My overall impression of the book is very positive. It is not only a comprehensive, rigorous and well-written overview of Rosen’s life-long contributions to theoretical biology, but it also contains some additional contributions by Louie himself to this area. I consider the book very relevant to all readers of this journal, not only those interested in biology. The book presents the material at two levels, a level of conceptual/philosophical discussion and a level of rigorous mathematical treatment. Understanding the latter requires substantial mathematical maturity. I suspect that the most challenging aspect of the book for many readers will be the heavy use of category theory, which plays an important role in Rosen’s system theory. Although requisite mathematical preliminaries are concisely presented in the book, more extensive knowledge, especially in category theory, is likely to be needed for full understanding of the material covered.

References

[1] Klir, G. 2010. Book Review of “More than life itself: A synthetic continuation in relational biology”. IJGS 39(7):783 – 797. DOI:10.1080/03081079.2010.504338.

[2] Louie, A. 2009. More Than Life itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag. ISBN 978-3-86838-044-6.

There are deep underlying similarities between Rosen’s (M,R) systems as a definition of life and the RAF sets (Reflexive Autocatalytic systems generated by a Food source) introduced by Hordijk and Steel as a way of analyzing autocatalytic sets of reactions. Using RAF concepts we have systematically explored the set of possible small idealized metabolic networks, searching for instances of (M,R) systems. This exhaustive search has shown that the central requirement of Rosen’s framework, unicity of Φ, becomes harder and harder to obtain as the network grows in size. In addition, we give an expression for operators f, β and in terms of RAF sets.

The Proceedings are available as an Open Access e-book from MIT Press here.

References

[1] Jaramillo, S., Honorato-Zimmer, R., Pereira, U., Contreras, D.,  Reynaert, B., Hernández, V., Soto-Andrade, J., Cárdenas, M.L., Cornish-Bowden, A., Letelier, J. C. 2010. “(M,R) Systems and RAF Sets: Common Ideas, Tools and Projections”. Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems.

[2] 2010. Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems. MIT Press. ISBN-10:0-262-29075-8 ISBN-13:978-0-262-29075-3

If complexity is a necessary but not sufficient premise for the existence and expression of the living, anticipation is the distinguishing characteristic of what is alive. Anticipation is at work even at levels of existence where we cannot refer to intelligence. The prospect of artificially generating aesthetic artifacts and ethical constructs of relevance to a world in which the natural and the artificial are coexistent cannot be subsumed as yet another product of scientific and technological advancement. Beyond the artificial, the synthetic conjures the understanding of aesthetics and ethics no longer from the perspective of the How? type of question, but rather the Why? Given the current infatuation with synthetic biology (i.e., making life from non-life), there is a practical consequence to such considerations. Synthetic life, as any other form of life, implies the possibility of evolution. Anticipation, which is the underlying factor of evolution, is thus expected. At the level of human existence, anticipation is expressed, for instance (but not exclusively), in aesthetic forms and ethical values. This translates, in turn, into an argument for the role aesthetics and ethics play in the process. Consequently, to qualify as life, the synthesis of the physical and the living will have to efficiently handle ambiguity. Current computational facilities, regardless of their nature or performance, operate exclusively in the semiotic domain of the well defined non-ambiguous.

A preprint PDF version is available here.

References

[1] Nadin, M. 2010. “Anticipation and the artificial: aesthetics, ethics, and synthetic life”. AI & Society 25(1):103-118. DOI: 10.1007/s00146-009-0243-0.

This essay is an attempt to construct an artificial dialog loosely modeled after that sought by Robert Maynard Hutchins who was a significant influence on many of us including and especially Robert Rosen. The dialog is needed to counter the deep and devastating effects of Cartesian reductionism on today’s world. The success of such a dialog is made more probable thanks to the recent book by A. Louie. This book makes a rigorous basis for a new paradigm, the one pioneered by the late Robert Rosen. If we are to make such a paradigm shift happen, it has to be in the spirit of the dialog. The relationship between science, economics, technology and politics has to be openly recognized and dealt with. The message that Rosen sent to us has to be told outside small select circles of devotees. The situation has even been described by some as resembling a cult. This is no way for universal truths like these to be seen. The essay examines why this present situation has happened and identifies the systemic nature of the problem in terms of Rosen’s concepts about systems. The dialog involves works by George Lakoff, W. Brian Arthur, N. Katherine Hayles, Robert Reich and Dorion Sagan. These scholars each have their own approach to identifying the nature of the interacting systems that involve human activity and the importance of identifying levels of abstraction in analyzing systems. Pooling their insights into different facets of a complex system is very useful in constructing a model of the self referential system that humans and their technology have shaped. The role of the human component in the whole earth system is the goal of the analysis. The impact of the Cartesian reductionist paradigm on science and the related aspects of human activity are examined to establish an explanation for the isolation of Rosen’s paradigm. The possible way to proceed is examined in the conclusion.

