Friday, October 14, 2005

From disorganization into organization: of language and biology.

Perspectives in Biology and Medicine 48.3 (2005) 317-327

"Meaning-Making" in Language and Biology

Yair Neuman

Ben-Gurion University of the Negev, Beer-Sheva, Israel.


The linguistic metaphor in biology adheres to a representational theory that seeks similarities between pre-given domains. The point of departure of this paper is the generative and nonrepresentational conception of metaphor. This paper argues that by adopting the nonrepresentational conception of metaphor, meaning-making may be the appropriate perspective for understanding biological systems. In both cases (the linguistic and the biological), boundary conditions between different levels of organization use micro-level disorganization to create macro-level organization.

Human Thinking Is Metaphorical, and metaphors are the sine qua non of any process of understanding (Lakoff and Johnson 1980). Thus, a scientific theory must critically examine its reservoir of metaphors and seek alternative metaphors for enlarging its scope and transcending its boundaries. As Tauber (1996) argues, "Theory must grope for its footing in common experience and language. By its very nature the metaphor evokes and suggests but cannot precisely detail the phenomenon in concern" (p. 18). Indeed, metaphors are creatively generated rather than mechanically applied to a pre-given world (Shanon 1992), and therefore they cannot "detail the phenomenon in concern"—an activity which is the role of the scientific model—but only guide the inquiry.

Human language has been used metaphorically to understand biological [End Page 317] processes, and vice versa (e.g., Atlan and Cohen 1998; Novak and Komarova 2001). This paper concerns the linguistic metaphor in biology. Can the linguistic metaphor productively guide investigation into biological systems? To address this difficult issue, we should be familiar with an important distinction between the representational and the nonrepresentational approaches to metaphor.

As Shanon argues, the discussion of metaphors in cognition and related disciplines commonly assumes that metaphor is a relationship established between two given entities whose attributes are defined prior to the establishment of their relationship. This representational theory of metaphor is evident in Gentner's (1983) seminal work on metaphor as a form of structural mapping between two domains. For example, the metaphor "An atom is like the solar system" is interpreted as a mapping of known, deep-structure similarities (similar relations) between one domain (the atom) and another (the solar system); electrons revolve around the nucleus just as the earth revolves around the sun. Although in some cases the use of metaphors may be interpreted by the representational theory, Shanon propounds the alternative that in most cases a metaphor has generative power that creates the similarities rather than simply assuming them. That is, the "metaphoric relationship is more basic than its constituents," and the metaphor "creates new features and senses" (Shanon 1992, p. 674).

The linguistic metaphor in biology has mainly employed the representational theory of metaphor to look for similarities between human language and biological systems as two pre-given domains. The benefit of moving along this line of inquiry is questionable. If one is familiar with the pre-given properties of two domains, finding similarities between them is of little use. Indeed, students of linguistics do not have to read Essential Cell Biology in order to understand human language, and students of medicine do not need to master Chomsky to understand cell biology. This critique of the representational theory of metaphor, while not new to those familiar with theories of metaphor, casts serious doubt on the possible contribution of the linguistic metaphor to biology.

If we adopt the nonrepresentational approach, our strategy should be different: first we should draw the metaphor and only then examine the similarities that emerge from its use. To illustrate this strategy, let us examine a difficulty that results from the representational approach to the linguistic metaphor.

The linguistic metaphor in biology has focused almost exclusively on similarities between the syntax of linguistic and biological systems for example, as evident in the structure of DNA. This is no surprise. Our knowledge of syntax has reached a high level of abstraction and formality that makes it easy to draw the analogy between the syntax of language and the "syntax" of DNA. However, the scope of linguistics is much broader than the study of syntax, and in order to have a full grasp of a linguistic activity one must also study, for example, the pragmatics of language (Yule 1998). Pragmatics is a field of linguistics that deals with language usage in context—in other words, the field of linguistics that deals with the generation of meaning-in-context (Levinson 1998). Although the generation [End Page 318] of meaning-in-context is crucial for understanding biological systems (Neuman 2004a), the linguistic metaphor in biology has, for the most part, ignored pragmatics. For example, Ji (1997), who propounds the idea of cell language, describes human language as consisting of lexicon, grammar, phonetics/phonology, and semantics, but he ignores pragmatics. This may be explained by the tremendous difficulty facing pragmatics even in linguistics (Yule 1998). This difficulty, however, holds great promise for biology and linguistics/semiotics alike. The analogy between human language and biological systems may teach both biology and linguistics an important lesson on a difficult subject: how meaning emerges in context. This paper intends to make the first moves toward this kind of inquiry.

