Project

Biocommunication and Natural Genome Editing

Goal: Biocommunication and Natural Genome Editing.

The biocommunicative approach investigates both communication processes within and among cells, tissues, organs and organisms as sign-mediated interactions, and nucleotide sequences as code, i.e. language-like text, which follows in parallel three (3) kinds of rules: combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic).

Natural genome editing from a biocommunicative perspective is 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.

The biocommunication method investigates both

• cells, tissues, organs and organisms coordinate and organize by communication processes, i.e. sign.mediated interactions
• nucleotide sequence order and the ratio of genome architecture are structured language-like, i.e. follow combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic) rules

My investigations therefore focus on

• sign-mediated interactions within and between all kind of cellular organisms
• (archaea, bacteria, eukarya)
• the role of persistent viruses and subviral agents in replication, transcription,
translation, repair and recombination
• persistent viral agents and the evolution of their persistence
• applied linguistic competences of natural genetic identity producers
• the role of viruses in the evolution of tissues and organs
• the role of subviral RNAs in the generation of viral identities
• communal and cooperative evolutionary processes
• natural invention and integration of novel nucleotide sequences
• Multiply (re)usable nucleotide sequence contents and regulatory agents
• immunity: pragmatic conditions, syntactic sequence order, semantic content flow

Date: 15 August 1986 - 15 August 2020

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Guenther Witzany
added 2 research items
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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.
Guenther Witzany
added a research item
Denis Nobel looks at four important misinterpretations of molecular biology concerning evolutionary processes and demonstrates that the new synthesis today looks rather outdated. The modern synthesis is nearly 80 years old. The proponents who worked out the modern synthesis had no access to the current knowledge on cell biology, genetics, epigenetics, RNA biology and virology. Therefore this contribution adds several aspects which Nobel’s article does not explicitly mention, providing some examples for a better understanding of evolutionary novelty.
Guenther Witzany
added an update
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,
 
Guenther Witzany
added an update
Denis Nobel looks at four important misinterpretations of molecular biology
concerning evolutionary processes and demonstrates that the new synthesis today looks
rather outdated. The modern synthesis is nearly 80 years old. The proponents who
worked out the modern synthesis had no access to the current knowledge on cell
biology, genetics, epigenetics, RNA biology and virology. Therefore this contribution
adds several aspects which Nobel’s article does not explicitly mention, providing some
examples for a better understanding of evolutionary novelty.
 
Guenther Witzany
added an update
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.
 
Guenther Witzany
added an update
Denis Nobel looks at four important misinterpretations of molecular biology
concerning evolutionary processes and demonstrates that the new synthesis today looks
rather outdated. The modern synthesis is nearly 80 years old. The proponents who
worked out the modern synthesis had no access to the current knowledge on cell
biology, genetics, epigenetics, RNA biology and virology. Therefore this contribution
adds several aspects which Nobel’s article does not explicitly mention, providing some
examples for a better understanding of evolutionary novelty.
 
Guenther Witzany
added 4 research items
Far from being mechanistic interactions, communication processes within and between organisms are sign-mediated interactions. Such interactions are the precondition for all cooperation and coordination between at least two biological agents such as organisms, organs, tissues, cells and even subcellular components. In most cases these communication processes are of a fine-tuned interconnected structure within a highly sophisticated hierarchical order. Signs of biocommunicative processes in most cases are chemical molecules. The signs that are used in a great variety of signaling processes follow syntactic, pragmatic and semantic rules. These three levels of semiotic rules are helpful tools in the investigation of the communication processes of unicellular and multicellular organisms. This article demonstrates a coherent biosemiotic categorization of communication processes found in the kingdoms of bacteria, fungi and plants. The investigation further shows that, apart from biotic sign use, a common trait is to interpret abiotic influences as indicators to generate appropriate adaptational behavior.
The role of viruses in the evolution of life has traditionally been seen to result from a predator/prey virus/host relationship in which viruses are selfish toxic replicators. Viral information found in host DNA was historically considered as mostly defective junk. Viral persistence or symbiosis is seldom considered, although these are exceedingly common states and highly mediated by defective virus. Here, we outline how colonizing persisting viruses acting as consortia (quasispecies) provides editing competence to create complex new virus/host identity and network regulation. Viruses via ‘virolution’ are a main editors of emerging host complexity and therefore main drivers that generate complement functions.
Guenther Witzany
added an update
The role of viruses in the evolution of life has traditionally been seen to result from a predator/prey virus/host relationship in which viruses are selfish toxic replicators. Viral information found in host DNA was historically considered as mostly defective junk. Viral persistence or symbiosis is seldom considered, although these are exceedingly common states and highly mediated by defective virus.
Here, we outline how colonizing persisting viruses acting as consortia (quasispecies) provides editing competence to create complex new virus/host identity and network regulation. Viruses via ‘virolution’ are a main editors of emerging host complexity and therefore main drivers that generate complement functions.
 
