Biosemiotics DOI 10.

1007/s12304-010-9102-0 ORIGINAL PAPER

An Answer to Schrdingers What Is Life?

Grard Battail

Received: 2 August 2010 / Accepted: 4 October 2010 Springer Science+Business Media B.V. 2010

Abstract That semiosis is specific to the living world is the cornerstone of biosemiotics. For checking an information-theoretic interpretation of this statement already proposed at the 2009 Biosemiotics Gathering in Prague, it is first attempted here to answer a question asked by Kupiec and Sonigo in Ni Dieu ni Gne (2000) on what differentiates living objects and those resulting from a geophysical process. Similar questions were asked by Schrdinger in his essay What Is Life? where the emphasis was laid on the relationship of the atomic scale of the genes and the macroscopic scale of living beings. This essay was published in 1944, before information was introduced as a scientific entity, at a time when DNA was not yet identified as the vector of heredity. We undertake answering some of these questions, arguing that the living world is made of organisms, i.e., of assemblies possessing in a genome the information needed for their replication and their maintenance while the inanimate world only contains aggregates. In short, a biological process keeps its order through the use of information. For defining order, it is proposed that an orderly object can be produced by a construction (e.g., the copy of a template) using available data within some given context. In other words, replicating an orderly object does not bring new information into its context. Order in this meaning appears as specific to the living world, at variance with the inanimate world which is basically disorderly. A better understanding of what separates the living world from the inanimate world results: the

Retired from E.N.S.T., Paris. Parts of this paper were presented at the 10-th Biosemiotics Gathering in Braga, Portugal, 2227 June 2010, under the title Identity, Species, Order. G. Battail (B ) La Chanatte, Le Guimand, 26120, Chabeuil, France e-mail: gbattail@club-internet.fr

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use of information is the distinguishing feature which defines their border. Any living thing contains a symbolic information, referred to as its genome, inscribed into DNA molecules. This genome can indeed be copied but, its support being embedded in the physical world, it incurs disturbances which result in symbol errors. Keeping its order thus needs endowing any genome with error correction ability: it must belong to a redundant code, i.e., a set of sequences separated by some minimum distance. The larger its minimum distance, the more immune to errors are the elements of a code. Then genomes become as distinct as to ensure order. Identity and specificity result. Although conservative according to the above definition of order, the living world actually exhibits an extreme diversity which even tends to increase as evolution proceeds. In sharp contrast, homogeneity and monotony are observed in the inanimate world, assumed however non-conservative. In order to solve this paradox and justify the proposed definition of order, it is argued that the errorcorrecting means which ensure the conservation of genomes fail with some low, but non-zero, probability. Although very infrequent, regeneration errors result in genomes largely different from the initial ones; and the correction mechanisms conserve the mutated genomes just as the original ones. The operation of life changes scales, since the regeneration errors which originate in atomic events have observable consequences at the macroscopic scale. Keywords Change of scale Decoding errors Error-correcting code Identity Order Species

Purpose That semiosis is coextensive to the living world is a basic tenet of Biosemiotics. We intend to illustrate the information-theoretic interpretation of this statement we already proposed in Battail (2009a, b) by first attempting to answer the following question asked by Kupiec and Sonigo in (2000, p. 33): [. . . ] pourquoi un processus biologique qui produit des organismes se ressemblant, et que lon appelle hommes, lapins ou chnes, confrerait ces regroupements une ralit plus grande que celle quun processus gophysique, tout aussi naturel, confre aux objets qui se ressemblent et que lon appelle pierres, montagnes ou rivires ? ([. . . ] why a biological process which produces like organisms referred to as humans, rabbits or oaks, would endow such kind of things with a greater reality than is endowed by a geophysical process, also natural, on like objects referred to as stones, mountains or rivers?; my translation, corrected using suggestions of a referee). This question looks utterly naive but it has been asked in 2000 by renowned biologists. It reveals that biology is unable to answer the most basic question regarding its very object, a strange situation which does not seem to much worry its upholders. Nevertheless, answering the question asked by Kupiec

An Answer to Schrdingers What Is Life?

and Sonigo is very easy once the role of information in the living world is recognized: living things possess a genetic memory which bears the information needed for instructing their development and maintenance, inanimate things do not. Making use of information, or not, makes all the difference. Kupiec and Sonigo ask the above question because they deny the role of genomes (understood as a set of genes, rather than the whole informational content of an individuals DNA) in heredity, considering the Darwinian selection as the only, or at least the main, factor of heredity. Stones, mountains or rivers are entirely subjected to geophysical forces like gravity, plate tectonics, volcanism, erosion, . . . , but they escape natural selection for lack of the ability to proliferate, a property that only information can provide. DNA molecules are the sole legacy from the past hence the only possible support of hereditary information. In short, the living world is made of organisms where information resides and controls their own construction and maintenance, and enables their proliferation. The inanimate world contains mere aggregates.