Living Systems and Boundary Conditions

Biological systems are open systems that exist on several distinct, complementary, and irreducible levels of organization. These levels constitute the systemic closure of the living system through feedback loops. In other words, they are recursive-hierarchical systems (Bateson 1979; Harries-Jones 1999). This unique form of organization, which also characterizes the structure of text, contrasts sharply with the organization of information-processing devices. Information, as classically defined by Shannon, is a probabilistic measure. As Emmeche and Hoffmeyer (1991) argue, unpredictable events are an essential part of life, and thus it is impossible to assign distinct probabilities to new events: "The quantitative concept of information needs a closed possibility space. If the set of possibilities is open, one cannot ascribe precise probabilities to any single possibility and thus no information value" (p. 3). Their conclusion is that biological information must embrace the "semantic openness" that is evident, for example, in human communication, and that we should abandon the probabilistic conception of information. Indeed, the semantic openness of language allows the free interplay of ideas and concepts, just as a certain level of disorganization in living systems is necessary for the emergence of new forms. Without a basic level of disorganization, semantic openness cannot exist.

Following Bateson (1979), Hoffmeyer and Emmeche (1991) also propound the idea that living systems have two different codes: a digital binary code for memory (as in DNA) and a gestalt-type analog code for behavior. The syntactic approach to language has emphasized the digital aspect without paying attention to the analog one. However, if we want to understand living systems as meaning-making systems, then the analog mode is indispensable. Indeed, several scholars have argued that living systems are reactive rather than transformatory (information-processing) (Cohen 2000; Neuman 2003). Transformational systems are sequential, linear systems that transform information in a specific order to achieve a specific goal (Cohen 2000). In contrast, reactive systems are multilevel, nonlinear, ongoing systems that interact constantly with their internal and external [End Page 319] environment to create sense out of the environment in an integrative gestalt manner that cannot be reduced to a digital binary code. In other words, living systems are meaning-making machines rather than information-processing devices.

The recursive-hierarchical and semantically open structure of living systems is evident in protein conformation. Although a protein folds to assume an energetically favorable structure, we cannot understand its final conformation without taking into account several distinct and complementary levels of organization and the boundary conditions imposed by the higher levels, as well as the context or environment—its interactions with solvent and with ligands. To understand protein folding, we must take into account not only different levels of organization but also interaction-in-context. Metaphorically speaking, we must take into account the "pragmatics" of this process.

The idea that the living organism is composed of an irreducible structure was introduced by Michael Polanyi (1968). One of Polanyi's main arguments is that an organism is a system whose structure serves as "a boundary condition harnessing the physical-chemical processes by which its organs perform their functions" (p. 1308). In other words, "if the structure of living things is a set of boundary conditions, this structure is extraneous to the laws of physics and chemistry which the organism is harnessing" (Polanyi 1968, p. 1309). If each level imposes a boundary on the operation of a lower level, then the higher level forms the meaning of the lower level, as evident in the folding of proteins.

Polanyi illustrates his thesis by analogy with linguistics. According to Polanyi, the boundary conditions in living systems are analogous to the boundary conditions in linguistics. The meaning of a word is determined by the sentence in which it is located, and the meaning of a sentence is determined by the text in which it is located. This analogy should be qualified. First, although we cannot understand the words without understanding the sentence, neither can we understand a sentence without understanding its words. This "hermeneutic circularity" was recognized long ago, and it seems to characterize the operation of living systems (Neuman 2003). However, due to a misunderstanding of the recursion process and the recursive-hierarchical organization of living systems, this hermeneutic circularity has been considered, at least by some philosophers, something to be avoided rather than a constitutive principle of living systems. Second, biological systems may be metaphorically described as "texts." However, there is no text without a reader. There is no meaning without an interaction. Therefore, both recursive-hierarchical organization and interaction are crucial for describing biological systems in linguistic terms.

