The biosemiotics of emergent properties
in a pluralist ontology

Claus Emmeche

Published in:   Edwina Taborsky, ed. (1999): Semiosis. Evolution. Energy: Towards a Reconceptualization of the Sign. Shaker Verlag, Aachen. (pp. 89-108).
The book is based on the meeting "Semiosis. Evolution. Energy, Third International Conference on Semiotics", Victoria Collage, University of Toronto, Canada, October 17-19, 1997 (programme and list of papers, see the SEE web page:

ABSTRACT. Semiotic inquiry relating the natural sciences to an evolutionary philosophy of nature must address the relations between physical, biologic and psychic systems. This can be done in various ways that either emphasize substantial differences between extensional and intensional descriptions, or strive to bridge the gap between theories of mind and matter be means of semiotic notions. Biosemiotics can contribute to integrate our concepts of matter, energy and sign systems such as the notion of a basic molecular code, which is not merely a chemical notion. It is argued that a semiotics of biological systems is in harmony with a pluralist ontology of emergent levels of organization.

Scientific research forms a special part of the global semiotic web by a specific set of approaches and attempts to understand and interpret material, living, mental and social phenomena of the world. Without being naïve, we would like to believe that one of the tasks of science is to provide conceptual tools to grasp this world of differences, change, emergent processes and coherent evolutionary continuity. Science in the twentieth Century has specialized into a tremendous net of semi-autonomous subdisciplines. Differences and diversity dominate the picture of modern science, and coherence and continuity between the fields seems often difficult to find. We have acquired a habit of renouncing coherence and unity for the sake of deeper details and stronger tools for specific purposes. It is possible, nevertheless, to advocate for a coherent picture in which crucial differences between physical, biological, psychological and sociological processes all can be seen within one ontology, which is non-reductionist with irreducible levels of organization, and where the existence of emerging properties on different levels does not contradict the evolutionary continuity between them (Emmeche et al. 1997). I shall pursue a part this picture by focusing on the emergence of `biological meaning' in a physical world after a brief digression into semiotics as a philosophy of nature.

The science of signs as understood in the tradition of Charles Sanders Peirce's semiotics may be a profitable place to start bringing together some major findings of the sciences. These are much more fragmented today than in 1914, the year Peirce died, but his thoughts bear relevance to the attempts to bridge the gap between specialized disciplines, and to investigate what might be called the evolutionary semiotics of energy. Peirce himself was deeply occupied with not only outlining the principles of nature's tendency to self-organize and form habits, but also with overcoming some boundaries, already firmly established in his time, between physics, biology and psychology. Continuity and evolution are fundamental categories in his philosophy. One is reminded of his essay "Man's Glassy Essence" from The Monist (vol.3, p.1-22, 1892), where he writes about matter as something not completely dead, but rather mind hidebound with habits,

"Hence, it would be a mistake to conceive of the psychical and the physical aspects of matter as two aspects absolutely distinct. Viewing a thing from the outside, considering its relation of action and reaction with other things , it appears as matter. Viewing it from the inside, looking at its immediate character as feeling, it appears as consciousness. These two views are combined when we remember that mechanical laws are nothing but acquired habits, like all the regularities of mind, including the tendency to take habits, itself; and that this action of habit is nothing but generalization, and generalization is nothing but spreading of feelings." (CP 6.268).

It is hard for the modern mind to embrace (or even understand) all aspects of Peirce's philosophy, a peculiar form of objective idealism, which might have taken slightly different and more concrete form if it was developed after the advent of molecular biology. For Peirce, there was no doubt that a `gob of protoplasm', say an amoeba or a slime-mould, feels, and that feeling has a substantial spatial extension which is subjective. Today very few philosophers (and virtually no biologists [1]) dare to speak about feelings in single-cell organisms, and for higher organisms with specialized sense organs, the inner side of feelings are discussed only within philosophy of mind under the technical term qualia (for which Peirce's term qualisign may be more precise). Nevertheless, it is important to remember the phenomenological or `inner side' of matter and ask if its qualities are accounted for when someone claims to have succeeded in bringing physics and psychology on one footing.

Let us identify distinct positions, formulated here as a set of theses. Some of these summarize ideas that have motivated the conference on which the present volume is based, but in this note they are all so briefly formulated that hardly any person would subscribe to a particular thesis without further qualification; they are merely listed here for discursive convenience.

1. The integration thesis: In the past, physical energy, biological evolution and cultural signification have been considered as denoting fundamentally different phenomena, and the relations between them, if any, have been seen as spurious (e.g., the former are seen as just some general preconditions for the latter). In order to make progress, we ought to integrate semiotics, biology and physics into a new framework in which these phenomena are understood as deeply related, because only this will help us to comprehend the emergence of new orders of complexity.