Guenther Witzany
added a research item
Durch den Rückgang auf die Regeln kommunikativer Rationalität eröffönet sich die Möglichkeit, die Frage nach der Evolutionslogik und der Evolutionsdynamik als Frage der Interaktionslogik und Interaktionsdynamik beantworten zu können. Evolutionsgeschichte wäre als Entwicklungsgeschichte von Interaktionssemiosen verstehbar. Könnten wir weiters feststellen, daß die Regeln, nach denen Evolution möglich und wirklich ist, Kommunikationsregeln einer Interaktionsgeschichte sind, so wäre die Rede vom regelgeleiteten Verhalten nicht nur der menschlichen, sondern gerade auch der nicht-menschlichen Natur begründbar.
Guenther Witzany
added a research item
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’ (complement same, preclude others). 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 (intra-organismic), between the same, related and different phage species (interorganismic), and between phages and non-phage organisms (transorganismic). This is crucial in coordinating infection strategies (lytic vs. lysogenic) 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 (non-lytic, non-prokaryotic) in these highly dynamic interactional networks.
Guenther Witzany
added 2 research items
The shifting perspective from a read-only-memory genome with copying errors to a readand-write genome with competent change operators is fundamental: For decades it was assumed that driving force of evolution is mutation (error) and selection. Now it is recognized that errors cannot explain genetic novelty and complexity. A variety of RNA based agents play essential roles in evolution and regulation in all DNA/Protein based life: basic non-coding RNA secondary structures built of (paired) stems and (not-paired) loops. RNA stem-loop swarms such as group I introns, group II introns, viroids, viral (RNA viruses, retrotransposons, LTRs, non-LTRs) and subviral networks (SINEs, LINEs, Alus) cooperate within cellular genomes as modular tools with its abundance of regulatory functions. Some noncoding RNAs built complementary consortia such as rRNAs, tRNAs, spliceosomes, editosomes, and other RNPs. Additionally counterbalancing modules such as toxin/antitoxin (TA) -, restriction/modification (RM) -, and insertion/deletion (INDEL) - modules assure identity (self/non-self) of cells, tissues, organs and even organisms. Infectious RNAgents manipulate host genomes for (i) selfish replicative purposes or (ii) persistent co-evolutionary integration. The latter in most cases remain as defectives, i.e. abundance of parts that now serve as co-opted modular tools for cellular needs or as full function elements that regulate complex developmental processes such as placentation in mammals. Also mixed consortia of RNA- and DNA virus-derived parts that integrate in host genomes have been found. All fine-tuned steps and substeps of key cellular processes such as gene expression, transcription, translation, DNA recombination and repair, epigenetic imprinting (memory, learning), as well as various forms of innate and adaptive immunity are essentially constituted by such natural genetic content operators.The Proceedings were published as Annals of the New York Academy of Sciences, Volume 1341, in April 2015
The 2018 symposium entitled “EVOLUTION—Genetic Novelty/Genomic Variations by RNA-Networks and Viruses” followed on “Natural Genetic Engineering and Natural Genome Editing” in 2008 (Ann. N.Y. Acad. Sci. Vol. 1178) and “DNA Habitats and Its RNA Inhabitants” in 2014 (Ann. N.Y. Acad. Sci. Vol. 1341). All three symposia were organized by philosopher Guenther Witzany. The 2018 symposium, upon which this issue is based, included 60 experts to discuss a new paradigmatic understanding of genetic novelty, as well as code-generating and genome-formatting agents such as RNA networks and viruses, and their roles in gene regulation. The 2018 symposium took place on July 4–8 at the St. Virgil Conference Center in Salzburg, Austria. Corrado Spadafora, from the Italian National Research Council, and Luis Villarreal, from the Center for Virus Research, University of California, Irvine were cooperating partners. Head administrator Hiltrud Oman managed all the details before and during the meeting. Andreas Oman and Martin Koller assisted directly at the conference center. Land Salzburg and Stadt Salzburg supported the symposium. Kostas Tosidis performed as the guitar soloist at the conference dinner.
Guenther Witzany
added a research item
Two starting points of this dialogue, which is really unique in the history of science, are the basic knowledge on language and communication from an action theoretical perspective and on the other point, basic knowledge of virology and all the detailed interactional motifs of viruses on RNA networks, subviral agents and cellular organisms that constitute this communicative interaction within a dialogue between 2006 and 2020. Cells must coordinate their behavior within and with other cells, being single cells or multicellular organisms, by signaling molecules, i.e. sign-mediated interactions. This is what we define „communication.“ Additionally it was clear that the genetic code is a real natural code. Empirical knowledge indicates that no natural code codes itself as no natural language speaks itself. In all cases such codes need competent code using agents of natural real lifeworld. What then are these agents, how do they generate sign sequences, combine and recombine, edit, re-edit and care for de novo generation of such sequences? The current dialogue assembles our thoughts, speculations, inspirations of how to think on code generating and code editing agents on the genetic and subgenetic level not strictly in the terms of physics and chemistry but in terms of biology as a social science. The result are preliminary remarks to a sociology of viruses and a RNA sociology. The lineup of our dialogue is not always coherent; is sometimes redundant with typical ‘real life’ errors, has some breaks with many answers as questions are seemingly not related. But the whole documentary is coherent and gives a good overview how to reach a complete new and integrated understanding of the genetic code and its editors, i.e., viruses, their relatives and subviral RNA networks. We dedicate this book to young minds and the next generations of the 21st century.
Guenther Witzany
added an update
The starting points of this dialogue, which is really unique in the history of
science, are basic knowledge on language and communication from an action
theoretical perspective and on the other side basic knowledge of virology and
all the detailed interactional motifs of viruses on RNA networks, subviral agents
and cellular organisms that constitute this communicative interaction within a
dialogue between 2006 and 2020.
Cells coordinate their behavior with other cells, being single cell or multicellular
organisms, by signaling molecules, i.e. sign-mediated interactions. This is what
we define „communication.“ Additionally it was clear that the genetic code is a
real natural code. Empirical knowledge indicates that no natural code codes
itself as no natural language speaks itself. In all cases such codes need
competent code using agents of natural real lifeworld. What are these agents,
how do they generate sign sequences, combine and recombine, edit, re-edit
and care for de novo generation of such sequences?
The current dialogue assembles our thoughts, speculations, inspirations of how
to think on code generating and code editing agents on the genetic and
subgenetic level not strictly in the terms of physics and chemistry but in terms
of biology as a social science. The result are preliminary remarks to a sociology
of viruses and a RNA sociology.
The lineup of the dialogue is not always coherent, sometimes redundant, some
breaks are usual and many answers as questions are seemingly not related. But
the whole documentary gives a good overview how to reach a complete new
and integrated understanding of the genetic code and its editors, i.e., viruses,
their relatives and subviral RNA networks.
We dedicate this book to young minds and the next generations of the 21st
century.
 
