Computers and Chemistry 26 (2002) 397 401 www.elsevier.

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Editorial

Grand metaphors of biology in the genome era

The advent of molecular biology, the rise of biotechnology and the (hopefully!) public availability of sequences of several genomes puts us in a peculiar situation in which our factual knowledge can no longer be managed without a synthesis of facts, theories and modeling techniques. In contrast to the recent past, working with wisely chosen models and asking the right questions become more important than increasing the number of known facts. An integrative (systemic) approach to understand biological processes has been postulated in this respect but solid methods for systems biology do not seem to be even imagined by its practitioners. Here again, we need to realize that very complex biological systems are better understood with well-chosen metaphors than without them. We also need to realize that in biology understanding meanings of our metaphors is crucial for avoidance of misconceptions and misinterpretation of factual data. To my knowledge, no comprehensive classication of biological metaphors has been done before even if profound discussion of selected individual cases has been conducted in biological literature of the recent two decades or so. That is why this brief article is devoted to compilation and classication of metaphors used by biologists today. in fact indispensable in concept formation and communication. The implication of this modern view is that we cannot avoid metaphors while formulating our thoughts. Moreover, because metaphors are believed to operate at the pre-linguistic levels of concept formation (or thinking) they are bound to appear in our language at least in an implicit or tacit form1. Although the importance of metaphors in science has long been recognized, leading thinkers of the past two millennia clearly advised to avoid metaphoric language while studying natural systems and phenomena. For instance, Aristotle believed that (literary) metaphors should not be used for making denitions2. Other intellectual giants of the past two millennia (such as C.S. Peirce) also displayed unhappiness with metaphors. A common pejorative characterization pictured them as something parallel to the truth (i.e. not really true) that stands for the true meaning of statements but not always corresponds to this true meaning3. Naturally, this alleged reputation of pretenders made metaphors unwanted guests in the language of scientists.
1 See Lakoff and Johnson (1980), Lakoff (1993) for the state-of-the-art details. 2 Aristotle writes: And if one should not argue in metaphors, it is clear too that one should not dene either by metaphors or what is said in metaphors; for then one will necessarily argue in metaphors. [Posterior Analytic Book 2] 3 Peirce writes: No thought in itself, then, no feeling in itself, contains any others, but is absolutely simple and unanalyzable; and to say that it is composed of other thoughts and feelings, is like saying that a movement upon a straight line is composed of the two movements of which it is the resultant; that is to say, it is a metaphor, or ction, parallel to the truth. [Collected Papers, CP 5.289]. Peirces approach to the concept of complexity via introduction of thirdness into denitions of symbolic objects (signs) appears very timely today but was probably too counter-intuitive for several generations of scholars before the end of the 20th century. Peircean semiotics did not have much inuence on development of paradigms of todays science. Some linguists and cognitive scientists do mention the existence of semiotics a la Peirce but their own work seems to be directed towards the dyadic and monadic (original Peircean terms for ordinary relations) theories of lexicography, grammar and knowledge.

1. Metaphors in general Effective inquiry has always been based on comparison of new (i.e. previously unknown) phenomena to those we feel familiar with. Whenever we encounter (or discover) new previously unknown things, facts or processes, we need to represent them in terms of the elements of our past knowledge. Without such representation, we are unlikely to conceptualize, understand and communicate their descriptions. In this sense metaphors and analogies constitute means for representing novelty (i.e. new knowledge) as well as for generating new concepts with the help of these new representations. Originally, metaphors were thought of as rhetoric tricks to enhance or extend meanings of artistic symbols in literature and other forms of art. Today, since at least the 1980s, the dominant paradigm is that metaphors are

