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Immunity
Immunity
The Evolution of an Idea
A L F R E D I . TA U B E R
1
1
Oxford University Press is a department of the University of Oxford. It furthers
the University’s objective of excellence in research, scholarship, and education
by publishing worldwide. Oxford is a registered trade mark of Oxford University
Press in the UK and certain other countries.
9 8 7 6 5 4 3 2 1
Printed by Sheridan Books, Inc., United States of America
In memory of Lynn Margulis
Immunology has always seemed to me more a problem in philos-
ophy than a practical science.
Burnet (1965, p. 17)
Our imperative need for cause and effect is satisfied when each
process has one demonstrable cause. In reality, outside us this is
hardly so; each event seems to be over-determined and turns out
to be the effect of several converging causes. Intimidated by the
countless complications of events research takes the part of one
chain of events against another, stipulates contrasts that do not
exist and that are created merely through tearing apart more com-
prehensive relations. … I do not mean to say that the world is so
complicated that every assertion must hit the truth somewhere.
No, our thinking has preserved the liberty of inventing dependen-
cies and connections that have no equivalent in reality. It obvi-
ously prizes this gift very highly, since it makes such ample use of
it—inside as well as outside of science.
Freud (Moses and Monotheism 1939, p. 137)
CONTENTS
Preface╇ ix
Acknowledgments╇ xvii
Introduction╇ 1
3. Individuality Revised╇ 89
5. Eco-╉immunology╇ 163
Epilogue╇ 219
Notes╇ 229
References╇ 255
Index╇ 295
PREFACE
This book is about how ideas structure and orient the practice and the-
ory of a science. Such foundational ideas for the most part remain hid-
den, or at least implicit to the immediate goals of research. Indeed, the
most evident task of science is a practical enterprise; nevertheless, the tacit
dimension of intellectual (and often ideological) commitments is always
at play, guiding interpretations of data and the assembling of facts into
models and then theory. So, although Frank Macfarlane Burnet used a
bit of hyperbole when observing that immunology was “more a problem
in philosophy than a practical science” (Burnet 1965, p. 17), I fully con-
cur with his basic insight: Much of immunology fascinates because of its
intellectual challenges, the vibrancy of its key ideas, and the scope of phil-
osophical issues the study of immunology might address.
Immunology, from its earliest inception, has been concerned with
biological identity— its establishment and maintenance. Three key
characteristics— individuality, immunity, and identification— together
define immune identity, and as one notion changes meaning, so do the
others. Individuality framed immune theory from its inception, for the
attack of pathogens on a vulnerable patient (individual) defined the task
of immunity, namely to defend a self pitted against alien others. In this
scenario, distinct borders confer guarded individuality, and immunity
is the response to the violation of those boundaries. Simply, the individ-
ual is “self-contained.” Contemporary immunology now recognizes the
fluidity of borders in the dialectical exchange of the organism with its
x Preface
The basic position developed here is that the idea of immunity is insep-
arable from how immune identity is construed because (1) differing
constructions of identity yield different notions of immunity and, recip-
rocally, (2) different modalities of immunity confer distinctive con-
ceptions of agency. The story of this mutual dependence begins at the
origins of immunology. With the discovery of infectious diseases, the vio-
lated organism, regarded as an autonomous entity, required protection.
However, the insularity characterizing such an animal proved unstable,
and so when we peer at immunology’s development, the striking ways
xii Preface
in which the meanings of immune agency have shifted mark the disci-
pline’s history. The science is now expanding beyond an exclusive focus
on defense to a broadened ecological orientation in which immunity
becomes a mediator of environmental exchange of both the dangerous
and the benign. This broadened bidirectionality—attack balanced against
(active) tolerance—is radically altering the science’s organizing principles
and its corresponding research agenda. In short, moving from a defensive
posture to a fully ecological alignment heralds a major shift in immunol-
ogy’s governing theory and a correction of its understanding of immune
selfhood at the heart of the discipline’s conceptual history. Note that I do
not envision immunology devoid of its semantic and theoretical depen-
dence on notions of agency, but simple dichotomies characterizing cur-
rent models fail to capture the dynamic forces at play.
This study presents a scientific, linguistic, and philosophical analysis
of immune identity along two thematic lines. The historically dominant
model asserts that the immune system protects a self, a conception that
incorporates the following three cardinal features: (1) A “self ” exists;
(2) this entity has certain identifying characteristics, of which immune
tolerance distinguishes that which is “self ” from “the other” (or non-
self); and (3) identity arises as a developmental process, which may be
modulated throughout life but essentially represents a protected “space”
of immune silence (nonreactivity). This account of demarcation derives
from a prominent Western anthropocentric extrapolation, one that may
be directly traced to the original clinical orientation in which immunol-
ogy emerged—a threatened self. As previously mentioned, this theoretical
scenario has been challenged by what I call the “ecological imperative,”
which works by an altogether different construction, one that displaces
immunology as the science of self-defense for one in which organismal
identity emerges in dialogue with both internal and external environ-
ments. According to this alternate point of view, a biology that ignores the
larger context in which immune mechanisms operate will fail to explain
immunity’s full functional panoply.