This attractive suggestion opens some questions. Who should do the integration and by what methods -- philosophical, scientific -- or do these very distinctions mislead us? One could think of integration of relative autonomous frames of description (semiotics, biology, chemistry, physics), within a loose metaphysical framework (e.g., such as the evolutionary world view), eventually supplied by a field of research labeled `philosophy of nature' dealing with specific epistemological and ontological questions related to the interpretation of this framework. The development of a more process-oriented philosophy of nature that attempts to integrate the findings of science with a critical understanding of the epistemological characteristics of scientific inquiry and modelling and also with other sources of knowledge of nature (everyday and other non-scientific experiental practices) is a very important enterprise. However, `integration' could be interpreted as effectively more or less the situation of today where basic reseach is very specialized and is done separately within the social, human and natural sciences with occasional contacts between the main areas, and meta-theortical reflections are done exclusively by philosophers. This situation may sustain the separation of knowledge and conserve the lack of real dialogue between the fields.

A less modest alternative is to strive towards a generalized coherent scientific description of all kinds of phenomena, in which one has redefined the basic notions and eventually invented a whole new paradigm based on the intuition that the three realms -- of semiosis, of evolution of function, and of dissipation of energy -- are deeply interdependent processes. Some versions exists of this idea:

2. The pansemiotic thesis: The universe is perfused with signs, semiosis is not only a process found in all living nature among beings which are organic, functional wholes (organisms as interpreters, or interpretants). The sign, its object and its interpretant are universal categories, which existed (eventually in degenerate form) even before the origin of life.

The pansemiotic thesis may be read as a version of panpsychism; the idea that matter is effete mind, or that the qualities of experience, sensation, pain or feeling come in degrees, and that even inorganic systems may have, eventually to very small degrees, such qualities. If one does not like the idea of emergence (as a sudden appearance of qualitative new irreductible properties, cf. Baas and Emmeche 1997), and embraces a continuity thesis (that mind is continuous with matter, and that systems with meaning-attributing capacities have originated from, or are a certain organization of, material systems), one is more inclined to such a view of nature, according to which mental phenomena are not simply found in the brain (and presuppose the body of a whole multicellular organism) because also single cells of any kind, not only complexes of nerve cells, have `mind', `feeling', `consciousness' (or semiotic capacity) -- at least to a tiny degree. Of course, a problem with this idea is that it is painfully difficult to give precise scientific meaning to the claim that single cells or even non-cellular systems have feeling, even to a very tiny degree, if one by meaning demands clear and fulfilled conditions of verification (or assertability or falsifiability) and not just appeals to special intuitions that seem to differ among semioticians as well as metaphysicists. This demand of clarity may be perceived by general semiotics as unnecessarily restrictive, but its fulfilment should facilitate communication between scientists and semioticians.[2] A less metaphysical version of the integration thesis is

3. The physical codification thesis. The sign should be reconceptualized as something that enables a change of state to be brought about between energetic entities, and thus semiosis is the transformation of energy into signs, relatively stable spatio-temporal units occurring within particular orders of matter-energy configurations. These orders are systems of knowledge and of molecular organization as well; they are organized codal actions (of codification of energy) that provide both continuity of knowledge and transformation of energy.

Note that the third is not entailed by the second thesis; you can endorse the attempt to analyse signs in terms of codified configurations of physical states without endorsing the view that everything in the universe is perfused, as Peirce said, with signs. But if one succeeds in this analysis, it could be used as an argument for the metaphysical thesis of pansemiotics. If signs are merely "relatively stable spatio-temporal units occurring within particular orders of matter-energy configurations", then (depending upon what orders one refers to) there could be a lot of semiosis going on in the non-living world.[3] Can we accept such a change in our conceptual inventory? The answer would be positive if it allows us to explain, in a bottom-up way, the origin of signification and meaning in the universe.

However, it is not clear what we exactly mean by `explanation' here. Usually, in the physical sciences, we like explanations to be causal effective ones, i.e., by reference to observable components and physical laws, by specification of boundary and initial conditions, and formulated in a purely extensional context (involving no reference to semiotic notions of the beliefs, desires, and intentions of the involved observables). Within this scheme of explanation, the system is fixed within a certain state space where it certainly can `evolve' but where this evolution is simply movement (whether deterministic or not) through the state space. Here, other principles must be added `from outside' so to speak, in addition to the physical description for which structures of `meaning' cannot be intrinsic to the system but are observer-relative.

