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Home , Biosemiotics, Interpretant, Jesper Hoffmeyer, Meaning (semiotics), Semiosis

Introduction to Introduction to Biosemiotics

The New Biological Synthesis

Edited by

Marcello Barbieri University of Ferrara, Italy Library of Congress Control Number: 2008922939

ISBN978-1-4020-4813-5 (HB) ISBN 978-1-4020-8344-0 (PB) ISBN 978-1-4020-4814-2 (e-book)

Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. www.springer.com

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All Rights Reserved © 2008 Springer Science+Business Media B.V. No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. To (1920–2001) and to his vision of a synthesis between Biology and TABLE OF CONTENTS

Editorial ix Marcello Barbieri

Part 1 – Historical Background

1. The Evolutionary History of Biosemiotics 1 Donald Favareau

2. in Evolution 69 Tuomo Jämsä

3. Has Biosemiotics Come of Age? and Postscript 101 Marcello Barbieri

Part 2 – Theoretical Issues

4. The Necessity of Biosemiotics: Matter-Symbol Complementarity 115 H. H. Pattee

5. What is the Scope of Biosemiotics? Information in Living Systems 133 Stanley N. Salthe

6. Semiotic Scaffolding of Living Systems 149

7. Biosemiotics and Biophysics – The Fundamental Approaches to the Study of Life 167

8. Is the Cell a Semiotic System? 179 Marcello Barbieri

9. Computing Codes versus Interpreting Life 209 Stefan Artmann vii viii Table of Contents

10. Towards a Darwinian Biosemiotics. Life as Mutual Understanding 235 Anton Markoš, Filip Grygar, Karel Kleisner, and Zdenekˇ Neubauer

11. From the of Science to the Logic of the Living. The Relevance of Charles Peirce to Biosemiotics 257 Tommi Vehkavaara

12. Towards a Standard Terminology for (Bio)semiotics 283

13. and Error-Correcting Codes in Genetics and Biological Evolution 299 Gérard Battail

Part 3 – Biosemiotic Research

14. RNA as Makers: A Biosemiotic View of RNAi and Cell Immunity 347 Marcella Faria

15. Cellular Semiotics and Signal Transduction 365 Luis Emilio Bruni

16. Inner Representations and in Animals 409 Stephen Philip Pain

17. A Biosemiotic Approach to Epigenetics: Constructivist Aspects of Oocyte-to-Embryo Transition 457 Johannes Huber and Ingolf Schmid-Tannwald

