The Affirmation of Life, A New Perspective of the Immune System

The Affirmation of Self: A NewPerspective on the ImmuneSystem

John StewartCNRSCOSTECHCentre Pierre GuillaumatUniversite de CompiegneBP 6064960206 [email protected]

Antonio CoutinhoInstituto Gulbenkian de CienciaPT-2781-901 [email protected]

KeywordsAutopoiesis, immune system, idio-typic network, self, non-self

Abstract The fundamental concepts of autopoiesis, whichemphasize the circular organization underlying both livingorganisms and cognition, have been criticized on the groundsthat since they are conceived as a tight logical chain ofdefinitions and implications, it is often not clear whether theyare indeed a scientific theory or rather just a potentialscientific vocabulary of doubtful utility to working scientists.This article presents the deployment of the concepts ofautopoiesis in the field of immunology, a discipline whereworking biologists themselves spontaneously have long hadrecourse to “cognitive” metaphors: “recognition”; a“repertoire” of recognized molecular shapes; “learning” and“memory”; and, most striking of all, a “self versus non-self”distinction. It is shown that in immunology, the concepts ofautopoiesis can be employed to generate clear novelhypotheses, models demonstrating these ideas, testablepredictions, and novel therapeutic procedures.Epistemologically, it is shown that the self–non-selfdistinction, while quite real, is misleadingly named. When areal mechanism for generating this distinction is identified, itappears that the actual operational distinction is between (a)a sufficiently numerous set of initial antigens, present fromthe start of ontogeny, in conditions that allow for theirparticipation in the construction of the system’s organizationand operation, and (b) single antigens that are first presentedto the system after two successive phases of maturation. Tocall this a self–non-self distinction obscures the issue bypresupposing what it ought to be the job of scientificinvestigation to explain.

1 Introduction

The concept of autopoiesis is one of the major contributions that Francisco Varela madeboth to biology and to cognitive science.

Living organisms are characterized by their circular organization: they are metabolicprocesses, pure fluxes of matter and energy, that have the very special property of pro-ducing themselves. They are dynamic dissipative structures; but unlike purely physicaland/or chemical structures, which are intrinsically ephemeral, living organisms functionin such a way that they can go on producing themselves indefinitely; in other words,although they can of course die at any moment if an accident befalls them, they arepotentially immortal.

c© 2004 Massachusetts Institute of Technology Artificial Life 10: 261–276 (2004)

J. Stewart and A. Coutinho The Affirmation of Self

Cognition is also characterized by a circular organization: the objects of cognition(for example, colors) are not given in advance, and do not even exist as such inde-pendently of the perceiving subject; these objects are brought forth together with thesubject, and are inseparable from the organization of that subject. Along with Hum-berto Maturana, Francisco Varela had the deep insight that these two forms of circularorganization are, at root, one and the same: this insight can be summed up by theformula “life=cognition=autopoiesis.”

These were, and still are, heady ideas, with an extraordinary capacity to evokean immediate intuitive conviction that they have to be right. However, it is equallyobvious that in order to make a substantial contribution to science these ideas need tobe deployed quite concretely; they have to do some real work in relation to precise,detailed experimental observations. In the 1980s it appeared to a number of people—Varela himself, the Brazilian immunologist Nelson Vaz, and the authors of this articleamong others—that the immune system offered a particularly promising field for puttingthese ideas into practice. It is a historical fact that immunology is an area where workingbiologists themselves spontaneously have long had recourse to “cognitive” metaphors:“recognition”; a “repertoire” of recognized molecular shapes; “learning” and “memory”;and of course, most striking of all, a “self versus non-self” distinction. And it did indeedturn out that the application of the concept of autopoiesis to the immune system ledwith extraordinary rapidity to a dramatic reversal in perspective. The aim of this articleis to explain what is involved in this potential paradigm shift.

2 Classical Immunology and a Potential Paradigm-Shift

In classical immunology, the immune system is conceived as a linear input-output sys-tem. The inputs are antigens: substances, generally foreign to the body of the animal,which trigger the production as an output of antibodies, each of which specifically rec-ognizes the antigen that evoked it. The specificity of this recognition is impressive: thenumber of different antigens that the immune system of a mammal is able to recognizehas been estimated to be of the order of 1017. Moreover, immunologists consider thatthe repertoire of antibodies is complete: the mammalian immune system is capableof recognizing the totality of all possible molecular shapes (of an appropriate size),including molecules that have never before existed in the course of biological evolu-tion because they were synthesized for the first time by human chemists. Classicallyagain, immunologists consider that the function of the immune system is to protectthe body against foreign antigens (typically, those that belong to pathological micro-organisms); more precisely, it is considered that the function of an antibody is to triggerthe destruction of the antigens that it recognizes (Figure 1).

This classical scheme can be summed up by saying that the immune system canpotentially perceive everything, and that it triggers the destruction of everything that itactually perceives. Now this bald schematic formulation raises a troublesome question:what about the relation between the immune system and the body in which it is housed?This body is composed of molecules, many of which are of the appropriate size forbeing “perceived” by the immune system; the proof of this is that if such molecules areinjected into another animal, they do indeed provoke a destructive immune response.It is for this reason that grafts of tissues or organs are practically impossible in mammals,whereas they are easy in plants or invertebrate animals such as insects. But now, ifwe apply the classical schema literally, we arrive at an astonishing conclusion: theprediction is that the immune system should systematically destroy the body in whichit is housed.

