The Meaning(s) of Information, Code â¦ and Meaning

ORIGINAL PAPER

The Meaning(s) of Information, Code … and Meaning

Anton Markoš & Fatima Cvrčková

Received: 13 December 2010 /Accepted: 22 November 2011 /Published online: 25 April 2012# Springer Science+Business Media B.V. 2012

Abstract Meaning is a central concept of (bio)semiotics. At the same time, it is alsoa word of everyday language. Here, on the example of the world information, wediscuss the “reduction-inflation model” of evolution of a common word into ascientific concept, to return subsequently into everyday circulation with new con-notations. Such may be, in the near future, also the fate of the word meaning if, flexedthrough objectified semantics, will become considered an objective conceptusable in semiotics. We argue that reducing meaning to a technical term essen-tially synonymous to code and stripped of most of the original semantic field is not anecessary prerequisite for a meaningful application of the concept in semiotics and inbiology.

Keywords Meaning . Information . Reduction-inflation model

The conclusion seems inescapable that cells are able to sense the presence intheir nuclei of ruptured ends of chromosomes, and then to activate a mechanismthat will bring together and then unite these ends, one with another. […] [This]is a particularly revealing example of the sensitivity of cells to all that is goingon within them. They make wise decisions and act upon them.B. McClintock, Nobel lecture, 8 Dec. 1983Genes and proteins, in short, are assembled by molecular robots on the basis ofoutside instructions. They are manufactured molecules, as different from

Biosemiotics (2013) 6:61–75DOI 10.1007/s12304-012-9155-3

A. Markoš (*)Department of Philosophy and History of Science, Charles University Prague, Faculty of Sciences,Viničná 7, CZ-128 44 Praha 2, Czechiae-mail: [email protected]

F. CvrčkováDepartment of Experimental Plant Biology, Charles University Prague, Faculty of Sciences, Viničná 5,CZ-128 44 Praha 2, Czechia

ordinary molecules as artificial objects are from natural ones. Indeed, if weaccept the commonsense view that molecules are natural when their structure isdetermined from within and artificial when it is determined from without, thengenes and proteins can truly be referred to as artificial molecules, as artifactsmade by molecular machines. This in turn implies that all biological objects areartifacts, and we arrive at the general conclusion that life is artifact-making.M. Barbieri 2008a, 579

Prologue

Situation 1, April 10, 2010: The Polish radio broadcasting (in Polish) the newsabout the demise of the Polish President in an air crash.Situation 2, April 6, 1994: The Polish radio broadcasting (in Polish) the newsabout the demise of the Presidents of Rwanda and Burundi in an air crash.

On hearing the first message, an average Polish listener remains in a deep shockand grief. An average Polish listener understands, of course, perfectly also the secondmessage, but no emotions will follow – well, it happens from time to time that this orthat potentate goes down in an accident.

On hearing the first message, an average citizen of Rwanda remains inert – even ifhe may guess from the discomfit voice of the speaker (and by distinguishing wordslike “Prezydent”, or “Polska”) that probably some tragedy has happened in Poland.The second message leaves him completely indifferent – he hardly notices from themonotonous flow of foreign speech that the message marks the beginning of hiscountry’s tragedy. An average inhabitant of, say, Bolivia, overhearing accidentally thePolish broadcast, will probably react similarly as the Rwandan, but no consequenceswill follow for him from any of both messages.

Disregarding the static, all three listeners received the same information, thoughfor two of them one of the messages was of utmost importance (even more for theRwandan). Only the Pole got rightly both, because he had an access to the languagecode in which the messages were transmitted. In addition, in Situation 1 the universalhuman code for sorrow was recognizable in the speaker’s voice – and all threelisteners realized it, but it was only part of the information. What fraction ofinformation, then, was contained in the message proper in Polish (which can be putdown on paper, or perhaps even quantified according to some criteria), and what inthe tremble of the speaker’s voice?

Both broadcasts represented signs of a tragedy – to or for a receiver who had theaccess to a code. If our Bolivian and Rwandan would speak Polish, they wouldinterpret them in a different way, if a Bolivian has a Rwandan (or Polish) partner, shewould react differently, if… Each message (identical information) would repre-sent a different, specific, perhaps personal meaning for any of the humanbeings involved.

Here we are: In human affairs, information, sign, or meaning is always informa-tion, sign, or meaning to somebody or for somebody. Information must become asign, and the sign will be interpreted uniquely, according to the nature of the person

62 A. Markoš, F. Cvrčková

deciphering it: the result of such interpretation will be its meaning to or for someperson, here and now. The meaning may change with contexts, of course.

