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Life is more than a computer running DNA software

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World Journal of Biological Chemistry 2014年第3期5卷 275-278页

作者： Frantiek Baluka Guenther Witzany IZMB University of Bonn telos-philosophische praxis

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.

关键词： DNA Genome Information Life Non-coding RNA Synthetic biology Virus

At the dawn of a new revolution in life sciences

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World Journal of Biological Chemistry 2013年第2期4卷 13-15页

作者： Frantiek Baluka Guenther Witzany IZMB University of Bonn telos-philosophische praxis

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 *** fundamental concept that integrates this new biological "information" with matter and energy is the universal Turing machine and von Neumann's self-reproducing *** this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce *** current knowledge on the roles of noncoding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.

关键词： History of science Paradigm shift Information Non-coding RNAs

Rethinking quasispecies theory: From fittest type to cooperative consortia

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World Journal of Biological Chemistry 2013年第4期4卷 79-90页

作者： Luis P Villarreal Guenther Witzany Department of Molecular Biology and Biochemistry University of California telos-philosophische praxis

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 competencenot 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. Fromsuch 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.

关键词： Quasispecies RNA stem-loops Infectious agents Cooperative interactions Evolution

Biocommunication and natural genome editing

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World Journal of Biological Chemistry 2010年第11期1卷 348-352页

作者： Guenther Witzany telos-philosophische praxis Vogelsangstrasse 18cA-5111-BuermoosAustria

The biocommunicative approach investigates communication processes within and among cells,tissues,organs and organisms as sign-mediated interactions,and nucleotide sequences as code,***-like text,which follows in parallel three kinds of rules:combinatorial (syntactic),context-sensitive(pragmatic),and contentspecific(semantic).Natural genome editing from a bio-communicative 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(***) purposes of the host organism.

关键词： Biotic agents Signs Molecular syntax Communication Nucleotide sequence editing

Pragmatic turn in biology: From biological molecules to genetic content operators

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World Journal of Biological Chemistry 2014年第3期5卷 279-285页

作者： Guenther Witzany telos-philosophische praxis

Erwin Schrdinger‘s question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

关键词： Life Information Quasi-species Incompleteness theorem Genetic content operators

Uniform categorization of biocommunication in bacteria,fungi and plants

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World Journal of Biological Chemistry 2010年第5期1卷 160-180页

作者： Günther Witzany telos-philosophische praxis Vogelsangstrasse 18cA-5111-BuermoosAustria

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 *** from being mechanistic interactions,communication processes within organisms and between organisms are sign-mediated ***-mediated interactions are the precondition for every cooperation and coordination between at least two biological agents such as cells,tissues,organs and *** of biocommunicative processes are chemical molecules in most *** signs that are used in a great variety of signaling processes follow syntactic(combinatorial) ,pragmatic(context-dependent) and semantic(contentspecific) *** three levels of semiotic rules are helpful tools to investigate communication processes throughout all organismic *** 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.

关键词： Trans-organismic communicative competence Bacteria Fungi Plants