Schrdingers What Is Life? Questions similar to that of Kupiec and Sonigo have been asked much earlier, especially by Schrdinger, one of the founding fathers of quantum physics who moreover had a deep philosophical culture. He published in 1944 a short essay entitled What is life? (Schrdinger 1967). When he wrote it, DNA was not identified as the vector of heredity: this identification occurred in Avery et al. (1944) and how it replicates was understood after Watson and Crick elucidated its molecular structure in 1953 (Watson and Crick 2003). Information Theory was not formulated prior to Shannon (1948). Schrdinger could thus not answer the above question as we just did. Many questions he asked in this book remain relevant so it is worth trying to answer them at the light of the experience gained during the last six decades by researches about information theory and communication engineering. The following question asked by Schrdinger is especially crucial (Schrdinger 1967, p. 21): [. . . ] incredibly small groups of atoms, much too small to display exact statistical laws, do play a dominating role in the very orderly and lawful events within a living organism. They have control of the observable large-scale features which this organism acquires in the course of its development, they determine important characteristics of its functioning; and in all this very sharp and very strict biological laws are displayed. Schrdinger wonders how a small group of atoms can display very sharp and strict biological laws when controlling features of living things because, according to statistical physics, the quantities associated with an object made of n atoms or molecules are defined with an uncertainty of about n, hence are not sharply defined when n is small.

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Gibbs and Boltzmann describe indeed the world as made of a huge number of atoms moving and interacting with each other at random. Then, in sharp contrast with classical physics which depicted the Universe as a huge clockwork, impermanence becomes an intrinsic property of the physical world. Physical quantities are mere averages. Their seeming constancy results from the law of large numbers but they are actually random with a variance of the same order as their mean. Schrdinger thought that statistical physics should have deeply changed our vision of the world, and he wondered why it was not so for many. Discussing the evolution of ideas about physical reality, he wrote in Mind and Matter (Schrdinger 1967, p. 161): Now between Kant and Einstein, about a generation before the latter, physical science has witnessed a momentus event which might have seemed calculated to stir the thoughts of philosophers, men-in-the-street and ladies in the drawing-room at least as much as the theory of relativity, if not more so. That this was not the case is, I believe, due to the fact that this turn of thought is even more difficult to understand and was therefore grasped by very few among the three categories of persons, at the best by one or another philosopher. This event is attached to the names of the American Willard Gibbs and the Austrian Ludwig Boltzmann.

Answering the Question Schrdingers Conjecture For answering the crucial question quoted above, Schrdinger suggested that (Schrdinger 1967, p. 73) [. . . ] living matter, while not eluding the laws of physics as established up to date, is likely to involve other laws of physics hitherto unknown, which, however, once they have been revealed, will form just as integral part of this science as the former. No yet unknown laws of physics have been revealed since Schrdinger wrote his essay and it is generally agreed that it is unlikely to occur. We suggest instead that what is lacking is still more important than yet unknown laws of physics: a fundamental scientif ic entity, besides matter and energy, which is needed for describing the world: information. Barbieri commented the same suggested answer as follows (Barbieri 2008): Schrdingers prophecy seems to have been shipwrecked in a sea of hydrogen bounds, but in reality that is true in only a very superficial sense. The essence of the prophecy was about the existence of something fundamentally new, and that turned out to be true. As we have seen, life is based on organic information and organic meaning, and these are indeed new fundamental entities of Nature. Schrdinger invokes the

An Answer to Schrdingers What Is Life?