In biology, functional explanations (referring to the purpose or role of the part in maintaining the whole) are allowed for, because it is implied that they are backed up by a causal account of the origin of functional wholes in evolution by natural selection (and other physical origins of organization) which are usually seen as a purely causal process in the physical sense. This backing-up or justification may be possible only `in principle' because of the organizational complexity of the organism and the historical contingency of the evolutionary process, but still no non-extensional properties (such as `meaning' in the sense of content or Sinn) are referred to in traditional biologic explanations. Only in psychology (except behaviourism) and in the social sciences one finds explanations that, first, rely on the stipulated legitimacy of intentional explanations referring to intentions, purposes, beliefs, desires (which may be non-observable) of the involved agents, and second, are given in a semantics that allow for intensional contexts (such as `N believes that P is the case'). Here, this semantics and the existence of intentionality are taken as given, and can thus be allowed for as explanatory resource. The deep challenge of formulating a bottom-up account in energetic terms of the origin of semiotic activity on the highest scale of complexity, where language, consciousness and society are present, is exactly that these phenomena cannot be taken as given, but must be accounted for by purely non-intensional explanatory contexts. Various boot-strapping strategies have been proposed (what other possibility than boot-strapping do we have for this challenge?), and they have all specific problems,[4] but my point here is just to emphasize the hard problem of coming from a purely extensional explanatory context to an account for genuine semiotic intentional phenomena.

The integration thesis is best contrasted by some positions in philosophy which are dualistic or `separatistic' in aim, that is, they hold that to save the phenomena (e.g., the phenomena of psychology, such as the experience of being a conscious person), one has to work with at least two (but sometimes more) irreducible areas of existence, mind and matter, or mental intentional phenomena and physical extensional properties, and we should not expect to bridge this explanatory gap between physical, neurobiological events in the brain and subjective experience. It is not my farfetched purpose to list or discuss all the positions in the philosophy of mind, instead, I'll give a few distinct versions of such `disintegration' or `disunification' theses:

a. The substance dualist thesis: A sign signifies only because it is interpreted by an active mind to be signifying something and thus having some (mental or intentional) content, which is a substantially different phenomenon from being a sheer physical thing. Thus, semiosis can only be of what we as intentional subjects can intend (or believe, or hope for, or know), while matter, energy and organisms are physically organized phenomena. We can never hope for a unified science of everything. (Or the moral version: We should never have such hopes. That's hubris!).

b. The property dualist thesis: There is only one kind of substance in the physical and biological and mental world, namely the material one. However, when organisms develop complex nervous systems with brains, the property of being conscious (or of signifying something to an interpreter) emerges as an irreducible but still natural phenomenon. That a material sign (e.g., the pixels in a picture; the marks on paper that stand for a text) has intentional content is not intrinsic to the sign (sign carrier) but derived from the emergent conscious ascription of meaning or signification to the sign when `decoded' by an intentional agent.[5]

For distinct reasons, both positions hold (explicitly or by implication) that the semiosis is a process located in the inner of the semiotic agent. Both of these positions would be very skeptical at attempts to reformulate the notion of sign in purely energetic terms, because they see a danger that this would lead to a reducing away the primary intentional property of signification processes, or to such a broad re-defined notion of signification and intentionality, that what the original concepts covered must now be renamed, without really having bridged the new (generalized or just `diluted'?) and the old (specific) meanings of the concepts of `sign' and `intention'. A third position would argue for disintegration on other grounds:

c. The multiple fundamental systems thesis: We simply observe that within the special sciences there exist several kinds of different systems that cannot be reduced to one another, because in order to describe different systems -- such as those which are (a) mechanical deterministic and predictive, or (b) deterministic and chaotic, or (c) stochastic, or (d) computational, or (e) conscious, or (f) intentional and technical -- we have to use different conceptual frames which are logically partly independent, i.e., they cannot be fully deduced from or translated into each other without further specifications. Therefore, a unified science is not possible, science is and should remain a pluralist undertaking.[6]

There is a further variety which combines the irreducibility between systems (as in a.) and between properties (as in b.) with integration (as in 1.) in a more general, less radical sense (not as integration by reduction, or theory-intertranslability). This is

4. The ontological level thesis: The world is material, but all matter is organized into forms and these again can be further organized. There are qualitative differences between these organized forms. What exist are not just fundamental particles, energetic fields, and their organization: Reality has during its evolution become organized into characteristic primary levels (the physical, biological, psychical and social). Entities at higher levels possess emergent [7] properties, some of which are ontologically irreducible to lower level properties. (Also called material pluralism or irreductive physicalism). Semiotic phenomena may be characteristic of some, but not necessarily all levels.

We are now prepared to sketch another member of the integration family, namely biosemiotics, which have some reservations against the pansemiotic stance:

5. The biosemiotic thesis: We have not only semiosis in the cultural domain, but also in the biological domain of living cells (information based autocatalysis). In parts of the physical universe where living organisms (sign interpreters) do not exists, signs can only be potential in their mode of existence. Organisms require for their very existence to be thermodynamically organized like dissipative structures (such as the open Sun-Earth-Universe system); this is a necessary but not sufficient condition. A further condition is that biochemical semiosis is based on a genetic code which is necessary for maintaining the autopoietic network of biofunctionality. Thus, together with the organism, we have the emergence of the sign, the autopoiesis, the code, and the evolution of further complex biological structures. One such structure is the higher level code of human language.