It is clear that this is not what happens; or more precisely, when something of this sorthappens, one speaks of “autoimmune disease,” but autoimmune diseases are relatively

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Figure 1. The linear input-output system of classical immunology. An antigen triggers the production of an antibodythat specifically recognizes and destroys the antigen.

rare, and when they do occur, they are far less catastrophic than the scheme predicts.In fact, quite apart from empirical observations, it is obvious that this prediction cannotbe fulfilled, because systematic autoimmunity would be horribly dysteleological andquite incompatible with the constraints of viability and natural selection. The classicalimmunologists invented a term, “horror autotoxicus,” to indicate that this prediction oftheir theory was not and indeed could not be systematically verified. Now, contrary tothe opinion of Karl Popper, a refutation does not necessarily induce scientists to aban-don the theory in question. In classical immunology, the refutation was circumventedby a straightforward adjustment to the theory: the immune system perceives every-thing except its own body. One suspects that this bald-faced adjustment, which is quiteshamelessly ad hoc in order to avoid what would otherwise be a straight refutation,caused a certain unease, which may be subliminally expressed by the very term “horrorautotoxicus,” quite horrible indeed in its mixture of Greek and Latin roots. Howeverthat may be, the conclusion—that the immune system perceives everything except itsown body—is quite inescapable, given the premises of the argument; and it is for thisreason that the so-called “self versus non-self” distinction plays such a central role inclassical immunology.

What light does the perspective of autopoiesis shed on this rather murky situation?According to the notion of autopoiesis, the objects of cognition are specified, consti-tuted, by the organism itself. This can be summed up very neatly by a verse of thePortuguese poet Pessoa:

What we seeIs not what we seeBut what we are

The point is, in a way, a very simple one; but it runs so radically counter to ordinarycommon sense that a few words of explanation may not be amiss. The usual point ofview is to consider that the objects of perception are ontologically primary: they exist,and are what they are, quite independently of any perception that there may or maynot be concerning them. A perception by a cognitive subject then corresponds to aninternal “representation” of the referential object; ideally, the representation will tendto be more or less isomorphic with the pre-existing referent. Technically, this point ofview is termed “objectivist”; we may note that it corresponds to the point of view of anexternal observer who is presumed to be omniscient, and is thus able to examine boththe object and the representation and to check out on the degree of correspondence or

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isomorphism between them. The perspective of autopoiesis is radically critical of theobjectivist position. The difficulty is that, from the point of view of a cognitive subject,there is no way of getting “out of its skin” and perceiving the “object in itself” directly assuch. The only thing that an organism can know is the effect that its interaction with anobject has on its own functioning; having access to only one of the two terms, there isjust no way that an organism can judge whether the content of its percept is, or is not,an adequate representation of an external object. Thus, the percept is not separablefrom the cognitive subject. This is reminiscent of Berkeley’s position, “to be is to beperceived,” with the difference that an organism is subject to a viability constraint, sothat its percept cannot be an arbitrary hallucination but must bear significantly on theorganism’s interactions with its environment.

In other words, in this new perspective, whatever one perceives is, by the very factof being perceived, the self; and whatever is not perceived is, ipso facto, non-self.This amounts to an exact reversal of classical immunology, according to which theimmune system does not perceive, ignores, the self (otherwise it would destroy it),and perceives only the non-self. Varela was the first to develop these considerations,in close collaboration with Vaz; together, they proposed that in order to denote thisradical reversal in perspective, it might be better to speak of a distinction between “self”and “nonsense” [16].

Before going further, it may be well to say a few words to try and dispel some confu-sion that has quite understandably arisen. It is abundantly clear that a major (if not nec-essarily the exclusive) function of the immune system is to protect the organism againstinfectious diseases caused by pathological microorganisms. This is demonstrated quitestraightforwardly by the simple observation that severely immunodeficient mice—andhumans—do indeed die of uncontrolled infectious disease. It is equally clear that inorder to do this, the immune system must make a distinction between pathological mi-croorganisms and the body of the organism itself. The perspective of autopoiesis doesnot gainsay any of this. What is at stake is the choice of an appropriate nomenclaturein order to designate the two terms of this distinction. The key here is a remark thatHumberto Maturana never tired of repeating: “Everything said is said by an observer.”In particular, whenever a distinction is being made, we should always ask: “Who ismaking the distinction?” In the case of classical immunology, the distinction is beingmade by an external human observer: it is the immunologist who can see the differ-ence between the organism on the one hand and pathological microorganisms on theother; it is the immunologist who designates molecules from the body of the organismas “self,” and molecules that he knows came from a microorganism (or another sourceexternal to the organism) as “non-self.” By contrast, when we employ the conceptualframework of autopoiesis, we are in a certain sense looking at things from the pointof view of the immune system itself.1 It is from this point of view that a self–non-selfdistinction is impossible, because, unlike a human immunologist, the immune systemitself has no means of knowing where the molecules came from. The immune sys-tem is composed of cells, the lymphocytes; at the level of a local interaction betweenan individual lymphocyte and a molecule, there is nothing that distinguishes what theimmunologist calls a “self” molecule from a “non-self” molecule. The conceptual frame-work of autopoiesis is thus the more appropriate one if we are trying to understand themechanisms and mode of operation of the immune system itself. As we shall see, theimmune system as a whole, considered over the history of its development, is capableof making a distinction that, to all practical intents and purposes, does roughly coincide