To compose a more comprehensive design, I argue that immunity is
fundamentally an information-processing faculty, and like the nervous
Preface xiii
that symbiosis of eubacteria and archaebacteria into early cells gave rise
to intracellular organelles: Mitochondria were descended from parasitoid
bacteria, and chloroplasts arose from once free-living photosynthetic bac-
teria. Robert Schwartz and Margaret Dayhoff proved the symbiogenesis
hypothesis in 1978 by showing that mitochondria and chloroplasts pos-
sess their own genes and their own translation machinery (reviewed in
Lang, Gray, and Burger 1999).
The evolutionary role of symbioses had been repeatedly postulated
throughout the twentieth century, but it was dismissed and ridiculed
insomuch as it conflicted with the main tenets of classical biology. In
promoting the ubiquity of symbiosis, Lynn radically shifted the “thought
collective” (Fleck 1979). Given the lineal heterogeneity of all organisms,
Lynn not only challenged the gradualism of Darwinian evolution but also
further envisioned a dynamic biology that broke the bounds of previous
thinking about the classification of life. She upset the entrenched dogma,
which divided the organic world into plants and animals, by proposing
a modification of Robert Whittaker’s five kingdoms taxonomy (Margulis
and Chapman 2009). This perspective, namely a view framed by efforts to
explain the evolution of microbiota, contrasted with the prevalent orien-
tation of neo-Darwinist evolutionary biologists trained in the tradition of
zoology. She asserted that the focus on animal evolution ignored nearly
90% of the evolution of life on Earth, including the most fundamental
evolutionary innovation. In short, by championing symbiosis, Margulis
effectively challenged the modern synthesis that had dominated evolu-
tionary biology for a more complex theory that included neutral fixation
by random drift, horizontal gene transfer, punctuated equilibrium, and
gene duplication (Koonin 2012).
Lynn holds a legitimate claim as “the master architect for re-thinking
biology in terms of interacting consortia” (Gilbert, Sapp, and Tauber
2012, p. 336). Drawing upon genetics, cell biology, protistology, earth sys-
tems science, and taxonomy, she reconceived notions of atomistic organ-
isms that characterized a biology she sought radically to revise. As she
stated, “Each of us is a colossus of nanobeasts, a coordinated bestiary”
(Margulis 2004, p. 80), a formulation in which such associations create
xvi Preface
Immunity: The Evolution of an Idea is both the synthesis and the capstone
of work published during the past 17 years. Although the key insights
presented in these earlier studies have not fundamentally changed, I have
modified certain views and, I hope, deepened my own understanding of
the conceptual structure of immunology’s theory and the various func-
tions of immunity. To acknowledge all those who have guided, provoked,
and aided me during this period is simply beyond my memory. I trust
all recognize my gratitude, and to any who feel slighted, I apologize.
However, a special acknowledgment is due to several colleagues: Eshel
ben Jacob (of blessed memory), Irun Cohen, and Nelson Vaz. Each gener-
ously explored with me questions of mutual interest concerning cognition
and information. They enlightened my own knowledge and perspectives
in varied and important ways about the basic mechanisms of immune reg-
ulation and how we might conceive the structure of the immune system.
Ilana Löwy introduced me to Ludwig Fleck’s critical appraisal of organism
as a ‘construction’ and thus anticipated much of the current philosophical
discussion about identity and individuality, which comprise the intellec-
tual scaffolding for my own work (Fleck 1979). The notion of organism
remains problematic because of the prevalence of symbiosis (thus obscur-
ing boundaries) and the deeper conceptual directives at work that define
individuals according to particular research interests. Ilana’s seminal
paper, long dormant in the literature, deserves special recognition for sow-
ing the early seeds of what finally emerged as key elements of Immunity’s
xviii Acknowledgments
and Fenner 1949). This “hole” (or “negative space”) is the “immune self.”
The implicit presence of the self emerged with the formalized self/nonself
distinction, which has been widely designated as immunology’s govern-
ing paradigm (Golub and Green 1991, p. 15) and consistently defended by
those committed to the self/nonself discrimination as the basis of immune
function (Cohn 2015; Bretscher 2016).