Here the crucial difference is that between, on the one hand, complex chemical, thermodynamical open systems (as have been described by Prigogine, 1955, see also Prigogine and Stengers 1984) with no `organismic' (or cell-related) properties (e.g., self-reproduction), and on the other hand, bounded macromolecular autocatalytic systems undergoing open-ended evolution (such as the first real cells on Earth). The latter are seen not merely as a further increased level of molecular organization, but as systems in which something completely new has emerged, namely: Signs, that signify something for someone -- or for `somecell'. That is, the origin of life. Thus, life is here essentially conceived or defined as a semiotic phenomenon (see Hoffmeyer 1996).[8]

Biosemiotics is distinctive, both in relation to the dominating theoretical paradigms in biology and in relation to other kinds of semiotics. In biosemiotics, the focus of attention it is neither the natural selection of replicating molecules or genotypes (as it is in the traditional and still dominating paradigm of neodarwinism), nor the operational closure of an autopoietic system (as it is in the alternative paradigm of autonomous systems [9]), but the sign-links and interpretants of various semiotic agents on all biological scales; from molecular recognition to cellular self/non-self-distinction; from the molecular semantics of gene expression and regulation to the semantics of inter-organism communication from E. coli to elephants; from individual cognition to the swarm intelligence of ants and humans.

There are deep implications of viewing not just human language but life as such as a semiotic phenomenon. For instance, if we explicitly define life by reference to biosemiotic processes, these have to be specified in relation to organisms conceived as sign-interpreters and their functions. Let us propose that life is defined as functional interpretation of signs in self-organized material code-systems making their own umwelts (Emmeche 1998a). The definition expresses central features of the biosemiotic view of life as being: natural processes that realize events of sign interpretation which are functional in the evolutionary sense (allowing the organism to self-maintain and self-reproduce and thus contribute to a genealogical lineage); natural processes which are based on some general self-organizing capacities of complex physical systems; natural processes that are guided by (or `dependent on', to avoid the `central governor'-connotation of the guidance metaphor for the genetic programme) a special chemically realized code system (the genetic code, cf. the notion of code-duality in Hoffmeyer 1996); and natural processes that gives rise to species-specific subjective `points of view' or experiental worlds or umwelts that constitute an actively constructed reality for each organism within a given species. Such a definition raises a lot of issues, two of which will be considered briefly here, (i) the problem of demarcating the interface between signs which are within the subjective umwelt and signs which are just functioning as parts of the organism's general semiotic web of cellular and intracellular communication; (ii) the problem of the generation of the original meaning of biosemiosis.

(i) There seems to be an ambiguity in the biosemiotic sign concept which appears when the general Peircean sign notion (which may apply to basic endosemiotic processes within single cells such as molecular recognition) is brought together with the Uexküllian almost phenomenological idea of signs in an organism's subjectively experienced umwelt. The latter has some affinity to the vernacular notion of a sign as a consciously experienced event with a particular meaning ("that sound was a crucial sign to me to be more careful"). The ambiguity is that between on the one hand the sign conceived as something that can be determined from without (e.g., a triadic relation that we as scientists can discover in, say, a bacterium or in the nervous system of a humming bird, such as the sign functions realized by the neuropeptides of the neurons' synapses) and, on the other hand, the sign as something that is experienced directly (e.g., my perception of the sound of a bullet ricocheting from the wall beside me; or the humming bird's perception of the sweet smell of honey). In direct experience we are tempted to say that it is experienced `from within' which is in some sense right -- we are here dealing with the qualitative aspects of the semiotic function -- and in another sense wrong, because in direct experience we are suspended in signs, there is no inside or outside, only the `thisness' or `here and now' of the signifying event (haecceity). However, this ambiguity is not one between an `objective' peircean sign notion and a `subjective' Uexküllian one, because Peirce's general sign concept is not tied to be either objective or subjective; its triadic structure encompasses firstness (the qualisign) and thus has a phenomenal dimension, as well as the referential and the functional (final cause) dimensions. Rather, the ambiguity derives from the biosemiotic attempt to combine science and semiotics, that is, the use (e.g., in Hoffmeyer 1996) of scientific descriptions originally framed in the `objective' language of detached observers (observing, e.g., the neuropeptides of humming birds or the swarm behavior of ants, or brain cells, or whatever) transposed to a semiotic frame of description in which subjective qualitative experience are either the very focus of investigation (as in von Uexküll's Umwelt research) or a kind of presupposed phaneroscopic ground for the sign concept (in Peirce). We will not worry long about the metaphysical aspects of this problem, let us here just pragmatically say that this ambiguity may simply appear as a demarcation problem and an observation problem: First, how to identify, among the totality of signs which simply acts (biofunctionally) as part of the total endo- and exosemiotic process of an organism, those ones that passes above the threshold of experiential quality (or awareness, attention, etc.) and thus enter in the realm of the organism's umwelt? Second, how to observe (by some kind of participatory empathy?) the umwelt experienced by other species? (for some answers to the later problem, see Cariani 1998 and Kawade 1998). After all, it may not be so strange that, using objective methods of neurophysiology and ethology, we can establish that a bat's umwelt is based on a kind of sonar system, but we can never experience its umwelt. Similarly, by for instance PET scanning we have access to a lot of non-conscious semiosis in a human's brain which never enter into that human's umwelt.