1 It is well to acknowledge that this is something of a rhetorical flourish: the point of view in question is not really that of the“immune system itself,” but rather that of a human biologist acting as “spokesman” for the immune system. This being said, thereremains a valid and important distinction between the two points of view—that of the classical immunologist, and that of the“spokesman.”



with the immunologist’s “self versus non-self” distinction. However, when we identifythe mechanisms whereby the immune system is capable of making this distinction,we shall appreciate that calling this a “self versus non-self” distinction is a misnomer.We shall return to this point; but the time has come to present the understanding ofthe actual functioning of the immune system that comes from adopting the conceptualframework of autopoiesis.

3 A Mathematical Model of the Immune Network

A key element that made it possible to apply the framework of autopoiesis to theworkings of the immune system was the work of the great Danish immunologist, NielsJerne. The starting point of Jerne’s theory is this: if the repertoire of antibodies reallyis complete (or “open-ended,” as he called it), then it is logically inescapable that theantibodies themselves should be included in this repertoire. After all, antibodies areprotein molecules of the same size as many other antigens. In other words, there arestrong a priori grounds for supposing that the set of “antibodies” forms a connectednetwork, where each “antibody” is recognized by other antibodies in the system. Wehave put the term “antibody” in scare quotes because it is clear that in this perspectivethat recognition does not necessarily lead to total and immediate destruction. For thisreason, it is preferable to use the term “immunoglobulin” to designate the moleculesproduced by the lymphocytes. In order to designate this sort of interaction betweenimmunoglobulins we employ the term “idiotypic”; consequently, the sort of networkpredicted by Jerne is an idiotypic network.

When Varela came to Paris in 1985, he worked with Antonio Coutinho (himself a stu-dent of Jerne’s) to set down the basis of a mathematical model of idiotypic networks.This is not the place to enter into technical details and the mathematical equations[13, 14]. Qualitatively, in natural language, the basic idea was the following. Thesurvival of a lymphocyte, its proliferation, and its capacity to secrete immunoglobu-lins depended on the field that it received as a result of its idiotypic interactions withother immunoglobulins. The dynamics of the network were highly nonlinear: if thereceived field was below a lower threshold, the lymphocyte perished (Vaz expressedthis by saying that the lymphocyte died of “loneliness”); if the field was above an up-per threshold, the lymphocyte died of “suffocation”; however, if the field was in thefavorable window between the two thresholds, the lymphocyte could survive and/or orproliferate and produce immunoglobulins (Figure 2).2 Now, the immunoglobulins thatprovide for the field itself, in the form of idiotypic interactions with the immunoglob-ulin receptors of the newly emerging lymphocytes, are produced as a consequenceof these very interactions. Hence the field determines itself and its maintenance, butit is never the same, as the emerging lymphocytes never repeat the same repertoireof diverse immunoglobulins. That is, the field is self-producing, and it selects newlyformed lymphocytes into its own operation, so that these dynamics are supplementedby a process of meta-dynamics. We have already indicated that a lymphocyte coulddisappear from the system (if its received field lay outside the window); but at each timestep, it was also possible to recruit new lymphocytes into the network from a sample of“random” lymphocytes freshly produced by the bone marrow. Specifically, a candidatelymphocyte would be recruited if, but only if, its received field was situated within thewindow between the lower and upper thresholds. There was thus a circular relation-ship between the dynamics and the meta-dynamics (Figure 3). On the one hand, thedynamics of the concentrations of the different lymphocytes determined the field at all

2 These rules for lymphocyte stability (survival within a favorable window of sensed field) are analogous to Conway’s well-knowngame of life. They are also similar to the neural homeostasis that is currently being implemented in evolved robot controllers.



Figure 2. The bell-shaped activation curve for lymphocytes as a function of the received field. Below the lowerthreshold LT, and above the upper threshold UT, the lymphocyte declines; between the two thresholds, there is awindow where the lymphocyte survives and/or proliferates and secretes immunoglobulins.

Figure 3. The circular relationship between dynamics and meta-dynamics. The dynamics presupposes a set list ofvariables (the concentrations of the clones) and a fixed matrix of pairwise affinities between these clones. Thetemporal variation in the concentration of each of the clones is then determined by a set of differential equations. Atany one point in time, the concentrations of the clones determine the field at all points in shape space. This in turndetermines the meta-dynamical processes of maintenance and elimination of existing clones, and the recruitment ofnew clones: a clone will be maintained or recruited if the field that it receives lies within the window between lowerand upper threshold; it will be eliminated or not recruited otherwise. Thus, the meta-dynamics determines the listof variables and the matrix of affinities; which brings us full circle.



points in shape space, and so the dynamics determined the meta-dynamics; conversely,the meta-dynamics gave rise to the structure and connectivity of the network at eachinstant, and so the meta-dynamics determined the dynamics.