Two questions will be dealt with in this paper:

1. Can information, sign, and meaning become scientific terms? Our tentativeanswer is No; if Yes, only at a cost – we will, perhaps inevitably, have to ignoreexactly those aspects of our shared experience we wanted to grasp.

2. Can tentative concepts of information, sign, and meaning, as known in humanaffairs, be extrapolated to the affairs of all living beings (including, e.g., bacteria,plants…), and to different level of description (cells, embryos, individuals in theirecosystem, etc.)? Our tentative answer is Yes.

It may be worth emphasizing that the wording of the second question alreadyshows that, unlike some biosemioticians (e.g. Brier 2003), we do not aim towardsunderstanding, ultimately, the functioning of the human mind, brain or conscious-ness. Our main interest are those aspects of communication as signification thatappear to be common to all living beings – and our uniquely first-person experiencewith the human affairs can provide nothing more, and nothing less, than a modelguiding our thinking about the processes taking place in, or performed by, beings notendowed with a human-like mind.

It follows from our answers that some aspects of the living of utmost importancecannot be formulated, i.e. studied, in the realm of contemporary biological science, atleast as far as this science claims to aim towards explaining (away) all biologicalphenomena in terms ultimately reducible to those of chemistry and physics. In thissense (and only in this sense) our position is vitalist, if we accept the Drieschian (i.e.not the Bergsonian), definition of vitalism sensu lato: as the acceptance of thepremise that some aspects of living beings are specific to them and not foundelsewhere (Eigengesetzlichkeit, Driesch 1905), and that current concepts of sciencessuch as chemistry or physics thus cannot grasp them in principle. It has to be,however, noted that we do not follow Hans Driesch in his demands for somemeasurable quantity specific to living matter (which is how his entelechy may beunderstood). That elusive “own law” of life may well be… semiosis. Below, we shallput our answers to the above two questions into contrast with opposite views,personified mainly by one of leading figures of contemporary biosemiotics, MarcelloBarbieri.

What is in a Word: The Reduction-Inflation Model

Let us first examine the tangled pathways whereby a common word evolves into aterm, using as an example the generally accepted (though sometimes ill-defined)concept of information, which, incidentally, also happens to be rather central to ourcurrent discussion.

History of science has witnessed many examples of terminological misconductroughly corresponding to the following scheme: (1) Take a word of broad usage andnarrow its semantic field (scope) substantially, generating a technical term used in alimited area. (2) Inflate this technical usage back to the whole realm of the previous

The Meaning(s) of Information, Code … and Meaning 63

semantic field. (3) Proudly state that “today, in contrast to the dark ages of previousgenerations, we already know what the term means.”

We shall pay attention to the concept of information here, but the same develop-ment can be demonstrated in many other scientific terms taken from ordinarylanguage, like force, light, heat, or black hole: everybody knows the words and hasdeveloped a private semantic field (feeling) for them. When it comes to science, it isvery difficult to narrow the semantic field of such words, to apply scientific objec-tivism (sensu Lakoff 1987) and to work with the concept in frames of formal,objective language.

It would perhaps be much more convenient to invent a new term with no counter-part in natural language, say “phenomenon Φ” for the black hole (or “guf” instead offorce). Perhaps cosmology would not be that popular in public as it is today. Butwords have their fates. Entropy is an artificial word; in the 1950s, it seems, it stillremained somehow suspect in the vernacular. That is why C.P. Snow (2003) haddifficulties with “literary intellectuals” when he asked them to explain the term (andshould he have asked, say, biologists, he would be disillusioned too). By now,however, it found its home in ordinary language as, roughly, a synonym of “disorder”and everybody feels that he/she is at home with it. Even more illustrative is the“transcription” of the term in different writing systems, like Chinese: the ideogram for“entropy” tends to be read as an ordinary Chinese word (“shang”) having some 15different meanings, none directly connected with the physics (see Mackay 2001).

In-formatio was understood since the Middle Ages as a process of molding of themind or character, by training, instruction, teaching, or even divine inspiration. Laterits meaning was somewhat narrowed to communication of knowledge concerningfacts, subjects, or events: intelligence, news, but not raw data! (see, e.g., The compactOxford Dictionary). For an early 20th century physiologist, information is somethingthat causes differences in response in the living body or its parts. Hence, the informedsubject had been gradually replaced by a contraption (e.g. a feedback device), andinformation itself became but a difference that makes a difference (Bateson 1972).Yet, even information in such a sense cannot be treated formally, nor can it bemeasured, only discerned: it can affect its addressee through its quality or meaningfor this particular addressee, but there is no objective definition of information.

