Review: Marcello Barbieri (Ed) (2007) Introduction to Biosemiotics. the New Biological Synthesis

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tripleC 5(3): 104-109, 2007 ISSN 1726-670X http://tripleC.uti.at

Review: Marcello Barbieri (Ed) (2007) Introduction to Biosemiotics. The new biological synthesis. Dordrecht: Springer

Günther Witzany

telos – Philosophische Praxis Vogelsangstr. 18c A-5111-Buermoos/Salzburg Austria E-mail: [email protected]

1 Thematic background without utterances we act as non-uttering indi- viduals being dependent on the discourse de- Maybe it is no chance that the discovery of the rived meaning processes of a linguistic (e.g. sci- genetic code occurred during the hot phase of entific) community. philosophy of science discourse about the role of This position marks the primary difference to language in generating models of scientific ex- the subject of knowledge of Kantian knowledge planation. The code-metaphor was introduced theories wherein one subject alone in principle parallel to other linguistic terms to denote lan- could be able to generate sentences in which it guage like features of the nucleic acid sequence generates knowledge. This abstractive fallacy molecules such as “code without commas” was ruled out in the early 50s of the last century (Francis Crick). At the same time the 30 years of being replaced by the “community of investiga- trying to establish an exact scientific language to tors” (Peirce) represented by the scientific com- delimit objective sentences from non-objective munity in which every single scientist is able the ones derived one of his peaks in the linguistic place his utterance looking for being integrated turn. in the discourse community in which his utterances will be proven whether they are good ar- 1.1 Changing subjects of knowledge guments or not. Definitively the solus ipse subject of knowledge was replaced by the “indefinite The crucial steps of early Wittgenstein and community of investigators” which doesn’t not scholars of logical empiricism to delimitate scien- produce ever lasting knowledge principles about tific sentences from non-scientific ones, the fol- scientific areas, but try to get forward in discur- lowing failure of all trials to establish a scientific sive truthfulness “in the long run” (Peirce) princi- language of theory which would be coherent with pally ending with human species in an “ultimate the language of observations, or to define a sci- opinion” (Peirce) of the things which are dis- entific language which could be able to depict cussed. objective reality in a one to one fashion, lead to the unescapeable effort to get clear how we can 1.2 Anthropomorphistic use of language me- define human language according to its main tapher in early molecular biology principles; i.e., all three semiotic levels of rules not only from the (objective) observer perspec- The code-metaphor introduced on modern biol- tive but even more from the (subjective) perspec- ogy therefore was an escape of pure physics tive of participants. This would be coherent to the and chemistry because it introduced certain fea- evidence, that without utterances we can not in- tures of languages into the description of chemi- tegrate our position into any discourse. Even cal structures. What seemed to be an obvious