This circularity between the dynamics and the meta-dynamics was quite deliberatelyin the spirit of the circular organization so fundamental to the general theory of au-topoiesis. Whether the circularity as expressed in this particular mathematical model isreally adequate to fully capture the circularity of autopoiesis is an open question—ofgreat importance, of course, but outside the scope of the present article. What wemay note, however, is that this model aimed at a good compromise between biologicalrealism on one hand, and maximal simplification on the other. All the components,properties, and relations in the model were based on entities and processes that wereknown to exist on grounds of actual biological observations; on the other hand, theseelements were represented in the model in the simplest possible form that would stillgive rise to interesting emergent properties of the system as a whole.

4 Morphogenesis in Shape Space

In 1988, John Stewart joined the group that had formed around Varela and Coutinho atthe Pasteur Institute in Paris. His contribution was to run computer simulations, basedon the model that we have just described, in order to examine the emergent propertiesof an idiotypic network. The immediate result of this was to reveal the necessity ofa method for specifying the structure of connectivity of an idiotypic network—morespecifically, of defining the matrix of all possible pairwise affinities between a given setof immunoglobulins. The experimental data on this point were (and still are) scantyand quite insufficient; in addition, we needed a mode of representation that wouldrender the evolution of the connectivity structure as the system matured over timegraphically visible and comprehensible. We solved this problem by adopting a mod-ified version of the shape space concept originally suggested by Perelson & Oster [9]and developed by Segel & Perelson [11]. According to this concept, the universe ofstereochemical shapes that determine intermolecular affinities can be represented aspoints in a multi-dimensional shape space. In our version, we used a two-dimensionalspace (for obvious reasons of graphical visualization), and each point in shape spacewas taken as representing a pair of perfectly complementary shapes with maximumaffinity (conventionally, the members of a pair are labeled black and white). This modeof representation has the following advantages: firstly, relations of similarity in molec-ular shape (and hence affinity profiles) are immediately perceptible as the proximity ofcorresponding points of the same color in the shape space; and secondly, relations ofcomplementarity (and hence high affinity) are also immediately perceptible in the formof proximity between black and white points. The generation of random immunoglob-ulins as candidates for meta-dynamical recruitment was then quite straightforward: itwas effected by generating black or white shapes at random positions in the totalshape space. Mathematically, the affinity between two clones i and j , mij , is definedas follows:

mij ={0 if i and j are the same color;exp(−d2

ij ) if i and j are of opposite colors(1)

where dij is the scaled distance between i and j in shape space.The dynamics were deliberately reduced to their simplest expression: at each time

step in the simulation, a clone was maintained at unit concentration if its received fieldlay within the window, and eliminated otherwise. At each time step, candidate cloneswere generated randomly until one new clone was recruited.



Figure 4. Schematized results of a simulated morphogenesis in shape space. Lymphocyte clones are represented byblack and white circles. Clones of the same color have no affinity with each other. Clones of one color create afield for clones of the opposite color that are close to them in shape space. (a) The self-organization of clones inthe absence of external antigens. The clones form chains of the same color, which face chains of the opposite color.In the region between chains of opposite color, shaded with dots, the field is high; in the region enclosed by chainsof the same color, the field is low; the clones are all situated in the region where the field has an intermediate valuewithin the window of activation (see Figure 2). (b) The adjustment of the emergent pattern induced by the presenceof two antigens, represented by a white square and a black square. It can be seen that the patterns of Figure 4a areadjusted so that the antigens are included in chains of the same color.

Using this procedure,3 we very rapidly obtained some promising results [12]. Firstly,we showed that under these conditions, a self-sustaining idiotypic network couldarise—without either collapsing or exploding. We quite deliberately started by studyingthe behavior of the system in the absence of external antigens, in order to characterizeits eigen-behavior. The idiotypic network did indeed exhibit interesting properties ofself-organization: as can be seen in Figure 4a, the combined dynamic and meta-dynamicprocess gives rise to clear patterns in shape space: there are chains of lymphocytes ofthe same color, and the chains of complementary shapes mutually sustain each other.We can consider that these patterns correspond to the identity of a molecular self asdefined and indeed constituted by the autonomous dynamics of the immune systemitself.

Secondly, we studied the modulation of this eigen-behavior when the system wasperturbed by the introduction of external antigens, modeled here as points in shapespace, which produced a field for the lymphocytes, but whose own concentration wasconstant irrespective of the field they themselves received. Typical results are shownin Figure 4b. What we see is that the idiotypic network adjusts smoothly so as tointegrate the antigens harmoniously into its own pattern of behavior; in other words,the antigens are effectively assimilated as a part of the molecular self constituted by thenetwork. More precisely: We see in Figure 4b that all the antigens of a certain color

3 Technically, it may be noted that these results were obtained by computer simulation. It would be practically impossible to obtainthese results analytically, not only because the meta-dynamical process of recruitment and disappearance of clones changes the listof variables, but because the process itself depends on relations between individual clones distributed in shape space and theserelations are historically contingent during the ontogeny of the system. In general, models that can only be resolved by simulationare at a strong disadvantage because they are difficult to interpret, compared to mathematical models based on differentialequations; the latter, even if they cannot be solved analytically but only by numerical methods, can be described qualitatively interms of attractor dynamics. This latter resource is not available in the case of simulation models. However, in the present casethis was not an overwhelming difficulty: as shown by the subsequent discussion, it proved possible to interpret the emergentpatterns—probably thanks to the choice of an appropriate mode of graphical representation.



