they differentially implement tenets of the major evolution schools that were discussed in the previous chapter. Traditional evolutionary epistemology and biosemiotics bring in a mesoevolutionary outlook by drawing on early Darwinism and evolutionary developmental biology movements that emphasize the role of the organism in evolution. Communication studies instead originally take on a microevolutionary perspective by investigating how units of information are transmitted across generations through time. Only later do they integrate studies on meaning-making at the organismal level. Sociobiology complements a microevolutionary with a macroevolutionary outlook by implementing population genetic approaches, typical of the Modern Synthesis, into studies on individual and group behavior. The new symbolic evolutionary sciences build upon these traditions and include disciplines such as evolutionary psychology, evolutionary linguistics, evolutionary anthropology, evolutionary archaeology, evolutionary sociology, and evolutionary economics. Originally centered on implementing Darwinian selection theory, these fields are now including ecological and evolutionary developmental biology as well as reticulate evolutionary paradigms. As diverse in outlook and scope as they are, no discipline holds a privileged position over the other and all have made valuable contributions to our understanding of human symbolic evolution. (shrink)

: Decisions about funding health services are crucial to controlling costs in health care insurance plans, yet they encounter serious challenges from intellectual property protection—e.g., patents—of health care services. Using Myriad Genetics' commercial genetic susceptibility test for hereditary breast cancer (BRCA testing) in the context of the Canadian health insurance system as a case study, this paper applies concepts from social contract theory to help develop more just and rational approaches to health care decision making. Specifically, Daniels's and Sabin's (...) "accountability for reasonableness" is compared to broader notions of public consultation, demonstrating that expert assessments in specific decisions must be transparent and accountable and supplemented by public consultation. (shrink)

We describe an approach to measuring biological information where ‘information’ is understood in the sense found in Francis Crick’s foundational contributions to molecular biology. Genes contain information in this sense, but so do epigenetic factors, as many biologists have recognized. The term ‘epigenetic’ is ambiguous, and we introduce a distinction between epigenetic and exogenetic inheritance to clarify one aspect of this ambiguity. These three heredity systems play complementary roles in supplying information for development. -/- We then consider the evolutionary significance (...) of the three inheritance systems. Whilst the genetic inheritance system was the key innovation in the evolution of heredity, in modern organisms the three systems each play important and complementary roles in heredity and evolution. -/- Our focus in the earlier part of the paper is on ‘proximate biology’, where information is a substantial causal factor that causes organisms to develop and causes offspring to resemble their parents. But much philosophical work has focused on information in ‘ultimate biology’. Ultimate information is a way of talking about the evolutionary design of the mechanisms of development and inheritance. We conclude by clarifying the relationship between the two. Ultimate information is not a causal factor that acts in development or heredity, but it can help to explain the evolution of proximate information, which is. (shrink)

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

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)

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)

The generation of viral mutants in vitro was demonstrated by treatment of the isolated RNA of Tobacco Mosaic Virus by nitrous acid. This agent causes deaminations converting cytosine into uracil, and adenine into hypoxanthine. Our assay for mutagenesis was the production of local lesions on a tobacco variety on which the untreated strain produces systemic infections only. A variety of different mutants are generated in this way. Quantitative analysis of the kinetics of mutagenesis leads to the conclusion that alteration (...) of a single out of the 6000 nucleotides of the viral RNA is sufficient for causing a mutation. (shrink)

This thesis studies the enabling properties of ICT and their effects and potential for social change, and prepares the ground for a sustainability-oriented ethico-political assessment of this technology. It primarily builds on interdisciplinary scholarship to describe and explain the multifaceted co-evolution between the global deployment of ICTs and the emergence of the Information Society, understood as a socioeconomic restructuring of capitalism. Beyond the role of ICTs in this regime transition, the thesis delivers other philosophical insights about crucial aspects (...) of ICT development, applications and management. These include arguments about how we should conceptualize ICTs on the basis of their different roles in extending human communication and in performing or facilitating the remote control of humans and animals, machines and systems operations; about the entanglement between telecommunications, transport networks, urban development and work and organization; and about the relations between ICTs, culture and human values. Examples are offered to illustrate the potential that these empirical and philosophical lessons may hold for the construction of a framework for the ethico-political assessment of ICTs. (shrink)