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anthropomorphism was the introduction of lin- This knowledge marked the importance of epi- guistic terms on biological sciences and medi- genetics, i.e. of environmental influences on pro- cine when they used phrases like “communica- tein level which can influence via second mes- tion within cells”, “communication between cells”, sengers the amino acid level, even in coding “genetic code”, “genetic text sequence”, “chemi- functions (which would be a neo-lamarckian per- cal messengers”, “neuronal communication”, spective). For long this view has been ignored or “hormonal communication”, “transcription of the in the realm of Neo-Darwinism dogmatically ta- nucleic acid language”, “amino acid language”, booed, it now becomes more and more impor- “translation of RNA in DNA”, “Letter pairs of tant. Now we know that in the human genome DNA”, and so on. only 3 % of the complete genetic data-set are protein coding sequences. The formerly termed The investigations of biological disciplines and “junk DNA”, the noncoding DNA sequences, is subdisciplines according the knowledge of the now being recognized as higher order regulatory genetic code are legendary. It led to the most functions which are crucial for an appropriate de- developing field of science we know today. termination of the protein coding sequences. The It started the first 3 decades that main investi- difference in the protein coding sequence be- gation focused on the “molecular syntax” tween human and mouse is only 12 %, so the (Manfred Eigen), i.e. the combinatorial patterns differences depend on the higher order regula- of nucleic acids and its corresponding protein tory functions. acid sequences which determined protein structures being the constituents of both of any uni- 1.4 Superficial and deep grammar of genome cellular until most complex multicellular organism storage medium and its developmental substeps. This lead to the complete deciphering of the human genome in This different development in the awareness of late 1990ies. But immediately it became clear different levels of nucleic acid storage medium that the knowledge of a complete sequence or- DNA is important because it marks the difference der of an organism doesn’t mean to know the of nucleic acid language to a one to one depic- complete meaning function which is really inher- tion of meaning functions in the genetic code. ent in the genome storage medium. Obviously there is a superficial grammar (which in the case of the human genome is deciphered 1.3 Genetic expression is no one way since the human genome project) and a hierarchical network of higher order regulatory func- This marks a development which arose in early tions which could be termed as a genome-editing 1980ies where it became clear more and more, MetaCode (Witzany 2006) characterized by the that behind the superficial grammar of molecular strong hierarchical interdependency of all higher syntax there is something like a deep grammar order regulatory modules which we are far away of regulation networks which determines the to know in all details. meaning function of a nucleic sequence order. According to the general features of any real Interestingly this structure of language features language – a real language is a sign system was detected in the early 60s also in human lan- which functions according to the complementary guage according to the change of linguistic turn syntactic, pragmatic and semantic rules – there to pragmatic turn in the theory of science discus- are several levels of higher order regulatory sion when reflecting on the validity claims being functions which are decisive for the expression held with any utterance in speech acts which and replication patterns of nucleic acid se- showed both: quences: it means that different environmental a) that speech acts are apriori social ac- influences, i.e. the situational context an organ- tions i.e. intersubjective actions which ismic individual is interwoven, determines the avoid the omnipresent problem of phi- higher order regulation of replication patterns. losophies of consciousness how to make This means that of the defined nucleic acid order the move from a state of private (solus sequence it is possible to express a great variety ipse) consciousness (sender/coding- of different expression patterns which may be receiver/decoding narrative) to a state of even contradictory: from the same nucleic acid mutual agreement and mutual coopera- order it is possible to produce different protein tion; meanings. And these different protein meanings b) that pure analyses of language and lan- may even derive without altering the genetic guage like structures based on syntactic code or being inheritable. Under certain circum- or syntactic/semantic investigations are stances these alterations may even be heritable not able to extract illocutionary meanings at all. hidden in the pragmatic (situational) con- texts which determines different mean-