Guenther Witzany
added 3 research items
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(aling)-mediated communication processes within ciliates (intra-organismic), between the same, related and different ciliate species (inter-organismic), and between ciliates and non-ciliate organisms (trans-organismic). 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.
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.
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(aling)- mediated communication processes within archaeal cells (intra-organismic), between the same, related and different archaeal species (interorganismic), and between archaea and nonarchaeal organisms (transorganismic). 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.
Guenther Witzany
added 3 research items
The crucial difference of quasispecies consortia with former quasispecies-concepts (fittest type – mutant spectra) is the basically consortial organisation of functional RNA ensembles.
The Table show the differences between molecular biological descriptions and the biocommunication approach
Guenther Witzany
added a research item
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.
Guenther Witzany
added a research item
Is there any reason, to believe a modern natural philosophy makes sense? The history of natural philosophy is marked by the search for principles that determine all beings independently whether they are abiotic matter or living organisms. Empirical data on the key features of life contradict even the possibility to find such principles because life in contrast to abiotic matter offers some main characteristics that are completely absent on abiotic planets. This means, if a modern natural philosophy should have any benefit it must be divided into a natural philosophy of physics or cosmology and a natural philosophy of life. If it is possible to give an updated definition of life, empirically based, non-reductive, non-mechanistic and without metaphysical assumptions, this would be an appropriate basis for a global consensus how future of humans may be generated in symbiosis with global biosphere. If we think on billions invested in health and drug research a new natural philosophy of life could orientate future of research on health and new drugs and avoid misinvestments.
Guenther Witzany
added a research item
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’ (complement same, preclude others). 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 (intra-organismic), between the same, related and different phage species (interorganismic), and between phages and non-phage organisms (transorganismic). This is crucial in coordinating infection strategies (lytic vs. lysogenic) 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 (non-lytic, non-prokaryotic) in these highly dynamic interactional networks.
Guenther Witzany
added 2 research items
Phages have serious effects on global energy and nutrient cycles. Phages actively compete for host. They can distinguish between ‘self’ and ‘non-self’ (complement same, preclude others). 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 (intra-organismic), between the same, related and different phage species (interorganismic), and between phages and non-phage organisms (transorganismic). This is crucial in coordinating infection strategies (lytic vs. lysogenic) and recombination in phage genomes. Therefore it is essential to investigate what communication of phages means and to identify the difference of the biocommunication approach to investigations that are restricted to the molecular biological perspective.
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.
Guenther Witzany
added an update
Guenther Witzany
added a research item
Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns – mediated by signs.
Guenther Witzany
added a research item
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.
Guenther Witzany
added a research item
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.
Guenther Witzany
added 2 research items
The development and growth of fungal organisms depend on successful communication processes (a) within the organism and between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic environment. However, these communication and interpretation processes can also fail. In such cases the overall results can induce disease-causing and even lethal consequences for the organism. This review will not enrich the knowledge of specialists in fungal research, but will demonstrate to a broader readership the different levels of fungal communication and how versatile fungal communicative competences really are. Interestingly, certain rules of fungal communication are very similar to those of animals, while others resemble those of plants. The correspondence between all three eukaryotic kingdoms has two aspects: (1) the context determines the meaning of trans-, inter- and intra-organismic (inter- and intracellular) communication, while (2) differences in abiotic and biotic signal perception determine the content arrangement of response behaviour.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms, and between bacteria of the same or related species. In a third stage I will focus on the relationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multiviral colonisation and virally-determined order of nucleic acid sequences.
Guenther Witzany
added 21 research items
