Panmere

A special issue of Axiomathes [1] has been published which is a series of essays about the book More Than Life Itself: A Synthetic Continuation in Relation Biology by mathematical biologist Aloisius Louie. The authors include: J. A. Prideaux, John J. Kineman, Donald C. Mikulecky, and Claudio Gutiérrez, Sebastián Jaramillo, Jorge Soto-Andrade.

In addition, Louie comments on these writings in an essay of his own, providing a helpful feedback loop. For me, this was particularly useful in the case of the Gutiérrez et al essay, which I found to be a bizarre, erroneous and illogical screed. Louie pulls no punches in laying bare their errors, incoherencies, and misconceptions.

References

[1] Issue: Essays on More Than Life Itself. 2011. Axiomathes 21(3):373-489.

A paper by Juan-Carlos Letelier, María Luz Cárdenas and Athel Cornish-Bowden entitled “From L’Homme Machine to metabolic closure: Steps towards understanding life” [1] has been published in the October 2011 issue of the Journal of Theoretical Biology. The abstract:

The nature of life has been a topic of interest from the earliest of times, and efforts to explain it in mechanistic terms date at least from the 18th century. However, the impressive development of molecular biology since the 1950s has tended to have the question put on one side while biologists explore mechanisms in greater and greater detail, with the result that studies of life as such have been confined to a rather small group of researchers who have ignored one another’s work almost completely, often using quite different terminology to present very similar ideas. Central among these ideas is that of closure, which implies that all of the catalysts needed for an organism to stay alive must be produced by the organism itself, relying on nothing apart from food (and hence chemical energy) from outside. The theories that embody this idea to a greater or less degree are known by a variety of names, including (M,R) systems, autopoiesis, the chemoton, the hypercycle, symbiosis, autocatalytic sets, sysers and RAF sets. These are not all the same, but they are not completely different either, and in this review we examine their similarities and differences, with the aim of working towards the formulation of a unified theory of life.

UPDATE: If the reader desires a copy of this paper, Athel Cornish-Bowden has graciously offered to provide them with a PDF. Athel may be contacted at: acornish@ifr88.cnrs-mrs.fr

References

[1] Letelier,J.-C. Cárdenas, M. L., Cornish-Bowden, A. 2011. “From L’Homme Machine to metabolic closure: Steps towards understanding life”. J. of Theoretical Biology 286:100-113. DOI:10.1016/j.jtbi.2011.06.033

Juan-Carlos Letelier will be presenting two papers on (M,R)-systems at the ECAL 2011 (European Conference on Artificial Life). The conference is Aug 8-12 in Paris, France.

The theme of the conference sounds quite interesting:

Refocusing on biology and complex systems

Back then, in the early 1990’s, the first two ECAL conferences in Paris and Brussels were mainly centered on theoretical biology and the physics of complex systems. Today, we feel that Alife can look back on these origins and take more inspiration from new developments at the intersection between computer science and theoretical biology—thus it is our wish to refocus the conference on complex biological systems. Closing a loop, this ECAL will mark the 20th anniversary of the 1st ECAL and will be framed as a tribute to the late Francisco Varela, co-organizer in 1991 with two of this year’s committee members (Paul Bourgine, CREA, and Hugues Bersini, IRIDIA).

Scheduled for July 17, 2011 at the 55th Meeting of the ISSS in Hull, England:

10:00 to 16:30 Relational Science: A Synthesis

John Kineman and Judith Rosen, Derwent SR5

Workshop sponsored by the “Relational Science” SIG (formerly “What is Life/Living” SIG)

In this workshop we will work through concepts that take us from mechanism to relational complexity and we will gain a deep understanding of what this debate is about: that we can learn more about the causal nature of reality by exploring the full nature of complex systems rather than building knowledge from simple systems. We will see that the two views are not really in conflict, but that the traditional view in physics is retained for consistency with previous non-complex theory structures. We will see clearly how the world described by physics is a reduction of the complex reality, and how complexity appears naturally in physical, biological, and ecological systems. We will not explore the equations of physics, but will present the relational approach with examples in physics, biology, and ecology. We will discuss the underlying principles and theory structure in terms of a re-interpretation of Aristotle’s four causes and their closure in nature. We will introduce new techniques for analyzing complex systems in terms of category theory mappings, which bridge between quantitative and qualitative analysis, and also explore how to apply statistical and probability theory to practical problems in complex system analysis. The workshop will be at an advanced level conceptually and a basic level mathematically and computationally. The aim of the workshop is to sketch conceptual and computational tools for applying relational science in the natural and human world.

John Kineman notes:

A workshop and SIG website has been established by the graces of Jeff Prideaux. At this site you can access relevant information about the workshop and related materials. In particular you will find the key papers for the workshop posted there under the "Papers" tab. The URL is:

www.relationalscience.org

If we can work out the technical details there will be a livestream of the workshop and those viewing may communicate via the relational science website or the livestream chat function. The URL for the live stream, if it happens, will be:

http://www.livestream.com/relationalscience

Published in the December issue of Axiomathes. The abstract:

I formulate in relational terms the ubiquitous biological interaction of symbiosis. I explicate the topology of the different modes of relational interactions of (M, R)-networks, the entailment diagrams that model the host and the symbiont. These modes all have biological realizations as various categories of symbiotic relationships, ranging from mutualism to parasitism to infection.

I also note the final paragraph of the paper, whereby relational biology leads to a potent result:

Symbiosis—in our general sense of commensalism and parasitism in addition to mutualism—is ubiquitous in the living world and is, indeed, an essential aspect of life itself. It may even be said that competition and symbiosis are the two driving forces of the biosphere. The importance of symbiosis in evolutionary innovation is evident when one understands its role in the determination of phenotypes and genotypes, as illustrated by the various entailment modes between symbiont and host. One may even extend the definition of ‘organism’ to be more than single genetic entities, and include symbiotic units. But in relational biological terms, this generalization is already made: a union of interacting (M, R)-systems (or better, their join in the lattice of (M, R)-systems) is itself an (M, R)-system.

References

[1] Louie, A. H. 2010. “Relational Biology of Symbiosis”. Axiomathes 20(4):495-509. DOI: 10.1007/s10516-010-9117-9.

Published in the December issue of Axiomathes[1]. The abstract:

We develop a general method for applying functional models to natural systems and cite recent progress in protein modeling that demonstrates the power of this approach. Functional modeling constrains the range of acceptable structural models of a system, reduces the difficulty of finding them, and improves their fidelity. However, functional models are distinctly different from the structural models that are more commonly applied in science. In particular, structural and functional models ask different questions and provide different kinds of answers. As we clarify these differences and articulate how to use these models jointly, we extend our ability to do science and gain insight into the proper use of the terms organization, order, and emergence when describing systems in nature.

References

[1] Levin, A. 2010. “A Top-Down Approach to a Complex Natural System: Protein Folding”. Axiomathes 20(4):423-437. DOI: 10.1007/s10516-009-9093-0