The fact that Polanyi and several celebrated biologists (e.g., Atlan and Cohen 1998; Cohen 2000; Jerne 1984) use the linguistic metaphor for understanding biological systems is not due to an intellectual whim. Meaning-making in natural language and the behavior of living systems do have something is common: both take advantage of disorganization on the micro level to create organization [End Page 320] on the macro level, through a recursive-hierarchical structure and interaction. Both operate on the boundary of organization and disorganization to create meaning-in-context.


Meaning-making can be defined as a process that yields the system's differentiated response to an indeterminate signal (Neuman 2004a). For example, being an antigen is not an attribute that is explicitly or directly expressed by a molecule (i.e., the signal). The meaning of being an antigen is the result of a complex deliberation process (i.e., a meaning-making process) that is finally evident in the specific immune response (Cohen 2000). In this sense, meaning-making is a process of computation in the classical etymological sense of assembling a whole from pieces.

The term computation is usually used in the technical, modern sense of a deductive process following a deterministic algorithmic program. Von Foerster and Poerksen (2002) have suggested restoring the original meaning of this word: computation is derived from the Latin computare, where com means "together" and putare means "to contemplate" or "to consider." Meaning-making involves bringing together different perspectives to achieve a specific response. For example, the decision as to whether a specific agent is an antigen or not involves a variety of immune agents (macrophages, T cells, B cells, cytokines) that contemplate (putare) together (com) to yield the final immune response. In other words, the signal (e.g., an antigen) is contextualized in a wider network of immune agents to achieve a specific response (Neuman 2004a). Meaning-making is thus a process of computation in the analog, holistic, and gestalt senses.

If there are no degrees of freedom in the system's response to a given signal, then by definition this system is not involved in meaning-making. The potentiality of a signal is an important economical principle underlying communication processes in living systems. This flexibility may be illustrated through natural language, in which the same sign can be used in different contexts to express different things. The specific term for this phenomenon is polysemy. The benefit of polysemy is clear: it "allows the use of the same word in different contexts and thus endows language with indispensable flexibility" (Shanon 1993, p. 45). This point is crucial for understanding both meaning-making and the organization of living systems. In both cases, there is maximum potentiality (of the sign or the molecule) at the micro level that endows the system with tremendous flexibility for making sense (linguistic or biological) on the macro level. [End Page 321]

Meaning-Making, Organization, and Disorganization

The term sense may have different meanings and connotations in biology and linguistics. In this paper, I use the term as being closely associated with organization. Thus a signal (in biology) or a sign (in linguistics) has meaning, or makes "sense," if it is embedded in a higher-order structure of components (i.e., context) that enables the system to produce a specific response.

The interesting thing about meaning-making is its quasi-paradoxical nature and the fact that it operates on the boundary of organization and disorganization. Let me explain this argument in semiotic terms. The generation of meaning requires that the system have maximum freedom on the micro level, but minimum freedom on the macro level. That is, disorganization in the sense of flexibility and dynamics is a necessary component of meaning-making. In natural language, for example, we can produce an infinite number of "meanings" (responses, senses) with a limited number of words. Saussure pointed out that the meaning of a sign is determined by its location in a broader network of signs. In other words, the meaning of a sign is determined by different organizations of the signs among which it is contextualized. Thus, a "virgin" sign lacks any sense and can be linked to myriad organizations of signs; therefore its degrees of freedom are potentially limitless. A sign is always a potential before it is mapped onto the macro level of the sentence (Neuman 2003).

The above argument may be formulated in terms of Peirce's (1955) three modes of being. The first mode, "firstness," concerns pure potentiality. In the meaning-making process, it is associated with the most basic level of organization and with the potential variability of the signal. As Peirce argues: "Freedom can only manifest itself in unlimited and uncontrolled variety and multiplicity; and thus the first becomes predominant in the ideas of measureless variety and multiplicity" (p. 79). While "firstness" concerns pure potentiality, "secondness" deals with actualization of the potential through relations established between various components of the system. In this sense, secondness is a constraint—a form of organization—imposed on the first mode. In meaning-making, the second mode of being is associated with a process of contextualization in which a given sign is woven into a network of other signs. In immunology, secondness as a type of relationship is evident when a specific signal is patterned (contextualized) into the web of immune agents and through this context obtains its meaning as an antigen (Cohen 2000).