The study of DNA virus persistence and RNA virus evolution has defined the concepts of addiction modules and quasispecies which can respectively explain the persistence of virus information and the cooperative evolution of viral populations (including defective virus). Together, these concepts can be applied to a wide array of phenomena that emerge from stable virus colonization of host. Since viruses are naturally competent in host code but also extend that code, they are natural agents for code editing. They are also natural agents to create new host identity (self), although this typically involves cooperative populations of agents. In this chapter I outline how the combined concepts of addiction modules and quasispecies can be applied to understand a wide array of phenomena, involving cooperation, network formation, symbiosis, immunity and group identity, all of which are also examined from a virus first perspective. I trace how essentially all systems of host identity and immunity can be examined from this way and show viral involvement. I also examine the emergence of human social identity from this perspective which provides many new insights for the origin of social cooperation.
All life must survive their corresponding viruses. Thus antiviral systems are essential in all living organisms. Remnants of virus derived information are also found in all life forms but have historically been considered mostly as junk DNA. However, such virus derived information can strongly affect host susceptibility to viruses. In this review, I evaluate the role viruses have had in the origin and evolution of host antiviral systems. From Archaea through bacteria and from simple to complex eukaryotes I trace the viral components that became essential elements of antiviral immunity. I conclude with a reexamination of the 'Big Bang' theory for the emergence of the adaptive immune system in vertebrates by horizontal transfer and note how viruses could have and did provide crucial and coordinated features.
Guenther Witzany
added a research item
All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated 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 and RNA 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.
Guenther Witzany
added 6 research items
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. KeywordsNatural languages/codes–Code concepts–Viral origins–Ribo-agents consortia
IntroductionBy ‘philosophy of consciousness’ we mean an assembly of different approaches such as philosophy of mind (mind-body problems, natural mind vs. artificial 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 ...
Guenther Witzany
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Far from being mechanistic interactions, communication processes within and between organisms are sign-mediated interactions. Such interactions are the precondition for all cooperation and coordination between at least two biological agents such as organisms, organs, tissues, cells and even subcellular components. In most cases these communication processes are of a fine-tuned interconnected structure within a highly sophisticated hierarchical order. Signs of biocommunicative processes in most cases are chemical molecules. The signs that are used in a great variety of signaling processes follow syntactic, pragmatic and semantic rules. These three levels of semiotic rules are helpful tools in the investigation of the communication processes of unicellular and multicellular organisms. This article demonstrates a coherent biosemiotic categorization of communication processes found in the kingdoms of bacteria, fungi and plants. The investigation further shows that, apart from biotic sign use, a common trait is to interpret abiotic influences as indicators to generate appropriate adaptational behavior.
Guenther Witzany
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The change could not be more radical. Biology, as a classical natural science, has celebrated numerous successes. Examining its subject matter from a reductionistic, materialistic point of view has led to exceptional knowledge and given rise to dozens of sub-disciplines. Unfortunately, by pursuing such detail, satisfactory answers to central questions – What is life? How did it originate and how do we view ourselves as living beings? – have been lost in a universe of analytical units. Yet not entirely! A transdisciplinary network is evolving: it goes beyond reductionistic biology, beyond vitalism or a rekindled (metaphysical) enchantment of nature. It is increasingly able to provide better answers to these questions than firmly established, traditional, mechanistic biology: (1.) a semiotics that transcends Peirce, James and Morris to serve as a basis for the interpretation of sign processes in biosemiotics (Kull 2005), (2.) developmental biologists, embryologists and epigeneticists who have turned the paradigm “DNA-RNA-Protein-everything else” (Arthur Kornberg) on its head and who try to understand protein bodies as context-dependent interpreters of the genetic text, (3.) a philosophy that reconstructs biology as an understanding social science which describes the rule-governed sign-mediated interactions of cell individuals to mega-populations in their lifeworlds.
Guenther Witzany
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Guenther Witzany
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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.
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Editorial: Genome Invading RNA Networks
 