(ii) The mentioned definition seems to imply that signs (or information or meaning) is conceptually primary while organisms, metabolism and evolutionary replication are secondary with respect to the semiotical processes. When biosemioticians apply semiotical concepts to natural systems, this primacy of the sign as a basic notion is often taken for granted. However, in order to bridge the gab between (physical) nature and (semiotical) culture,[10] we have to develop a theory of the causal nature of sign-interpretation that can account for the generation of the so-called original meaning (not just ascribed observer-dependent meaning but intrinsic meaning, the content in one's own experienced umwelt) as part of the natural activity of physical systems under specific boundary conditions. A similar search for such a theory is going on in cognitive science and the neurosciences.[11] As we have not yet seen convincing accounts of the emergence of sign-functions in a purely physical system (cf. discussion in Emmeche 1994), such a theory will probably be closely dependent on a future biological understanding of the origin of life (living cells, metabolism and the semiotical machinery of the genetic memory), as it is precisely here we can detect the first primitive semiotic systems. As biological life is functional -- i.e., dependent upon system-maintaining relations between parts which are not living (such as a single molecule of sugar or a single protein) and wholes which are living (such an amoeba or a cat) -- it remains to be seen precisely how the causal nature of the part-whole relations is constituted. Furthermore, a deeper analyses of the relation between the concepts of biotic functionality and sign action in biotic systems has to be given, which is, but for a few hints, beyond the scope of this note.

If the first cells in the primordial soup were emergent entities (or represented a new type of systems with emergent properties such as metabolism and self-reproduction), this entails the existence of a kind of `upward causation' from the physical collection of individual macromolecules (lacking such properties) to a functional whole. One has to answer if this process entails just the emergence of functionality, as many biologists would be inclined to say, or if functionality is an inherently semiotical phenomenon, so that for any kind of complex system (above the von Neumann threshold [12]) this kind of part-whole relation can only be realized by being based upon a sign-interpretation capacity of the very system itself. (In the latter case, the emergence of the first living cells coincided -- from the biosemiotic point of view -- with the emergence of genuine semiosis in natural evolution, such that signs and life are almost co-extensive; or -- within a pansemiotic perspective -- both life and semiosis were to some extant already processually present under pre-biotic conditions although not as developed or full-blown as after the invention of cells). With respect to the cell, its metabolism is based upon proteins, and these are partly specified semiotically by the genome (the primary sequence of amino acids are coded in the cell's DNA sequence via the genetic code), partly being self-assembled in the folding process following the protein synthesis. Here, functionality, as revealed by molecular biology, is not `purely physical'; it is biological, and in that respect, also semiotical.[13] In the genome of an eukaryotic cell there is sequence information specifying a set u of roughly 50,000 to 100,000 specific species of protein molecules of which roughly 10,000 may be in use in a given cell type. The cell's DNA-based selective construction of one specific protein (from the set u) for synthesis -- out of the astronomically huge number of possible proteins of a given size -- is really the original meaning of `biological specificity' as the term for the distinctive character of biochemical reactions, which was later identified as being based upon the `biological information' in the genome.[14] The secret of biological complexity lies in that `right' semiotically specified selection. The biosemiotical claim is that by casting molecular biology as just `biology with chemical and physical methods', we tend to forget the intrinsically biological meaningfulness in the cell, which is the basic and "minimal semiosic unit" (Sebeok 1986: 347). The cell as a semiotical whole causes (by a kind of `downward causation') another much more ordered distribution of materials and kinds of molecules than what would have existed without this emergent semiotical unit.

