Entailment of ambiguity

Everything in Rosen's work flows from the principle of 'closure to efficient cause', the necessary and sufficient distinguishing feature of complexity, and a necessary distinguishing feature of an organism. Some students of Rosen find considerable confusion over the meaning of 'closure to efficient cause'. Such confusion is unnecessary. The matter is entirely cleared up by the (M,R)-system, a set of three algebraic maps. Each map must include one of the others in its co-domain, and is itself in the co-domain of the remaining map. Structurally, the three maps form a circular hierarchy of containment. This peculiar structure is Rosen's closure. Since each map represents an efficient cause, they reveal the character of efficient cause. The efficient cause of a process is represented as its 'dynamical law', and is a constraint that arises from the intersection of the morphology of the process and the inherent constraints in reality represented by the 'laws of Nature'. A critical, observable property (evidently unnoticed by Rosen), entailed by the closure, is its inherent ambiguity. From a foundation of ambiguity, the bizarre properties of complexity (e.g., non-computability, non-fractionability, undecidability, and incompleteness) follow in a straightforward manner, often with proofs simpler than those that Rosen discovered.     

Topological Patterns in Metazoan Evolution and Development

Topological patterns in the development and evolution of metazoa, from sponges to chordates, are considered by means of previously elaborated methodology, with the genus of the surface used as a topological invariant. By this means metazoan morphogenesis may be represented as topological modification(s) of the epithelial surfaces of an animal body. The animal body surface is an interface between an organism and its environment, and topological transformations of the body surface during metazoan development and evolution results in better distribution of flows to and from the external medium, regarded as the source of nutrients and oxygen and the sink of excreta, so ensuring greater metabolic intensity. In sponges and some Cnidaria, the increase of this genus up to high values and the shaping of topologically complicated fractal-like systems are evident. In most Bilateria, a stable topological pattern with a through digestive tube is formed, and the subsequent topological complications of other systems can also appear. The present paper provides a topological interpretation of some developmental events through the use of well-known mathematical concepts and theorems; the relationship between local and global orders in metazoan development, i.e., between local morphogenetic processes and integral developmental patterns, is established. Thus, this methodology reveals a “topological imperative”: A certain set of topological rules that constrains and directs biological morphogenesis.     

Overcoming the Newtonian paradigm: The unfinished project of theoretical biology from a Schellingian perspective

Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics.     

On the Semio-Mathematical Nature of Codes

The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing systems but “meaning-making” systems. Therefore, what flows in the genetic system is not “information” but “value.” We define meaning, meaning-making, and value and then use these terms to explain the abstract dynamics of coding, which can illuminate many forms of sign-mediated activities in biosystems.     

Creating parts that allow for rational design: Synthetic biology and the problem of context-sensitivity

The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins’ account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.     

Closure to efficient causation, computability and artificial life

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.     

The Romantic Conception of Robert J. Richards

In his new book, The RomanticConception of Life: Science and Philosophyin the Age of Goethe, Robert J. Richardsargues that Charles Darwin's trueevolutionary roots lie in the German Romanticbiology that flourished around thebeginning of the nineteenth century. It isargued that Richards is quite wrong in thisclaim and that Darwin's roots are in theBritish society within which he was born,educated, and lived.