Guenther Witzany
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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.
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Evolution – Genetic Novelty/Genomic Variations by RNA Networks and Viruses 4 – 8 July 2018 Salzburg – Austria
Meeting
 
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Archaea 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. These competences are made possible by sign-mediated communication processes within the archaeal body (intraorganismic), between the same, related and different archaea species (interorganismic) and between archaea and non-archaea organisms (transorganismic). In order to generate an appropriate response behavior archaea must be able not only to sense but also to interpret and memorize indices from the biotic and abiotic environment and adapt to them accordingly. This is decisive in concerted coordination of growth and development, mating, shape and dynamics. However, these communication, interpretation and memory processes can also fail. In such cases the overall consequences can mean individual or community collapse or even death for the archaea.
Guenther Witzany
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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(aling)-mediated communication processes within archaeal cells (intra-organismic), between the same, related and different archaeal species (interorganismic), and between archaea and nonarchaeal organisms (transorganismic). 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. © Springer International Publishing AG 2017. All rights reserved.
Guenther Witzany
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In contrast with former definitions of life limited to membrane-bound cellular life forms which feed, grow, metabolise and replicate (i) a role of viruses as genetic symbionts, (ii) along with peripheral phenomena such as cryptobiosis and (iii) the horizontal nature of genetic information acquisition and processing broaden our view of the tree of life. Some researchers insist on the traditional textbook conviction of what is part of the community of life. In a recent review [Moreira, D., Lopez-Garcia, P., 2009. Ten reasons to exclude viruses from the tree of life. Nat. Rev. Microbiol. 7, 306-311.] they assemble four main arguments which should exclude viruses from the tree of life because of their inability to self-sustain and self-replicate, their polyphyly, the cellular origin of their cell-like genes and the volatility of their genomes. In this article we will show that these features are not coherent with current knowledge about viruses but that viral agents play key roles within the roots and stem of the tree of life.
Guenther Witzany
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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 noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. 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 behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics.
In a recently published article Sydney Brenner argued that the most relevant scientific revolution in biology at his time was the breakthrough of the role of "information" in biology. The fundamental concept that integrates this new biological "information" with matter and energy is the universal Turing machine and von Neumann's self-reproducing machines. In this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce themselves. Additionally current knowledge on the roles of non-coding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.
Guenther Witzany
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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 (not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (qs-c) 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 (immunity) 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.
Tropical coral reefs harbour some of the most diverse biological communities on our planet and as such rival tropical forests communities in species diversity and number of individuals from all domains. The cooperative interplay of prokaryotes, eukaryotes – particularly – the interactions among plantae and animalia shape this delicate balance, which ultimately culminate in the beauty of the coral reef biome. Some algal species but especially scleractinian corals with their interconnected organizational structure precipitate a calcium-carbonate skeleton that, upon generation after generation, form and shape structures that can even be seen from space. Yet this process is limited by light penetrability – either by depth or by visibility – that provides endosymbiotic algae with the energetic flux to convert light quanta into biochemically available energy. As a result, the sheer dominance of coral species somewhat camouflages the delicate balance between reef builders and bioerosive processes. This intrinsically interwoven biocommunicative dynamics is a key issue in order to comprehend how such structures can evolve and stretch out over 1,000s of km. Neglecting the importance of these processes compromises a full understanding of reef-dynamics and in turn promotes accelerated reef degradation due to improper use of reef resources to those who rely on them. Doing so simply increments reef instability and as such its long-term survival. This article attempts to shed light on the crucial role of biocommunicative processes and how these are manifested across taxa. In fact biocommunication is so essential in assigning each organism a specific role in this network of interdependences that the elegance even within organisms themselves – seen from a biomic perspective –attain self-similar properties. In turn and regardless of the taxa involved, self-similarity in coral reef ecosystems is an underlying feature that relies on intact and efficient biocommunicative pathways.