existence of new laws rather than of new entities, but that was only a minor imperfection and should not have been allowed to obscure the substance of the prophecy (Barbieris italics). We fully concur with this statement. Rather than several new entities, however, what we propose is a single but multifaceted one. Information was unknown as a fundamental entity when Schrdinger wrote. It acquired the status of a scientific entity a few years later, starting with Shannons seminal work (Shannon 1948). It is only the lack of understanding between scientific disciplines that prevented as yet biologists to recognize the most fundamental entity of communication engineering in the supposedly lacking ones. We claimed indeed that the border between the living and the inanimate is that the former bears and uses information, while the latter does not (humanmade artifacts should be appended to the living world, as both products of living things and prostheses to them, to make this statement fully valid) (Battail 2009b). It is thus suggested that it is not a physical quantity associated with a small number of atoms, hence intrinsically imprecise, but an information, as a nominal entity, which controls the features of a living thing. No wonder then if very sharp and very strict biological laws are displayed. We first explain what is intended here as nominal entity. Nominal Entities What we mean by nominal entity is best illustrated by examples. One of them is provided by a telephone number. I want to call Mr Dupont whose phone number is 0123456789 but I erroneously dial 0123456788. As a result, I fail to call him. The number I actually dialled differs only in one digit from that of Mr Dupont but this proximity does not matter: it has the same negative result as a sequence which differs from the correct one in all its 10 digits, for instance 1234567890. Clearly phone numbers which correspond to different users cannot be said to be more or less close to each other: each one is unique. They are referred to as nominal entities. As another example of a nominal entity, an individual is identified in France (for instance) by a 13-digit number which indicates his/her sex, year, month and place of birth, plus the rank of the line where the birth has been registered. As uniquely identifying someone, this sequence is a nominal entity, too. Barbieri introduced the term nominable entity in the same meaning as nominal entity here. He wrote indeed (Barbieri 2007, p. 200): Organic information, organic signs and organic meaning are neither quantities nor qualities. They are a new kind of natural entities which are referred to as nominable entities. The idea of nominal entity is not so new. Kupiec and Sonigo actually trace the origin of nominal entities to a philosophical disputation which opposed in the Middle Age realists and nominalists, the former believing that species

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are intrinsically real but the latter denying it, considering that only individuals (nominal entities) are real. This quarrel had itself its origin in the divergent Platonic and Aristotelian interpretations which were made of Porphyrys book Isagoge (Kupiec and Sonigo 2000). It has however been completely forgotten by modern scientists. Information as a Fundamental Entity The concept of information is foreign to classical physics. Information plays the capital role, not fully identified, of linking the abstract and the concrete. As a consequence, it exhibits properties radically different from that of matter and energy, which need be fully understood. Before we examine these points, we must be aware of a lexical problem, which makes dealing with the information concept difficult. It is met because the single word information is used for meaning at the same time an entity, its quantitative measure, and an object having this entity as an attribute. To illustrate this polysemy by an analogy with a better understood entity we assume that the single word mass is available to designate a massive object, its ability of resisting change in its motion as well as the quantitative measure of this ability. Similarly, information is used for designating an equivalence class among sequences, the entity it communicates and the quantitative measure of its ability to communicate. A further conceptual difficulty met here is that an information, as an equivalence class, is a very abstract concept and the other meanings of the word information are still more so. We already published attempted definitions of information and discussed its several meanings in Battail (2009b), and a paper on this subject is currently being written (Battail 2010a). Compared Properties of Matter, Energy, and Information Matter and energy are conserved, hence can only be exchanged. Information has no autonomous existence in the physical world, but needs to be borne by some physical medium, substrate or wave, to be referred to below as its physical support. This entails, in sharp contrast with matter and energy, that it is not conserved. An information is annihilated when another information is written on its support. It can also be shared: the information written on some support can be copied on another one without being lost. Hence it can be reproduced, which entails that an initial information can proliferate. Interestingly, this property of information is typical of life. The physical support of an information has itself the properties of matter and energy, radically foreign to those of information. The inscription of an information on a physical support, however, is necessary for enabling any interaction of information with the physical world, thereby endowing it with reality. Moreover, an information is a nominal entity, as introduced above in Nominal Entities. As an equivalence class among sequences, an information

An Answer to Schrdingers What Is Life?