The third mode ("thirdness") is that "which is what it is by virtue of imparting a quality to reactions in the future" (Peirce 1955, p. 91). In other words, it is the law, the habit that governs the behavior of the phenomenon, and our ability to predict its future behavior based on the law. It is the "conception of mediation, whereby a first and second are brought into relation" (Peirce 1978, p. 25). In meaning-making, the third mode of being is evident when the system's different [End Page 322] perspectives converge and are integrated to achieve a specific response in a given context, a process described by myself (2004a), following Bakhtin, as "transgradience." In immunological recognition as a process of meaning-making, this mode of being is evident when the immune agents "co-respond" to each other through a complex communication network to reach the final decision as to whether a molecule is an antigen (Cohen 2000).

Meaning and Interaction

The movement from disorder (firstness) to order (thirdness) is not random. This point can be illustrated through protein folding. One might imagine that protein molecules search through all possible conformations at random "until they are frozen at the lowest energy in the conformation of the native state" (Branden and Tooze 1999, p. 91). However, this "random walk" would require far more than the actual folding time. In this sense, it is ridiculous to expect order on the macro scale of a living system to simply pop up from firstness, just as it is ridiculous to expect a meaningful theory to emerge out of the uncontrolled delirium of a schizophrenic patient. In the case of proteins, Branden and Tooze (1999) have suggested that "the folding process must be directed in some way through a kinetic pathway of unstable intermediates to escape sampling a large number of irrelevant conformations" (p. 91). As Peirce argues, one cannot explain meaning by reducing it to lower levels of analysis; meaning is evident only once there is a triadic (or higher-order) relation between components—in other words, only through the mediating force of thirdness. In this sense, intermediates are needed to produce sense from senseless microelements.

The protein-folding process is a riddle. It is known, however, that the decrease in free energy is not linear. During the folding process, the protein proceeds from a high-energy, unfolded state (high potentiality) to a low-energy, native state through "metastable intermediate states with local low energy minima separated by unstable transition states of higher energy" (Branden and Tooze 1999, p. 93). To understand this process in semiotic terms, think about a word. It is transformed from a state of high potentiality to concrete actuality through the regulatory power of the higher linguistic levels of analysis, such as a sentence or text. However, every move from one linguistic level of analysis to a higher level of analysis gives the word new potential for a different response. The word love, for example, has the potential to mean different things in different contexts. The potential is actualized and the meaning of love is constrained when it is in a sentence. However, placing the sentence in a broader, extra-linguistic context may result in a totally different response than the one expected from the sentence alone. In the context of protein folding, this process suggests that between the micro and the macro levels of analysis there is a process of organization—one that has been described as the "middle way" or the "logic of in-between" [End Page 323] (Laughlin et al. 2000; Neuman 2004b). This process seeks to overcome high-energy barriers to folding (constraints). Producing order from chaos is energy-consuming, but without the system's basic tendency to reduce its free energy or to revert to a more basic mode of being, no work can be done and no meaning can be created. In this sense, the protein's natural entropic path to disorganization is subject to meta-regulatory processes (boundary conditions) that channel it so as to increase order.

These meta-stable processes can be discussed in terms of interaction. The transfer of energy involves a weak coupling/interaction between at least two systems (e.g., ligand-receptor binding). This coupling is weak in the sense of the weak interactions discussed in research on synchronization. That is, one system/level of organization transfers energy to the other system/level of organization, but they remain two autonomous and separate systems/levels of organization. Weak interactions are a necessary condition for meaning-making, whether in biology (e.g., non-covalent forces) or in linguistics. Returning to Peirce, we can understand that the pure potentiality of the micro level is actualized by the repeated, habitual, or synchronized interaction of the third level. It is the third level that completes the triadic structure of meaning-making. Interaction is what mediates the emergence of meaning, whether in linguistics or in biology.

Although meaning-making assumes disorder, the specificity of response demands order on the macro level. When a sign is located in a context, its degrees of freedom are significantly reduced. Thus, we need minimal potentiality on the macro level. For example, when using the sign shoot, we would like to have maximum freedom to use the same word once to express an order given to a soldier, and in a different context as a synonym for speak. In a given context, however, we want the sign to communicate only one of the meanings and not the other. To achieve this stability, the system has to be habituated through socialization, in the case of human learning of signs, or through evolutionary processes, in the case of a biological response. In both cases, interaction plays a crucial role. One must pay close attention to the fact that this "habituation" is not domestication. When we use language, we would like to be understood through the social habituation of language practices. On the other hand, we always preserve the opportunity to be incomprehensible and vague through jokes, paradoxes, inventions, and other forms of nonsense that are crucial for flexible life.