This downward causation should not be interpreted in a certain strong sense; it does not mean that the `causal closure' of the physical universe is disturbed `from without' by supernatural forces (as if we are invoking a semiotic analogy to a vitalistic `life force') or that physical laws are violated or something of that sort. However, to talk about the causal closure of the physical universe is somehow to take a transcendental `God's eye view' on the whole of nature. We cannot attach much pragmatic scientific meaning to such a proposition as `the whole nature is causally closed'.[15] As finite semiotical beings we should not invoke such demons of traditional physics as a complete micro-determinism. A more modest stance will emphasize the necessity of choosing a particular frame of description and particular observables in the quest for understanding life, and here we are forced to surpass the purely micro-deterministic stance. Downward causation is only a problem for an ontology that allows only strictly efficient causation, because efficient downward causation surely leads to contradictions.[16] But semiotical causation is different. It involves other causal modes (or modes of explanation), almost forgotten but still helpful to us, from the Aristotelian tradition, namely material, formal and `final' [functional] causation.

Biosemiotics is also distinctive with respect to other kinds of semiotics. For the sake of simplicity, one can distinguish between anthroposemiotics, biosemiotics and pansemiotics as three answers to the question of what a science of signs should deal with, namely, that sign production and sign interpretation is just a human phenomenon, or a general biologic process, or a universal physical phenomenon (see scheme 1).[17] This division reflect to some degree different metaphysical commitments to the theses we have outlinet above. Thus, an anthroposemiotic stance could be based on a dualist conception of the mind/body relation where only people can have mental representational states with intrinsic intentionality. However, particular theoreticians may expound views that cannot just be put under one of these headings (e.g., the article of Anderson et al. 1984 is representative of biosemiotics with strong stains of pansemiotic metaphysics).

As indicated in scheme 1, another great challenge for biosemiotics is to account for the emergence of the specific human language, which has certain formal similarities with the genetic code, but where the dissimilarities are of higher interest for the origin problem. The origin of linguistic `meaning' will be related to the complex behavioural and communicative interactions in the groups of hominids that developed internal modelling systems for representing more and more complex aspects of the psychic and social environment in parallel with the pre-existing `body language' for communication. In that sense, the emergence of linguistic syntax, semantics and pragmatics is a coherent process of evolution on both social, cognitive and biological levels.

Scheme 1.

Is there semiosis (sign-activity) going on in system X according to semiotics Y ?

Y: Kind of se-




of system:






Uexküll, Morris,







language users


[^]?    *


[^]?    *



Biochemical cycles,
Cells, Organisms,



[^]?    *



(equilibrium or non-equilibrium) systems

NO !!!



Scheme 1: A simple map of the ways to answer the question "Is there semiosis (sign-activity) going on in system X according to semiotics Y?". The sign [^]? marks that at this point the type of semiotics is challenged by the question of how to explain the emergence of semiosis or `meaning' at the given level. Due to the idea of continuity in pansemiotics, meaning or significations comes always in degrees. Similarly, the * sign marks the challenge of explaining how and why the level in question is different from the level below. The number of !-signs is an index, as usual, of the emphasis.

The emergence problem on both levels, from proto-biology to biosemiosis, and from proto-language to language, actualizes the need for specifying frames of observation and property-attribution mechanisms to complex systems, that allow for self-generation in such systems of new observational frames in the dynamic description as a way to boot-strap oneself up from the simple to the complex. It may lead to a more general understanding of the semiotics of emergent complex phenomena in which observation, description, evolution and cognition are closely coupled.

In what sense could the physical codification thesis contribute to an explanatory bottom-up model of the evolutionary emergence of the processes of biosemiosis and anthroposemiosis as specific types of signification? It may be hard to say as that thesis is still in the making (though see Taborsky, this volume), however, an interesting way to approach the question is not so much from the abstract conceptual level of general semiotics and physics as from the specific point of view of biochemistry and molecular biology. We noted earlier that "the secret of biological complexity lies in that `right' semiotically specified selection" of the truly functional proteins out of the finite but gigantic number of possible but non-functional proteins (as well as the specimens of rRNA, tRNA that forms part of the semiotic metabolic web of the cell). The closed organization of the metabolism within the cell and its membrane (its autopoietic structure) thus depends upon the functionality of the individual macromolecules and their chemical energetic exchanges (a brief course in biochemistry would be relevant here, but see, for instance Fox 1982).

The controlled nature of these reactions, their selectivity and the high number of intermediary steps in the total energy transduction in living cells, crucially depend upon the mentioned `biological specificity' of the macromolecules, e.g., the specific three-dimensional structure of the enzymes that makes reversible coupling between an enzyme and its substrate or between proteins and DNAs (or mRNAs or ribosomes, etc.) possible. These functional properties of a living system is indeed emergent, and, as Root-Bernstein and Dillon (1997: 453) put it, "the critical question posed by the evolution of living systems is how self-assembling systems create new contexts in which naturally occurring processes "reinterpret" or "abstract" new and higher-level hierarchical properties from a background of more elemental components and processes. How, in other words, do cybernetic controls emerge".