can be represented by its information message, defined as the shortest binary sequence which belongs to this class. The binary numeration establishes a one-to-one correspondence between any information message and a natural integer, which is a nominal entity owing to its unique arithmetic properties. Any two nominal entities are either identical or different. In sharp contrast, a physical quantity is generally known through a measurement intended to provide a real number (a mathematical entity obtained by an abstract construction actually unrelated to any physical reality: the word real is misleading) but unavoidably imprecise. A physical quantity is actually a real random variable known with an uncertainty of about n if it concerns an object made of n atoms or molecules. At variance with nominal entities, physical quantities can be more or less close to each others. Representing Nominal Entities by Sequences, Hamming Metric Nominal entities are unique but must be represented by sequences which, in the presence of errors, incur the risk of being confused with others. Errors originate in physical processes which cannot be controlled, and occur with some non-zero probability. How then is it possible to ensure the conservation of a nominal entity during arbitrarily long time intervals? More specifically, how is it possible to conserve the genetic information at the time scale of geology? The only way for doing so consists of representing nominal entities by sequences made resilient to errors, which means that they should belong to an error-correcting code. To briefly explain how such codes work, we must first introduce the Hamming metric which measures the risk that sequences are confused with each others in the presence of errors. The set of n-symbol sequences from a certain alphabet (e.g., binary) can be endowed with the Hamming metric, which is relevant when errors possibly affect their symbols. The Hamming distance between two sequences of same length is defined as the number of positions where their symbols are different. The larger their Hamming distance, the more unlikely an error pattern can change one of them into the other. An error-correcting code is thus a set of nsymbol sequences such that the minimum Hamming distance d between them is as large as possible so as to make them as distinct to each others as possible. Then nominal entities, say, k-bit information messages, must be represented by n-bit words belonging to an error-correcting code. The inequality k < n must be satisfied for obtaining a large enough minimum distance d. In other words, the code must be redundant. Physical Inscription of Sequences In the physical world, the symbols of a q-ary alphabet are associated with q possible physical states (q = 2 in the binary case, the most usual and simplest one). Sequences are then represented by a series of such states which succeed

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to each other in a one-dimensional space at well-defined locations. For states succeeding to each other in time, a binary state can be the value that a process referred to as modulation imparts to a parameter (amplitude or phase) of an acoustic or electro-magnetic wave. A series of time-successive states representing a sequence will be referred to as a digital message, as currently used in data transmission or telephony. When the physical support of information is material, a binary state can be for instance the magnetization of a ferrite core or one of the two possible states of a bistable mechanical or electronic device. A series of such devices in a spatial dimension of the physical world will be referred to as a memory, as used in computers and recording devices. DNA molecules are typical examples of memories, using the quaternary alphabet {A, T, G, C}. Digital messages and memories enable the interaction of informations, as abstract nominal entities, with the physical world. Informations can act on the physical world only through their agency. An interaction also exists in the other way: the intrinsic randomness of physical states entails that any symbol in a sequence has a non-zero probability of error. Some energy E must be used for changing the state associated with a symbol in a digital message or a memory. At an absolute temperature T , the average energy of thermal noise is kB T /2 per dimension, where kB denotes Boltzmanns constant, so the probability p of a random change of state (error) is a steeply decreasing function of E/ kT . Increasing E appears as the simplest way to decrease it. Only moderate energies, however, are available in living things so very small values of p cannot result from increasing E. Securing a minimum Hamming distance of d between sequences results in a probability P of sequence error proportional to pd/2 which is much smaller than p if p is small enough. Using a means which makes d large, i.e., an error-correcting code, is thus much more efficient than increasing E for ensuring the integrity of an information borne by a modulated electromagnetic wave or physically inscribed in a memory. Decoding and Regeneration Then, the exact recovery of the original sequence despite symbol errors becomes possible. This decoding process fails with a very small error probability P, provided the average number of erroneous symbols in the sequence remains less than d/2. Fulfilling this condition implies a short enough time interval between successive decodings because the probability of an error is an increasing function of time, as just shown below. Successful decoding will be referred to as regeneration of the original sequence. If too many symbols are in error within the sequence, regeneration of the original sequence fails. Then the decoding process results in a widely different sequence, at a Hamming distance of at least d from the initial one. The probability of a symbol error is actually a function of time. During an infinitesimal time interval dt, the probability d p of an error is proportional to this time interval: d p = dt, where is referred to as the error frequency.

