Scientific Autobiography – 2

Code Biology

1       A book review

In March 2001 I sent to Thomas Sebeok the draft of ‘The Organic Codes’, a manuscript where I underlined that there are many organic codes in Nature and that their existence requires that we introduce in biology not only the concept of information, but also the concept of meaning.

    Sebeok acknowledged the manuscript and a few weeks later invited me to review a special issue of Semiotica that was dedicated to the coming of age of biosemiotics and to celebrating Jakob von Uexküll as the chief architect of that new discipline (Kull 2001). I accepted and I acknowledged that the two main points of the special issue – the making of biosemiotics and the recovery of Jakob von Uexküll from oblivion – came out with clarity and force, and were a success.

    There was however a third point that I did not agree with. It was the idea that biosemiotics was the crowning achievement of the idealistic tradition that goes back to Goethe, Schelling, Saint-Hilaire, von Baer and Driesch, a ‘vitalistic’ approach that has been the historical antagonist of the ‘mechanistic’ approach of Galileo, Newton, Lamarck, Darwin and Mendel. I fully agreed with the project of introducing meaning in biology, but I argued that vitalism was not the right approach.

    I sent my review to Sebeok in August 2001, saying that I had not been able to write an impartial report and therefore that I would not be surprised if he turned it down. To my surprise, however, Sebeok accepted it (Barbieri 2002) and to me that meant that in principle he was not against the mechanistic approach.

    His implicit message, in my opinion, was that vitalism is not compulsory in Biosemiotics. A mechanistic approach to meaning cannot be ruled out, and people who are proposing it should be listened to.

    Sebeok died a few months later, on December 21, 2001, and that implicit message was probably his last contribution to biosemiotics. Personally, I took it as an invitation to join the biosemiotic community and I decided to give it a try.

    The decisive change came in 2004, at the fourth Gathering in Biosemiotics organized by Anton Markoš in Prague. Jesper Hoffmeyer, Claus Emmeche, Kalevi Kull, Anton Markoš and myself decided that what was uniting us – the introduction of meaning in biology – was more important than our divisions, and we should make that visible.

    Up until then, I had been referring to the study of biological meaning as Semantic Biology, whereas Markoš had been calling it Biohermeneuthics, but we accepted to give up our favourite names and to adopt the term Biosemiotics that Sebeok had been campaigning for with so much passion and vigour.

    I also proposed to start a new journal and a few years later I became the founder and first editor-in-chief of the Springer journal Biosemiotics.

    My hope was to gradually turn biosemiotics into an increasingly scientific field but there was a great obstacle on the way: most biosemioticians were supporting the Peirce model of semiosis, the idea that the cell is capable of interpreting what goes on in the world.

2       Interpretation at the cellular level

    Free-living single cells (bacteria and protozoa) make up the great majority of the living world, and countless studies have shown that they have a context-dependent behaviour in the sense that they can react in different ways to different environmental conditions. Thomas Sebeok argued that a context-dependent behaviour comes from an ‘interpretation’ of the environment, and concluded that all living systems, from bacteria to animals, have the ability to interpret the world.

    In reality, the behaviour of bacteria and protozoa is accounted far more naturally by the combination of two or more organic codes. A context-dependent behaviour means a context-dependent expression of genes, and this is obtained simply by associating a signal transduction code to the genetic code. It takes only two context-free codes, in short, to produce a context-dependent behaviour.

    Coding and decoding, on the other hand, are far simpler than interpretation, and there is no need to assume anything more complicated than that in single cells, especially in those that appeared at the beginning of the history of life.

    Free-living single cells are semiotic creatures because they make use of codes, but there is no evidence of interpretation at the molecular level, and this conclusion is supported by the fact that the genetic code has been conserved in all living organisms and in all environments ever since the origin of life, which clearly means that it does not depend on interpretation.

    The evidence, in short, tells us that coding and decoding is all that goes on at the cellular level, and yet the followers of Peircean biosemiotics have claimed that interpretation does exist at that level because we can define decoding as a form of interpretation. There are many examples of this trick in the literature, and these are two of them.

    (a) In the paper “What Does It Take to Produce Interpretation?”, Søren Brier and Cliff Joslyn (2013) proposed to solve the problem in this way: “…we can identify interpretation in general as any process which encounters a sign and takes it for its meaning in virtue of some code…Thus a ribosome is an interpreter. And the right amino acid is its interpretation of some codon.”

    (b) In the paper “Anticipatory Functions, Digital-Analog forms and Biosemiotics”, Argyris Arnellos, Luis Emilio Bruni, Charbel Niño El-Hani and John Collier (2012) claimed that signal transduction is a process of interpretation because “…receptors act as interpreting systems”.

    This is what Peircean biosemiotics is about: it claims that interpretation takes place at the cellular level simply because we can define interpretation in such a way that it is present at the cellular level.

    In reality, the existence of meaning in living systems is an outstanding scientific problem and we can only learn from Nature, not from ad hoc definitions, whether or not meaning is present in the processes that take place in the cell.

3       The birth of Code Biology

    As editor-in-chief of Biosemiotics I was committed to publish contributions from all schools of biosemiotics, including those which claimed that ribosomes ‘interpret’ the messenger-RNAs. The codons of a messenger- RNA are recognized by the complementary anticodons of the transfer-RNAs and saying that a ribosome is interpreting a messenger RNA is like saying that a key is interpreting a lock in order to open a door.

    I realized that my editorial commitment was becoming incompatible with a scientific approach, and the sole solution therefore was for me to resign from the journal. That decision however was pre-emptied by an unexpected event: at the 2012 Gathering in Biosemiotics that took place in Tartu, I was expelled from the governing board of the biosemiotic society with a public vote of the general assembly.

    That put an end to my project to turn Biosemiotics into a scientific field, and I went back to my previous field but with a difference. The term Semantic Biology was replaced by Code Biology because it is codes that give us the experimental proof that meaning exists in living systems.

    This is why at the end of 2012, I resigned as editor-in-chief of Biosemiotics and together with a few colleagues I founded the International Society of Code Biology. We also decided to leave no doubt about the scientific nature of our project, and to this end we explicitly wrote in the constitution of the new society that “Code Biology is the study of all codes of life with the standard methods of science”.

    Code Biology, in conclusion, started in 1985 with the name of Semantic Biology and the publication of its major ideas, but was officially established with its present name in 2012, when the International Society of Code Biology was founded.

    Any society requires of course congresses and publications, and it is for this reason that we have had international conferences in Code Biology since 2014 and special issues dedicated to Code Biology have been published in BioSystems since 2018.