The Clonal Selection Antibody Theory (1957)

Immunology does not suffer from a lack of experimental data, but still some of the most elementary questions are undecided, and it is not yet possible to choose between instructive and elective theories.”

Joshua Ledergerg, Genes and Antibodies https://doi.org/10.1126/science.129.3364.1649

Every scientific theory relies on the scientific method. A scientist may make an observation and devise a hypothesis to explain that observation, then design an experiment to test that hypothesis. If the hypothesis is shown to be incorrect, the scientist will develop a new hypothesis and begin the process again. If the hypothesis is supported by the results of the experiment, it will go on to be tested again. If the hypothesis isn’t disproven or surpassed by a better explanation, the scientist may incorporate it into a larger theory that helps to explain the observed phenomenon and relates it to other phenomena, according to the Field Museum. 

A scientific theory is not the end result of the scientific method; theories can be proven or rejected, just like hypotheses. And theories are continually improved or modified as more information is gathered, so that the accuracy of the prediction becomes greater over time.

https://www.livescience.com/21491-what-is-a-scientific-theory-definition-of-theory.html

At the time that Frank MacFarlane Burnet proposed the Clonal Selection theory of antibody formation in 1957, there were a few different explanations floating about, including Burnet’s own Indirect Template theory which was suggested almost a decade earlier. They included:

1. Side Chain Theory
2. Direct Template Theory
3. Indirect Template Theory
4. Natural Selection Theory

Each of these theories proposed different ways antibodies formed based on the “scientific” evidence of the time. Naturally, Burnet saw the burning need to discredit his previous theory in order to throw a new one into the mix. To do so, he utilized Niels Jerne’s Natural Selection theory and reworked it so that he could cover-up the holes and lack of evidence in his previous attempt. Thus, the Clonal Selection theory was born and it has gone on to become the most widely accepted explanation for the formation of the unseen particles assumed to be within the blood. The acceptance of this “theory” is clearly pointed out by these first three sources, which use some interesting wording describing Burnet’s last contribution to the antibody narrative:

“Clonal selection theory is a scientific theory in immunology that explains the functions of cells of the immune system (lymphocytes) in response to specific antigens invading the body. The concept was introduced by Australian doctor Frank Macfarlane Burnet in 1957, in an attempt to explain the great diversity of antibodies formed during initiation of the immune response.^[1][2] The theory has become the widely accepted model for how the human immune system responds to infection and how certain types of B and T lymphocytes are selected for destruction of specific antigens.^[3]“

https://en.m.wikipedia.org/wiki/Clonal_selection

“The clonal selection hypothesis is a widely accepted model for the immune system’s response to infection.

“clonal selection: An hypothesis which states that an individual lymphocyte (specifically, a B cell) expresses receptors specific to the distinct antigen, determined before the antibody ever encounters the antigen. Binding of Ag to a cell activates the cell, causing a proliferation of clone daughter cells.

The clonal selection hypothesis has become a widely accepted model for how the immune system responds to infection and how certain types of B and T lymphocytes are selected for destruction of specific antigens invading the body.”

https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/11%3A_Immunology/11.07%3A_Antibodies/11.7C%3A_Clonal_Selection_of_Antibody-Producing_Cells

“In 1957, Burnet proposed that central tolerance to self-antigens occurred by clonal deletion of self-reactive lymphocytes [7]. However, as we will discuss, this model has been ‘updated’ on several occasions.”

https://www.cell.com/trends/immunology/fulltext/S1471-4906(04)00311-4

Notice the words hypothesis and model thrown about in these descriptions of what is considered to be the most widely accepted scientific theory for antibody production? What could they possibly be referring to? Let’s see if we can clear this up by looking at the definitions:

scientific hypothesis, an idea that proposes a tentative explanation about a phenomenon or a narrow set of phenomena observed in the natural world. 

https://www.britannica.com/science/scientific-hypothesis

scientific modeling, the generation of a physical, conceptual, or mathematical representation of a real phenomenon that is difficult to observe directly. 

https://www.britannica.com/science/scientific-modeling

scientific theory, systematic ideational structure of broad scope, conceived by the human imagination, that encompasses a family of empirical (experiential) laws regarding regularities existing in objects and events, both observed and posited. A scientific theory is a structure suggested by these laws and is devised to explain them in a scientifically rational manner.

https://www.britannica.com/science/scientific-theory

Putting it all together, Burnet’s Clonal Selection theory conceived of by the human imagination, which can be rejected just like any other tentative explanation otherwise known as a hypothesis, is the current model, which is a conceptual representation of a real phenomenon that is “difficult to observe directly.” This explanation obviously creates a bit of a problem. In order for this hypothesis/model/theory to be considered scientific, it must adhere to the scientific method:

“A theory is a carefully thought-out explanation for observations of the natural world that has been constructed using the scientific method, and which brings together many facts and hypotheses.”