ings of identical syntactic data-sets (Wit- and a linguistic/semiotic approach to nucleic acid zany 2000). language and protein language. Biosemiotics in- tegrates these approaches by investigating a va- It is obvious that the language games which are riety of organic codes, which means that the de- played in recent research are not fully compati- cisive difference between life and non-life is the ble. On the one side biological sciences (which generation and use of codes. define themselves as natural sciences investigating observations according to the universal natu- 3 The contributions ral laws of physics and chemistry) which now have to deal with linguistic rules with features The book is divided into three parts. which cannot be deduced of natural laws. On the other side a coherent language and communica- Part 1 – “Historical Background” with contribution theory which is limited to the human self- tions by Donald Favareau (The Evolutionary His- understanding. tory of Biosemiotics), Tuomo Jämsä (Semiosis in Evolution), Marcello Barbieri (Has Biosemiotics 2 The new player in this universal discourse: Come of Age? and Postscript). Biosemiotics Part 2 – “Theoretical Issues” with contributions At this point a new discipline holds validity claims by Howard Pattee (The Necessity of Biosemiot- in this universal discourse: Biosemiotics. ics: Matter-Symbol Complementarity), Stanley Biosemiotics investigates rule-governed sign- Salthe (What is the Scope of Biosemiotics? In- mediated interactions within and between cells, formation in Living Systems), Jesper Hoffmeyer tissues, organs and organisms. As Howard Pat- (Semiotic Scaffolding of Living Systems), Kalevi tee (2005, pp.299) stated: “Life is distinguished Kull (Biosemiotics and Biophysics – The Funda- from the nonliving world by its dependence on mental Approaches to the Study of Life), signs”. Biosemiotics also investigates processes Marcello Barbieri (Is the Cell a Semiotic Sys- and interdependences in the realm of genetics/ tem?), Stefan Artmann (Computing Codes ver- genomics/proteomics which have features of sus Interpreting Life), Anton Markos and co- icons, indices or symbols. The first “Introduction workers (Towards a Darwinian Biosemiotics. Life to Biosemiotics” has now been published. as Mutual Understanding), Tommi Vehkavaara (From the Logic of Science to the Logic of the ”Introduction to Biosemiotics” combines ap- Living. The Relevance of Charles Peirce to proaches from semiotics, linguistics, semantics, Biosemiotics), Marcel Danesi (Towards a Stan- biology, philosophy, systems theory, theory of dard Terminology for (Bio)semiotics), Gérard science, physics and information theory. All con- Battail (Information Theory and Error-Correcting tributions share the conviction that the main Codes in Genetics and Biological Evolution). processes of coordination and information ex- change within and between living organisms, Part 3 – “Biosemiotic Research” with contribu- from single cell to most complex multicellular life, tions by Marcella Faria (RNA as Code Makers: A are mediated by the use of signs. Every sign Biosemiotic View of RNAi and Cell Immunity), process (=semiosis) is coherent with the laws of Luis Emilio Bruni (Cellular Semiotics and Signal physics and chemistry. But in difference to phys- Transduction), Stephen Philip Pain (Inner Rep- ico-chemical interactions in the non-living world resentations and Signs in Animals), Johannes semioses are inherently connected with semiotic Huber and Ingolf Schmid-Tannwald (A Biosemi- rules. According to Charles Morris and Charles otic Approach to Epigenetics: Constructivist as- Sanders Peirce, every sign use is characterized pects of Oocyte-to-Embryo transition), Dario by rules of combination (syntax), context (prag- Martinelli (Language and Interspecific Communi- matics) and content (semantics). The comple- cation Experiments: a Case to Re-open?). mentarity of these 3 levels of rules in every sign- process enables de novo generation of signs, 4 The editorial combinatorial changes, and alternative use of the same sequences to transport different mes- In an Editorial, Marcello Barbieri gives a short in- sages with different meanings. Biosemiotics, as troduction on biosemiotics. He distinguishes 4 introduced by this book, strives to do more than major approaches or schools in biosemiotics. merely promote the biological disciplines from The first is based on the model of Peirce, pro- the perspective of rule-governed sign-mediated posing that interpretation is a crucial element of interactions between living organisms; its validity semiosis and that every semiotic system is char- claim is also to better understand the linguistic acterized by a triad (sign, object and interpre- features of nucleic acid sequences and their tant). regulations. Biosemiotics therefore proclaims In 1974, Marcel Florkin proposed a second both a communicative approach to sign- model for biosemiotics, namely the dualistic sys- mediated interactions among living organisms tem of Saussure, i.e. that a “signifier and signi-

