Organisms that share the capability of storing information about experiences in the past have an actively generated background resource on which they can compare and evaluate more recent experiences in order to quickly or even better react than in previous situations. This is an essential competence for all reaction and adaptation purposes of living organisms. Such memory/learning skills can be found from akaryotes up to unicellular eukaryotes, fungi, animals and plants, although until recently, it had been mentioned only as a (...) capability of higher animals. With the rise of epigenetics, the context-dependent marking of experiences at both the phenotype and the genotype level is an essential perspective to understand memory and learning in all organisms. Both memory and learning depend on a variety of successful communication processes within the whole organism. (shrink)

This is the first book to systemize all levels of communicative behavior of phages. Phages represent the most diverse inhabitants on this planet. Until today they are completely underestimated in their number, skills and competences and still remain the dark matter of biology. Phages have serious effects on global energy and nutrient cycles. Phages actively compete for host. They can distinguish between ‘self’ and ‘non-self’. They process and evaluate available information and then modify their behaviour accordingly. These diverse competences show (...) us that this capacity to evaluate information is possible owing to communication processes within phages, between the same, related and different phage species, and between phages and non-phage organisms. This is crucial in coordinating infection strategies and recombination in phage genomes. In 22 chapters, expert contributors review current research into the varying forms of phage biocommunication and Phagetherapy. Biocommunication of Phages aims to assess the current state of research, to orient further investigations on how phages communicate with each other to coordinate their behavioral patterns, and to inspire further investigation of the role of non-phage viruses in these highly dynamic interactional networks. (shrink)

First, I offer a short overview on the classical occidental philosophy as propounded by the ancient Greeks and the natural philosophies of the last 2000 years until the dawn of the empiricist logic of science in the twentieth century, which wanted to delimitate classical metaphysics from empirical sciences. In contrast to metaphysical concepts which didn’t reflect on the language with which they tried to explain the whole realm of entities empiricist logic of science initiated the end of metaphysical theories by (...) reflecting on the preconditions for foundation and justification of sentences about objects of investigation, i.e. a coherent definition of language in general, which was not the aim of classical metaphysics. Unexpectedly empiricist logic of science in the linguistic turn failed in the physical and mathematical reductionism of language and its use in communication, as will be discussed below in further detail. Nevertheless, such reflection on language and communication also introduced this vocabulary into biology. Manfred Eigen and bioinformatics, later on biolinguistics, used ‘language’ applied linguistic turn thinking to biology coherent to the logic of science and its formalisable aims. This changed significantly with the birth of biosemiotics and biohermeneutics. At the end of this introduction it will be outlined why and how all these approaches reproduced the deficiencies of the logic of science and why the biocommunicative approach avoids their abstractive fallacies. (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)

IntroductionBy ‘philosophy of consciousness’ we mean an assembly of different approaches such as philosophy of mind , perception, rational conclusions, information processing and contradictory conceptions such as holistic ‘all is mind’ perspectives and their atomistic counterparts.Since ancient Greeks philosophy has provided widespread debates on pneuma, nous, psyche, spiritus, mind, and Geist. In more recent times the philosophy of consciousness has become part of psychology, sociology, neuroscience, cognitive science, linguistics, communication science, information theory, cybernetic systems theory, synthetic biology, biolinguistics, bioinformatics and (...) biosemiotics.However, no matter what each of these approaches presents as a coherent explanation of the human mind, thinking, and consciousness, they remain alien to our self-awareness and self-reflection-based understanding because they do not offer a rational and at the same time .. (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)

Plants are sessile, highly sensitive organisms that actively compete for environmental resources both above and below the ground. They assess their surroundings, estimate how much energy they need for particular goals, and then realise the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behaviour accordingly. These highly diverse competences are made possible by parallel sign(alling)-mediated communication processes within the plant (...) body (intraorganismic), between the same, related and different species (interorganismic), and between plants and non-plant organisms (transorganismic). Intraorganismic communication involves sign-mediated interactions within cells (intracellular) and between cells (intercellular). This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated plant parts. This allows plants to coordinate appropriate response behaviours in a differentiated manner, depending on their current developmental status and physiological influences. Lastly, this volume documents how plant ecosphere inhabitants communicate with each other to coordinate their behavioural patterns, as well as the role of viruses in these highly dynamic interactional networks. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication (...) between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