(black or white) are surrounded by lymphocytes of the same color. We know that allthe lymphocytes in a chain of a certain colour receive a field (from lymphocytes inthe facing chain of the opposite color) that is within the limits of the window (if thiswere not the case, the lymphocytes would already have been eliminated). Since, underthese network conditions, the antigens receive the same field as the lymphocytes ofthe same color that surround them, there is an important corollary: the field receivedby the antigens remains within the limits of the window, that is, it is at most equalto the upper threshold. Thus, if we suppose (as is reasonable) that the destruction ofantigens is only triggered by fields well above the upper threshold, in the presence ofan idiotypic network antigens will not be destroyed, but will be tolerated.

Thirdly, we can compare these results with what happens if the idiotypic network isabolished. This would be difficult to realize experimentally in a real biological situation,but in the model it can be achieved by a stroke of the pen—for example, by recruitinglymphocytes of only one color, which have zero affinities with each other. In thiscase, the lymphocytes are activated only by the antigens; consequently, lymphocytescomplementary to the antigen are recruited without limit, and the field received by theantigens increases indefinitely until it reaches levels that we may suppose do triggerdestruction of the antigens.

The results of these computer simulations contributed to a renewal of interest innetwork ideas. When Jerne [6] first presented his concept of an idiotypic network in1974, the idea received quite a favorable reception from the community of immunol-ogists. However, over the years, the idea gradually fell into disrepute. What seems tohave happened is this. As we have seen, classical immunology is centered around thephenomenon of strong, destructive immune responses to external antigens. Thus it wasquite natural that in the first-generation models of the immune network, the aim was tomake the network produce immune responses. However, the result of these attemptswas general failure: there seemed to be no way that an idiotypic network could be gotto produce a good immune response.4 Retrospectively, it seems clear that this failurestemmed from the fact that the first-generation models were trying to make the networkdo exactly the wrong thing. In order to produce classical immune responses, Burnet’smechanism consisting of the selection of unconnected clones is both straightforwardand perfectly adequate; at this level, a network organization is not only unnecessarybut actually counterproductive, because the network prevents the development of astrong immune response. A much more appropriate role for the immune network, forwhich its natural emergent properties are an advantage rather than a handicap, is topromote tolerance by protecting the antigens of the body from attack by the immunesystem. These considerations led Varela and Coutinho [15] to make a proposal for“second-generation immune networks,” whose distinctive feature is that the immunesystem is composed of two complementary compartments: the central immune systemand the peripheral immune system.

5 The Central Immune System and the Peripheral Immune System

It is important to note that these theoretical considerations were undertaken in closeconjunction with the ongoing experimental work in Coutinho’s laboratory at the Pasteur

4 Theoretical immunology was, and still is, a flourishing field with a strong international community [10]. Around 1990 there wasa certain interest in idiotypic networks. However, as explained in the text, mainstream work in this area focused on immuneresponses, immune “memory,” and vaccination. The work of Perelson and others showed that vaccination could only be obtainedby mini-networks composed of groups of two or three clones unconnected to each other. Global network connectivity gave riseto results that could not be interpreted in this classical framework; this is poignantly expressed by the title of an article by de Boerand Hogeweg [4]: “Unreasonable implications of reasonable idiotypic network assumptions.” On the other hand, when Perelsonand de Boer studied the emergent properties of an idiotypic network, without presupposing that the network should mediateimmune responses, they obtained results comparable to those presented here [5].



Institute. In particular, there was great interest in the so-called natural antibodies, thecirculating immunoglobulins that are found in the sera of all normal vertebrates evenwhen they are secluded from all antigenic contact with the environment. These naturalantibodies are produced in a seemingly spontaneous manner, and thus appear to be theresult of the autonomous internal activity of the immune system. Following previouswork of Avrameas at the Pasteur Institute [1], Coutinho’s group quickly found thatthese antibodies bind to self (i.e., antigens of the body) and are often multi-reactive.Further work demonstrated that increases or decreases in the concentration of certainspecific natural antibodies had an influence on the natural antibody repertoire as awhole. The natural antibodies are produced by naturally activated lymphocytes, whichrepresent about 10% of total lymphocyte numbers; the remaining 90% are resting cells,which are mitotically inactive, do not secrete immunoglobulins, and are thus devoid ofeffector functions. Fitting nicely to all these facts were the observations, independentlyproduced in John Kearney’s [8] and Coutinho’s groups, that spontaneously producedantibodies often reacted with each other, while the connectivity of antibodies producedupon activation of naturally resting lymphocytes was orders of magnitude lower.