In 1948, Claude Shannon introduced the catchy technical term information to givea name to the probability of transmission of a digital string of symbols through achannel (Shannon 1948). Defined in such a way, suddenly information could bemathematically defined, measured, quantified, stored, and manipulated by machines.Even more, it became context-free (it requires no addressee to or for whom it confersany meaning) and thus completely decoupled from meaning, hence objective andpalatable for scientific use. Consequently, such particular usage of the word hadimmediately gained on popularity in scientific circles, and from there it quicklyinfested many areas that had nothing in common with the original territory of use;finally entering school curricula and creating thus a “memetic trap” that shapes ourthinking ever since. Both general public and experts now “know” precisely whatinformation is. One can, for example, find calculations of how many bits of infor-mation is contained in the human genome, in the net of the brains’ neuron connections,etc. (e.g. Christley et al. 2008; Wang et al. 2003; Reber 2010). Even more, one oftenencounters a statement that information belongs to fundamental physical quantities,


besides matter and energy (e.g., Barbieri 2003). Note that the narrowing, reductionthe semantic field of the word was quickly followed by an inflation – a bubble of newcontexts where “information” is now being used in the vernacular. Yet, the old naturallanguage meaning of the word information still somehow manages to survive in theeveryday life. As much as we might argue about bits and bytes, hardly anyone wouldthink of looking for them at the information kiosk of a train station.

Claude Shannon is not to be blamed for the above-mentioned reduction (the lessfor the inflation). His classical paper from 1948 contains also a warning, notoriouslyknown from basic textbooks in informatics: “Frequently the messages have meaning;that is they refer to or are correlated according to some system with certain physicalor conceptual entities. These semantic aspects of communication are irrelevant to theengineering problem.” Indeed, two messages of very different meanings, or even ameaningful message and a meaningless one, may be indistinguishable in terms of“information content” according to the technical definition (Shannon and Weaver1949).

In other words, once we have accepted the Shannonian definition of information,we should give up the notion of contents – or, rather, we should delegate it tosomething else than information. Meaning?

Incidentally, Shannon’s warning contains also a summary of what meaning means:reference, correlation, i.e. putting a message (a word, a letter, a sound) into thecontext of a physical or conceptual entity. Even the most elementary usage of theword (as in the phrase “different meanings of the same word”), not to speak about itsmore sophisticated uses (e.g. intention, purpose, spirit of the told or written word,interpretation, signification) points towards an intimate connection between meaningand context; the same sentence, statement or text may mean different things fordifferent readers, or, occasionally, nothing at all, if a certain background context isabsent (just imagine the situation from the prologue, only substituting a Polishnewspaper to the radio broadcast). As P. Heelan (1998) noted, for a written text“there is no single legitimate meaning relevant to all readers of, say, a text (orsuchlike material), for meanings depend on use.”

Thus, the external world, both synchronous and diachronous (acting throughmemory and experience) always enters the discourse as a modulator of interpretation.Only when we accept this, can we speak – in a natural language – of semiotics oreven hermeneutics performed by the living (Markoš 2002).

But can all this be extrapolated to non-human beings?

Organic Information – and Meaning

There is another brave attempt of introducing the term into science: M. Barbieri (e.g.2008a) coins the term organic information as a basic physical entity (irreducible, i.e.not derived from other physical entities) that is not a quantity but a nominable: itcannot be measured but only named. He explicitly means aperiodic biologicalpolymers like DNA, RNA that cannot come into existence spontaneously (e.g.through ordinary chemical reaction or by crystallization), but exclusively by copyingof pre-existing molecules of the same kind that serve as a template for the newlymade polymer. Similarly, proteins that can be synthesized, in cells, only thanks to the


existence of the genetic code. In short, for nominables – both molecules or man-madetexts – only a copying process, or some translating algorithm, will ensure theircontinuing existence (or evolution) in time. (Note that both kinds of nominablesare, then, artifacts: below we shall return to the question of who wrote the templates.)

There are no rules – physical or chemical – how to decipher the sequence ofbuilding block in such a nominable, they must be read one by one, and, if in a stringof 500 nucleotides or amino acids we know 499 units, we still have no hints what the500th item (base, amino acid) would be.1 Thus, two such strings differing in a singleitem represent two different, nominable, physical entities. Describing the sequencesin terms of Shannonian information would lead to two identical numbers revealingbut a trivial fact that the strings are of the same length.