The modern historiography of immunology has followed the Burnet-
authored framework and has accepted the centrality of self/nonself dis-
crimination as its fundamental theme. But adopting this version of
immunology’s history omits the deeper perplexities of the science that
remain largely unstated and thus ignored. An alternate history begins
with Elie Metchnikoff ’s theory of immunity (Chernyak and Tauber 1990;
Tauber and Chernyak 1991; Tauber 1991a, 1994a, 2003). Unlike Burnet’s
proposal of a firm demarcation between self and nonself, Metchnikoff
regarded immune processes as mediating the organism’s identity through
a continuous, lifelong developmental process. Accordingly, immunity is
that function which supervises the integrity of the organism in its inter-
nal economy of repair, cell turnover, and surveillance. On this view, host
defense becomes a subordinate aspect of a more general identification
process. Thus, the notion of a self, transcendentally cohesive and fixed,
was displaced by a conception of the organism with a dynamic identity,
whose boundaries and structure evolved in the face of internal and exter-
nal challenges (Tauber 1994a, 1994c, 2003). My revisionist theme is based
on this insight.
Whereas immunology as a science has been defined as the “science of
self/nonself discrimination,” from a philosophical point of view, follow-
ing Metchnikoff, immunology is the science concerned with establish-
ing and maintaining the immune identity of the organism. This more
expansive designation allows for conceiving immune processes in their
broadest biological context, namely in addition to defensive and restor-
ative processes, the immune system also may be understood as engaged
in information processing and cognition, exchange with the environment
to allow for benign intercourse, and tolerance for symbiotic relationships
constitutive of an organism conceived as a complex holobiont. Placing the
4 I m m u n it y: T h e E v o l u ti o n o f a n I d e a
organism in its full ecological context displaces the defensive insular con-
ception of a host (a “self ”)—╉originally defined as requiring protection—╉
to one in which the immune system arbitrates the organism’s dialectical
exchanges with its environment. “Dialectical”—╉the conceptual basis of an
ecological orientation—╉refers broadly to immunity as enacting the organ-
ism’s capacities to control its environment and in turn be determined by
it. Immunity establishes the balance between these two engagements by
addressing both defensive and benign interactive functions. And upon
that platform, philosophical issues pertaining to identity, individuality,
cognition, information, biological causation, mechanism, model, and
metaphor assume more complex meanings than those used in a dichoto-
mous self/╉other framework. Here, the significance of these differing con-
ceptions of immune identity for philosophy of biology is reviewed.
the camp of the Lord] i.e. (in the language of Deuteronomy) “the
place which the Lord chose,” Jerusalem or, more exactly, the Temple
area. Compare 1 Chronicles ix. 18, note.
and that which is left is this great store] The Hebrew requires
some correction. Read as the LXX., καὶ κατελίπομεν ἐπὶ τὸ πλῆθος
τοῦτο, “we leave (‘have left’) this great store and more.”
as the duty of every day required] Or, as margin, for his daily
portion.
18. and them that] Render, and the registration included all
their little ones, etc. The connection of the last part of the verse is
very obscure.
their set office] Or, as margin, their trust (so also above verse
15).
Chapter XXXII.
1‒8 (compare 2 Kings xviii. 13‒16).
Sennacherib’s threatened Invasion. Hezekiah’s Precautions.
² Or, another.
the other wall] In Isaiah xxii. 9‒11 the preparations to meet the
Assyrian attack are described by the prophet who speaks of a “ditch”
(Revised Version “reservoir”) made at this time between “the two
walls.” In Excavations at Jerusalem, 1894‒1897, Dr Bliss describes
a buttressed wall (pp. 96 ff.) built without lime (see his frontispiece
for an illustration of it) and enclosing the pool of Siloam on the south-
east, which, he says, “may date back as far as Hezekiah” (pp. 325
f.). Dr Bliss also, following up a clue given by earlier explorers, found
a second wall (running at an angle to the first) enclosing the pool on
the west. This second wall was probably due to Herod, but Dr Bliss
suggests that the line it follows may have been defended by a wall
as early as Hezekiah’s day (p. 326). For further discussion see G. A.
Smith, Jerusalem, I. 182, 207.
with us is the Lord] Compare xv. 2, xx. 17; Isaiah viii. 10.
9‒19 (compare 2 Kings xviii. 17‒35).
Sennacherib’s Threatening Messages.
13. the peoples of the lands] In 2 Kings xviii. 34 the lands are
specified and include Samaria.
17. to rail on] Or, to defy (the same Hebrew word as in 2 Kings
xix. 4, 16, 22, 33, and there rendered “reproach”).
24. Remark that this single verse epitomises 2 Kings xx. 1‒11.
In those days] The phrase is taken over from 2 Kings xx. 1, and it
cannot be determined what date is intended, though we may
conclude from 2 Kings xx. 6 that it was a time at which the Assyrian
danger was not yet past, and that it was about the fourteenth year of
Hezekiah (compare Barnes on 2 Kings xx. 1).