Panmere

Robert Rosen’s anticipatory systems are the focus of the first in a series of thematic issues of the International Journal of General Systems [1], as noted by George Klir in the issue editorial:

The primary distinction is that thematic issues are invited and written by one author or, possibly, by one team of authors. The purpose of publishing each of these thematic issues is not only to stimulate interest in the covered area, but also to convey a message that this area is central to the aims of the journal, thus encouraging submission of papers contributing to it.

This is the first thematic issue. It is devoted to anticipatory systems and its author, Mihai Nadin, is one of the most distinguished contributors to this area. While the idea was introduced in two papers published by Robert Rosen in 1974 in the first volume of this journal, virtually nothing on anticipatory systems has been covered in the following 37 volumes. It is, thus, timely to report on the tremendous developments since those early papers and express in this way the ongoing interest of the International Journal of General Systems in this important area. It is my hope that this thematic issue will stimulate the basic and applied research in anticipatory systems and, at the same time, encourage researchers working in the area to submit papers describing their work to this journal. Finally, I would like to express my gratitude to Professor Mihai Nadin for accepting my invitation and preparing, within a relatively short time, this interesting and comprehensive overview of the rapidly growing area of anticipatory systems.

The issue features a paper by Mihai Nadin, “Anticipation and dynamics: Rosen’s anticipation in the perspective of time” [2].

* Notably, the issue is currently free to download.

* In addition, it appears that Taylor & Francis have made access to issues of the International Journal of General Systems and the International Journal of System Science available for free, for at least this month. So, do a sitewide search for “Robert Rosen” as the Author Name and download his papers now!

References

[1] International Journal of General Systems, Volume 39 Issue 1 2010.

[2] Nadin, M. 2010. “Anticipation and dynamics: Rosen’s anticipation in the perspective of time“. IJGS 39(1):3-33. DOI: 10.1080/03081070903453685.

The folks at the n-Category Café have been discussing the possible relationships between time and category structure. For example, these comments from John Baez on the post “Kan Lifts”:

Why is Set so different than Set^op? It’s because the morphisms are functions: relations that can be many-to-one, but not one-to-many.

Why do many-to-one but not one-to-many relations get singled out for single treatment and dubbed ‘functions’? Because functions are supposed to be ‘deterministic’: the cause must determine the effect. We don’t care if the effect fails to determine the cause.

Why does our customary concept of determinism have this asymmetry built in? Well, we see it a lot in ordinary life. It’s often (though not always) true that the initial state of an experiment determines the final outcome. But it’s much less common for the final outcome to determine the initial state… at least, not in an easily visible way.

For example, take a heat distribution and run it forwards to equilibrium. We always get the same equilibrium, regardless of the initial conditions.

This asymmetry is built into equations like the heat equation, but it seems absent from the fundamental laws of physics — so far, anyway. This leads to a big puzzle: “why is there this ‘arrow of time’?”

Nobody knows the answer, except “that’s how this universe is: there’s a low-entropy big bang in the past, and a high-entropy expansion in the future, as far as we can see.”

So, the beautiful time-symmetric formalism of quantum theory, so nicely modelled by the dagger-categories we’ve learned to love, is far removed from common experience, where functions rule the roost.

See also the recent post “The Arrow of Time in Cat“.

Because in the encyclopedia of nature, wheels are rarely mentioned.

The Journal of Biology has begun an interesting thematic series entitled “Ockham’s Broom“[1], which they describe thusly:

Ockham’s broom is an implement conceived by Sydney Brenner as the device whereby inconvenient facts are swept under the carpet. This is common practice in biological research where the facts often cannot be explained all at once; but in due course the edge of the carpet must be lifted and the untidy reality confronted. In this eclectic series, contributors examine the sweepings from their fields and offer a fresh perspective on generally accepted views. (Ockham’s broom should not be confused with the more familiar Ockham’s razor which inspired this less philosophically correct concept.)