What might be the fundamental psychology of intelligence naturally selected in biological evolution to minimize, prevent, and cure social and personal issues like war, crime, commit suicide, homicide, theft, drug addictions, and so on? How to achieve a higher level of well-being? I found a primary cognitive limiting factor called mind viruses (MV)(more than 3000) which regresses intelligence and well-being and makes the grand delusion: remedies are healthy mind viruses(HMV)(3000). Here, I show the disclosed core of early Buddhist (...) teachings (on learning, training the mind, and behavior on the 8-fold psychological course psychologically 'program' for better (intelligent) decisions. A theoretical 3D graph might represent the state of evolution of intelligence, nature, nurture, X-ultra quantum unique consciousness particle (X-UQUPC), and psychological well-being with the psychological time of a person. To this hypothesis, if the afterlife occurs, the natural selection of vacant zygote/early embryo neurons of the next life and their quality might depend on the finally evolved X-ultra quantum genomic particle of consciousness (X-UQGPC). Therefore, the quality, including the species of the new life and its nurture in the universe/s, depends on the quality of the finally evolved X-UQGPC. Such natural selection of a new nurturing environment for future (promising)life might be uncertain and, therefore, a high risk of finding a life-consciousness in great nature and nurture. However, there may be more mysterious issues to be solved in future research; therefore, the article might not discuss a theory of everything on the central theme. -/- . (shrink)

“Denn das Maß der Widerwärtigkeiten und Schlechtigkeiten wird augenblicklich wieder durch neue aufgefüllt, als glitte das eine Bein der Welt immer wieder zurück, wenn sich das andere vorschiebt. Daran müßte man die Ursache und den Geheimmechanismus erkennen!” (Robert Musil, Der Mann ohne Eigenschaften, I, 27) Die Frage, ob Evolution eine Fortschrittskomponente beinhalte, oder zumindest einen Trend zur Komplexität der Organismen oder der Ökosysteme, beschäftigt nicht nur Romanschreiber, sondern Biologen wie Philosophen (Ruse 1993). Ist Anpassung ein Schritt vorwärts? Wovon weg (...) - worauf zu? Ist der komplexere Organismus besser an seine Umwelt angepaßt? Wenn ja, was sind die Konsequenzen und Kosten solchen Fortschritts? Ludwig von Bertalanffy wunderte sich über den Sinn eines evolutionären Dramas, in dem das Leben sich umständlich immer höher schraubt, um für jede erreichte Ebene einen neuen Preis zu zahlen: für Vielzelligkeit den Tod des Individuums, für das Nervensystem den Schmerz, für das Bewußtsein die Angst (Davidson 1983). Daß Evolution nicht, wie man lange glauben wollte, partout der Komplexität zustrebt, zeigt sich am Verlust der Flugfähigkeit bei vielen Inselvögeln in Abwesenheit terrestrischer Räuber, oder an der strukturellen Vereinfachung der meisten Parasiten, wird aber besonders deutlich in den klassischen Experimenten von Spiegelman (1967). Spiegelman inkubierte die RNA eines Virus in einer konstant gehaltenen Brühe aus freien Monomeren und Replikase. Unter artifizieller Selektion für rapide Reproduktion etablierte sich in diesem Experiment nach nur 75 Generationen eine stabile Mutante, die sich zwar fünfzehnmal so schnell vermehrte, sich aber von ursprünglich 4200 Nukleotiden auf nur mehr 220 reduziert hatte, nicht viel mehr als die Erkennungsstelle für die Replikase. Im Schlaraffenland, wo Ressourcen nie weniger werden, Abfälle sich nie anhäufen und Feinde nicht existieren, in einer Umwelt also, in welcher der Organismus weder bedroht noch von den Rückwirkungen seiner eigenen Handlungen betroffen wird, verläuft die Evolution anscheinend nicht in Richtung auf zunehmende Größe und Komplexität, wie dies Bonner (1988) für die reale Welt zu zeigen versuchte, sondern genau umgekehrt. Ich werde im folgenden eine Antwort auf dieses Paradoxon skizzieren, die aus den folgenden Thesen besteht: 1. Jeder Adaptivschritt eines evoluierenden Organismus zieht einen Komplementärschritt seiner unbelebten und seiner belebten Umwelt nach sich. Die Umwelt weicht vom sich adaptierenden Organismus zurück. Der Organismus von heute ist an die Umwelt von gestern angepaßt. 2. Während die unbelebte Umwelt lediglich in passiver Weise auf das energetische Vordringen des Organismus reagiert, sind Wechselwirkungen zwischen Organismus und belebter Umwelt, also anderen Organismen, teleonomisch. Wechselwirkungen, die im Energiefluß asymmetrisch sind (wie zum Beispiel zwischen Räuber und Beute), sind im Informationsfluß komplementär asymmetrisch. In dem Maße wie Energie zum erfolgreichen Räuber fließt, fließt Information zur erfolgreichen Beute. Der Räuber von heute erbt das Beutebild von gestern. 3. Einmalige Individualität, das Resultat sexueller Fortpflanzung, vermittelt diese asymmetrische Rückkoppelung und puffert die daraus resultierende zeitverschobene Eskalation. Der Trend zur Individualisierung ist selbstverstärkend und führt zu zunehmender räumlicher und zeitlicher Komplexität von Organismen und Umwelten. Individualität ist die stärkste Triebfeder in der Gestaltung der Biosphäre. (shrink)