An Answer to Schrdingers What Is Life?

Assuming that is constant entails that the probability p(t) that an error with respect to its initial value has occurred at time t equals p(t) = q q1 1 exp t q q1 ,

where q is the alphabet size (it reduces in the binary case to p(t) = 1 [1 2 exp(2 t)]) (Battail 2008a). This is an increasing function of t approximately equal to t when t is small enough. Notice that, for t approaching infinity, the asymptotic value of this probability is p() = (q 1)/q (= 1/2 in the binary case), i.e., that of a purely random choice. In other words, after a large enough time interval a received symbol no longer depends on its initial value so the content of the memory is eventually forgotten. As a consequence, its ability to communicate information, i.e., its information-theoretic capacity, is an asymptotically vanishing function of time (Battail 2008b, 2010b). The probability that more than d/2 symbol errors occur, which entails a high probability of decoding error, is much smaller than p(t) when t is small but increases faster with time. Decoding must therefore be performed after a time interval as short as to make the probability of regeneration failure ignorable. The regenerated information is then subjected again to the occurrence of symbol errors, so its conservation implies that decoding is effected frequently enough, say, almost periodically. Notice that the word error does not refer to any abnormality or misfunctioning. It just means that some symbol or sequence is replaced by another, equally legitimate, one. This is a random event that can occur since digital messages and memories are embedded in the world of statistical physics. Provided its probability is non-zero, ergodicity tells that an error occurs sooner or later. The average lifetime of an information represented by a sequence incurring an error with probability P is proportional to 1/ P. Informations thus survive in a physical memory the longer, the smaller is P, but P can never be strictly zero. In more adamant words: no memory is permanent. Using larger and larger error-correcting codes, which secure an increasing minimum Hamming distance d between the sequences, is the only means for making P vanishingly small when the energy E is limited. It merely costs redundancy, i.e., an increase in sequence length. This theoretical result looks paradoxical since the longer is a sequence, the larger the average number of erroneous symbols it contains, but it is fully confirmed by the engineering practice. To summarize, we may think of an error-correcting code as substituting a high probability of receiving a sequence slightly different from the original one for a very low probability of receiving a very different sequence. Since a nominal entity does not suffer any approximation but can only be either correct (identical) or wrong (different), representing it by a word of an errorcorrecting code widely diminishes the probability of its erroneous reception, thereby increasing its longevity.

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Identity, Species, Order Potential, Symbolic and Structural Information We briefly recall here distinctions already introduced in Battail (2009b). We define any set of random events as bearing potential information. Potential information will be able to interact with physical devices only if it generates a one-dimensional sequence of symbols from some alphabet inscribed on a physical support: say, if it is recorded. This sequence then bears symbolic information. It can be copied because its support is one-dimensional: an initial sequence can then act as a template. Associated with semantic rules, symbolic information can act as a recipe for building a phenotype, i.e., a 4-dimensional object (three spatial dimensions plus time). This object then bears structural (or Aristotelian) information. The simplest example of such a recipe is the genetic code where semantic rules associate triplets of nucleotides (codons) with amino-acids. Proliferation of Objects, Species Repeatedly copying a symbolic information and using it as a recipe results in the proliferation of identical objects, which together constitute a species. Its physical support being no longer one-dimensional, structural information cannot be copied nor used as a recipe for replicating the object which bears it. Von Neumann has indeed shown in 1966 that an object cannot be replicated unless it bears its own description in symbolic form (von Neumann 1966), and the biological implications of this most important result were discussed by Pattee, e.g., in Pattee (2008). The symbolic information used as a recipe for replicating a living object is referred to as its genome. Potential information possibly becomes symbolic information through recording. Symbolic information results in structural information through the semantic rules of a recipe. These transformations are irreversible, which may be thought of as extending the central dogma of molecular biology to genetic information. Only the symbolic information borne by the genome can be copied, thus enabling the proliferation of identical objects. Identity within a Species Consider an object some part of which is the physical support of a symbolic sequence, for instance the genome which is necessary for replicating a living object. The information message associated with this sequence, as a nominal entity, may be defined as the identity of this object. Since the support of the symbolic sequence belongs to the world of statistical physics, this object will keep its identity only insofar as a low enough probability P of confusion with another nominal entity is secured, which implies that the sequence which represents it belongs to an efficient enough error-correcting code, which moreover is decoded frequently enough (Battail 2008a, b, 2010b). The object then keeps

