Bio-communication and Natural Genome Editing A new concept for the - - PowerPoint PPT Presentation

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Bio-communication and Natural Genome Editing A new concept for the - - PowerPoint PPT Presentation

May 13, 2023 127 likes •399 views

Bio-communication and Natural Genome Editing A new concept for the emergence of biological information Guenther Witzany Telos Philosophische Praxis 5111-Buermoos, Austria www.biocommunication.at www.biocommunication.at Introduction

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www.biocommunication.at

Bio-communication and Natural Genome Editing

A new concept for the emergence of biological information

Guenther Witzany Telos – Philosophische Praxis 5111-Buermoos, Austria www.biocommunication.at

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Natural Codes Persistent Viruses RNA Behaviour Introduction Conclusion

Life = Material Reality = Physics + Chemistry

  • Life emerges out of atoms and molecules
  • Life = physics + chemistry (E.Schrödinger)
  • Life can be depicted by mathematical

equations

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Natural Codes Persistent Viruses RNA Behaviour Introduction Conclusion

Life = physics + chemistry + information

  • DNA is a information storage medium
  • DNA consists of atoms and molecules
  • Information is a molecular feature (M. Eigen)
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Introduction Persistent Viruses RNA Behaviour Conclusion Natural Codes

Mathematical Theories of Language involved in Biochemistry

  • systems theory,
  • information theory,
  • biolinguistics,
  • bioinformatics,
  • synthetic biology,
  • mathematical biology
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Introduction Persistent Viruses RNA Behaviour Conclusion Natural Codes

Falsified: Mathematical theories of natural languages

  • Ludwig Wittgensteins pragmatic turn:
  • natural languages depend on social groups
  • „the meaning is its use“ (depends on context, not syntax)
  • Kurt Gödels incompleteness theorem

The construction of a contradiction-free axiomatic system is impossible (as suggested by Hilbert, Russel, Whitehead)

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  • ne gene - one Protein
  • non-coding DNA is JUNK
  • DNA - RNA - Proteins - anything else
  • Mutations (replication errors) drive genetic variation

Falsified: main assumptions in molecular biology

Introduction Persistent Viruses RNA Behaviour Conclusion Natural Codes

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  • No natural code codes itself
  • There must be agents which use such codes.
  • Code user follow syntactic, semantic, pragmatic

rules.

  • Rule-following is inherently a kind of social

interaction

Results: Empirical Knowledge about Natural Codes

Introduction Persistent Viruses RNA Behaviour Conclusion Natural Codes

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Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

Essential Agents in Cellular Life

If the genetic code is really a natural code there must be agents that

  • generate code sequences de novo
  • identify sequence-specific target sites
  • integrate in pre-existing genetic content arrangements

without destruction of former content

  • recombine according adaptational needs
  • mark sequence sites to epigentically vary meaning

What are these agents?

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Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

Essential Agents in Cellular Life

2009

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Examples of viruses/viral parts that insert into and recombine host genetic content

  • Viruses are the most abundant biological agents on this planet (10 times)
  • Only viruses assemble double stranded or single stranded RNA or DNA (+ and –)
  • Omnipresent phages in prokaryotes
  • The eukaryotic nucleus has a variety of

large dsDNA virus features

  • Persistent viral parts in mitochondria and other organelles
  • Endogenous retroviruses (active and/or defective)
  • Intronic regions that are spliced out during exon assembly

Essential Agents in Cellular Life

Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

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Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

Mitchell RS, Beitzel BF, Schroder ARW, Shinn P, Chen H, et al. (2004) Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol 2(8): e234.

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  • DNA-Viruses
  • DNA-transposons
  • RNA-Viruses
  • non-retroviral RNA viruses
  • endogenous retroviruses
  • LTRs-retrotransposons
  • non-LTRs (SINEs, LINEs, ALUs)
  • group II introns
  • group I introns
  • non-coding RNAs

Some persistent viruses/virus-derived parts

Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

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  • Transcription
  • Post-transcriptional RNA-Editing + RNA Splicing
  • Translation
  • DNA replication
  • Chromatin organisation
  • Epigenetic modifications
  • DNA recombination
.

Viral derived parts are active in

Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses

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Biocommunication and Natural Genome Editing

Introduction Natural Codes RNA Behaviour Conclusion Persistent Viruses 2009

Annals of the New York Academy of Sciences

2012

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Introduction Natural Codes Persistent Viruses Conclusion RNA Behaviour

Non-Coding RNAs: Viral derived Moduls

  • 1,5 % of the human genome code for proteins
  • 98,5% represent non-coding RNAs
  • C.Elegans and Home Sapiens share app. 20,000 genes

The difference is regulation of these genes

  • ncRNAs are co-opted adaptations of former genetic

colonizers that now act as regulatory elements

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Introduction Natural Codes Persistent Viruses Conclusion RNA Behaviour

Grammar rules of RNAs: basepairung and non-base-pairing Nucleotides

Smit S, Yarus M, Knight R Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories. RNA. 2006 Jan;12(1):1-14.

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories

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Introduction Natural Codes Persistent Viruses Conclusion RNA Behaviour

Briones C, Stich M, Manrubia SC (2009) The dawn of the RNA world: toward functional complexity through ligation of random RNA oligomers. RNA 15:743–749

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Witwer C1, Rauscher S, Hofacker IL, Stadler PF Conserved RNA secondary structures in Picornaviridae genomes. Nucleic Acids Res. 2001 Dec 15;29(24):5079-89s

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Villarreal LP, Witzany G (2013b) Rethinking quasispecies theory: from fittest type to cooperative consortia. World J Biol Chem 4:71–82

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RNA stem loops: Group Building

Jessica C. Bowman • Nicholas V. Hud • Loren Dean Williams. The Ribosome Challenge to the RNA World. J Mol Evol DOI 10.1007/s00239-015-9669-9

J Mol Evol DOI 10.1007/s00239-015-9669-9

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Introduction Natural Codes Persistent Viruses RNA-Behaviour Conclusion

Life = Physics + Chemistry + Communication

  • Genetic Information is not randomly derived
  • RNA Agents generate, identify, integrate, recombine and mark

nucleic acid sequences

  • Natural genome editing is the result of consortial interactions of

viral and subviral agents with cellular host

  • Natural genome editing agents follow syntactic, semantic and

pragmatic rules (optimizes energy cost)

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non-mechanistic explanation of

Consortial interactions

  • From single RNA stem loops to group (identity) building
  • Emergence of biological identity

(self/non-self identification competence)

  • Context dependent interactions

De novo generation of

  • Nucleic acid sequences
  • Coherent integration into pre-existing ones
  • Innovation by variations in RNA stem loops
  • Genetic identity

Introduction Natural Codes Persistent Viruses RNA Behaviour Conclusion

RNA Sociology

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Introduction Natural Codes Persistent Viruses Summary Conclusion

Leben = Physik + Chemie (1944) (Erwin Schrödinger) Leben = Physik + Chemie + (zeichenbasierte) Kommunikation (1993) (Günther Witzany)

Einleitung Natürliche Sprachen Beispiele: Pflanzen, Bakterien Sesshafte Viren Zusammenfassu

Zusammenfassung

Thank you very much for your attention!