The need for macro stability is evident in protein conformation. A given sequence of amino acids forms a stable structure through the covalent forces that bind its molecules. However, this order is subject to non-covalent forces that interact to yield a specific conformation. Although a protein has an enormous number of potential conformations, it finally folds into one main conformation capable of responding (for example) to a given ligand. In other words, the final conformation of the protein is determined through interaction with another biological entity in a given context (Cohen 2000). This description should be qualified, too. Although meaning-making requires stability at the macro level, it [End Page 324] is not a total, rigid stability. The function of a protein requires structural flexibility and not rigid stability. The function of a word requires the same flexibility. You may want your word to achieve a specific response in a specific context, but you always want to reserve the ability to take your word back. Both in life and language, pragmatics assumes flexibility.


Previous uses of the linguistic metaphor in biology have been based on a representational theory. I propose investigating biological systems through another perspective, which emphasizes the pragmatic and contextual side of language. If we are prepared to do this, then our next step is to discuss several aspects of biological meaning-making along the lines we drew previously. First, we should emphasize the idea of biological organization rather than biological order. Whereas the term order usually pertains to information theory and the idea that a phenomenon can be represented (and quantified) through a unidimensional string of characters, organization emphasizes the multi-level structure of biological systems and the interconnections among the components of the system. As Denbigh (1989) argues, wallpaper with a repeating pattern may be highly ordered but poorly organized. In contrast, a painting by Cezanne has a low level of order but a high (but not quantifiable) level of organization. Language usage is organized rather than ordered. Any attempt to reduce meaning to order is doomed to failure. Following this line of reasoning, we may interpret the pathology of a biological system, as in the case of autoimmune diseases, as a problem of disorganization and meaning-making—a problem with the system's ability to make sense out of signals by patterning them into a broader network of meaning. In this case, something happens in between the levels of organization; the boundary conditions do not function in such a way as to avoid the system's natural "entropic" reversion to firstness.

As Harries-Jones (n.d.) argues, following Bateson, the death of a living system is more likely to be related to its loss of flexibility/resilience and to the devastation of its capacity to self-organize than to an outright loss of energy. The death of an organism might be the result of a vicious pathogen, but blaming the pathogen is of no help. This phenomenon should be investigated primarily through the failure of the immune system to make sense out of signals. For example, cytokines have been considered crucial to immune recognition. Under certain conditions, however, knocking out genes responsible for the production of cytokines does not destroy the immune system (Cohen 2000). This is not a surprising finding if one realizes that biological systems in general are characterized by overlapping and redundant feedback mechanisms. In this specific case, the immune system had organized itself to function properly. In other words, the immune system shows resilience, in the sense that it renews itself and can therefore flexibly use other opportunities for meaning-making and immune recognition (Neuman 2004a). [End Page 325]

A mature understanding of a living system is possible only when the descriptions of the different levels are synthesized into a working whole. This is evident in immunology, where we have acquired knowledge about micro elements and their interaction in the immune system but without an encompassing synthesis (Cohen 2000). For example, cytokines play an important role in communication among immune agents, and there is a flood of information about cytokines. However, "practically nothing is known about the behavior of the [cytokine] network as a whole" (Callard, George, and Stark 1999). This problem should not be underestimated. As Paton (2000, p. 63) argues, "From a biological system's point-of-view there is a lack of tools of thought for dealing with integrative issues." Unless several distinct but complementary levels of organization are integrated and it is shown how they influence each other, the behavior of the immune system is to a large extent incomprehensible. This conclusion is, in fact, an invitation for researchers to investigate the recursive-hierarchical structure of living systems and the unique way these systems make sense out of their environment.

The author wishes to thank Irun Cohen and Peter Harries-Jones for ongoing discussions and their constant support, Jesper Hoffmeyer for his constructive comments on an earlier draft, and the anonymous reviewers for their helpful comments.

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