Two problems should be further elaborated with organic information reified,connected with nominability of strings at different levels of description.

Let us for this moment keep the paradigm of the central dogma stating that“information [sic] flow can proceed from nucleic acids to proteins, not backwards”(Crick 1958). In its simplest case, the unique (nominable) string of DNA is eithertrans-coded into a complementary string of DNA (in a process called “replication”),or trans-coded into a complementary string of RNA (in a process called “transcrip-tion”). One class of RNAs (called mRNA) may then be translated into the polypeptidestring of a nascent protein according to the genetic code. There is a match, viamRNA, between the sequence of nucleotides in DNA, and the sequence of aminoacids in the nascent protein; almost as perfect as, say “A” is a match of “▪ –” in Morse.Barbieri has a credit that he pointed to the fact that the existence of such codes is notself-evident from the laws of physics as we know them: codes are products ofhistorical coincidence, i. e. proteosynthesis is “artifact-making”, not an ordinarychemical reaction of polymerization (e.g. Barbieri 2008a). He goes on, however, bystating that in this particular case the nominables in the set of DNA string represent“signs”, whereas those in the set of proteins (results of decoding the information)represent the “meaning” of those bits and pieces of information. “Meaning is anobject, which is related to another object via a code”, says Barbieri (2003, 5). “A” isthe meaning of “▪ –“(and vice versa, in this particular case). He then insists that thismay be the scientific, i.e. objective and reproducible, definition of meaning. It followsfrom such a reduction (comparable to Shannonian treatment of information) that theexistence of codes is a necessary and sufficient condition for semiotic processes; i. e.semiosis is completely decipherable in scientific terms provided that the codes areknown. Indeed, to model life as a hierarchy of codes (e.g. Trifonov 2008) is a verycatchy and respectful idea, yet, we feel that modeling living processes as a determin-istic program-run machine (like a computer) belongs to physiology rather than tosemiotics – and physiology can do without the concept of meaning. Barbieri tries toencompass the term of meaning in lines of the most venerable tradition of modernscience: by developing mechanistic models of life and especially levels of semiosispresent in living beings (see, e.g. Barbieri 2011a, b). As is apparent, we follow adifferent path of investigation that, in future, may, or may not be, encompassed byscience.

1 But grammar may sometimes help with such a spelling: not all sequences will give sense.


The description above aspires to belong to the realm of objectivist semantics(Lakoff 1987). Here, meaning and rationality become transcendent, i.e. perfectlycommunicable and identical to all participants of such an information exchange. Aswill be further discussed below, semiotics has no place in such an objective construct;semiotic processes will confer meaning to or for a particular being. Indeed, Barbieriin his earlier work (2003) uses the term semantic biology; the switch towards semi-otics was, on our opinion, infelicitous.

Code

What, then, is a code? If we put aside juridical and biblical usage of the word, we areleft with signals, abbreviations, or signs serving for either simplified (compacted) orprotected (encrypted) transmission of messages, originally in fields such as e.g. themilitary, transport or telegraphy. For instance, shortwave radio enthusiasts are, evennow, using not only the notorious Morse code, but also the “92 code” originallydesigned in 1859 by Western Union railway telegraph operators, and the “Q code”originating from the abbreviations established for communication among Britishcommercial ships before WW I.

Nowadays, cybernetics, computing or molecular biology are just additional situa-tions where one-to-one correspondence between the original and received message –transmitted via the code – is often necessary or at least desirable. It follows thatmachines or machine-like devices able to perform the coding and decoding (or evencode-breaking) can be built. They do so using hardwired tables of codes, which can bestored, transferred, public or hidden. No intrusion of mind, intentionality, understandingof the context – some of the basic components of meaning in the old, broad senseknown from the natural language – is required, despite the fact that the code is aspecific case of meaning.

To return to the definition quoted above: meaning0mutual relation of two objectsvia a code. The narrowed contents of such a technically defined meaning coverstherefore only a fraction of the original semantic field of the word – as is usual whenobjectivization is desired. Like in the case of information, we are at risk of falling intoanother version of the old memetic trap: the technical, narrowed-down definition ofmeaning may come back into the natural language. Everyone will know from now onthat meaning is just a matter of coding and decoding – maybe more complicated thanthe Morse code, but “in principle” one only needs to understand how Morse works tograsp it all.

