Questions about cell biology / organization environment boundaries

William P. Hall

17 April 2005


The last week's discussion on autopoiesis-dialognet has been interesting, as several of the topics are central to the paper I am currently working on, focusing on the autopoietic basis of biological systems. Peter Bond's latest contribution on "organization and structure" - especially his paper on "Technology as Knowledge, as paradigm, as culture, and as an ecology of ideas-in-practice" (http://www.knowledgeboard.com/cgi-bin/library.cgi?action=detail&id=5242)  and Steven Hoath's latest on "questions about cell biology" are particularly relevant.

I'm currently assembling ideas relating to applications of the following questions relating to cellular forms of life (i.e., cells to colonial organisms and biological species) from a number of different paradigms: 

This project extends the approach introduced in my paper just published in The Learning Organization 12(2):169-188 (eprint available on - http://www.hotkey.net.au/~bill.hall/TheBiologicalNatureshortrevjmf1bh3.pdf). This is based on analyzing the nature of cognition and "knowledge" in autopoietic systems in the epistemological framework provided by Karl Popper's theory of knowledge based on a concept of three worlds or ontological domains. In to trying to account for/describe the growth of knowledge within autopoietic systems in physically materialistic terms, my research has faced some very interesting epistemological issues relating to observers and observations that also greatly troubled Maturana and Varela.

As I was only dimly beginning to understand in my Learning Organization paper, Howard Pattee's concept of epistemic cuts provides a robust physical foundation for Popper's three worlds and defining the various forms of knowledge that can be formed within autopoietic systems. A brief sketch is presented below. This is followed by a working bibliography of papers relating to the epistemological issues raised by Pattee's ideas.

World 1

World 1 is the dynamic reality that exists independently from the cognition of any observer. However world 1  includes observers and their cognitive processes within this dynamic reality. In the sense that I believe world 1 exists independently from my perceptions of it, I am a realist even though I fully accept that all my knowledge of this reality is constructed within my mind. 

Autopoietic entities are complex dynamic systems that emerge within the framework of universal laws and constraints of world 1. Hugo Urrestarazu has made an excellent start towards describing what autopoiesis looks like in this world (http://autopoietic.net/boundaries.pdf).

The existence and growth of knowledge is purely a consequence of the existence and evolution of complex, autopoietic systems. Existence and evolution of complex systems takes place in W1. Knowledge that persists in the structure of autopoietic systems consists of those persistent aspects of the autopoietic system's structure that enable the system to survive perturbations through time. 

World 2

Following Pattee and his student Luis M Rocha, there is an ontological or epistemic "cut" between the real world (W1) and the representation or map of that world in the active cognition of autopoietic entities that guides their regulatory responses to that world. The "cut" separates the world that is from some form of observation or representation of that world.

For reasons elucidated by Popper, Maturana and Varela, and the radical constructivists such as von Glaserfeld and Riegler, world representations in the autopoietic systems cannot reasonably be exact and perfect in all respects. The processes of autopoiesis reflect the existence of a form of semantic (or organizational) closure the incorporates enough experience of from a history of existence that the autopoietic entity in some way "knows" what it has to do in order to self-regulate its autopoiesis in response to perturbations in the world. However, where the world representations do reflect regularities in existence, Popper and the other evolutionary epistemologists, and Pattee and Rocha have shown that the process of "blind variation" and error elimination will lead to the growth of increasingly more functional representations of those regularities.

At this level, the knowledge is dispositionally representational - basically as a consequence of the inheritance of various regularities of structure and dynamics within the autopoietic system that reflect regularities of world 1. This is the only kind of knowledge available to newly emerged autopoietic systems.

In this Popperian framework, I would regard technological infrastructure described by Peter Bond as belonging in world 2. Technology comprises tools that extend our reach or cognition. Technology is as much a part of human dispositional "knowledge" as are the cells of our brains, muscles and digestive systems.