18. and Interspecific Experiments: A Case to Re-open? 473 Dario Martinelli

Author Index 519

Subject Index 525 EDITORIAL

MARCELLO BARBIERI

THE CHALLENGE OF BIOSEMIOTICS

Semiotics, literally, is the study of signs and initially it was thought to be concerned only with the products of culture. Mental phenomena, however, exist also in animals, and cultural semiotics can be regarded as a special case of biological semiotics,or biosemiotics, a science that started by studying semiotic phenomena in animals and then was gradually extended to other living creatures. Eventually, the discovery of the genetic code suggested that the cell itself has a semiotic structure, and the goal of biosemiotics became the idea that all living creatures are semiotic systems. But what is a semiotic system? According to cultural semiotics, there are two answers to this question. One is the model proposed by , who defined a semiotic system as a duality of “signifier and signified” or “ and ”. The other is the model of Charles Peirce, who pointed out that interpretation is an essential component of semiosis and defined a semiotic system as a triad of “sign, object and ”. In 1974 Marcel Florkin argued that “signifier and signified” are equiv- alent to “genotype and phenotype” and proposed for biosemiotics the dualistic model of Saussure. He underlined however that “in the sign is arbitrary with reference to the relation between its two faces. In molecular biosemiotics, on the other hand, signifier and signified are in a necessary relation imposed by the natural relations of material realities”. According to Florkin, in other words, in molecular biosemiotics there is no arbitrary relationship between signifier and signified, and he explicitly declared that “A bioseme carries no Bedeutung or Sinn (no meaning). Its signifier is an aspect of molecular configuration and its signified is an aspect of biological activity”. In the 1960s and 70s Thomas Sebeok started a lifelong campaign in favor of the idea that language has biological roots, but rather than following Saussure he adopted the triadic scheme of Peirce first in , in 1963, and then in the more general field of biosemiotics (Sebeok, 1963, 1972, 1986). According to Sebeok, any semiosis is necessarily a triadic relationship, and interpretation is its sine qua non condition. He insisted that “there can be no semiosis without interpretability” and that interpretation is “a necessary and sufficient condition for something to be a semiosis” (Sebeok, 2001). The Peirce-Sebeok model of semiosis has become extremely popular and it has been adopted by most biosemioticians, in ix x Barbieri particular by the Copenhagen-Tartu school (Claus Emmeche, Jesper Hoffmeyer and Kalevi Kull) and (in a hermeneutic version) by the Prague school (Anton Markoš). A third model of semiosis, however, does exist and was suggested in the 1980s by the theory that the cell is a triad of genotype, phenotype and ribotype, where the ribotype is the ribonucleoprotein system of the cell and represents its “codemaker”, i.e. the seat of the genetic code (Barbieri 1981, 1985, 2003). This amounts to saying that the cell contains a “codemaker” but not an “interpreter”, because the rules of the genetic code do not depend on interpretation. They are virtually the same in all living systems and in all circumstances, and that has been true for almost the entire history of life on Earth. In this framework, the simplest semiotic system is a triad made of “sign, meaning and code” and the origin of semiosis (the semiotic threshold) does not coincide with the origin of interpretation (the hermeneutic threshold). Another approach to biosemiotics has been proposed by Howard Pattee who investigated the physical conditions that are necessary for codes and symbolic controls. Pattee introduced the concept of epistemic threshold, the boundary region where local matter has not only its intrinsic physical properties governed by universal laws, but where it is also “about” something else. Epistemic matter, in other words, “stands for” something, and the “standing for” relation is usually considered an emergent process that leads necessarily to a triadic Peircean relationship of “matter, interpreter and referent” (Pattee, 1969, 1972, 2001). Today, in short, we have four different models of biological semiosis and at least four different schools of biosemiotics. Despite all that, biosemiotics remains an isolated discipline and many perceive it as a small field that lies at the outskirts of science, somewhere between biology and linguistics. This is because there is a very strange paradox at the heart of modern science. On the one hand it is acknowledged that the genetic code is the bedrock of life, and on the other hand it is underlined that it is not a real code. The argument is that the genetic code would be real only if it was associated with the production of meaning, but modern science does not deal with meaning and is bound therefore to deny any reality to the code of life. According to the dominant paradigm, the genetic code is fundamentally a metaphor. It is a linguistic construction that we use in order to avoid long periphrases when we talk about living systems, but no more than that. It is like those computer programs that allow us to write our instructions in English, thus saving us the trouble to write them in binary digits. Ultimately, however, there are only binary digits in the machine language of the computer, and in the same way, it is argued, there are only physical quantities at the most fundamental level of Nature. This conclusion, known as physicalism,orthe physicalist thesis, has been proposed in various ways by a number of scientists and philosophers (Chargaff, 1963; Sarkar, 1996; 2000; Mahner and Bunge, 1997; Griffiths and Knight, 1998; Griffith, 2001, Boniolo, 2003). It is probably one of the most deeply dividing issues of modern science. Many biologists are convinced that the genetic Editorial xi code is a real and fundamental component of life, but physicalists insist that it is real only in a very superficial sense and that there is nothing fundamental about it because it must be reducible in principle, to physical quantities. This, in fact, is the only answer that allows people to say that there are no signs and meanings at the basis of life, and that semiotic processes are not fundamental events. But what a price to pay! It is perfectly right to mention the genetic code practically in every single problem of biology, provided one keeps in mind that it is not meant to be serious. On the face of this, many biologists prefer to avoid the issue altogether, which is hardly surprising. But some do not. The issue is not so much the physicalist thesis as the nature of life itself. The experimental reality is that proteins are manufactured by molecular machines based on the rules of the genetic code and there is little point in saying that the code must be a metaphor simply because modern science does not know how to cope with meaning. That is the challenge of biosemiotics: the codes are a fundamental reality of life and we simply have to learn how to introduce signs and meanings in science. This book is addressed to students, researchers and academics who are not familiar with biosemiotics and want to know more about it. It is a highly qualified introduction to this new field because it is written by many of its major contributors. At the same time, it contains the most recent developments in the basic issues of biosemiotics and provides therefore a fairly accurate portrait of the present state of the . The book is divided into three parts. The first is dedicated to a brief historical account and the last to a few research applications, whereas the central, and longest, part of the book is devoted to theoretical issues.This is because the real obstacle to biological progress, today, is not lack of data but a pervasive theoretical paradigm that continues to deny the semiotic nature of life, or to pay only lip-service to it, thus depriving the biological codes of all their revolutionary potential. Biosemiotics is truly a new biological “synthesis” because it brings together biology and linguistics, and effectively brings down the old divide between the “Two Cultures”. Its main challenge, as we have seen, is to introduce meaning in biology, on the grounds that organic codes and processes of interpretation are fundamental components of the living world. Biosemiotics has become in this way the leading edge of the research in the fundamentals of life, and is a young exciting field on the move. This book wants to bring it out of the small niche in which it has been developed so far and make it available to all those who are prepared to accept the challenge raised by the discovery of the genetic code and of biological meaning.

ACKNOWLEDGEMENTS

I wish to thank Jacco Flipsen, at Springer-Netherlands, for proposing the project of this book in the first place, and Catherine Cotton for organizing the reviewing of its chapters and for taking care of countless editorial problems. I am also grateful to Catherine for bringing the ideas of this book to the attention of science journalists and for taking part in the 6th Gathering in Biosemiotics, thus proving to be not xii Barbieri only a highly professional editor but also an enthusiastic supporter of the emerging field of biosemiotics.The actual production of the book has been directed by Ria Kanters at Springer-Netherlands with wonderful care and I wish I could adequately express my gratitude for the splendid job that she has done.

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