https://www.fieldmuseum.org/blog/what-do-we-mean-theory-science

The scientific method requires the observation of a real phenomena in nature. In fact, this is the very first step:

1. Observe a natural phenomenon
2. Alternate hypothesis
   • Independent variable (the presumed cause)
   • Dependent variable (the observed effect)
   • Control variables
3. Null hypothesis
4. Test/experiment
5. Analyze the observation/data
6. Validate/invalidate hypothesis

It requires the use of a valid independent variable, i.e. purified/isolated particles assumed to be antibodies, to vary and manipulate in order to determine a cause and effect relationship. In other words, the independent variable must be something that has been shown to physically exist in reality. As antibodies have never been purified and isolated directly from humans in order to be used as a valid independent variable and these particles can not be observed directly in nature, none of the indirect experimental data generated and utilized to formulate these theories was scientific. None of the antibody “theories” adhered to the scientific method in order to develop the hypotheses which were used to craft the experiments that were needed to produce the data which was utilized to create the theory. They all started by presupposing the existence of the very entity they were trying to conjure up evidence for in order to formulate a theory to explain the effects seen as well as the shape and function of the presupposed entity for which they could not observe directly.

Basically, this is a long way of saying that we can exclude scientific from the definition of the word “theory” used to describe Burnet’s Clonal Selection as it is obvious that it did not adhere to the scientific method and is thus not scientific at all. Therefore, we can replace the scientific definition with the common definition:

theory, an idea that is suggested or presented as possibly true but that is not known or proven to be true

https://www.britannica.com/dictionary/theory

This can be applied to all antibody theories which amount to nothing more than dreamt up speculative fantasies crafted from non-scientific experimental data which combined human and animal blood with various chemicals to create a non-specific reaction in order to blame on invisible entities. These mad science experiments are obviously the exact opposite of a natural phenoma observed in nature. All antibody theories therefore start from a fraudulent foundation.

In any case, as the previous theories/models of this unseen entity were unscientific and could not hold up to scrutiny, they were eventually unceremoniously thrown out in favor of Burnet’s Clonal theory. For decades it was considered as the “truth” even though it was nothing but speculation masquerading as science. However, even the unscientific Clonal theory has being challenged recently. In 1992, Irun Cohen, an immunologist at the Weizmann Institute of Science in Israel who developed the theory of the immunological homunculus in 1989, wrote a paper challenging the Clonal Selection theory. Unfortunately, I was unable to aquire the whole paper. However, the abstract gives us an idea as to the grounds Cohen challenged the theory on:

The cognitive principle challenges clonal selection

“Here, Irun Cohen argues that the clonal selection paradigm is no longer a convenient paradigm for organizing thinking about the immune system. He contends that most immunologists now investigate questions for which the clonal selection paradigm makes no provision and that one of its major tenets is contradicted by the prevalence of natural autoimmunity. Instead, he proposes a cognitive paradigm.”

https://pubmed.ncbi.nlm.nih.gov/1476598/

In a page referencing the work of Cohen, further light can be shed on his criticisms as he claimed that the tenets of classic Clonal Selection are not compatible with the findings reported in a paper on the success of a therapeutic peptide vaccination. Cohen felt that the success of the clinical trial was compatible instead with the homunculus concept of autoimmunity:

DiaPep277 Peptide and Type 1 Diabetes

Raz I., Elias D., Avron A., Tamir M., Metzger M., Cohen I.R.
-cell function in new-onset type 1 diabetes and immunomodulation with a heat-shock protein peptide (DiaPep277): A randomized, double-blind, phase II trial. The Lancet, 2001; 358: 1749-53.

“At the practical level, this paper shows that autoimmune destruction of beta cells in patients with newly diagnosed type 1 diabetes can be arrested by the administration of DiaPep277, a peptide fragment of the 60kDa heat shock protein molecule. Three subcutaneous injection of the peptide, 1 mg each in an oil vehicle, were effective. The optimal dose of peptide and the most effective schedule of injections remain to be worked out. Nevertheless, the confirmation of effectiveness and safety in continuing trials would indicate that immunologically specific treatment of autoimmune disease is feasible.

At the theoretical level, these results serve as a proof-of-concept in the controversy between contending theories regarding the basic organization of the immune system. The classical clonal selection theory holds that:

1. Self-non-self discrimination is the aim of the immune system;
2. Autoimmunity is deleted from the healthy repertoire of antigen receptors;
3. Autoimmunity arises by accident;
4. Autoimmune disease therapy requires blocking self-recognition, or removal of self-recognizing lymphocytes.