A preprint version is available here.

References

[1] Mikulecky, D. 2010. “Even More than Life Itself: Beyond Complexity”. Axiomathes 4(20). DOI: 10.1007/s10516-010-9119-7.

The unanimous Declaration of the thirteen united States of America,

When in the Course of human events, it becomes necessary for one people to dissolve the political bands which have connected them with another, and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature’s God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.–That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, –That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness. Prudence, indeed, will dictate that Governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn, that mankind are more disposed to suffer, while evils are sufferable, than to right themselves by abolishing the forms to which they are accustomed. But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute Despotism, it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security.–Such has been the patient sufferance of these Colonies; and such is now the necessity which constrains them to alter their former Systems of Government. The history of the present King of Great Britain is a history of repeated injuries and usurpations, all having in direct object the establishment of an absolute Tyranny over these States. To prove this, let Facts be submitted to a candid world.

(more…)

References:

[1] Miller, R. (ed.), Poli, R. (ed.). 2010. Special Issue: Anticipatory systems and the philosophical foundations of futures studies. foresight 12(3).

[2] http://fumee.co.cc/?page_id=7

The important and consequential Venter achievement is an impressive one in technology, but no synthetic life, alas, has been made. An achievement is diminished if it is accompanied by overreaching claims of success, when such hyperbolic ‘accomplishment’ is illusory, and not entailed from what has actually been done.

References

[1] Louie, A. 2009. More Than Life itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag.

[2] Louie, A. 2010. “Artificial Claims About Synthetic Life: The View from Relational Biology”. Jrnl of Cosmology. Vol 8. Article 19. 

[3] Gibson et al. 2010. “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome”. Science. DOI: 10.1126/science.1190719

Chitosan, a non-toxic biodegradable polycationic polymer with low immunogenicity, has been extensively investigated in various biomedical applications. In this work, chitosan has been demonstrated to seal compromised nerve cell membranes thus serving as a potent neuroprotector following acute spinal cord trauma. Topical application of chitosan after complete transection or compression of the guinea pig spinal cord facilitated sealing of neuronal membranes in ex vivo tests, and restored the conduction of nerve impulses through the length of spinal cords in vivo, using somatosensory evoked potential recordings. Moreover, chitosan preferentially targeted damaged tissues, served as a suppressor of reactive oxygen species (free radical) generation, and the resultant lipid peroxidation of membranes, as shown in ex vivo spinal cord samples. These findings suggest a novel medical approach to reduce the catastrophic loss of behavior after acute spinal cord and brain injury.

References

[1] Knight, K. 2010. “CHITOSAN REPAIRS DAMAGED SPINAL CORD“. J. of Exp. Biol. 213:i-a. DOI:10.1242/jeb.045039.

[2] Cho, Y., Shi, R., Borgens, R. “Chitosan produces potent neuroprotection and physiological recovery following traumatic spinal cord injury“. J. of Exp. Biol. 213:1513-1520. DOI:10.1242/jeb.035162

]]> http://www.panmere.com/?feed=rss2&p=107 http://www.panmere.com/?p=106 http://www.panmere.com/?p=106#comments Sun, 21 Mar 2010 14:15:02 +0000 Tim Gwinn http://www.panmere.com/?p=106 I missed the publication of this last month. The abstract [1]:

The major insight in Robert Rosen’s view of a living organism as an (M,R)-system was the realization that an organism must be “closed to efficient causation”, which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure.

This is a wide-ranging paper which seeks to illuminate and clarify “closed to efficient causation” and its consequences. In the relatively short space of 14 pages, the authors manage not only to delve into some of the mathematical aspects of “closed to efficient causation”, but also counter the arguments of a number of previous critics who had erroneously claimed that “closed to efficient causation” models are simulable.

References

[1] Cárdenas,M.L., Letelier,J.-C., Gutierrez,C., Cornish-Bowden,A., Soto-Andrade,J. 2010. “Closure to efficient causation, computability and artificial life”. J. of Theoretical Biology. 263(1):79-92. DOI:10.1016/j.jtbi.2009.11.010.

Although the author does provide a historical overview of various interpretations of ‘holism’ and ‘reductionism’, the end result remains: a lack of clarity, specificity and agreement over the meaning of these terms. In addition, the term ’systems biology’ is arguably equally nebulous.