Within the last decade, thousands of studies have described communication processes in and between organisms. Pragmatic philosophy of biology views communication processes as rule-governed sign-mediated interactions (rsi's). As sign-using individuals exhibit a relationship to following or not-following these rules, the rsi's of living individuals dier fundamentally from cause-and-effect reactions with and between non-living matter, which exclusively underlie natural laws. Umwelt thus becomes a term in investigating physiological influences on organisms that are not components of rsi's. Mitwelt is a term for (...) the investigation of all rsi's of organisms. Living organisms are never solus ipse subjects of semioses, but share common sets of rules and signs. Life depends decisively on symbiotic communities. Serial Endosymbiotic Theory proved that the evolution of the eukaryotic super-kingdom was a merger of anchestral bacteria. The integration of bacterial genomes into eukaryotic genomes was also a step from analog to symbolic genetic codes. Now we know, that so-called ‘junk DNA’ has higher order regulatory functions on genome architecture and protein coding DNA plays only the role of a structural vocabulary. (shrink)

Kant’s critique/doctrine distinction tracks the difference between a canon for the understanding’s proper use and an organon for its dialectical misuse. The latter reflects the dogmatic use of reason to attain a doctrine of knowledge with no antecedent critique. In the 1790s, Fichte collapses Kant’s distinction and redefines dogmatism. He argues that deriving a canon is essentially dialectical and thus yields an organon: critical idealism is properly a doctrine of science or Wissenschaftslehre. Criticism is furthermore said to refute dogmatism, by (...) which Fichte means Spinozism. Schelling repudiates Fichte’s position in his Philosophical Letters by reviving Kant’s distinction. First, ‘critique’ for Schelling names a canon that is valid for all systems—including Spinozism—and thus favours none—not even the Wissenschaftslehre. Second, Schelling coins ‘dogmaticism’ to refer to what Kant calls ‘dogmatism’: reason’s uncritical claim to doctrine. Hence, he says all systems—even Fichte’s—are susceptible to the ‘enthusiasm’ of mistaking themselves for doctrines or ‘objects of knowledge’, instead of subjectively valid ‘objects of freedom’. I reconstruct Schelling’s argument for reviving Kant’s distinction, while noting two consequences for German idealism. First, if criticism favours no system, a system’s origin cannot be an act of knowledge, e.g., intellectual intuition, but only an act of endorsement. Second, if dogmaticism entails enthusiasm, a system’s goal cannot be absolute knowledge, but only infinite striving. Hence, by retrieving Schelling’s notion of dogmaticism, we can both gain a better understanding of the Letters and register the impact of a core Kantian distinction on the German idealist project. (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)

This is the first coherent description of all levels of communication of ciliates. Ciliates are highly sensitive organisms that actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realise the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behaviour accordingly. These highly diverse competences show us that this is (...) possible owing to sign-mediated communication processes within ciliates, between the same, related and different ciliate species, and between ciliates and non-ciliate organisms. This is crucial in coordinating growth and development, shape and dynamics. This book further serves as a learning tool for research aspects in biocommunication in ciliates. It will guide scientists in further investigations on ciliate behavior, how they mediate signaling processes between themselves and the environment. (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)

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)

Manfred Eigen employs the terms language and communication to explain key recombination processes of DNA as well as to explain the self-organization of human language and communication: Life processes as well as language and communication processes are governed by the logic of a molecular syntax, which is the exact depiction of a principally formalizable reality. The author of the present contribution demonstrates that this view of Manfred Eigen’s cannot be sufficiently substantiated and that it must be supplemented by an approach (...) based on linguistic pragmatics. (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)

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)

Archaea represent a third domain of life with unique properties not found in the other domains. Archaea actively compete for environmental resources. They perceive themselves and can distinguish between 'self' and 'non-self'. They process and evaluate available information and then modify their behaviour accordingly. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. These highly diverse competences show us that this is possible owing to sign- mediated communication processes within archaeal (...) cells, between the same, related and different archaeal species, and between archaea and non-archaeal organisms. This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated colony parts. This allows archaea to coordinate appropriate response behaviors in a differentiated manner to their current developmental status and physiological influences. This book will orientate further investigations on how archaeal ecosphere inhabitants communicate with each other to coordinate their behavioral patterns and whats the role of viruses in this highly dynamic interactional networks. (shrink)

A renaissance of virus research is taking centre stage in biology. Empirical data from the last decade indicate the important roles of viruses, both in the evolution of all life and as symbionts of host organisms. There is increasing evidence that all cellular life is colonized by exogenous and/or endogenous viruses in a non-lytic but persistent lifestyle. Viruses and viral parts form the most numerous genetic matter on this planet.