However, even in the realm of codes, old meaning is not dead, as long as humanbeings enter the chain of message transmission and interpretation. The railway tele-graph operators who designed the “92 code” more than 150 years ago were undoubt-edly busy men working with low-throughput transmission channels of limitedreliability, and the code table is thus as compact as possible. Yet, since the verybeginning, 73 has been reserved for “best regards” – nowadays perhaps the mostfrequently used code word of this table (and 88 stood for “love and kisses”, longbefore the neo-Nazis gave it another, more sinister meaning). For deciphering mean-ing, codes will represent only a subset of necessary preconditions to understand signswhich never are objects.


Objects and Signs

Let us first examine the seemingly innocuous notion of an “object”, the conceptwhich plays such a prominent part in M. Barbieri’s definition of meaning. We shallfollow the terminology of J. Deely (2008, 2009a, b, 2010), who works up thetradition of semiotics going through Middle Ages via C.S. Peirce up to our Post-modern times – contrasting to the tradition of Modernity. We should start with a littleterminology we are rather unused to, or even worse, the same words have an oppositemeaning in the terminology of Modernity.

According to this concept, the world is full of things – known or unknown to us –which abound with different qualities and relations, all modeled by their history.2

Nobody is able to list all the properties of a thing – however well known. Suchsubjectivities of the surrounding world can give themselves (or can be perceived) tosenses, receptor molecules and/or structures of a living being: we stress again – anyliving being, not only that endowed with mind.

What follows, however, has been elaborated for humans or – at most – animals;generalization of some semiotic concepts is our task here. Sensations, in cooperationwith our nature, experience, language competences, learned knowledge, historicaland community context, etc., will give rise to a suprasubjective sign. A sign cannot bepointed at with a finger – it is a relation. Signs then will be processed – interpreted –into objects of mind. Objective reality, then, is a product of our minds, and isinhabited by objects and their relations. Object may point toward some aspects ofthings (subjectivities) in the world, or they can even be created independently of theworld, inside the minds (like numbers, geometrical objects, or objects of physics.Objective reality – a transcendent artifact of human mind – can be communicated(and learnt) across the society by means of a class of signs called words. In short,objective reality is our creation, resulting from evaluating the meaning of ever-changing signs in the flow of our experience (remember our Prologue).

Objective reality is an evolutionary invention, characteristic for Homo sapiens,who is able to distinguish between things and objects. It may be that other animalsalso build their umwelten from objects that they, however, cannot distinguish fromthings. Yet we shall maintain here that creatures other than animals are also able –without access to objects and language – of deciphering sings and their meaning,depending on their nature, genetic databases and programs, evolutionary as well asindividual experience, learned knowledge, historical and community context, etc.,thus interpreting their situation in the world. In other words, we aspire to persuade thereader, that cells, plants, bacteria are able to “make wise decisions and act upon them”(see epigraph).

Here we enter an unsafe terrain. Neither Barbieri nor Deely will provide us aguide, (each for different reasons, see their exchange in Barbieri 2008b; Deely2009b), not only because they build on different premises (which, on itself, doesnot exclude the more than welcome possibility of reaching, independently, similarconclusions), but also because they differentiate between beings dwelling on differentlevels of scala naturae. Deely only grudgingly accepts zoosemiotics, but does not

2 Actually, Deely is very close to similar characteristic of things in Heidegger (e.g. 1971; see also Markošand Faltýnek 2011.)


admit semiotic accomplishments to beings devoid of brains or at least nervoussystem. Barbieri accepts Deely’s platform as one (the highest) step of his three-stepsemiosis, but he does not allow two lower steps any interpretative abilities; henceboth thinkers degrade beings different from humans (or humans plus some animals)to programmed machines.

The only difference from machines (or mechanistic models of reality – see Barbieri2011b) is that living beings are neither copied nor produced (made), but born fromother living beings. But this difference makes the very difference between livingbeings and automata. Life is not art, neither artifact-making: it’s life who makesartifacts and fine arts and even writes down its experience into quasi-digital strings ofbiological polymers (to read, i.e. interpret the script in various contexts). We endeavorto claim that there is only one and single “grade of semiosis”, accessible to all livingbeings – because all share the same world and all carry with them 4 billion years ofexperience – written in their genetic material, or – somehow – transmitted by theirbodies and interactions with other living beings – conspecific or not. We shall furtherconcentrate on the first “level”: aperiodic linear biopolymers and their interactions.