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2. Metaphors and models in science Today scientists recognize that metaphors are needed to make missing connections between facts and interpretations. In their pioneering treatise on meaning, Ogden and Richards (1923) discussed massive evidence for a double potential role of metaphors: viz. (1) enhancement of symbolic informative accuracy and (2) evocation of meaningful emotions. The rst (symbolicinformative) role is usually associated with a great concept-generating power of metaphors while the second (emotive capacity) can lead to misconceptions and vagueness. This is in fact the enhanced symbolic role combined with a suppressed (or neutral) evocative role that characterizes a good choice of scientic metaphor which can then serve as a powerful tool of formulating questions and interpreting answers. As far as science is concerned, metaphors relate to models and their representation in terms of other (new) models. More often than not, a given natural system is inaccessible for direct observation (interpretative reasoning included) in which case we need a model to represent it and to talk about it. The model may still be inaccessible for observations in which case we need a model of a model that in turn may require yet another model. The process of modeling consecutive levels of models may continue until we feel comfortable with the sensual and conceptual categories generated by a nal model in the cascade (series) of models. Of course each time we map a model onto another model we take a risk of missing or misrepresenting some properties of the input model as well as adding new properties which originally were not there. We also take a risk of misrepresenting original relations between properties. That is to say, ideally, our intended mapping should preserve the relational structure of the input model. In practice this invariance of mapping may not always be achieved because of profoundly convoluted (complex) properties of relations that should be preserved or simply because of human errors in perceiving the outcome of the mapping. At this point metaphors enter the methodological picture: instead of modeling a natural system (or its earlier-generation model) we can model its metaphor. The advantage of this deviant but common procedure is the fact that an intuitive understanding of the system provided by a good metaphor helps us to create workable models within which we can ask adequate questions and judge the completeness (or incompleteness) of answers. This in turn is an effective way of deciding if we need further models in the cascade or if we are satised with the current model as a nal one. [Metaphors are particularly useful for representing complex systems or their aspects.]

3. Metaphors in biology Living things are difcult to model because they are genuinely complex. The explanation of their functioning contains convoluted causal loops that, if not used wisely, lead to either paradoxes or open rhetoric questions. Since we do not yet seem to have a good methodology of dening and studying complex systems we seek to represent intellectually difcult cases in terms of examples believed to be already comprehended. That is one reason why understanding biological systems can be assisted by representing them with other concepts that appear to be easier to model. In other words in order to understand biological systems at all we need metaphors. Three main general metaphors have shaped research in biology for more than two millennia: 1. machine metaphor; 2. language metaphor and; 3. organic system metaphor (organism is an important case here). Each of these grand metaphors is related to a multitude of submetaphors (i.e. derived metaphors) each of which has a proven record of helping to create conceptual foundations and useful models to explain aspects of the phenomenon of life. The denitions of grand metaphors in terms of their submetaphors are schematically illustrated in Fig. 1. Due to the advent of genetics and molecular biology, the machine metaphor is perhaps the most powerful conceptual tool of modern biology. It is believed to have originated in 1637 with Descartes Discourse on Method (Descartes, 1988/1637). Ironically, Descartes himself did not seem to intend to create a research program for biology with this metaphor4. However his followers, the Cartesians, were many, and some of them truly worth their master in terms of depth and originality of their thought in the Cartesian spirit of systematic doubt. In addition to these qualities it took courage and determination of a true intellectual pioneer Julien Offray de La Mattrie to publish Man a Machine in 1747 (about a century after Descartes death)5.

To the contrary, his apparent goal in evoking the machine metaphor was an attempt to demonstrate superiority of humans (not machines) over animals (machines). The Cartesian famous motto I think therefore I am clearly indicates that for Descartes the complex I could not be explained in terms of clockwork mechanisms whose behavior can be determined by properties and coordination of their parts. 5 The rst printing of this anonymously written essay was reportedly burned by the order of Consistory of the Church of Leyden but the second and further printings survived thanks to the courage and integrity of the printer Elie Luzac. (I personally would not mind if some of my current publishers cared to display this kind of integrity.)

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Fig. 1. The simplied bullet chart of three grand metaphors dened in terms of their many submetaphors. Each of the submetaphors has been tested and proven a useful conceptual tool of biology over the years. This particular chart is limited (pruned) to three levels of depth but there are many more submetaphors in use today that would pertain to deeper levels of derivation. The connections (overlaps) between the three grand metaphors could in principle be made via concepts of code, meaning or function. However, for the purpose of this brief paper, I preferred to leave the possibility of such overlaps open for discussion rather than denite. In fact the conceptual overlap of metaphors can be misleading and thereby could bring more misconceptions than useful insights.