This book assembles recent research on memory and learning in plants. Organisms that share a capability to store information about experiences in the past have an actively generated background resource on which they can compare and evaluate coming experiences in order to react faster or even better. This is an essential tool for all adaptation purposes. Such memory/learning skills can be found from bacteria up to fungi, animals and plants, although until recently it had been mentioned only as capabilities of (...) higher animals. With the rise of epigenetics the context dependent marking of experiences on the genetic level is an essential perspective to understand memory and learning in organisms. -/- Plants are highly sensitive organisms that actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behavior accordingly. -/- The book will guide scientists in further investigations on these skills of plant behavior and on how plants mediate signaling processes between themselves and the environment in memory and learning processes. (shrink)

A stationary subset S of a regular uncountable cardinal κ reflects fully at regular cardinals if for every stationary set $T \subseteq \kappa$ of higher order consisting of regular cardinals there exists an α ∈ T such that S ∩ α is a stationary subset of α. Full Reflection states that every stationary set reflects fully at regular cardinals. We will prove that under a slightly weaker assumption than κ having the Mitchell order κ++ it is consistent that Full Reflection (...) holds at every λ ≤ κ and κ is measurable. (shrink)

Meillassoux seeks knowledge of transcendental reality, blaming Kant for the ‘correlationist’ proscription of independent access to either thought or being. For Meillassoux, correlationism blocks an account of the meaning of ‘ancestral statements’ regarding reality prior to humans. I examine three charges on which Meillassoux’s argument depends: (1) Kant distorts ancestral statements’ meaning; (2) Kant fallaciously infers causality’s necessity; (3) Kant’s transcendental idealism cannot grasp ‘the great outdoors’. I reject these charges: (1) imposes a Cartesian misreading, hence Meillassoux’s false assumption that, (...) for Kant, objects don’t exist without subjects; (2) misreads Kant, who infers causality’s necessity from the possibility of experience; (3) casts Kant’s idealism as subjective, ignoring his perspectival portrayal of it. (shrink)

First uniform description of all key levels of communication in the organismic kingdoms of plants, fungi, animals (bees and corals), bacteria and additionally the natural genome editing competences of viruses based on the most recent empirical data. The biocommunicative approach presented is based on the results of the philosophy of science discourse concerning coherent definitions of 'language' and 'communication'.

Every coordination within or between animals depends on communication processes. Although the signaling molecules, vocal and tactile signs, gestures and its combinations differ throughout all species according their evolutionary origins and variety of adaptation processes, certain levels of biocommunication can be found in all animal species: Abiotic environmental indices such as temperature, light, water, etc. that affect the local ecosphere of an organism and are sensed, interpreted. Trans-specific communication with non-related organisms. Species-specific communication between same or related species. Intraorganismic communication, (...) i.e., sign-mediated coordination within the body of the organism. This book gives an overview of the manifold levels of animal communication exemplified by a variety of species and thereby broadens the understanding of these organisms. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular (...) biocommunication between soil microorganisms. Th is includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

Fungi are sessile, highly sensitive organisms that actively compete for environmental resources both above and below the ground. They assess their surroundings, estimate how much energy they need for particular goals, and then realise the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behaviour accordingly. These highly diverse competences show us that this is possible owing to sign-mediated communication processes (...) within fungal cells, between the same, related and different fungal species, and between fungi and non-fungal organisms. Intraorganismic communication involves sign-mediated interactions within cells and between cells. This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated mycelium parts. This allows fungi to coordinate appropriate response behaviors in a differentiated manner to their current developmental status and physiological influences. (shrink)