Levels of String Classification

Let us explain the difficulties on the simplest model, that of the information-transmission pathway DNA–RNA–protein as presented by Barbieri.

a. A protein-coding sequence in DNA may give birth to a single string of protein.This is a very simple example of simple decoding, as it can be demonstrated inlaboratory models. Nevertheless, it does not automatically follow that in the“world of bodies”, as discussed below, such a protein string will also reach thesame spatial conformation, as folding of the protein depends on the kineticparameters of its synthesis, which may well be affected even by the structure ofthe RNA being translated (Kimchi-Sarfaty et al. 2007). (Even at this level someparadoxes may arise: If two alleles of a protein-coding sequence in DNA differ ina single nucleotide, they represent two different nominables, i.e. they deserve 2names; yet due to the code degeneration, both may code but for a single protein.)

b. A protein-coding sequence in DNA can give rise – via alternative processing oftranscripts – to a plethora of unique, hence nominable, protein strings.

c. A native protein is often further processed by cutting or splicing peptide stringsand/or chemical modification of amino acid residues. In such a case the numberor quality of amino acids in the string will get changed, i.e. a set of uniquenominables, sometimes very large, would arise from a single native protein;moreover, the process may be reversible, hence we experience a floating worldof incessant name-changing (for histone proteins, see Markoš and Švorcová2009).

It follows from the last two points that the number of entities during the “infor-mation processing” (or better, transforming one class of organic information intoanother) may increase even into the innumerable. Moreover, if the final issue of thestring depends on a number of modifying “epigenetic” influences (like, e.g. proteinkinases/phosphatases, methylases/demethylases, acylases, etc.) a question arises how


much information is coded in the information entity (i.e. string of DNA) and howmuch arrives from the structured environment (structures, ecosystem of proteins, etc.,see below). Can one, then, put a sign of equation between “information processing indifferent contexts” and “interpretation dependent on context”?

To reflect the obvious fact (in case of the nucleic acid – protein relationships),Barbieri sticks to an idea of a “codes upon codes” contraption. As we said above, themodel is meaningful, but it has nothing to do with semiosis and seeking for meaningin the original sense (see the Prologue). Another reductionist move must thus be donein order to justify it. Barbieri (2008b, 2011b) introduces the idea of 3-steps semiosis,with steps evolving from code semiosis through signaling semiosis up to interpreta-tive (cultural) semiosis; hence, only the third step involves interpretation, and onlyhumans are capable of pursuing this last step. On the lower levels, then, interpretationdoes not take place, and meaning comes out of coding-decoding, i.e. of grammaticalor semantic processes. By such a trick, biosemiotics (at least its lower levels) could beincorporated into the standard science of biology. At the point when no interpretationexcept decoding is allowed, we can abandon the concept of semiosis easily – after all,most textbooks do so.

Body

The situation with sequence multiplicity in proteins will get even more complicatedwhen we abandon the string-focused view and take into consideration the fact that theprotein molecule is a body with a great plasticity of shapes. Even in the simplest casediscussed in point a above, the protein’s body (molecule) is not a crystal-likestructure, even if it tends to adopt some preferred shape(s). Not only physical factorslike temperature, pH, ionic strength etc. (such factors will in some way influence allproteins present) participate in “guiding” a nascent protein molecule towards thisshape, but above all targeted (allosteric) regulation of the given protein by a greatplethora of regulators that bind to the molecule – be it “messengers” or other proteinspresent in its surroundings here and now. Or should we reverse the optic? Should wesay that the protein (or a protein team – a supra-protein structures like, say a ribosomeor microfilaments) take all those inputs as cue, to be able to react in a meaningful way(to make wise decisions and act upon them in a given context)?

The role of highly structured cellular interior harboring thousands of differentproteins (who modify the nascent protein in a meaningful way allosterically orby”changing the name” of the very string (as above b,c), is, then, the very informa-tion matrix that gives the protein its final shape, location, or function. Not only this:even the very thesaurus of DNA sequence nominables represents bodily structures(not speaking of RNAs) and will be readily molded by the cellular interior (so thecentral dogma becomes somewhat blurred): simple bending of the string will changethe gene expression, not mentioning frequent recombination processes, and chemicalmodifications of particular bases. Is a bent string a different item from the straightone? Should a string with one cytosine modified to methylcytosine mark a newnominable, or should we ignore such “diacritics”?