An Answer to Schrdingers What Is Life?

its identity during an average time proportional to 1/ P, the reciprocal of the probability of a decoding error. It results from the above definition of identity that the members of a species share the same identity which is borne by their genome or, at least, by that part of the genome which is encoded by error-correcting codes: accounting for individual differences suggests that a small fraction of the symbolic sequence is left uncoded and thus incurs random variations. Decoding errors will eventually change the identity of a few members of the initial species, then originating in new species becoming the target of natural selection. This branching process moreover results in a hierarchical taxonomy due to the nested structure assumed by the genomic error-correcting code, which is itself needed for explaining that very old genomic sequences, like the HOX genes, are conserved (Battail 2008a, b, 2010b). Biological Order Order is most often implicitly likened to some kind of regularity like periodicity or symmetry. The paragon of order in this meaning is a crystal, i.e., a set of atoms chemically bound to each others in a way which maximizes the stability of their assembly. Likening order to regularity relies on subjective grounds and is far too restrictive. Schrdinger predicted that the vector of heredity, unidentified when he wrote, should be an aperiodic crystal (Schrdinger 1967, pp. 5 and 65). Indeed, this oxymoron adequately describes the DNA molecule as a one-dimensional polymer. It is generally agreed that life is characterized by a biological order left otherwise undefined. We suggest that an object is orderly in this meaning if it can be identically reproduced, hence if it bears its own symbolic description acting as a recipe for its construction and maintenance. In other words, replicating an orderly object does not bring any innovation into its context: it merely keeps the already existing information, which just becomes inscribed on one more physical support. A Paradox The picture of the living world and of its relationship with the inanimate world which results from the above statements reveals a deep paradox: The inanimate world, as described by statistical physics, is rich of an inconceivably huge number of random events. It thus bears a high quantity of potential information. The living world is dominated by the symbolic information borne by genomes and much of the life processes concur to its conservation, hence the quantity of information it bears increases only when the conservation mechanisms fail.

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Yet we perceive the inanimate world as uniform and monotonous. On the contrary, the living world appears to us as extremely diverse and contrasted, hence rich in information.

Life Changes Scales This paradox is due to the change of scales that life operates, such that some events at the atomic level entail observable consequences at our macroscopic scale. An inconceivably huge number of fleeting events occur in the inanimate world at the atomic level (Schrdinger asks, with feigned naivety: Why are the atoms so small? (Schrdinger 1967, p. 6)). Tending to conserve information, life results in lasting organisms which owe their longevity as species to the low probability that their genomes are confused with each others. Significantly, DNA molecules escape the atomic scale in one of their dimensions, bearing symbolic sequences as long as to enable an efficient enough error correction. The low probability of error thus acquired entails their persistency up to the geological timescale (Battail 2008b). The operation of life thus results in a wide change of spatial and temporal scales with respect to the atomic level through the agency of genomic errorcorrecting codes. The numerous fleeting and small-scale events of the atomic world merely result in very infrequent events in the living world, occurring only when the genetic error correction system fails to conserve identity. The outstanding diversity of life, the variety and constrasts it exhibits, result basically from decoding errors which, although they have their origin at the atomic level, produce long lasting events at the macroscopic scale. By eliminating a number of species, natural selection diminishes this variety, far from creating it as often stated.

Conclusion Using information as a fundamental scientific entity widely improves the understanding of life and of its relationship with the inanimate world. A very large amount of work remains to be done before this remark is fully beneficial to biology. Information itself should be better known and popularized among biologists. Researches in information theory should also tend to better fit the needs of biology: it originated indeed as an engineering discipline and remained mostly so. Not only biology, but physics itself, especially insofar as it tries to integrate the living observer as an unavoidable actor of any experiment, should benefit from similarly recognizing the prominent role of information and the singularity of its properties when compared with the fundamental entities of classical physics.

An Answer to Schrdingers What Is Life? Acknowledgements The author is deeply indebted to Marcello Barbieri. He specially acknowledges the influence of his concepts of organic codes and nominable entities. He also sincerely thanks the anonymous referees for their careful reading and relevant comments, which were very helpful for improving this paper.

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