In his recent interview for the Guardian Craig Venter is elaborating about a household appliance for the future, Digital Biological Converter (DBC). Current prototype, which can produce DNA, is a box attached to the computer which receives DNA sequences over the internet to synthesize DNA; later in future also viruses, proteins, and living cells. This would help the household members to produce, e.g. , insulin, virus vaccines or phages that fight antibiotic resistant bacteria. In more distant future, Craig Venter’s hope is that the DBC will generate living cells via so-called “Universal Recipient Cell”. This platform will allow digitally transformed genomes, downloaded from the internet, to form new cells fitted for the particular needs such as therapeutics, food, fuel or cleaning water. In contrast to this, the authors propose that DNA sequences of genomes do not represent 1:1 depictions of unequivocal coding structures such as genes. In light of the variety of epigenetic markings, DNA can store a multitude of further meanings hidden under the superficial grammar of nucleic acid sequences.
Guenther Witzany
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Like ants, bees derive evolutionarily from parasitoid wasps, the most numerous species in the animal kingdom with nearly 100,000 different species. Like other flying insects, bees are important pollinators for plants, which would not be able to produce fruits without them. Since Karl von Frisch’s work it has been evident that the highly complex social behaviour of bee swarms is organised and coordinated by sign-mediated interactions, i.e. communication. If communication processes are disturbed this may have fatal consequences for bee colonies. As in every other natural language the same sign sequences may have different meanings in different contexts. This means that bees with a limited repertoire of signs can transport different messages via identical semioses which trigger different response behaviours with far-reaching consequences. As in every other natural language, bee languages also differ in habitat-dependent dialects. The language of honey bees in colder hemispheres is the only known non-human language which uses body movements that represent symbolic meaning functions.
Guenther Witzany
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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.
Guenther Witzany
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The ecological crisis, characterized by the destruction and subsequent collapse of mutually supportive ecospheres, forces mankind - as the perpetrator - to enter into a relationship with living nature that can minimize the worst consequences. Do we proceed a destructive, parasitic relation of exploitation, pollution and extinct of species? What is urgently needed is a completely new understanding of Life. Based on this we may learn and develop a respectful behavior towards living nature. If we investigate and finally understand that every living cell of every organism since the beginning of life communicates within itself and in parallel outside with similar cells in a tissue or a population community, and additionally with non-related cells and organisms to coordinate and organize its behavior then we may imagine the communicative nature of life. The success of a communicative, i.e., a responsible, sustainable and symbiotic-like cooperation with living nature - in time - will decide in the long run, whether our self-understanding as the top of evolution was correct or in contrast human mankind was an evolutionary error.
Jesper Hoffmeyer shows us the direction of one of the next fundamental changes of paradigms in the history of science. In his intention to explain life processes in the light of semiotics he has gone beyond established biological mainstreams. He recognized, that models of explanation, wanting to explain the organisational structures of all living phenomena by the use of a physicalistic language, are not able to reach their goal of complete description of life processes.
Guenther Witzany
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If rules governing evolution are equivalent to communication rules which lie behind the history of interaction, then we could refer to the natural history of life as a history of communication logics and dynamics. Communication processes are rule governed sign mediated interactions (rsi) which may be described in the evolution of eukaryotic cells as well as - for example - in microbial and plant interactions. The first part of this article supports Margulis theory of symbiogenesis (Serial Endosymbiotic Theory) but questions the use of classical mechanistic language of natural science in describing highly complex interactions of symbiosis and, subsequently, of symbiogenesis. The alternative is to describe these as communication processes which are multi-leveled, regulative, constitutive and generative and whose success depends on sign processes which proceed in a rule- based manner. In my illustrations of rsi, I propose the existence of an innovation code (text- generating code, evolution code), a genome editing (ge) MetaCode hidden in the non-coding DNA. The second part argues that the community of investigators doesn’t consist of ‘pure observers’ but of performative participants of the communicating scientific community which are (a) parts of the investigation itself, (b) parts of the planetary symbiotic interdependence of communicating living nature. I summarize pragmatic turn results which lead to an adequate description of communicative rationality by investigating which formal preconditions must be fulfilled so that rule-governed sign-mediated interactions in and between communicating communities can function. This approach of a pragmatic philosophy of biology enables a three- levelled biosemiotics avoid reductionistic fallacies.
Guenther Witzany
added 4 research items
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.
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 di¤er fundamentally from cause-and-e¤ect reactions with and between non-living matter, which exclu-sively underlie natural laws. Umwelt thus becomes a term in investigating physiological influences on organisms that are not components of rsi's. Mit-welt is a term for the investigation of all rsi's of organisms. Living organ-isms 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 higher 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.
