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

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

Editorial preface to the fourth edition and modified translation -- The text of the Philosophische Untersuchungen -- Philosophische untersuchungen = Philosophical investigations -- Philosophie der psychologie, ein fragment = Philosophy of psychology, a fragment.

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

Die Leitgedanken meiner Untersuchungen über die Grundlagen der Mathematik, die ich - anknüpfend an frühere Ansätze - seit 1917 in Besprechungen mit P. BERNAYS wieder aufgenommen habe, sind von mir an verschiedenen Stellen eingehend dargelegt worden. Diesen Untersuchungen, an denen auch W. ACKERMANN beteiligt ist, haben sich seither noch verschiedene Mathematiker angeschlossen. Der hier in seinem ersten Teil vorliegende, von BERNAYS abgefaßte und noch fortzusetzende Lehrgang bezweckt eine Darstellung der Theorie nach ihren heutigen Ergebnissen. Dieser Ergebnisstand weist zugleich die Richtung (...) für die weitere Forschung in der Beweistheorie auf das Endziel hin, unsere üblichen Methoden der Mathematik samt und sonders als widerspruchsfrei zu erkennen. Im Hinblick auf dieses Ziel möchte ich hervorheben, daß die zeit weilig aufgekommene Meinung, aus gewissen neueren Ergebnissen von GÖDEL folge die Undurchführbarkeit meiner Beweistheorie, als irrtüm lich erwiesen ist. Jenes Ergebnis zeigt in der Tat auch nur, daß man für die weitergehenden Widerspruchsfreiheitsbeweise den finiten Stand punkt in einer schärferen Weise ausnutzen muß, als dieses bei der Be trachtung der elementaren Formallsmen erforderlich ist. Göttingen, im März 1934 HILBERT Vorwort zur ersten Auflage Eine Darstellung der Beweistheorie, welche aus dem HILBERTschen Ansatz zur Behandlung der mathematisch-logischen Grundlagenpro bleme erwachsen ist, wurde schon seit längerem von HILBERT ange kündigt. (shrink)

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

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