World 3 

Where this representational knowledge becomes codified (e.g., in nucleic acids, language, writing etc.) a second epistemic cut is created between the dispositional dynamics of the autopoietic entity and encoded representations of the "knowledge" used to guide and regulate that dispositional dynamics. Codification establishes Popper's world 3.

In world 3 the knowledge is not dispositional, as it is normally encoded via arbitrary regularities in a physical substrate that is energetically neutral or "degenerate" with regard to the semantic content of the coded information carried by the substrate, and can persist in stable form through time - in some cases even independently of the autopoietic entity that encoded the knowledge. The semantic meaning of the code is determined by its impact on the structure of the autopoietic system when the code is transcribed and translated into components that are dynamically active within the autopoietic structure.

Obviously a great deal more work will be required work out how these ideas are applicable to different focal levels of autopoietic systems based on living cells (e.g., monera, eukaryotes, multicellular organisms, colonial and social organisms, and biological species). However, I am confident that the ideas above are the key clues to understanding the origins and evolution of the various kinds of knowledge-based systems and activities in living things.

In the following bibliography, almost all of the cited references are available electronically, either directly through the Web (where I have given URLs) or via on-line services available to major research libraries. In my case I am able to achieve access thanks to an honorary fellowship provided to me by Monash University's Faculty of Information Technology.

Additional Bibliography on the Epistemology of Autopoietic Cognition 

(building on refs in my Learning Org paper) 