In their paper, they emphasize the role of biological specificity of the kind known in molecular recognition processes, the key-and-lock feature of macromolecules, the `molecular complementarity'.[18] Indeed, such attempts to formulate general principles for energy, `information' (as biological specificity) and `codes' may well prove to be a fruitful base for further development of the before mentioned physical codification thesis (as well as the biosemiotic thesis [19]), if only one is aware of the fact that `codification' in the sense of the genetic code (and implied, the whole machinery of DNA-duplication and protein synthesis) is a very in detail described and highly specific phenomenon in physical nature, and it may be extremely difficult to find `similar' examples of other systems in which `codification' (in some vague sense) is at play in the physical world which is not already described (on the biosemiotic and anthroposemiotic levels) better and in more detail by specific theories (e.g., the linguistic discipline of semantics).

The philosophical status of biosemiotics is best viewed as compatible with the ontological level thesis. This means that biosemiotics is not as such a research programme (or paradigm) that should be an alternative for existing biological research (in e.g., molecular biology, physiology, ecology, etc.). But it gives the research done here a broader interpretation, and helps to relate the findings of biology better to the general picture of the living world and the physical universe, a picture which has been dominated by atomistic and mechanistic notions of nature. In that sense, biosemiotics helps to provide a better `foundation' for biology (not to be understood here as a `first philosophy' or as positivist foundationalism), and to develop an alternative philosophy of nature in which the semiotic phenomena of thoughts, feelings, experiences, sensations and actions are seen as true natural parts of the world we live through. Furthermore, it contributes in an important way to general semiotics, by putting its research in closer contact with biology. The beginning of biologic life is the beginning of actual interpreters. Thus, it is my guess that the emergence of umwelts, from certain friendly or favourable environments, is the first event to signify the actual beginning of the life of signs in this universe.


I thank Edwina Taborsky for helpful comments to an earlier version of this paper, and the participants in the Semiosis/Evolution/Energy conference for stimulating discussions.

{In the printet volume, the notes run from no. 89 to 107}

{89} [1] Except in some special branches of modern theoretical biology and philosophy of biology (including biosemiotics) that could be called `qualitative organicism' which differs from `main stream organicism' which is also non-reductionist (claiming the autonomy of biology) but does not consider the qualitative, phenomenal, experiential aspects of life as an object of scientific inquiry; cf. Emmeche (submitted).

{90} [2] If the field of general semiotics of the Peirce-tradition wants to develop a fruitful dialogue with contemporary science and not just be Peirce-scholarship (which for sure has its own merits), the strive for clarity is not unimportant. Too much contemporary semiotics are of the type of each author having his or her own idiosyncratic and partly intuitive notions of the basic semiotic concepts. An interesting rhetorical experiment is to compare the often rather opaque prose of Merrell 1996 with the distinct exposition of Clarke 1987, and I am not sure whether it merely reflects the difference between a hegelian method of letting metaphysical concepts develop as it were by themselves, and an analytical method of establishing clear definitions; it may rather reflect the different consequences of synechistic pansemiotics and a restrained branch of comparative biosemiotics informed by philosophy of language, respectively, for the very mode of thought.

{91} [3] E.g., in a brick stone, in my litter basket, or in the atmosphere of Jupiter. Of course, such systems are not what the Physical Codification Thesis has in mind, because there are, as far as we know, no intrinsic codes in these systems; what is intended is perhaps the biological coding systems as the prime example, but then one has to specify them and it may well turn out that such a specification cannot be done adequately simply by physical means. Thus the non-equilibrium thermodynamics (of Prigogine, see below) does not in itself distinguish living from dead dissipative structures. Here Stuart Kauffman's contribution (Kauffman 1993, 1996) takes us further - and beyond physics. The notion of an agent, i.e. an organism, is indeed needed. What Kauffman describes as simple agents is a new, interesting and very important way of re-formulating -- within the light of his theories of the origins of biological organization from physical order -- the old notion of an organism in biology. Further reflections on agency in Emmeche 1998b. More on the notion of physical codification, see Taborsky 1999.

{92} [4] One such strategy is computational artificial life, in which, e.g., one has argued for the validity of Cellular Automata models of the emergence of information processing capabilities in a purely physical system. A critical discussion of this strategy (inspired by works of theoretical biologists H.H. Pattee, P. Cariani, A. Moreno and G. Kampis) is given in Emmeche 1994, which is accessible from the website Even though it might be possible some day to model the physical emergence of information processing capacities, this is still a far cry from any account of the emergence of intentional capacities from mere information processing.

{93} [5] The philosopher John R. Searle represents a position close to this thesis. However, influenzed by Wittgenstein's late philosophy as he is, he would not reduce semiosis to a pure `internal' phenomenon.

