On several occasions I have pointed out that the lesson taught us by recent developments in physics regarding the necessity of a constant extension of the frame of concepts appropriate for the classification of new experiences leads us to a general epistemological attitude which might help us to avoid apparent conceptual difficulties in other fields of science as well. Since, however, the opinion has been expressed from various sides that this attitude would appear to involve a mysticism incompatible with the (...) true spirit of science, I am very glad to use the present opportunity of addressing this assembly of scientists working in quite different fields but united in their striving to find a common ground for our knowledge, to come back to this question, and above all to try to clear up the misunderstandings which have arisen. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal (...) processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

Throughout the history of molecular biology, the primary meaning of biological information has been taken from the image of a word-based linguistic code. I want to argue that the metaphor of such a code does not begin to capture either the variety or the richness of the processes by which nucleotide sequences inform biological processes. Current research demonstrates that nucleotide sequences inform not only development but also heredity and evolution, and they do so in all sorts of ways. Even though (...) they do not exhaust the varieties of biological information employed in these processes, I claim that the power of DNA sequences to inform these processes is richer and perhaps far greater than the conventional understanding of genetic information permits, indeed richer than what any of our images of simple linguistic codes or of senders and receivers permits. Rather than a tape in a Turing machine or a message or signal sent through the generations, DNA is first and foremost a physicochemical structure with a range of potential uses by the physicochemical arsenal of biological cells that is so large as to expose the poverty of our most familiar metaphors. Recognition of this fact leads us to conclude that DNA is both more and less than we thought—more because it carries both symbolic and non-symbolic information and less because accepting that fact undermines its radical distinction from other biological molecules. (shrink)

The rise of the mechanistic worldview in the seventeenth century had a major impact on views of biological generation. Many seventeenth century naturalists rejected the old animist thesis. However, the alternative view of gradual mechanistic formation in embryology didn’t convince either. How to articulate the peculiarity of life? Researchers in the seventeenth century proposed both “animist” and mechanistic theories of life. In the eighteenth century again a controversy in biology arose regarding the explanation of generation. Some adhered to the view (...) that life is a physical property of matter (e.g. Buffon), others saw living entities as the result of the development of pre-existing germs (e.g. Bonnet). Naturalists, lacked a convincing account that could guide their research. In interaction with leading naturalists of his time Immanuel Kant articulated an approach to explaining generation. Kant’s account, delineated in his Kritik der Urteilskraft (Critique of the power of judgment) (1790), is a combination of Newtonian non-reductionist mechanism in explanation, and a concept of natural end comparable to Stahl’s formal conception of organic bodies. It consists of two claims: a) in biology only mechanical explanation is explanatory, and b) living entities contain some original organisation, which is mechanically unexplainable. In the nineteenth century this approach influenced naturalists as Müller, Virchow, and Von Baer, in their physiological research. Dissatisfied with a sheer mechanistic or, on the other hand, a sheer teleological approach, they appreciated the Kantian account of mechanical explanation of natural ends. In Germany, in the second halve of the nineteenth century, Ernst Haeckel reopened the debate about abiogenesis, which still continuous. (shrink)

A sign is something that refers to something else. Signs, whether of natural or cultural origin, act by provoking a receptive system, human or nonhuman, to form an interpretant (a movement or a brain activity) that somehow relates the system to this "something else." Semiotics sees meaning as connected to the formation of interpretants. In a biosemiotic understanding living systems are basically engaged in semiotic interactions, that is, interpretative processes, and organic evolution exhibits an inherent tendency toward an increase in (...) semiotic freedom. Mammals generally are equipped with more semiotic freedom than are their reptilian ancestor species, and fishes are more semiotically sophisticated than are invertebrates. The evolutionary trend toward the production of life forms with an increasing interpretative capacity or semiotic freedom implies that the production of meaning has become an essential survival parameter in later stages of evolution. (shrink)