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fied” are equivalent to “genotype and pheno- ally, evolution replaced the ribogenes with genes type”. Thomas Sebeok adopted the Peircian nar- and the riboproteins with proteins but the syn- rative for zoosemiotics. The Peirce-Sebeok thesizing ribosoids of the ribotype have never school was the first to be fully accepted by most been replaced. They are the oldest phylogenetic biosemioticians, especially the Copenhagen- molecules that exist on earth and they firmly re- Tartu School (Claus Emmeche, Jesper main at the heart of every living cell.” (186) Hoffmeyer, Kalevi Kull). That the Prague school In this thesis, Barbieri is a forerunner not only of Anton Markos also derived from this model as in biosemiotics: his approach gives a coherent suggested in this editorial seems to be risky be- explanation of fundamental processes of life with cause the biohermeneutic approach (first devel- its connection to early stages of evolution. This oped by Sergej Chebanov: Chebanov 1999) de- yields a quasi-subject of linguistic competence: rives from hermeneutic science founded by the ribotype, which throughout the history of life Hans-Georg Gadamer, whose methodological is able to produce codes by code-making. “The aim differs fundamentaly from that of the Peirce- codemaker is the agent, whereas signs and Sebeok school. meanings are the instruments of semiosis.” (187) As a third model, Barbieri introduces his se- Signs come into life in the coding process of this mantic theory. It states that the cell is a triad of code-maker. Thus, signs/meaning and code- genotype, phenotype and ribotype, wherein the maker/coding are true organic entities. ribotype is the “codemaker”, i.e. the generator of But the organic code of the ribotype is not the the molecular syntax of the nucleic acid lan- only conventional organic code – other natural guage. He furthermore suggests that, in his con- conventions share the three basic characteristics cept, the rules of the genetic code do not depend of all codes “(1): a correspondence between two on interpretational processes. independent worlds, (2) the presence of molecu- As a further (fourth) approach, Barbieri names lar adaptors and (3) a set of rules that guarantee the model of Howard Pattee and his concept of biological specificity.”(190) Barbieri identifies the epistemic threshold. It differentiates between (i) splicing codes, the signal transduction codes, the physical preconditions for the organic codes and compartment codes (which are crucial for the symbolic regulations and (ii) some kind of emer- “geographical” destination of a cell), the cy- gentism. toskeletal codes responsible for the necessary dynamic instability because the number of “dif- 5 Two examples of the main chapters ferent structures that cytoskeleton can create is potentially unlimited.”(193) Also important are Here, I briefly review two examples within the the sequence codes (such as transcription main chapters: Certainly, one of the key contri- codes, gene splicing codes, translation pausing butions is Barbieri’s chapter “Is the cell a semi- codes, the DNA structure code, the chromatin otic system?”, in which he attempts to give rea- code, the translation framing code, the modula- sons for his concept of organic codes. He de- tion code and the genome segmentation code). fines a semiotic system as a system “made of In a third chapter, Barbieri explains why these two independent worlds that are connected by codes are actually physical entities: they are ob- the conventional rules of a code.” (181) These jective, reproducible and defined by operative are two distinct entities for Barbieri, and he re- procedures. So “organic information and organic places the Peircean semiosis triad (sign, object, meaning are both the result of natural processes. interpretant) by his own triad (sign, meaning, Just as it is an act of copying that creates or- convention). Important in Barbieri’s concept are ganic information, so it is an act of coding that the “copying” and “coding”-processes that repre- creates organic meaning. Copying and coding sent crucial differences to the non-living world. are the processes, copymakers and codemakers Here, the codemaker is the ribosomal RNA, are their agents, organic information and organic which generates chromosomal sequences ac- meaning are their results.” (199) (In this context cording to the molecular syntax of the nucleic see also the interesting contribution of Marcella acid language. This initially involved simple copy Faria in part 3 of this book) functions. “The first protein-maker had to bring together three different types of molecules (mes- One of the leading positions in biosemiotics is senger, ribosomal and transfer RNAs) and was represented by the Prague-school. A contribution therefore much more complex than copymak- by its founder Anton Markos and his co-workers ers.” (184) Accordingly, gene sequences differ “Towards a Darwinian biosemiotics. Life as mu- from randomly assembled molecules in the non- tual understanding” investigates, in a first part, animated world because they are a real artefact the preconditions of understanding processes. produced by “molecular machines based on This is the only investigation the book contains in RNAs.” (185) This makes the cell a trinity of this field. It aims to understand our understand- genotype, phenotype and ribotype. And the early ing of sentences, meanings, codes and utter- RNA world appeared spontaneously. “Eventu- ances, which is not definable by formalistic pro-