These tenets of classic clonal selection are not compatible with the findings reported in the paper. On the contrary, the success of the clinical trial of therapeutic peptide vaccination is compatible with the homunculus concept of autoimmunity. This theory includes the following ideas:

1. The aim of the immune system is not to discriminate self from non-self, but to organize inflammation in a way that maintains, heals and, where possible, regenerates damaged cells and tissues; the healthy system is continuously responding to self.
2. The healthy repertoire includes a high frequency of lymphocytes that recognize key self-antigens: the immunological homunculus.
3. Autoimmune diseases arise from a failure of normal regulation, and the resulting diseases are predictably associated with collectives of particular self-antigens.
4. The natural cure to autoimmune disease is to activate and reinstate the regulatory mechanisms built into the homunculus.

The paper demonstrates that a single peptide can indeed activate regulation; the immune system is best controlled by supplying the immune information the system is organized to seek. The immune system is a cognitive system.”

https://www.weizmann.ac.il/immunology/sci/CohenPage2.html

In 2002, Arthur M. Silverstein, an American immunologist and science historian who has written extensively on the history of immunology, wrote a paper attempting to defend the Clonal Selection theory. However, in the paper, he noted the criticism of the Clonal Selection theory by Cohen and others as an obsolete and outdated theory and pointed to some very important questions that CST needed to answer which were largely unaddressed:

The Clonal Selection Theory: what it really is and why modern challenges are misplaced

“The Clonal Selection Theory (CST)2 of Macfarlane Burnet and David Talmage seems to be under fire currently from several directions. Irun Cohen, in considering the role of autoimmunity in the economy of the body, suggested that, “Progress in immunology appears to have rendered the clonal selection paradigm incomplete, if not
obsolete; true it accounts for the importance of clonal activation, but it fails to encompass, require, or explain most of the subjects being studied by immunologists today …”. Polly Matzinger has gone even further: based upon her view that the “danger theory” has negated Burnet’s classical view of self-nonself discrimination, she extends this to suggest that the entire clonal selection paradigm that has ruled immunology for some 35 years has been overthrown.”

“Even philosophers of science have occasionally blurred the important distinction between the core hypotheses of CST and the ancillary
hypotheses that may stem from it. In his book The Immune Self: Theory or Metaphor?, A. Tauber calls Burnet’s view of tolerance “…a cornerstone of his later immune theory [CST]”, and throughout appears to accept the various challenges to Burnet’s ideas on tolerance and self-nonself as challenges to the central meaning of CST. Again, in their book The Generation of Diversity, S. Podolsky and A. Tauber discuss the several challenges to Burnet’s idea of self-nonself and conclude that, “Specifically, we must ponder whether CST, as constructed by Burnet, Talmage, and Lederberg [sic!8] … is now being seriously challenged”. Kenneth Schaffner, in his elegant discussion of the philosophical bases of CST, Discovery and Explanation in Biology and Medicine, formally defines three levels of hypothesis in CST and actually assigns Burnet’s tolerance hypothesis to a secondary level. But even he sometimes seems to suggest that tolerance experiments may serve as tests of CST.

From instruction to selection

Between 1930 and the early 1960s, the accepted explanation for the large repertoire of antibody specificities was that antigen somehow acts as a template to transfer information to the globulin-producing mechanism. This was termed an “instruction theory” and was advanced in different forms. At a time when immunology was preoccupied with chemical approaches, and when little was known about how proteins are formed, these instruction theories seemed plausible. No matter that they could not explain such observations as the persistence of antibody formation, the accelerated and enhanced secondary response or what would later be termed affinity maturation.

Then in 1955, in the context of increasing interest in tissue transplantation, immunodeficiency diseases, autoimmunity and tolerance, Niels Jerne suggested that the information for all antibody specificities is inherent in the host and expressed as “natural” antibodies. Now the sole function of antigen was to select the matching antibody and transport it to the appropriate cells where, somehow, they would be stimulated to produce more of the same. Jerne’s idea attracted little support at the time; its surviving claim-to-fame lies in the fact that David Talmage and Macfarlane Burnet independently saw in its selectionist approach the seed of an interesting idea.”

Silverstein offered questions CST must answer that were largely unaddressed. I’m paraphrasing them here for length considerations:

1. If a “Landsteiner-size” repertoire arises spontaneously, what is the mechanism for its generation?
2. If a repertoire is generated randomly and somatically, why are destructive autoantibodies not formed against native antigens to engender immediate autoimmune disease?
3. Is there more than one type of receptor on a single cell?
4. If somatic mutation persists after clonal expansion, how can clonal specificity be maintained?
5. How can interaction of antigen with a surface antibody receptor induce cell proliferation and differentiation?
6. What determines and regulates which clonal daughters differentiate to form antibody and which survive as memory cells?