Confronted by the enormous body of data provided by contemporary biologicalresearch, we feel that biosemiotics can hardly aspire to become a (natural) science,


unless we accept that nearly all molecular biologists could be labeled as cryptobio-semioticians. The alternative is becoming, or remaining, a branch of semiotics proper.If so, interpretation should be admitted at all levels of the living, with non-reducedmeaning of the concept of meaning. This requires searching for analogies betweennatural language and the organization of the living (first attempts in such a directionsee Markoš et al. 2009; Markoš and Švorcová 2009; Markoš and Faltýnek 2011;comparison of Barbieri’s and our approach see Markoš 20103). Because proteins areborn into preexisting cells (and such preexisting cells give rise to a multicellularbody), the way (language) how cells process their heritage (be it DNA or not), howthey understand, interpret this heritage, may give us cues how to understand life. Butwe doubt that only pre-established, reifiable tables of codes work in the background.Cells do not arise by copying and they never emerge de novo according to a blueprint:they are born and they keep the tradition how to understand, among others, thegenetic script. They decide what should be processed in what contexts. The codes arenecessary but not sufficient preconditions for life (like vocabulary and grammaticalrules/codes are not sufficient for a meaningful speech or text).

A Place for Meaning – and for (Bio)Semiotics?

Meaning never sits somewhere ready to use; it must be negotiated all the time.Negotiation to extract meaning, negotiation to maintain its vigor, negotiation tocontrol its historical development. Let us now outline two strategies aimed towardsgrasping the living, both respectable but mutually incompatible to a large extent.

First, accepting the program of biologization of physics, we might discover life-like properties in the universe itself, and adjust our model accordingly (Markoš andCvrčková 2002). While remaining safely in the realm of objective sciences, we couldthus hope to get rid of the uneasiness associated with fitting the phenomenon of lifeinto an objective model of machine-like deterministic universe – as universe itselfwill be perceived alive (Jantsch 1979; Ruyer 1974; even Deely 2010 with hispansemiotic statements). Modeling epigenesis, or ontogeny, as reconstruction fromincomplete information (Barbieri 2003), or attempts to describe the inner workings ofa cell in terms of a network of modules connected by a set of protocols (e.g. Csete andDoyle 2002), may also fall into this category.

The second strategy will be expanding the study of living beings beyond the limitsof biology (understood as an objective science), and entering the realm of the “life-world” studies, of which classical biology would represents only a special case.Living beings will be recognized not as push-‘n-pulled objects, detached in adetached world, but as active participants in affairs that encounter on their life-paths, taking care of themselves, actively influencing their world, lives, ontogenyand even evolution by modifying the very rules how the universe behaves. The realmof the lifeworld can be reached even from within sciences – as demonstrated, e.g., byS. Kauffman’s (2000) model of the biosphere of autonomous agents, taking care of

3 Surprisingly, not only biological sciences succumbed to the reduced version of information: the sameprocess took place in linguistics, too. By language metaphor, then, we do not mean making analogies withformal languages that are subject to scientific study (Markoš and Faltýnek 2011).


themselves and incessantly changing the properties of the universe. Semiotics,hermeneutics, and similar disciplines of the humanities open the gate into this realm,supplying methods and thought patterns unknown in natural sciences (Markoš 2002).

However, such an enterprise is not free of risk. First of all, you will be givennames:”vitalist” the mildest among them. As we have already seen, not unjustly. The(not yet entirely consensual) biosemiotic axiom that life and semiosis are co-extensiveprovides a perfect example of “life’s own laws” that H. Driesch considered a definingfeature of his vitalist theory.4

Science is focused on measurable and repeatable phenomena, albeit in biologythese are usually reached only in special model organisms under strictly controlledconditions, and wise biologists are ready to accept this fact as a necessary limitationinherent to the scientific method (see, e.g., Trewavas 2003). Nevertheless, from suchdata obtained under specially designed circumstances, extrapolations are being madeto the whole realm of the living. Physiology, biochemistry, and molecular biology arefull of examples of molecular homeostatic machines. What cannot be forced into sucha mechanical model is considered deviation, non-standard behavior, or, at best,accepted as being out of the scope of the scientists’ interest. Hence difficulties withnon-cyclic and non-deterministic phenomena or events, like origins of life, or evolu-tion, as well as the frustration from our inability to construct an “epigenetic machine”(an oxymoron, on our opinion). This cozy certainty that phenomena of the real worldare deterministic, predictable, available to the tools of the scientists’ trade, will be, ofcourse, lost.

What, then, is the position and role of mechanisms, of the measurable andrepeatable? How can they be accommodated into the lifeworld? Let us conclude witha hypothesis, perhaps far-fetched, but at least suggesting a basis for mutual under-standing between classical biology and lifeworld studies.