Lifting the edge of the carpet and confronting the untidy reality was something which Rosen continually pursued. As he wrote in his Autobiographical Reminiscences[2]:

Quite early in my professional life, a colleague said to me in exasperation, “The trouble with you, Rosen, is that you keep trying to answer questions nobody wants to ask.” This is doubtless true. But I have no option in this; and in any event, the questions themselves are real, and will not go away by virtue of not being addressed.

The first article in the Ockham’s Broom series, “Molecular machines or pleiomorphic ensembles: signaling complexes revisited“[3] is almost certainly one Rosen would have appreciated. The article begins:

A cell must constantly monitor cues from its environment and adjust its activities accordingly. Faithful and reliable signal transduction is not only essential for normal life, but its malfunctioning underlies many human health problems. Enormous strides have been made in the past several decades toward understanding how this process works at the molecular level. It is notable that when describing the fruits of that work, those of us who work on cell signaling would be hard-pressed to avoid terms such as ‘machinery’ and ‘mechanism’. The analogy between cell signaling and man-made machines is all-pervasive, frequently adopting the imagery of elaborate clockwork mechanisms or electronic circuit boards. This perception is undoubtedly shaped by what we know: the machines that we use in our everyday life and the ways that we describe such machines in diagrams or in words. But is this really an accurate, or useful, description of the actual processes used by cells? We will argue that signaling complexes typically consist of pleiomorphic and highly dynamic molecular ensembles that are challenging to study and to describe accurately. Conventional mechanical descriptions not only misrepresent this reality, they can be actively counterproductive by misdirecting us from investigating critical issues.

The authors go on to explain how the systems involved have enormous number of potential states and so the systems themselves may have a range of behaviors far exceeding the behavior of machine-like models of those systems. In Rosennean terms, the physical systems are open to many interactions and degrees of freedom to which the machine-like models are closed.

Facing this situation, either one somehow has to demonstrate that the behaviors not captured by these models can be ignored as being “noise” or unimportant variations, or one has to widen the classes of models used in order to more fully capture the behavior of the systems being modeled. It does not suffice for this untidy situation to be ignored, to be “swept under the carpet”. As Rosen said, “the questions themselves are real, and will not go away by virtue of not being addressed”. The authors conclude:

The pleiomorphic, heterogeneous, non-stoichiometric nature of signaling complexes provides a serious conceptual challenge for biologists, who are naturally more comfortable thinking of mechanical devices with states that are clearly defined and limited in number. But the current practice of avoiding these properties because they are difficult to study and to describe is likely to be a mistake. Only by confronting this issue head-on will be able to assess, once and for all, its real impact on signal transduction.

References

[1] Editorial: Robertson, M. 2009. Journal of Biology. 8(9):79. DOI:10.1186/jbiol187 Series: http://jbiol.com/series/ockhams_broom

[2] Rosen, R. 2006. “Autobiographical Reminiscences of Robert Rosen”. Axiomathes 16(1-2):1-23. DOI:10.1007/s10516-006-0001-6

[3] Mayer, B., Blinov, M., Loew, L. 2009. “Molecular machines or pleiomorphic ensembles: signaling complexes revisited”. Journal of Biology. 8(9):81. DOI:10.1186/jbiol185

This PDF [1] contains the currently known errata for Aloisous Louie’s More Than Life Itself [2]. Aloisius has confirmed these. Fortunately, they are few, only typographical in nature, and none of them are too serious. If anyone happens to find any others, please let me know and I will update the PDF.

References

[1] ML Errata.pdf

[2] Louie, Aloisius H. 2009. More Than Life Itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag, Frankfurt. 388 pp. ISBN: 978-3-86838-044-6

Alan Levin has published the paper “A Top-Down Approach to a Complex Natural System: Protein Folding” in Axiomathes. 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.

A copy of the paper can also be downloaded from Alan Levin’s website.

References

[1] 2009. Levin, A. “A Top-Down Approach to a Complex Natural System: Protein Folding”. Axiomathes. DOI 10.1007/s10516-009-9093-0.