Hoffmeyer says that something is missing in modern biology. Understanding communication in biology requires seeing it as signs. He says:

True communication, biosemiotics argues, is based on semiosis, or sign processes... a sign is something that refers to something else — with the essential addition that it takes somebody (i.e., a receptive living system) to make the reference. The meaning conferred by a sign is thus acutely dependent on the nature and the context of its receptive system, the sensing body — and that body's relations with externality are mediated continually by the active establishment and disestablishment of such signs. A sign process, then, is more than just a mechanical transfer of information packets because the sign embraces a process of interpretation. And yet, it is precisely the biological phenomena that comprise this interpretative activity that is neglected — or at least not recognized as engendering its own measure of causal efficacy in the world — in both traditionally conceived Information Theory and in most contemporary mainstream Evolutionary Theory.

Yet by making just this slight and empirically well-justified expansion in our basic view of nature (i.e., to accept that semiosis and interpretative processes are essential components in the dynamics of natural systems), biosemiotics, as I hope to show, provides the conceptual tools necessary to explanatorily reintegrate living creatures (including, of course, human beings) into the natural world from which they came — but from which they have since been effectively excluded by a scientific ontology that has, at least since the time of Descartes, consistently encouraged scientists to de-semiotize all the naturally communicative and fundamentally interactive processes of living systems.

(Biosemiotics, p.xiv)

Hoffmeyer wants to move beyond the reductionism and deterministic mechanism in biology. The time is right for a scientific confrontation with "mechanicism," he says, because of the development in the last few decades of nonequilibrium thermodynamics, chaos theory, nonlinear dynamics, complexity theory, and biosemiotics.

But we need something more if we are to escape deterministic reductionism. The "order out of chaos" of Ilya Prigogine produces only material "information structures" like the galaxies, stars, and planets. They contain no "information processing," nothing semiotic, which is the essence of biology. Chaos and complexity theories are as deterministic as the Newtonian dynamics that drives them. Their sensitivity to initial conditions and computational unpredictability do not provide the kind of emergent freedom that Hoffmeyer wants for biology.

The most pronounced feature of organic evolution is not the creation of a multiplicity of amazing morphological structures, but the general expansion of "semiotic freedom,"that is to say the increase in richness or "depth" of meaning that can be communicated: From pheromones to birdsong and from antibodies to Japanese ceremonies of welcome.

I should be very surprised if the driving force behind evolution did not prove, at the end of the day, to be the self-same creativity and flexibility that are accorded to those systems engaging in ever subtler forms of semiotic interplay. The anatomical aspect of evolution may have controlled the earlier phases of life on Earth but my guess is that little by little, as semiotic freedom grew, the purely anatomical side of development was circumscribed by semiotic development and was thus forced to obey the boundary conditions placed on it by the semiosphere.

I had to think long and hard before choosing to speak of semiotic "freedom" rather than semiotic "depth." It was not an easy decision to make, since freedom is a rather ambiguous term. Semiotic freedom refers not only to the quantitative mass of semiotic processes involved but even more so to the quality of these processes. We could perhaps define it as the "depth of meaning" that an individual or a species is capable of communicating.

Over recent years it has become quite clear that some kind of term along the lines of "depth" is required in the communication sciences, to supplement the term "information."

(Signs of Meaning in the Universe, p.61-62)

Hoffmeyer laments the use of the term "information" as all the physical information in the universe, essentially the information a super-intelligent Laplacian demon needs to know to see the past and future, the positions and momenta, the motion paths, of all the particles in the universe. (It is this physical information that the second law of thermodynamics destroys, but the expansion of the universe creates - as negative entropy.)

Hoffmeyer prefers the definition of a bit of information as Gregory Bateson's "a difference that makes a difference." While this is vague, Hoffmeyer explains that he wants to limit the term information to biological information, to that intentionally created or meaningfully interpreted by an agent.

The essence of this definition is that information is something which is generated by a subject. Information is always information for "someone"; it is not something that is just hanging around "out there" in the world. For instance: If I happen, one evening, to hear a blackbird burst into song, I might look up into the tree to try and catch sight of it. In other words, the variations in sound reaching my ears prompt my brain to produce a piece of information to the effect that there must be a blackbird somewhere close at hand. For the moth clinging to a nearby wall, on the other hand, no information whatsoever is generated.The blackbird s song is a difference that makes absolutely no difference to it. Ergo, no information. And my small son might well contrive to say "bird," but not "blackbird." He has, in other words, produced another piece of information from the same sound.

The annoying thing about Bateson's definition is that it cannot be used to quantify information. Information is associated with an intentional creature of some kind or another, whether it be an amoeba registering a difference in nourishment levels and reacting by extending a pseudopodium toward the spot where the pickings are richest, or a human being seeing a ripe fruit on a tree and stretching out a hand to pluck it. Or—to put it another way—information is based on interpretation and, in this sense, corresponds to signs as defined by Peirce.

(Signs of Meaning in the Universe, p.66)

Hoffmeyer seems to want to identify "meaningful" information, but he also wants a measure (his semiotic freedom) of the complexity of the information.

the saturation degree of nutrient molecules upon bacterial receptors would be a message with a low depth of meaning, whereas the bird that pretends to have a broken wing in an attempt to lure the predator away from its nest might be said to have considerably more depth of meaning. In talking about semiotic freedom rather than semiotic depth, then, I try to avoid being misunderstood to claiming that semiotic freedom should possess a quantitative measurability; It does not. But it should also be noted that the term refers to an activity that is indeed free in the sense of being underdetermined by the constraints of natural lawfulness. Human speech, for instance, has a very high semiotic freedom in this respect, while the semiotic freedom of a bacterium that chooses to swim away from other bacteria of the same species is of course extremely small..

(Biosemiotics, p.187)

As a semiotic category, however, analog coding is perhaps not quite satisfactory, and I shall use it here primarily as a counter-concept to digital coding. Specifically, I will use analog coding as a common designation for codings based on some kind of similarity in the spatio-temporal continuity, or on internal relations such as part-to-whole, or cause-and-effect. Digital coding, in contrast, will be used to designate sign systems where the relations of sign to signified are due to a demarcation principle of purely conventional or habitual origin.

Code-duality therefore implies that the singularis of the digital code is placed on equal footing with the pluralis of analog codings that make up the biosemiosis of life. This positioning of the single digital code as in a sense equal to the totality of analog codings is justified by the unique properties of digital codes that I have discussed above. Moreover, it is precisely the play between these two types of coding that makes evolution possible, as analog and digital coding are two equally necessary forms of referential activity. They appeared, I would argue, as twins in the individuation process that gave rise to life's internal logic.

Had it not been for digital coding there would have been no stable access to the temporal world — i.e., the unidirectional continuum of pasts and futures — and therefore there could have been no true agency or communication. On the other hand, had it not been for the analog codes there could have been no true interaction with the world, no other-reference, and no preferences. To claim that only the digital twin is semiotic, whereas the analog twin remains in the sphere of classical dynamics, is to block the only possibility for transcending the epistemic cut of Howard Pattee. Code-duality and semiosis open up a dimension of our world and its evolution that is left underdetermined by thermodynamics. Organismic "context space" expands at an accelerating rate in proportion to the increase in the semiotic sophistication of species; for, simply put, there are so many more different ways to be smart than different ways to be simple (and this may be the reason why the speciation rate among mammals is five times higher than the speciation rate among lower vertebrates).

(Biosemiotics, p.89)