Guenther Witzany
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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.
As in all organisms, the evolution, development and growth of plants depends on the success of complex communication processes. These communication processes are primarily sign mediated interactions and not simply an exchange of information. They involve active coordination and active organization-conveyed by signs. A wide range of chemical substances and physical influences serve as signs.Different abiotic or biotic influences require different behaviors. Depending on the behavior, the core set of signs common to species, families, genera and organismic kingdoms is variously produced, combined and transported. This allows entirely different communication processes to be carried out with the same types of chemical molecules.Almost without exception, plant communication are parallel processes on multiple levels, (A) between plants and microorganisms, fungi, insects and other animals, (B) between different plant species as well as between members of the same plant species; (C), between cells and in cells of the plant organism.
Guenther Witzany
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Telomeres identify natural chromosome ends being different from broken DNA through differences in their "molecular syntax" (M.Eigen) which determines the functions of reverse transcriptase and its integrated RNA template, telomerase. Although telomeres play a crucial role in the linear chromosome organisation of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus. This talk will demonstrate certain advantages of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic) semiotic rules. Genetic/genomic organisation from the biosemiotic perspective is not seen any longer as an object of randomly derived alterations (mutations) but as functional innovation coherent with the broad variety of natural genome editing competences of viruses.
Guenther Witzany
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Telomeres in Evolution and Development from Biosemiotic Perspective
Whereas telomeres protect terminal ends of linear chromosomes, telomerases identify natural chromosome ends being different from broken DNA. Although telomeres play a crucial role in the linear chromosome organisation of eukaryotic cells, their molecular syntax descended from an ancient retroviral competence. This is an indicator for the early retroviral colonization of large double stranded DNA viruses, which are putative ancestors of the eukaryotic nucleus. This contribution will demonstrate an advantage of the biosemiotic approach towards our evolutionary understanding of telomeres: focus on the genetic/genomic structures as language-like text which follows combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic) semiotic rules. Genetic/genomic organisation from the biosemiotic perspective is not seen any longer as an object of randomly derived alterations (mutations) but as functional innovation coherent with the broad variety of natural genome editing competences of viruses.
Guenther Witzany
added 2 research items
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms, and between bacteria of the same or related species. In a third stage I will focus on the relationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multiviral colonisation and virally-determined order of nucleic acid sequences.
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 communication processes 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 interactions in which a plant organism is interwoven determines the content arrangement of its response behaviour. And as exemplified by the multiply semiotic roles played by 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 different meanings (semantics) that are determined by the different contexts (pragmatics) in which this sign is used.
Guenther Witzany
added 6 research items
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.
Communicative competences and the use of a semiochemical vocabulary enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like mul-ticellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitu-tion of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial compe-tences derive from the aptitude of viruses for natural genome editing. In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe transorganismic communication, i.e. the main catego-ries of sign-mediated interactions between bacterial and non-bacterial organisms, and interorganismic communication, i.e. between bacteria of the same or related species. In a third stage I will focus on intraorganismic communication, i.e. the re-lationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multi-viral colonisation and the virally-determined order of nucleic acid sequences, which has implications for our understand-ing of the evolutionary history of pre-cellular and cellular life.
Guenther Witzany
added 2 research items
From a biocommunicative perspective it is suggested that in the beginning of life there were single-stranded, unencapsulated RNA molecules with an aptitude for replicating themselves by copying. The crucial shift was the invention of coding capabilities, because this dramatically differs from pure copying in a function which assembles a molecular syntax, pragmatics (context) and semantics (content) in parallel. Because coded nucleotide sequences differ from a random mixture of nucleotides, in that coded sequences imply a molecular grammar whereas a random mixture of nucleotides does not, it is necessary to propose coding agents which are competent to differentiate self from non-self structures and colonize competing agents by new sequence inventions which would serve as advantage in both increasing genetic sequence-complexity and immune function against competing agents. These pre-requisites are fulfilled by consortial interacting ribozymes. i.e. last universal common pre-viruses. The fittest of them escaped by invention of consortial addiction modules and protein membranes
Guenther Witzany
added 6 research items