For my part, there is perhaps nothing more useless in science than arguing between two putatively contrary ill-defined concepts (holism and reductionism), especially if the argument is in relation to how those concepts apply to a third ill-defined concept (systems biology).

Even the author states:

We may not know exactly what modern holism in systems biology is – although we can perhaps generalise that it is usually explanatory ontological antireductionism with some tendencies to epistemological antireductionism - but we do know that it is against reductionism. That might be the end of the discussion, were it not for the fact that it is not entirely clear if we know what reductionism is either.

Rosen’s work arises during the discussion, but the author appears to misstate Rosen’s view:

Although neo-reductionism has had a low profile among systems biologists and biologists in general, a new kind of holism, Relational Biology, has attracted attention, mostly among those who are dissatisfied with traditional molecular biology but also sceptical about the explanatory capabilities of modern versions of holism. Developed over some years by Robert Rosen and a small band of disciples, relational biology does not dispense with the hierarchy of the Vienna Circle, but rather inverts it. Rosen, based on some earlier similar ideas by Elsasser, claimed that physics, by virtue of its application to homogeneous molecular structure is in fact not the fundamental science, but actually a special case. Biology, as the science of the complex, is the lowest level in the layer model.

The notion of a hierarchy (and its inversion) is unhelpful with respect to understanding Rosen’s view, nor did Rosen argue that biology was more fundamental than physics. Also, “Biology, as the science of the complex” can be a somewhat confusing phrasing.

Rosen realized and proved [2] (and Louie proved in even more detail [3]) that if all the models of a given system are simulable (i.e. Turing-computable) then the analytic models of the system coincide with the synthetic models of the system. That is, all the information one can have about such systems can be found in its synthetic models alone. Moreover, the entire collection of these synthetic models can be combined into one model, which is called the largest model of the system. As an immediate result of this coinciding, the properties of such systems are entirely fractionable and can thus possess no “emergent” properties. Rosen defined this class of systems to be the class of mechanisms or simple systems.

By contrast, the class of complex systems are those systems which possess at least one nonsimulable model and, as a consequence, possess at least one analytic model which does not coincide with a synthetic model. That is, there is at least one model (i.e., analytic model) of the system which describes properties of the system for which there is no corresponding model of an assemblage of parts of the system (i.e., synthetic model). In simpler terms, in such a case the system possesses properties which cannot be described by an assemblage of the properties of its parts.

This means of classification allows for a precise definition of ‘emergent property’, if one so desires.

It is important to point out, as Rosen did repeatedly, that complex systems can still possess many analytic models which coincide with synthetic models: “The failure of a system to be a mechanism does not at all mean that has no mechanical models; indeed, in some sense, these form a subcategory of the category of all its models.” If this were not the case, then all the obvious successes of reductionistic-oriented science to date would not have been possible. Thus one must be careful when stating that biology is “the science of the complex”.

As a corollary: the existence of an abundance of simple models in a system cannot, by itself, logically entail that simple models alone are exhaustive of all models of the system

The class of organisms, Rosen argued persuasively, form a subset of the class of complex systems; however, organisms are not the entire class of complex systems.

Rosen also proved that the very structure of the Newtonian paradigm (and its quantum mechanical variant) is such that it inherently treats physical systems as simple systems: that is all that this paradigm can encode (or “see”) about any system, simple or complex.

To put all this together, in the Rosennean picture:

• The class of all natural systems can be bifurcated into two non-intersecting subsets: simple systems and complex systems.
• The class of organisms are a subset of the class of complex systems.
• Modern physics is founded on a paradigm which can treat systems only as simple systems.
• Therefore, physics needs to alter/enlarge its paradigm if it is to more fully model  complex systems, such as organisms.
• Necessarily, some of those models will be nonsimulable.
• Likewise, systems biology will need alter/enlarge its paradigm to embrace nonsimulable models.

So, there is no “hierarchy” in the Rosennean view, nor is biology in any sense more fundamental than physics. Instead, the complex system nature of biological organisms is symptomatic of the need for more encompassing approaches in both biology and physics. As Rosen said, “Perhaps the first lesson to be learned from biology is that there are lessons to be learned from biology.” [4]

References

[1] Gatherer, D. 2010. “So what do we really mean when we say that systems biology is holistic?”. BMC Systems Biology. 4(22).DOI:10.1186/1752-0509-4-22

[2] Rosen, R. 1991. Life Itself: A Comprehensive Inquiry Into The Nature, Origin, and Fabrication of Life. Columbia Univ. Press

[3] Louie, A. 2009. More Than Life itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag.

[4] Rosen, R. 2000. Essays on Life Itself. Columbia Univ. Press.