The book was bluntly departing from Descartes religiosity and put forward the well justied claim that machine metaphor should be applied to humans because from the physiological point of view men are not different from animals. The claim has been pretty popular among educated individuals ever since. Today the machine metaphor inuences all elds of biology indeed. The cell is being metaphorically viewed as machinery of life, chemical factory, and even a computer. The same metaphor seems to be instrumental in discussion of specic cellular processes such as protein biosynthesis although it would be difcult to elucidate details of this process without the knowledge of the genetic code (i.e. without the language metaphor). Development, evolution, inheritance, and even epigenesis are being discussed with the help of concepts inspired by the machine metaphor. Of course, as it is a case of all metaphors, the concept of machine has limits even in biology. Despite the success of mechanistic thinking in molecular biology, genetics and evolutionary theory, living things are not machines because

they do have history. That is to say in addition to all material properties observed today, the emergence of these attributes in the past must be taken into account in all sensible descriptions of the phenomenon of life in general or individual living things (or processes) in particular. Because of the need for historic narrative in biological explanations, the machine metaphor is bound to fail as a serious scientic tool. It must break down sooner or later (it was more of a later in a recent past since 1950s and the rise of molecular biology). Yet it can remain an extraordinarily useful pedagogical tool in education of gifted non-specialists in local youth centers (including our Universities) all over the world. The exact origins of language metaphor are not clear. Early preformationist theories of embryogenesis could qualify as aspects of this metaphor. So do word-matter transformation mythologies (including the Old Testament versions thereof) of some religions. Certainly early studies in genetics enforced the idea that organisms contain their own description (or body plan) to be used for development of their following generations.

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After discovery of linear arrangement of genes on the chromosome and establishment of DNA as a genetic material, the language metaphor was instrumental for understanding the genetic code (translation code for polypeptide biosynthesis). Today the metaphor clearly points towards representing DNA (or RNA) genome as a text but it has many variants some of which are in fact convoluted with the other two grand metaphors (machine and organism). This is not always fortunate because the metaphor appears to exhaust its powers with the success of discovery of the genetic code. The slogan DNA makes RNA (that) makes protein has been discussed by many as misleading and factually incorrect. [Among the arguments against overextending the language metaphor beyond very simple processes (such as polypeptide synthesis) we could list the following: DNA does not make anything. The cell does. Polypeptides are not proteins without the folding and secretion to the place of cellular action. Epigenetic rules, not genes per se, are directly involved in adaptation and survival strategies and so on]. It is perhaps a paradox that a great success of molecular biology was inspired by language metaphor but today, partly because of this success, the metaphor seems to become nothing more than a convenient educational tool for gifted non-specialists in local youth centers over the world [it is not surprising that the somewhat related machine and language metaphors appear to share the same destiny for the same apparent reason]. The system (organism) metaphor exists in biology since at least the Hellenic period of ancient Athens. The original idea behind this metaphor was that whatever the material behavior of the living thing could be, there exists a superior level of integration/organization that makes the matter alive. Of course there were different speculations and theories of what this organizing factor could be, but this is an entirely different issue which will not be discussed in this brief paper. In the 18th century, the word organism had begun to be interpreted as a mechanism similar to musical instruments whose properties are a subtle combination of attributes of its parts. Because the organism is still the most popular use of organic system metaphor, the two metaphors (organism and machine) often overlap with each other. Today the original (primarily Aristotelean) holistic meaning for organism was restored for these living things that do not yield to explanatory powers of molecular biology. However, research in both developmental biology and ecology points toward a possibility that perhaps the concept of organic properties of a system (alive or not) is more appropriate for understanding biological phenomena than the conceptually closed metaphor of organism. For one thing such a metaphor of organic property could lead to an appropriate generalization of systems dynamics (Popper, 1990; Ulanowicz, 2001) that in turn would lead to non-mechanistic models within (still re-

ductionist) conceptual framework of todays biological disciplines. In contrast with the two other grand metaphors (machine and language) it seems unlikely that a very general metaphor of organism will disappear from biology research any time soon. Its strength and survival value lay precisely in its generality that in turn precludes any detailed modeling of properties of living things.

4. The legacy and the future of biological metaphors It is clear that metaphors of science (including biology) evolve and change according to what we already know as well as in response to the need of future models and interpretations. Each of the grand metaphors described in this note had their prime time of assisting our understanding over the years. Today biology and other life sciences seem to approach the stage in which asking a right question and having an adequate model will be more important than accumulating new data and descriptions. That is a reason why we can reasonably expect that new metaphors (yet to come) will pertain more to human qualities of sensibility and understanding than to machine-like mechanisms, automata or grammars. It can also be expected that the organism metaphor will stay as a very general descriptive term. However, more specic metaphoric concepts of organic system and organic property are likely to assist our modeling and inspire our interpretations to much greater extent than they did in the past. Finally, I hasten to add that current research in all elds of science (including biology inspired by genomics and its relatives) may bring about new discoveries of basic phenomena that in turn could become sources of new metaphors. Of course this is also a potentially interesting property of the future: the one that remains totally unpredictable and thereby unexpected.