Life sooner or later delegates to machine-like behavior all those processes whichcan reliably go on without continuous control. In such cases, hardwired coding willbe preferred to endless decision-making process and negotiation. We automaticallyperform activities like walking, breathing, digestion, protein synthesis, driving cars,pumping ions across membranes, even filling forms or answering our sweethearts,but we can jump out from such automatisms and behave as sentient beings wheneverthe context of situation becomes pushing. While we read poetry or write papers, ourcells and organs do their automatic jobs; similarly, we may not be aware when theyjump out from hardwired regimes. And let us not be mislead into anthropomorphism:a similar argument can be developed even for plants, possibly the least “sentient”macroscopic living beings imaginable (Trewavas 2003; Cvrčková et al. 2009).

If we extend this analogy to the whole realm of the living, we may came closer tounderstanding ontogeny as a hermeneutic achievement based in the experience of thegiven lineage, as opposed to a result of blind deterministic forces acting from theoutside. Lifeworld will become the true realm of information and meaning.

Back to biosemiotics: does biology gain more than what was lost by reducingmeaning to the result of decoding? If not, then we should perhaps renounce amanageable definition of meaning in favor of a more specific term that can be defined

4 You will also be accused of laziness, because instead of hard work in the lab you kill your time by“philosophizing”. But this is not the point we want to touch.


without substantial loss of contents. Code itself would probably do, and M. Barbieri’slater narrowing of meaning to organic meaning (Barbieri 2008a) can be taken as awelcome step in this direction. Another alternative may perhaps be the notion ofprotocols (analogous to those known from the computing field) connecting functionalmodules at various levels of biological organization (see, e.g., Csete and Doyle 2002).At the same time, we still believe that some aspects of meaning in the “old” sense, notcovered by the concept of code, remain highly important if we really strive tounderstand life (to more details see the “language metaphor” of life, see Markošand Faltýnek 2011). While we cannot prove our point, we hope we can at leastillustrate it using the analogy of the game of chess as a metaphor for some aspects ofthe scientific endeavor.

Coda

To make our view more palatable, we invite the reader to compare two games: chessand ice hockey. In chess, the chessboard, the pieces and the rules (a code) governingtheir behavior represent the world. The whole inventory of the world exists before-hand, objectively, no hidden elements (such as a piece called, say, Prime Minister) areallowed, and no new elements or rules can arise throughout the game. The game isdifferent every time, sometimes interesting, sometimes dull, depending on the qual-ities of the players (like the models of the world provided by science, and theirinterpretations). However, essentially it is nothing but push-‘n-pull of pieces on theboard, although the players may differ in their strategy. The pieces themselves haveno say in the ongoing game. The chess game is the analogy of the universe as studiedby scientists: those who push the keys are, of course, laws of nature. The world ofchess can be deduced from the properties of its elementary building blocks and fromlaws that determine their behavior. Knowing everything about this basic level ofdescription is the safest way towards revealing all properties of such a world anddeveloping a winning strategy. Of course, there is a price. There is no space for“Why?” questions like “Why is that piece called King, and why is it irreplaceable?”

Compare this with ice hockey: The world of the game is also limited by themantinels, rules (that evolve with time), and interpretation of those rules by thereferees. Yet, it’s the “pieces” – i.e. players, who create the game within the givenlimits. They are not pushed and pulled by external forces, they themselves govern –or better, “negotiate” – the dynamic of the match. Each of them enforces his fitnessupon the given world, they take risk, they recognize the meaning of their doings – andthe output is by far not the result of decoding. An interesting biological counterpart ofthe hockey game has come from the group of S. Linquist (Rutherford and Lindquist1998; Sangster et al. 2004; Taipale et al. 2010; see also Bergman and Siegal 2003).Evolution in their view is in hands of the dynamic protein networks (players?) whoseactivity is controlled, buffered, and kept in a chosen regime by special “chaperonin”proteins (referees?) in the hubs of such networks. Mutation of the code, effect of theenvironment, internal relations may be buffered for many generations (no changes inphenotyope, i.e., species-specific appearance of the game), just to switch suddenlyfrom time to tome (change of rules). Compare this with chess pieces, which simply“exist” and have no participation on rules applied from outside.


Let us allow to draw a primitive analogy between the ice hockey-like games andlife: the players (proteins, cells) are largely similar in different games (species), it isthe rules (genes, coded contraptions, etc.) and the overall settings (playground ofecological interactions and historical contingencies) that makes each game a distin-guishable “species”, with evolution. Such a historically achieved network of inter-actions allows the players to model their world “specifically”, to give it meaning.

Acknowledgements This work was supported by grants from the Czech Ministry of education(MSM0021620845 to AM and MSM0021620858 to FC).

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The Meaning(s) of Information, Code â¦ and Meaning

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