This draft investigates Genetic Networks as a special case with comparisons to other networks. The intention is to discover the mapping between generic and abstract network properties and specific case studies.

The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - one trait approch, which (...) has often proved to be effective, has been extended to cover even complex traits. This simplifying view has been appropriately criticized, and the movement called systems biology has taken off. Systems biology [Noble, 2006] emphasizes the presence of several feedback loops in biological systems, which severely limit the range of validity of explanations based upon linear causal chains (e.g. gene → behaviour). Mathematical modelling is one the favourite tools of systems biologists to analyze the possible effects of competing negative and positive feedback loops which can be observed at several levels (from molecules to organelles, cells, tissues, organs, organisms, ecosystems). Systems biology is by now a well-established field, as it can be inferred by the rapid growth in number of conferences and journals devoted to it, as well as by the existence of several grants and funded projects.Systems biology is mainly focused upon the description of specific biological items, like for example specific organisms, or specific organs in a class of animals, or specific genetic-metabolic circuits. It therefore leaves open the issue of the search for general principles of biological organization, which apply to all living beings or to at least to broad classes. We know indeed that there are some principles of this kind, biological evolution being the most famous one. The theory of cellular organization also qualifies as a general principle. But the main focus of biological research has been that of studying specific cases, with some reluctance to accept (and perhaps a limited interest for) broad generalizations. This may however change, and this is indeed the challenge of complex systems biology: looking for general principles in biological systems, in the spirit of complex systems science which searches for similar features and behaviours in various kinds of systems. The hope to find such general principles appears well founded, and I will show in Section 2 that there are indeed data which provide support to this claim. Besides data, there are also general ideas and models concerning the way in which biological systems work. The strategy, in this case, is that of introducing simplified models of biological organisms or processes, and to look for their generic properties: this term, borrowed from statistical physics, is used for those properties which are shared by a wide class of systems. In order to model these properties, the most effective approach has been so far that of using ensembles of systems, where each member can be different from another one, and to look for those properties which are widespread. This approach was introduced many years ago [Kauffman, 1971] in modelling gene regulatory networks. At that time one had very few information about the way in which the expression of a given gene affects that of other genes, apart from the fact that this influence is real and can be studied in few selected cases (like e.g. the lactose metabolism in E. coli). Today, after many years of triumphs of molecular biology, much more has been discovered, however the possibility of describing a complete map of gene-gene interactions in a moderately complex organism is still out of reach. Therefore the goal of fully describing a network of interacting genes in a real organism could not be (and still cannot be) achieved. But a different approach has proven very fruitful, that of asking what are the typical properties of such a set of interacting genes. Making some plausible hypotheses and introducing some simplifying assumptions, Kauffman was able to address some important problems. In particular, he drew attention to the fact that a dynamical system of interacting genes displays selforganizing properties which explain some key aspects of life, most notably the existence of a limited number of cellular types in every multicellular organism (these numbers are of the order of a few hundreds, while the number of theoretically possible types, absent interactions, would be much much larger than the number of protons in the universe). In section 3 I will describe the ensemble based approach in the context of gene regulatory networks, and I will show that it can describe some important experimental data. Finally, in section 4 I will discuss some methodological aspects. (shrink)