In the last decade it was found that the number of genes of some nematodes and humans was similar but their regulation was completely different. Today we know that the higher-order regulation of protein-coding datasets depends on complex interconnected networks of a great variety of non-coding RNAs that are read and transcribed in the developmental and growth processes of every cell within multicellular organisms. The evolutionary origins of these non-coding RNAs are not randomly-derived mixtures of nucleotide acids but formerly intact viral agents which infected all cellular host genomes in a non-lytic but persistent way. Although some of these viral agents still fulfill vital functions, e.g., endogenous retroviruses which are active in placentation of mammals, in most cases they split up (‘defectives’) into several functional parts which now serve as ‘effectives’, i.e. symbiogenetic integrated functional tools for cellular needs of host organisms.
The biocommunicative approach investigates rule-governed, sign-mediated interactions both within and among cells, tissues, organs and organisms. It also investigates genetic sequences as codes/texts that are coherent with the laws of physics and chemistry but, in addition, follow a complementary mix of combinatorial (syntactic), context-sensitive (pragmatic), content-specific (semantic) rules. In this respect, the roles of telomeres and telomerases in evolution, structure and content arrangement of genomes are of particular interest. This involves deciphering the relationships between the ‘molecular syntax’ of telomere repeats and their meaning, i.e. their function in the genomic content. This requires their evolutionary roots to be examined. The telomere replication process by telomerase is the most important feature here because it is processed by a very ancient competence, i.e. reverse transcriptase with a great variety of functions in most key processes of living nature.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioural patterns. Biocommunication of bacteria is the presupposition even for behavioural patterns in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. Bacteria seem to be the optimal biotic matrix for virus-induced genetic inventions.
Guenther Witzany
added 2 research items
This is the first uniform description of all key levels of communication in the organismic kingdoms of plants, fungi, animals and bacteria based on the most recent empirical data. Biocommunication occurs on three levels (A) intraorganismic, i.e. intra- and intercellular, (B) interorganismic, between the same or related species and (C) transorganismic, between organisms which are not related. The biocommunicative approach demonstrates both that cells, tissues, organs and organisms coordinate and organize by communication processes and genetic nucleotide sequence order in cellular and non-cellular genomes is structured language-like, i.e. follow combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic) rules. Without sign-mediated interactions no vital functions within and between organisms can be coordinated. Exactly this feature is absent in non-living matter. Additionally the biocommunicative approach investigates natural genome editing competences of viruses. Natural genome editing from a biocommunicative perspective is 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. The biocommunicative approach is an original scientific field of investigations. Readers must be competent in basic knowledge of biology and genetics.
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.
Guenther Witzany
added 2 research items
This article describes a coherent biocommunication categorization for the kingdoms of bacteria, fungi and plants. The investigation further shows that, besides biotic sign use in trans-, inter- and intraorganismic communication processes, a common trait is interpretation of abiotic influences as indicators to generate an appropriate adaptive behaviour. Far from being mechanistic interactions, communication processes within organisms and between organisms are sign-mediated interactions. Sign-mediated interactions are the precondition for every cooperation and coordination between at least two biological agents such as cells, tissues, organs and organisms. Signs of biocommunicative processes are chemical molecules in most cases. The signs that are used in a great variety of signaling processes follow syntactic (combinatorial), pragmatic (context-dependent) and semantic (content-specific) rules. These three levels of semiotic rules are helpful tools to investigate communication processes throughout all organismic kingdoms. It is not the aim to present the latest empirical data concerning communication in these three kingdoms but to present a unifying perspective that is able to interconnect transdisciplinary research on bacteria, fungi and plants.
Guenther Witzany
added 5 research items
In the second half of the twentieth century the physiological processes of all levels of cells, tissues, organs and organisms of all organismic kingdoms were the mainstream focus of biological research and experiments. In the 1970s, increasing use of ‘communication’-metaphor occurred. In the last decade of the twentieth century, communication (no longer used as metaphor) within and between organisms surpassed the pure physiological understanding of organisms. Cell-cell-communication dominated contemporary cell biology, including considerable knowledge about a great variety of signalling pathways serving as both organisation and coordination of production, release, uptake and information-processing within and between cells.
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 species-specific 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. Complementary to this, active biocommunication depends on the deoxyribonucleic acid (DNA) storage medium and the agents that generate coherent content of nucleic acid sequences. Therefore natural genome editing is not the result of replication errors but of group interactions of competent ribonucleic acid (RNA) agents.
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.