{94} [6] My best acquaintance with this thesis is the Danish philosopher Hans Siggaard Jensen (1990), but the view may be found in many versions, one such for biology is Dupré 1993. Jensen argues, that for some of the distinct fundamental types of systems, such as chaotic non-linear ones, there are instances of these at all of the so-called levels of organization (both economic, biological, and physical systems may be chaotic in the mathematical sense). This allows for an instrumentalist interpretation of scientific models, and he goes further and argues against the ontological level thesis. The non-translatability (which may only be a partial one) of different conceptual frames in which the different kinds of systems are described resonnates well with some of Kuhn's later characterizations incommensurability between scientific paradigms, see, e.g., Kuhn 1993.

{95} [7] A standard sense of emergence is that "a property of a complex system is said to be `emergent' just in case, although it arises out of the properties and relations characterizing simpler constituents, it is neither predictable from, nor reducible to, these lower-level characteristics" (Kim 1995).The standard notion of emergence does not specify if prediction or reduction is impossible in principle or in practice, or in what non-trivial senses one cannot predict such properties, or if the "arising" of such properties are a consequence of descriptive or physical processes, etc. Many philosophers prefer supervenience for emergence as a concept characterising the dependence relation between entities or properties at different levels. On the history of the notion, see Blitz 1992.

{96} [8] For en extensive multiple-review of Hoffmeyer's pioneering work, see the special issue of Semiotica 120 (3/3), 1998.

{97} [9] Based on the famous works of H. R. Maturana and F. J. Varela. I dare not refer to this work in the list of references, because it would be totally incomplete if I omitted the newer works by Varela, and hardly acceptable if I referred to papers of his that I have not read.

{98} [10] including the ecosystem as the semiotic `bio-culture'; compare the concept of `semiosphere' (Hoffmeyer, 1996).

{99} [11] I take the term `original meaning' from Haugeland, 1985. Though he uses it in a the context of AI (how to get meaning from pure syntax), the problem described here (how to get meaning from pure physics) is similar.

{100} [12] "There is a minimum number of parts below which complication is degenerative (...) but above which it is possible for an automaton to construct other automata of equal or higher complexity", von Neumann 1966, p. 80. (One may think of open-ended evolution above this threshold).

{101} [13] This semiotical aspect of the basic gene-to-protein relation is very important, but is often ignored or simply not articulated scientifically as such by molecular biologists, partly because of ignorance of semiotics, partly because the failure to understand that knowing the molecular and mechanical details of a systems does not imply that the system is nothing but mechanics or chemistry. It is for some reason easier to accept that the computer is (also) a semiotic engine and not simply fully describable as a physical system than to accept that a cell may not be fully describable by molecular concepts. Cf. Emmeche 1999.

{102} [14] Cf. the lucid analysis by Sarkar 1996.

{103} [15] This was what Niels Bohr emphasized: "When we attempt a unified description of which we ourselves are part we met with the problem of a wholeness where the observational standpoint is lost. (...) Only when a section [line] is drawn between a part of it and the rest, the idea of observation can be obtained." (Bohr, MSS, No.21, 19.8.1954, here cited from p. 100 in Favrholdt, 1994). Bohr believed that committing oneself to claims that "everything existing is material", or "everything existing is mental" (or semiotical for that matter!), one has committed a philosophical failure of presupposing `The Angelic Point of View'.

{104} [16] See also Emmeche, Køppe and Stjernfelt (in prep.), and the work of Jaegwon Kim. I thank Køppe, Stjernfelt and Charbel Niño El-Hani for valuable discussions about downward causation and efficient causality (as contrasted with other Aristotelian modes of causality).

{105} [17] Another definition of anthroposemiotics is that it is simply the branch of general semiotics that deal with human communication systems, while biosemiotics deal with all other communication systems, and include as well zoosemiotics, phytosemiotics, endosemiotics, etc. This is old the idea of "levels of envelopment" where the phytosemiotic level is contained within the zoosemiotic one at a new level of complexity (compare T. von Uexküll 1984). Thus in this sense, "biosemiotics" and "anthroposemiotics" are not in conflict.

{106} [18] Complementarity in this sense is a standard notion in biochemistry and molecular biology known, e.g., from the complementary bases that constitute DNA (i.e., A and T; G and C); or from cDNA (complementary DNA) produced by reverse transkriptase activity from mRNA. However, Dillon and Root-Bernstein (1997) give it a slightly more general meaning as the non-random reversible coupling between the elements of the cell.

{107} [19] "In a way I see these two papers [Root-Bernstein and Dillon 1997] as delivering a firmly built bio-molecular and physiological platform for biosemiotics to work on" (Jesper Hoffmeyer, pers. comm. 16/09/98 [on OCA list]).


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