In this book, well-known scholars describe new and exciting approaches to aesthetics, creativity, and psychology of the arts, approaching these topics from a point of view that is biological or related to biology and answering new questions with new methods and theories. All known societies produce and enjoy arts such as literature, music, and visual decoration or depiction. Judging from prehistoric archaeological evidence, this arose very early in human development. Furthermore, Darwin was explicit in attributing aesthetic sensitivity to lower (...) animals. These considerations lead us to wonder whether the arts might not be evolutionarily based. Although such an evolutionary basis is not obvious on the face of it, the idea has recently elicited considerable attention. The book begins with a consideration of ten theories on the evolutionary function of the arts, and this is followed by several chapters that consider the possible evolutionary function of specific arts such as music and literature. The theory of evolution was first drawn up in biology, but evolution is not confined to biology: genuinely evolutionary theories of sociocultural change can be formulated. That they need to be formulated is shown in several chapters that discuss regular trends in literature and scientific writings. Psychologists have recently rediscovered the obvious fact that thought and perception occur in the brain, so cognitive science moves ever closer to neuroscience. Several chapters give overviews of neurocognitive and neural network approaches to creativity and aesthetic appreciation. The book concludes with two exciting chapters describing brain-scan research on what happens in the brain during creativity and presenting a close examination of the relationship between genetically transmitted mental disorder and creativity. (shrink)

From mitochondria to meerkats, the natural world is full of spectacular examples of social behaviour. In the early 1960s W. D. Hamilton changed the way we think about how such behaviour evolves. He introduced three key innovations - now known as Hamilton's rule, kin selection, and inclusive fitness - and his pioneering work kick-started a research program now known as social evolution theory. This is a book about the philosophical foundations and future prospects of that program. [Note: only (...) the Introduction is available to download.]. (shrink)

A formalism is introduced to represent the connective organization of an evolving neuronal network and the effects of environment on this organization by stabilization or degeneration of labile synapses associated with functioning. Learning, or the acquisition of an associative property, is related to a characteristic variability of the connective organization: the interaction of the environment with the genetic program is printed as a particular pattern of such organization through neuronal functioning. An application of the theory to the development of (...) the neuromuscular junction is proposed and the basic selective aspect of learning emphasized. (shrink)

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with (...) the organism-level fitness. Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives. (shrink)

The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status (...) of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research. (shrink)

This paper explores the possibility of a standard legal language (e.g. English) for a principled evolution of law in line with technological development. In doing so, reference is made to blockchain networks and smart contracts to emphasise the discontinuity with the liberal legal tradition when it comes to decentralisation and binary code language. Methodologically, the argument is built on the underlying relation between law, semiotics and new forms of media adding to natural language; namely: code and symbols. In (...) what follows, I will concentrate on the study of factors that explain why such approach can be fruitful for the future of law and innovation. I have three reasons for selecting this topic. The first is a more pragmatic reason, based on my current research of law as a linguistic phenomenon. Secondly, the topic does also touch the matter on binary code language, rivalrous to legal alphabetic language. Lastly, the study aims at emphasizing the pivotal role of the jurist as an interpreter in a changing society accommodating diverging realms of reality. The study is structured as follows. Firstly, a quick exam of the traits of blockchain networks would provide the contextual link to establish the arguments in support of the need of a standard legal language. Secondly, a comparison between liberal legal institutions and theory of semiotics is set to perceive their functioning and ascertain their limits in the light of todays unprecedented changes. Thirdly, a summary on blockchain networks’ legal features would constitute the thrust behind the idea of a uniform legal language. Methodologically, the argument does also establish some relations with classical laws of physics and philosophy of media. Its aim is to demonstrate how the suggested legal interpretation and semiotic-based approach can contribute to overcome existing stumbling blocks including, but not limited to, the lack of cooperation at the international level as well as the gap in State norms when it comes to innovation. In this sense, the proposed strategies do not intend to replace current advances in the legal thought. In contrast, it seeks to harmonise their results providing a methodical approach that can concur to inform a new technique to address new controversial issues. In practice, the proposed method regarding the adoption of a uniform legal language would lower transactive costs in terms of normative coordination in the matter of international cooperation and in the definition of applicable law among different legal systems. Alternatively, it might contribute to the convergence of legal systems and/or their underlying concepts. Differently put, article’s contribution can be envisaged in fostering juridical consistency with regards to different forms of languages’ coexistence. (shrink)