The second-generation immune network model arose by putting together these em-pirical observations with the theoretical considerations outlined above. Every day, thebone marrow produces a large number of new lymphocytes, each of which carries aunique immunoglobulin receptor. The numbers produced are so large that the totalpopulation of lymphocytes can be replenished in a few days; in addition, the repertoireof these new lymphocytes is complete in the sense defined above, that is, it covers thetotality of all possible molecular shapes (of an appropriate size). If these new lym-phocytes are not stimulated, they remain in a resting state and die after 2 or 3 days.However, the rate of production is such that at any one time, these resting cells makeup 90% of total lymphocyte numbers. These resting cells constitute the peripheralimmune system (PIS); they have no functional idiotypic connections. The central im-mune system (CIS) is composed of the 10% of lymphocytes that are naturally activated;according to the model, this activation is primarily the result of idiotypic interactionsbetween these lymphocytes, so that they form a connected network. As predicted bythe computer simulations, the repertoire of the CIS incorporates all the antigens of thebody of the organism that are permanently present. Also in line with the computersimulations, it is the fact that body antigens are included in the repertoire of the CISwith a network organization that protects them from immune attack and thus accountsfor the phenomenon of tolerance.

It is to be noted that according to this model, the two compartments, CIS and PIS,are complementary. The CIS is composed of lymphocyte clones that have been res-cued from death within 2 or 3 days (their fate if they had remained in the PIS) by theirmeta-dynamical recruitment into the CIS. We may recall that the repertoire of lympho-cytes freshly emerged from the bone marrow is complete. Hence, by construction, therepertoire of the PIS is complete minus the repertoire of the CIS. Since the repertoire ofthe CIS includes all the body antigens, it follows that to a first approximation (but weshall have occasion to return to this point) the repertoire of the PIS is complete minusbody antigens. Since the lymphocytes in the PIS are isolated (unconnected by networkinteractions either with each other or with the CIS), if they are stimulated by a novelantigen (for example belonging to an invading microorganism), they will mount anunfettered immune response. Thus, the PIS is ideally constituted both by its repertoireand by its mode of functioning to the role of protecting the organism from pathologicalmicroorganisms. The relationship between the CIS and the PIS is illustrated in Figure 5.

Conceptually, a possible extension of this notion is that the PIS includes lympho-cytes that are rescued from death by minimal affinity to the idiotypic network, butthat affinity is too low to promote their activation to immunoglobulin secretion and



Figure 5. A schematic illustration of the relation between the central immune system (CIS) and the peripheralimmune system (PIS). The bone marrow continually exports large numbers of new lymphocytes. Over several days,the repertoire of these lymphocytes is complete, that is, they recognize the totality of possible molecular shapes (ofan appropriate size). A small proportion of these new cells are recruited into the CIS, defined as a set of cloneswith mutual affinities that sustain each other to form a connected network. The remainder of the new cells form aresidue of clones that are not stimulated and that will die after a few days; this residue constitutes the PIS. It followsthat the repertoire of the PIS is complete minus the CIS.

consequent participation in building the network itself. It follows that the CIS-PIS orga-nization makes it possible to maintain a set of lymphocytes that survive as resting cells,available to stimulation by microbial antigens (non-self), but capable of producing im-munoglobulins that are potentially within the limits of network control. This explainsthe fact that a number of conventional clonal immune responses may be submitted tonatural idiotypic regulation. In addition, this twist may well provide the mechanism forselection of the long life spans of a small fraction of all lymphocytes that participatedin conventional responses, such that they are currently called memory cells. In otherwords, memory of non-self is also a property of the network, which maintains alivesome specific cells even after the antigen has been eliminated from the body. How-ever, although these extensions are attractive and plausible for experimentalists, theywere never implemented in the computer simulations; to that extent, their theoreticalvalidity remains uncertain.

We may now compare this second-generation network model with the scheme ofclassical immunology. In a certain sense, the distinction between the CIS and the PIScorresponds to the classical distinction between self and non-self. This is comforting,and means that the new network view renders unto Caesar that which is Caesar’s. How-ever, there remains a major difference from classical immunology, which is interesting.The difference is that in classical immunology, tolerance to body antigens results fromeliminating all the lymphocytes that interact with them—the so-called clonal deletiontheory. According to the second-generation network model inspired by the concept ofautopoiesis, however, tolerance to body antigens is the result of a positive process: thelymphocytes that interact with the body are not eliminated, but on the contrary they are



activated by being incorporated into the dynamics of an idiotypic network. This hasa number of consequences—conceptual, experimental and practical—which are worthspelling out.

The conceptual difference is that the category of self is not defined by an externalhuman observer on the basis of knowledge that is intrinsically inaccessible to the im-mune system. In this new conception, self is first and foremost defined by the immunesystem itself on the basis of its autonomous functioning as a self-sustaining idiotypicnetwork. It is only subsequently that the body antigens are incorporated into the reper-toire of this network. The body antigens are not intrinsically self as such (and even lessbecause they are decreed to be self by an immunologist); they become self by virtueof being assimilated into an immunological self that has already been constituted bythe autonomous operation of the immune system. This notion has a sound empiricaldemonstration in a series of experiments carried out in the late 1980s by Le Douarinand colleagues in Paris [3]. Concerned with analyzing cell fate in embryonic devel-opment, this group conducted tissue grafts between embryos of related, yet different,species and strains, at a stage that preceded the existence of lymphocytes. Whereasconventional theory would have predicted that such grafts—present in the body frombefore the development of the immune system—would be taken as part of self and thustolerated, Le Douarin’s group discovered that all embryonic grafts were rejected oncethe animals reached immunological maturity. This observation was most surprising,and it was at the origin of the current concepts of dominant tolerance (see below),demonstrating that incorporation into the immunological self only occurs when thegrafted tissues share critical antigens with the cells that either make up the immunesystem (bone marrow) or ensure its development and self-restricted operation (thymicepithelial cells). We may also note here that even if we accept that the body antigensare normally incorporated into the immunological self, it does not follow that the im-munological self reduces to just the body antigens. As already mentioned, we shallhave occasion to return to this point.

