The mathematical theory of communication.

All sciences have epistemic assumptions, a language for expressing their theories or models, and symbols that reference observables that can be measured. In most sciences the language in which their models are expressed are not the focus of their attention, although the choice of language is often crucial for the model. On the contrary, biosemiotics, by definition, cannot escape focusing on the symbol–matter relationship. Symbol systems first controlled material construction at the origin of life. At this molecular level it is (...) only in the context of open-ended evolvability that symbol–matter systems and their functions can be objectively defined. Symbols are energy-degenerate structures not determined by laws that act locally as special boundary conditions or constraints on law-based energy-dependent matter in living systems. While this partial description holds for all symbol systems, cultural languages are much too complex to be adequately described only at the molecular level. Genetic language and cultural languages have common basic requirements, but there are many significant differences in their structures and functions. (shrink)

Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings of the word (...) ‘communication’. Since literal communication needs to be secured so as to enable semantics being communicated, information theory is a necessary prerequisite to biosemiotics. Moreover, heredity is a purely literal communication process of capital importance fully relevant to literal communication, hence to information theory. A short introduction to discrete information theory is proposed, which is centred on the concept of redundancy and its use in order to make sequences resilient to errors. Information theory has been an extremely active and fruitful domain of researches and the motor of the tremendous progress of communication engineering in the last decades. Its possible connections with semantics and linguistics are briefly considered. Its applications to biology are suggested especially as regards error-correcting codes which are mandatory for securing the conservation of genomes. Biology needs information theory so biologists and communication engineers should closely collaborate. (shrink)

This paper is intended to complement our previous works on the necessary existence of error-correcting codes endowing genomes with the ability of being regenerated, not merely copied. It sketchily recalls some fundamental definitions and results of information theory and error-correcting codes; provides an overview of our research; shows that the disjunction of replication and regeneration enlightens the divide between germinal and somatic cells; suggests that some phenomena referred to as epigenetic may possibly find an explanation within the framework of error-correcting (...) codes; points out some difficulties, especially those related to sexual reproduction; criticizes the template-replication paradigm, and prompts geneticists to become familiar with information theory. (shrink)

Since the beginning of the XX-th century, it became increasingly evident that information, besides matter and energy, is a major actor in the life processes. Moreover, communication of information has been recognized as differentiating living things from inanimate ones, hence as specific to the life processes. Therefore the sciences of matter and energy, chemistry and physics, do not suffice to deal with life processes. Biology should also rely on sciences of information. A majority of biologists, however, did not change their (...) mind and continued to describe life in terms of chemistry and physics. They merely borrowed some vocabulary from the information sciences. The first science of information available to biological applications, semiotics, appeared at the end of the XIX-th century. It is a qualitative and descriptive science which stemmed from efforts of linguists and philosophers to understand the human language and is thus mainly concerned with semantics. Applying semiotics to biology resulted in today’s Biosemiotics. Independently, an explosive expansion of communication engineering began in the second half of the XX-th century. Besides tremendous progresses in hardware technology, it was made possible by the onset of a science of literal communication: Information Theory (Shannon, Bell Syst Tech J 27:379–457, 623–656, 1948). Literal communication consists of faithfully transporting a message from a place to another, or from an instant to another. Because the meaning of a message does not matter for its transportation, information theory ignores semantics. This restriction enables defining information as a measurable quantity on which a mathematical theory of communication is founded. Although lacking implementation means at its beginning, information theory became later very successful for designing communication means. Modern ones, like mobile phones, can be thought of as experimentally proving the relevance and accuracy of information theory since their design and operation heavily rely on it. Information theory is plainly relevant to biological functions which involve literal communication, especially heredity. This paper is intended to compare the two approaches. It shows that, besides obvious differences, they have some points in common: for instance, the quantitative measurement of information obeys Peirce’s triadic paradigm. They also can mutually enlighten each other. Using information theory, which is closer to the basic communication mechanisms, may appear as a preliminary step prior to more elaborated investigations. Criticizing genetics from outside, information theory furthermore reveals that the ability of the template-replication paradigm to faithfully conserve genomes is but a prejudice. Heredity actually demands error-correcting means which impose severe constraints to the living world and must be recognized as biological facts. (shrink)

The traditional divide between nature and culture restricts to the latter the use of information. Biosemiotics claims instead that the divide between nature and culture is a mere subdivision within the living world but that semiosis is the specific feature which distinguishes the living from the inanimate. The present paper is intended to reformulate this basic tenet in information-theoretic terms, to support it using information-theoretic arguments, and to show that its consequences match reality. It first proposes a ‘receiver-oriented’ interpretation of (...) semiosis. This interpretation implies that the means for recording, storing and processing information exclusively reside in the living world (extended so as to include the artefacts it produces). Then it may be argued that the main difference between the inanimate world and the living one lies in the fact that the very existence of the latter relies on information, which on the contrary is not relevant to the former. Thus, besides matter and energy, information is an entity irreducible to them which must be taken into account in any attempt for describing and understanding life. Information can interact with the real world only provided it is borne by some physical support: it must be ‘physically inscribed’. Contrary to matter and energy, information can be shared, not necessarily exchanged, so a same information can be borne by a number of distinct supports. Any living thing possesses means for recording, storing and processing information which are necessary for keeping it alive and securing its progeny. In particular, its genome contains hereditary information, can be replicated, and instructs the construction and maintenance of a phenotype. The simultaneous existence of a phenotype and of a genome, where the latter bears the symbolic description of the former, is mandatory for enabling the self-reproduction of an organism. Bearing and using information then endows a living thing with the ability to decrease the physical entropy, hence to act as Maxwell’s demon. Not only its own life is maintained against physical entropy, but its self-reproduction multiplies clones of the demon. Taking information as the entity which differentiates the living from the inanimate also supports Rovelli’s ‘relational’ interpretation of quantum physics. Experimental apparatuses then appear as information-theoretic channels from the inanimate world to a living observer. Besides having its own perspective (as stated by Rovelli), each of these channels has its own horizon because its capacity is necessarily finite. As another consequence, we may assert that the physicists’ quest of a ‘theory of everything’ is doomed to failure since, for lack of considering information as a relevant entity, physicists deny the living world, hence themselves. (shrink)