© Vienna University of Technology 2003. Witzany, Günther 108 cedures or operationalistic theory of science hermeneutic foundation and background knowl- definitions. This is a crucial contribution for edge. A theory of science discussion about the biosemiotics if this new discipline desires to be status of language and communication in methodologically coherent. In a second part, the biosemiotics, or about the scientific foundation authors demonstrate an actual biosemiotic inves- and justification of sentences within biosemiotics tigation on “corporeality, life and language”, according to the linguistic and the pragmatic which is indeed one of the outstanding biosemi- turn, is missing in this book. The same holds true otic applications. Here, the authors find a defini- for the integration of a post-metaphysical (non- tion for a phenomenon observable in all life solus ipse) subject of knowledge. processes: homoplasy. “From the biosemiotic perspective, homoplasy is not newly derived: (3) Is this discipline merely an additional view on rather, it is a result of the persistence of a biological phenomenon, or does it have the morphogenetic system which became reawak- paradigmatic power to redefine our understand- ened or re-invented in an unusual context. ing of living nature? Hence, if organisms need to evolve a new adap- The recent main deficit of biosemiotics – the tive structure, they may activate remote morpho- lack of a uniform method for applied investiga- genetic systems and, under the current circum- tions – may turn out to be its driving force be- stances, an unexpected shape will appear. From cause it needs to integrate very different aims, the biosemiotic point of view, such “realization” traditions, paradigms. Especially the approach of refers both to understanding (becoming aware of Marcello Barbieri (and Marcella Faria) and his a “knowledge” – of the existence of an engram), differentiation between “copying” and “coding”- recognition of its significance (acknowledgement functions in the evolution of life gives an out- of a mute sign) and its bodily interpretation (to standing interpretation of recent biological re- know the how of the developmental process).” search: In genome rearrangements it is a usual (252) phenomenon, that in a first step parts of the genome are simply duplicated (copying) and in a 6 Conclusions second step the molecular syntax is recombined (coding) by a set of small RNAs, microRNAs and Ultimately, I try to evaluate the validity claim held higher order regulations inherent in the non- with this “Introduction to Biosemiotics” in the protein coding and repetitive elements of the ge- landscape of modern biological sciences. nome (Witzany 2007). This power of a coherent explanation biolinguistics or bioinformatics are (1) Is there any advantage which suggests using lacking. biosemiotics instead of established disciplines such as biolinguistics or bioinformatics? “Introduction to Biosemiotics” is a key step for- Whereas biolinguistics and bioinformatics are ward into this dynamic process of creating a new established sciences which are applied for in- scientific view on a language-like structure of the formational and bioengineering purposes by genome organization and storage medium as several biological disciplines, this is not (yet) the well as on rule-governed sign-mediated interac- case for biosemiotics. Applied biosemiotic re- tions within and between cells, tissues, organs search is less developed, although the research and organisms. Should this integration prove contributions in this book are interesting and successful in the long run, then biosemiotics useful. Biosemiotics in its present status has a could develop to a major discipline in biology. strong focus on theoretical investigations about the role, function and interpretation of signs ac- References cording to the concepts of Charles Sanders Peirce, Jakob von Uexküll, Stuart Kauffman, Barbieri, M. (ed.) (2007) Introduction to Biosemiotics. The Howard Pattee and the more recent publications new biological synthesis. Dordrecht: Springer. of Jesper Hoffmeyer, Anton Markos and Marcello Barbieri, M. (2007) Is the Cell a Semiotic System? In: Bar- Barbieri. Although this broader view is helpful to bieri, M. (ed.) (2007) Introduction to Biosemiotics. The new understand the whole dimension of sign proc- biological synthesis. Dordrecht: Springer. esses in living nature, biolinguistics and bioinformatics are without doubt currently the more Chebanov, S. (1999) Biohermeneutics and the Hermeneutics practical tools. of Biology. Semiotica 127: 215-226. Markos, A. Grygar, F; Kleisner K., Neubauer Z. (2007) To- (2) Is there a coherent method which serves as a wards a Darwinian Biosemiotics. Life as Mutual Under- powerful tool for investigations within all domains standing. In: Barbieri, M. (ed.) (2007) Introduction to of biological research? Biosemiotics. The new biological synthesis. Dordrecht: A unique coherent method of biosemiotics Springer. does not yet exist. Biosemiotic investigations rely Pattee, H. (2005) The Physics and Metaphysics of Biosemi- on ontological, systems theoretical, naturalistic, otics. Journal of Biosemiotics 1:281-301. physicalistic, mechanistic, idealistic, metaphysic,

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Witzany, G. (2000) Life: The Communicative Strucure. A New Philosophy of Biology. Norderstedt, Libri Books on Demand. Witzany, G. (2006) The Logos of the Bios 1. Contributions to the Foundation of a three-leveled Biosemiotics. Helsinki, Umweb. Witzany, G. (2007) The Logos of the Bios 2. Bio- Communication. Helsinki, Umweb.