The experimental difference is this. On the classical view, tolerance is due to theelimination of lymphocyte clones that interact with the antigen in question. Thus, ifa hybrid immune system is produced experimentally, tolerance should be recessive(i.e., a hybrid between a tolerant and a non-tolerant system should be non-tolerant).On the new view, tolerance is due to the positive effects of a functional network;thus, on condition that the hybridization is carried out in such a way that the networkis not disrupted, tolerance should be dominant (the hybrid, or chimeras containinga mixture of tolerant and non-tolerant cells, should be tolerant). Without going intodetails, we note that many experiments have been performed that amply demonstratethe phenomenon of dominant tolerance. It suffices to say that, after a few decadesof great predominance of recessive-tolerance theories, it is now widely accepted thatnatural tolerance is in fact dominant.

The practical, clinical difference is this. On the classical view, autoimmune diseasearises because the immune system is functioning overzealously; it is therefore quitelogical to treat autoimmune disease by immunosuppression. The results are generallynot very satisfactory: immunosuppressive treatments are, at best, symptomatic, andmay have serious side effects. To date, there are no observations indicating the cureof autoimmune patients by such treatments. On the new view, autoimmunity arisesfrom a deficiency in the normal ongoing activity of the immune system (and, quiteapart from treatment, it is a widespread clinical and experimental observation thatimmunodeficiency is indeed often associated with autoimmunity); the logical treatmentthus consists of an (appropriate) activation of the immune system. In line with thisprediction, the treatment of autoimmune disease by the injection of a balanced mixtureof normal serum immunoglobulins has had some very positive results [7].



6 Subsequent Developments

The second-generation network models described in the previous section had onemajor gap. What our work showed was that if the immune system functioned ina network mode, then the antigens that fall within its repertoire will be integratedinto the network dynamics and will hence be tolerated (this is the basis of the CIS);whereas if the immune system functioned in a non-network mode without idiotypicconnections, then the antigens that fall within its repertoire will provoke an immuneresponse leading to their destruction (this is the basis of the PIS). However, the majorissue that remained quite unresolved was to specify how the distinction between the CISand the PIS actually came about. In our first simple models, illustrated in Figure 4, thenetwork spread over the whole available shape space (the self-organized patterns onlyarose when the whole shape space was saturated), thus leaving no room for a residualPIS. It is true that if we abolished the network interactions by simple fiat—a “handof God,” as it were—then the system would function in a PIS mode. However, thissort of intervention (divine or otherwise), coming from outside the system, was quitecontrary to the spirit of autopoiesis, where the whole point is to explain phenomenaas resulting from the autonomous operation of the system itself. To be more precise,what was missing was an account of how the CIS-PIS distinction (the successor to theclassical self–non-self distinction) could arise through the autonomous ontogeny of thesystem itself.

After 1993, this problem was tackled with great energy and imagination by JorgeCarneiro, at that time a PhD student at the Pasteur Institute. Carneiro came to theconclusion that this problem could only be solved by extending the model to includenot only the B lymphocytes, which produce immunoglobulins, but also macrophages,which present digested fragments of antigens via the MHC molecules on their cellsurface, and the T lymphocytes, which recognize the MHC-presented antigens andprovide help to B lymphocytes. Without going into the details [2], we state that Carneirocame up with an aesthetically beautiful model that exhibited the emergent properties wewere looking for. The first condition was that the ontogeny of the system should startwith a sufficiently numerous and diverse set of antigens (these plausibly correspondto the body antigens already present when the immune system starts developing inembryonic life, but we will refer to them more prudently here as initial antigens). Onthis condition, the immune system went through several phases in its ontogeny. Firstly,T cells were activated, and these in turn recruited B cells. On condition that the initialset of antigens was sufficiently numerous, this process continued until the repertoireof the B cells was complete, and so the B cells started to exert a regulatory feedbackinfluence on the T cells. At this stage, the second phase commenced: now that thesystem was saturated and complete, competition set in amongst the B cells for the T-cellhelp that they themselves were limiting. Under these conditions, the repertoire of theB-cells shrank until only those with a B-cell receptor (BCR, an immunoglobulin) thatdirectly recognized a T-cell receptor (TCR) remained. It is aesthetically pleasing to notehere that since the TCRs are a mirror of the initial antigens, and these BCRs are a mirrorof the TCRs, the BCRs are a mirror of a mirror—a sort of “internal image” of the initialantigens. Thus, the B-cell repertoire in the mature CIS was far from complete, and infact was restricted to an internal image of the initial antigens. This set the stage for thethird phase in the ontogeny. If a single novel antigen, which the immune system hadnot seen so far, was now presented to the system after the maturation of the first twophases, then the global regulatory processes that occurred with the initial set of antigenswere not reproduced. The reason is that the B-cell repertoire was now tightly restrictedto an internal image of the initial antigens, and had virtually no chance of percolatingto include a BCR that would regulate the T cell activated by the novel antigen. The



result was that the immune system would mount an unfettered immune response tothe novel antigen.