5. Recommended further reading

Argos, P., 1992. The language of protein folding: many forked tongues. Comp. Chem. 16 (2), 93 102. Fiumara, G.C., 1995. The Metaphoric Process: Connections Between Language and Life. Rutlege, London. Haken, H., Karlqvist, A., Svedin, U. (Eds.), 1993. The Machine as Metaphor and Tool. Springer, Heidelberg. Konings, D.A.M., 1992. Coexistence of multiple codes is messenger RNA molecules. Comp. Chem. 16 (2), 153 163. Konopka, A.K., 1994. Sequences and codes: fundamentals of biomolecular cryptology. In: Smith, D. (Ed.), Biocomputing: Informatics and Genome Projects. Academic Press, San Diego, pp. 119 174. Konopka, A.K., 1997. Theoretical molecular biology. In: Meyers, R.A. (Ed.), Encyclopedia of Molecular Biology and Molecular Medicine, vol. 6. VCH Publishers, Weinheim, pp. 37 53.

Editorial Konopka, A.K., Salamon, P., 1992. Workshop on Computational Molecular Biology. Human Genome News, January 1992, 3 (5). Konopka, A.K., Salamon, P., 1993. Second International Workshop on Open Problems in Computational Molecular Biology. Human Genome News May 1993, 5 (1). La Mettrie de, J.O., 1994/1748. Man a Machine. Hackett Publishing Company, Indianapolis. Lewontin, R.C., 1996. Evolution as engineering. In: ColladoVides, J., Smith, T., Magasanik, B. (Eds.), Integrative Approaches to Molecular Biology. The MIT Press, Cambridge, MA. Lewontin, R., 2000. The Triple Helix: Gene Organism and Environment. Harvard University Press, Cambridge, MA. Pattee, H.H., 1969. How does a molecule become a message? In: Lang, A. (Ed.), Twenty-eighth Symposium of the Society of Developmental Biology. Academic Press, New York, pp. 1 16. Pattee, H.H., 2001. The physics of symbols: bridging the epistemic cut. BioSystems 60, 5 21. Rosen, R., 1985. Anticipatory Systems. Pergamon Press, New York. Rosen, R., 1991. Life Itself. Columbia University Press, New York. Rosen, R., 1994. What is Biology? Comp. Chem. 18 (3), 347 352. Rosen, R., 1996. Biology and the measurement problem. Comp. Chem. 20 (1), 95 100. Torgny, O., 1997. Metaphor A Working Concept. KTH, Royal Institute of Technology-CID, Stockholm, Sweden. Trifonov, E.N., 1989. The multiple codes of nucleotide sequences. Bull. Math. Biol. 51 (4), 417 432.

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Ulanowicz, R.E., 1999. Life after Newton: an ecological metaphysics. BioSystems 50, 127 142.

References
Descartes, R., 1988/1637. Discourse on the method of rightly conducting ones reason and seeking the truth in the sciences. In: Cottingham, J., Stoothoff, R., Murdoh, D. (Eds.), Descartes: Selected Philosophical Writings. Cambridge University Press, Cambridge, pp. 20 56. Lakoff, G., 1993. The contemporary theory of metaphor. In: Ortony, A. (Ed.), Metaphor and Thought, second ed. Cambridge University Press, Cambridge, pp. 11 52. Lakoff, G., Johnson, M., 1980. Metaphors We Live By. The University of Chicago Press, Chicago. Ogden, C.K., Richards, I.A., 1923. The Meaning of Meaning. Harcourt-Brace, New York. Popper, K.R., 1990. A World of Propensities. Thoemmes, Bristol. Ulanowicz, R.E., 2001. The organic in ecology. Ludus Vitalis 9 (15), 183 204.

Andrzej K. Konopka Center for Ad6anced Sequence Analysis, BioLingua Research Inc., 10331 Battleridge Place, Gaithersburg, MD 20886, USA E-mail: akk@blingua.org