  1. Andrade, E. 2002. The Organization of Nature: Semiotic Agents as Intermediaries between Digital and Analog Informational Spaces. SEED 2(1):56-84 - http://www.library.utoronto.ca/see/SEED/Vol2-1/Andrade/Andrade.htm
  2. Atmanspacher H. 1997. Cartesian cut, Heisenberg cut, and the concept of complexity. World Futures 49, 333-355. 
  3. Atmanspacher, H. 1999. Ontic and epistemic descriptions of chaotic systems. In: Proceedings of CASYS 99, ed. by D. Dubois, Springer, Berlin 2000, pp. 465-478 - http://www.igpp.de/english/tda/pdf/liege.pdf 
  4. Atmanspacher, H. 2004. Quantum theory and consciousness: An overview with selected examples. Discrete Dynamics in Nature and Society 1:51-73 - http://dx.doi.org/10.1155/S102602260440106X 
  5. Atmanspacher, H. 2004. Quantum Approaches to Consciousness, The Stanford Encyclopedia of Philosophy (Winter 2004 Edition), Edward N. Zalta (ed.), - http://plato.stanford.edu/archives/win2004/entries/qt-consciousness/ 
  6. Atmanspacher, H, Bishop, R.C. and Amann., A. 2001. Extrinsic and intrinsic irreversibility in probabilistic dynamical laws. In: Foundations of Probability and Physics, ed. by A. Khrennikov. World Scientific, Singapore, pp. 50-70 
  7. Atmanspacher, H, Kronz, F. 1998. Many Realisms. Acta Politechnica Scandanavica. Ma-91:31-43. - http://www.igpp.de/english/tda/pdf/echo3.pdf 
  8. Atmanspacher, H, Primas, H. 2003. Epistemic and ontic quantum realities. In: Time, Quantum, and Information, ed. by L. Castell and O. Ischebeck. Springer, Berlin pp. 301-321 - http://www.igpp.de/english/tda/pdf/cfvw.pdf 
  9. Atmanspacher, H. and Wiedenmann, G. 1999. Some basic problems with complex systems. In: Large Scale Systems: Theory and Applications, ed. by N. T. Koussoulas and P. Groumpos, Elsevier, Amsterdam, pp. 1059-1066. http://www.igpp.de/english/tda/pdf/patras.pdf 
  10. Bailly F., Longo, G. 2003 Objective and Epistemic Complexity in Biology (Towards a "conceptual organization"). Invited lecture, International Conference on Theoretical Neurobiology, National Brain Research Centre, New Delhi, INDIA, February , 2003. - http://www.nexial.org/Life/obj-epi-complex.pdf 
  11. Balazs, A. 2004. What does a molecule want? The myth of the self-replicating molecule (comments on the ýselfish-geneţ paradigm). BioSystems 73:1-11. 
  12. Balazs, A. 2004. Is there a ýmolecular Nirvana Principleţ? Towards a unified resolutional model of the biological symbol˝matter dichotomy. BioSystems 77:1˝10. 
  13. Bentolila, S. Forthcoming. ýLive memoryţ of the cell, the other hereditary memory of living systems. BioSystems [in press] 
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  15. Brier, S. 1996. From second-order cybernetics to cybersemiotics: A semiotic re-entry into the second-order cybernetics of Heinz von Foerster. SYSTEMS RESEARCH 13 (3): 229-244 
  16. Brier, S. 1998 Cybersemiotics: a transdisciplinary framework for information studies. BioSystems 46 (1998) 185˝191. 
  17. Brier, S. 1999: Biosemiotics and the foundation of cybersemiotics. Reconceptualizing the insights of Ethology, second order cybernetics and PeirceÝs semiotics in biosemiotics to create a non-Cartesian information science. Semiotica, 127-1/4, 1999, 169-198. Special issue on Biosemiotics. - http://www.flec.kvl.dk/sbr/full text documents/Reconceptualizing.pdf 
  18. Brier, S. 2001. Cybersemiotics: A reconceptualization of the foundation for information science. SYSTEMS RESEARCH AND BEHAVIORAL SCIENCE 18 (5): 421-427. 
  19. Brier, S. 2003. The Cybersemiotic Model of Communication: An Evolutionary View on the Threshold between Semiosis and Informational Exchange. tripleC 1(1): 71-94, 2003 http://triplec.uti.at/articles/tripleC1(1)_Brier.pdf 
  20. Brier, S. 2003. Information seen as part of the development of living intelligence: the five-leveled cybersemiotic framework for FIS. Entropy 5:88-99 - http://www.mdpi.org/entropy/papers/e5020088.pdf 
  21. Brooks, D.R. 2002. Taking Evolutionary Transitions Seriously. SEED 2(1):6-24 - http://www.library.utoronto.ca/see/SEED/Vol2-1/Brooks/Brooks.htm 
  22. Collier, J. 2003. Hierarchical dynamical information systems with a focus on biology. Entropy 5:100-124. - http://www.mdpi.org/entropy/papers/e5020100.pdf 
  23. Corning. P.A. 2001. "Control information": The missing element in Norbert Wiener's cybernetic paradigm? Kybernetes. London: 2001. Vol. 30, Iss. 9/10; pg. 1272, 17 pgs 
  24. Cottam, R., Ranson, W., Vounckx, R. 2004. Autocreative Hierarchy I: Structure, Ecosystemic Dependence and Autonomy. SEED 4(2):24-41 - http://www.library.utoronto.ca/see/SEED/Vol4-2/Cottam et al 2.htm 
  25. Cottam, R., Ranson, W., Vounckx, R. 2004a. Autocreative Hierarchy II: Dynamics Self-Organization, Emergence and Level-Changing. SEED 4(2):42-60 - http://www.library.utoronto.ca/see/SEED/Vol4-2/Cottam et al 2.htm
  26. Di Guilio, M. 2005. The origin of the genetic code: theories and their relationships, a review. BioSystems 80:175˝184
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  32. Emmeche, C. 2004. A-life, Organism and Body: the semiotics of emergent levels. Published pp. 117-124 in: Mark Bedeau, Phil Husbands, Tim Hutton, Sanjev Kumar and Hideaki Suzuki (eds.): Workshop and Tutorial Proceedings. Ninth International Conference on the Simulation and Synthesis of Living Systems (Alife IX), Boston Massachusetts, September 12th, 2004. - http://www.nbi.dk/~emmeche/cePubl/2004e.alife9_01e.pdf
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