Unfortunately, several straightforward predictions of this model are refuted by theobservations: for example, µ-knockout mice that have no B-cell receptors do not ex-hibit uncontrolled T-cell proliferation. Even more seriously (for after all, a “refutation”can always be overcome by an appropriate adjustment and/or subsequent experimen-tal findings—it should be said that very recent observations do show alterations in thedevelopment of TCR repertoires in the immune system of mice that produce no im-munoglobulins), this model has not given rise to experimental observations that wouldvalidate it positively. The most serious problem is that it is not at all sure that idio-typic interactions between the highly variable BCRs and TCRs have any physiologicalsignificance at all. Jerne’s initial argument in favor of idiotypic networks was purelylogical and qualitative: if the immunoglobulin repertoire is complete, then there mustlogically exist interactions between immunoglobulins. Incontrovertible as far as it goes,this is not enough to show that the concentrations and affinities involved are sufficientfor these interactions to have real physiological effects. Thus, for the moment at least,idiotypic network models have fallen again into the shade.

7 Epilogue

Francisco Varela left immunology in 1993, to return in a more focused way to brainbiology, which he had never left either in the laboratory or in his mind. His feel-ing was that neuroscience, to which he brought the highly original contribution ofneurophenomenology, was more likely to provide the system best able to test and il-lustrate his general, fundamental ideas. Interestingly, one of his major contributionsto neuroscience—the demonstration that a neural network selects what it pays atten-tion to, which in turn reverberates through a large part of the system and adds to thememory of past experiences in selecting what we next pay attention to—is closely akinto the second-generation immune networks that he offered to immunologists. So, tenyears later, what has become of Francisco’s contribution to immunology?

An interesting achievement of this work in immunology is to show that the con-cepts of autopoiesis can be employed to generate clear novel hypotheses and producemodels demonstrating these ideas. The concepts of autopoiesis have been criticizedon the grounds that since they are conceived as a tight logical chain of definitions andimplications, it is often not clear whether they are indeed a scientific theory or ratherjust a potential scientific vocabulary of doubtful utility to working scientists. Here wesee that ideas inspired by autopoiesis can provide clear and testable predictions andsuggest novel therapeutic procedures.

More precisely, as regards the field of immunology itself, we have noted that idiotypicnetwork models are not currently in vogue. However, whatever its ultimate empiricalvalidity, the culminating network model of Carneiro provides a very good illustrationof an important epistemological point raised at the end of Section 2 above. This modelprovides a mechanism, hypothetical certainly but quite precise and explicit, as to howthe demarcation between the CIS and the PIS could actually come about in the courseof an autonomous ontogeny, without the providential help of an omniscient externalagent. And to all practical intents and purposes, this demarcation does roughly coincidewith the classical immunologist’s self–non-self distinction. However, if the mechanism isindeed akin to that proposed by Carneiro, the actual operational distinction is between(a) a sufficiently numerous set of initial antigens, present from the start of ontogeny, and(b) single antigens that are first presented to the system after two successive phases ofmaturation. To call this a self–non-self distinction obscures the issue by presupposingwhat it ought to be the job of scientific investigation to explain—rather like Moliere’s



doctors, who grandiloquently claimed that the reason why opium makes you sleep isthat it contains a “dormitive principle.” If Carneiro’s model is not the right one, it willhave to be replaced by an alternative account with the same operational capacity toexplain how the CIS-PIS distinction does come about.

The focus of current research on the phenomena of tolerance to body antigens hasshifted to the so-called regulatory T cells. However, this recent work is complementaryrather than contradictory to the basic insights that came from the second-generationnetwork concepts. Firstly, the work on auto-reactive regulatory T cells has yet to addressthe questions of repertoire formation and the 20-year-old observations on reciprocaland recursive selection amongst naturally activated B and T cells. Secondly, and evenmore important, the basic renewal of perspective that came from the deployment ofthe concepts of autopoiesis in the field of immunology has become irreversible. Itis now clear that tolerance to body antigens is dominant, and so it cannot possiblybe explained on a “one-by-one“ clonal basis and certainly not by the elimination oflymphocytes that interact with the body. On the contrary, tolerance is primarily theresult of a positive, active process involving lymphocytes that interact productivelywith the body; these lymphocytes probably include the newly fashionable regulatoryT cells but are not necessarily restricted to them. To be sure, the concept of dominanttolerance as actually adopted by the immunological community is a rather watered-down version of what Varela proposed, and falls short of adopting the autopoieticperspective as such. Thus the intellectual potential for a paradigm shift, clearly presentin Varela’s ideas, has not fully materialized—to date, at any rate. However, the future isnot closed. Francisco liked to say that the central, primordial function of the immunesystem is that of “self-assertion”; and this insight, today more than ever, holds promisefor the future.

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The Affirmation of Life, A New Perspective of the Immune System

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