Whereas telomeres protect terminal ends of linear chromosomes, telomerases identify natural chromosome ends, which differ from broken DNA and replicate telomeres. Although telomeres play a crucial role in the linear chromosome organization of eukaryotic cells, their molecular syntax most probably descended from an ancient retroviral competence. This indicates an early retroviral colonization of large double-stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus. This contribution demonstrates an advantage of the biosemiotic approach towards our evolutionary understanding of telomeres, telomerases, (...) other reverse transcriptases and mobile elements. Their role in genetic/genomic content organization and maintenance is no longer viewed as an object of randomly derived alterations (mutations) but as a highly sophisticated hierarchy of regulatory networks organized and coordinated by natural genome-editing competences of viruses. (shrink)

Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life functions (...) through signaling processes. Signaling allows for real life coordination and organization and is a communicative action in which speciesspecific behavioral patterns and sign repertoires are used. Cells, tissues, organs, and organisms that communicate share several key levels that are essential to all life forms and which serve as a uniform tool for investigating biocommunication. (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)

This contribution demonstrates that the development and growth of plants depends on the success of complex communication processes. These communication processes are primarily sign-mediated interactions and are not simply an mechanical exchange of ‘information’, as that term has come to be understood (or misunderstood) in science. Rather, such interactions as I will be describing here involve the active coordination and organisation of a great variety of different behavioural patterns — all of which must be mediated by signs. Thus proposed, a (...) biosemiotics of plant communication investigates communicationprocesses both within and among the cells, tissues, and organs of plants as sign-mediated interactions which follow (1) combinatorial (syntactic), (2) context-sensitive (pragmatic) and (3) content-specific (semantic) levels of rules. As will be seen in the cases under investigation, the context of interactionsin which a plant organism is interwoven determines the content arrangement of its response behaviour. And as exemplified by the multiply semiotic roles playedby the plant hormone auxin that I will discuss below, this means that a molecule type of identical chemical structure may function in the instantiation of differentmeanings (semantics) that are determined by the different contexts (pragmatics) in which this sign is used. (shrink)

The Serial Endosymbiotic Theory explains the origin of nucleated eukaryotic cells by a merging of archaebacterial and eubacterial cells. The paradigmatic change is that the driving force behind evolution is not ramification but merging. Lynn Margulis describes the symbiogenetic processes in the language of mechanistic biology in such terms as “merging”, “fusion”, and “incorporation”. Biosemiotics argues that all cell-cell interactions are (rule-governed) sign-mediated interactions, i.e., communication processes. As the description of plant communication demonstrates, the biosemiotic approach is not limited to (...) the level of molecular biology, but is also helpful in examining all sign-mediated interactions between organisms on the phenotypic level. If biosemiotics also uses the notions of “language” and “communication” to describe non-human sign-mediated interactions, then the underlying scientific justification of such usage should be critically considered. Therefore, I summarize the history of this discussion held between 1920 and 1980 and present its result, the pragmatic turn. (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)

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)

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)

It is becoming increasingly evident that the driving forces of evolutionary novelty are not randomly derived chance mutations of the genetic text, but a precise genome editing by omnipresent viral agents. These competences integrate the whole toolbox of natural genetic engineering, replication, transcription, translation, genomic imprinting, genomic creativity, enzymatic inventions and all types of genetic repair patterns. Even the non-coding, repetitive DNA sequences which were interpreted as being ancient remnants of former evolutionary stages are now recognized as being of viral (...) descent and crucial for higher-order regulatory and constitutional functions of protein structural vocabulary. In this article I argue that non-randomly derived natural genome editing can be envisioned as (a) combinatorial (syntactic), (b) context-specific (pragmatic) and (c) content-sensitive (semantic) competences of viral agents. These three-leveled biosemiotic competences could explain the emergence of complex new phenotypes in single evolutionary events. After short descriptions of the non-coding regulatory networks, major viral life strategies and pre-cellular viral life three of the major steps in evolution serve as examples: There is growing evidence that natural genome-editing competences of viruses are essential (1) for the evolution of the eukaryotic nucleus, (2) the adaptive immune system and (3) the placental mammals. (shrink)

“DNA-RNA-Protein-everything else” (Arthur Kornberg) on its detail, satisfactory answers to central questions – What is life? head and who try to understand protein bodies as context- How did it originate and how do we view ourselves as living dependent interpreters of the genetic text, (3.) a philosophy that beings? – have been lost in a universe of analytical units.