“Any valid theory of antibody formation (and that is what CST is) must satisfactorily explain these and other questions. However, the central theory need not fall just because its promulgator was wrong in proposing a mechanism to answer one of its subsidiary questions. Some of these questions address the “selection” component of CST, whereas others deal with the “clonal” component; the former might survive the disproof of the latter. It is curious that CST has been challenged based upon Burnet’s error in explaining self-nonself discrimination, but no one has suggested that CST might be challenged because Burnet was wrong about the mechanism for the generation of diversity, although these are hierarchically equal hypotheses. Yet self-nonself is chosen among all the other possibilities, for reasons that we will explore below.”

“Burnet became so involved with the question of self and with his explanation of the mechanism of tolerance that even he began to view it as an integral part and even a test of CST, rather than as merely a subsidiary question to be approached by trial and error. In discussing the foundations of CST, Burnet admitted that if immunologists are correct in doubting that “tolerance is wholly a matter of the absence of the immunocyte … an extensive reorientation [of CST] will become necessary”. No wonder that others might feel the same! (We might note also that Burnet came close to giving up on CST in 1962, when reports came in of two and even four different antibody specificities produced by a single cell; when Szenberg et al. found too many pocks on the chorioallantoic membrane of chick embryos injected with small numbers of lymphocytes (that is, the proportion of cells specific for MHC alloantigens appeared to be much too high)40; and when Trentin and Fahlberg found that a single clone of cells used to reconstitute a lethally irradiated mouse seemed able to form antibodies of different specificities.)”

“Given this wide-open theoretical terrain, it is no wonder that debate continues on such questions as a “big bang” versus the continuous generation of diversity, the relative roles of central versus peripheral mechanisms of tolerance, the number and type of signals required for one or the other response, whether autoimmunity is dangerous or beneficial (Cohen) and whether the immune apparatus evolved to recognize infectious pathogens (Cohn and Janeway), “danger” (Matzinger) or, following Jerne, “self” (Coutinho and Cohen).”

“In the end, however, we must not lose sight of the fact that the CST is only a theory of how antibodies are formed, not a theory of why they are formed.”

DOI:10.1038/ni0902-793

As can be seen, Burnet’s theory, while presented as the truth regarding antibody production and formation, is not without its detractors. Even Burnet himself waffled on the correctness of his own theory in 1962, stated in 1967 that it was incomplete and the terms were obscure and meaningless, and considered his work speculative in his own paper. The entire 1957 paper detailing his ideas is presented below:

A Modification of Jerne’s Theory of Antibody Production using the
Concept of Clonal Selection

There are three current theoretical interpretations of antibody production which, following Talmage (1957), may be referred to as the direct template theory in which the antigen serves as a template against which the specific pattern of the antibody is synthesized, the indirect template theory which postulates a secondary template incorporated into the genetic-synthetic processes of the antibody producing cells (Burnet, 1956), and the natural selection theory in which the antigen acts essentially by selection for excess production of natural antibody molecules of corresponding type (Jerne, 1955).

The two latter theories were devised primarily to account for two sets of phenomena for which the direct template theory seems quite irrelevant. The first is the absence of immunological response to “self” constituents and the related phenomena of immunological tolerance; the second is the evidence that antibody production can continue in the absence of antigen. Some means for the recognition and differentiation of potentially antigenic components of the body from foreign organic material must be provided in any acceptable formulation. In Burnet and Fenner’s (1949) account, a positive recognition of “self” material was ascribed to the presence of “self
markers” in all potentially antigenic
macromolecules, and corresponding recognition units in the scavenger cells of the body. At the time it was regarded as inconceivable that a mechanism could exist which would recognise in positive fashion all foreign material and no attempt was made to devise one, despite the fact that we have always recognised the clumsy character of the self-marker, self-recognition scheme.

It is the great virtue of Jerne’s hypothesis that it provides an approach to this alternative method of recognising self from not self. There is no doubt about the presence in all mammalian or avian sera of a wide range of reactive globulins which can legitimately be called “natural antibodies.” Jerne assumed that amongst these globulin molecules were all the possible patterns needed for specific immunological type reaction with any antigen, except for those patterns corresponding to body antigens which would be eliminated by in vivo absorption. When a foreign antigen enters the blood it unites, according to Jerne’s scheme, with one of the corresponding natural antibody molecules. The complex is taken up by a phagocytic cell in which the antigen plays no further part, but the antibody globulin provokes the production by the cell of a fresh crop of similar molecules which are liberated as antibody. If this basis is accepted, most immunological phenomena can be well described in terms of the theory. Its major objection is the absence of any precedent for, and the intrinsic unlikelihood of, the suggestion that a molecule of partially denatured antibody could stimulate a cell, into which it had been taken, to produce a series of replicas of the molecule.

Talmage (1957) has suggested that Jerne’s view is basically an extension of Ehrlich’side chain theory of antitoxin production and that it would be more satisfactory if the replicating elements essential to any such theory were cellular in character ab initio rather than extracellular protein which can replicate only when taken into an appropriate cell. Talmage does not elaborate this point of view but clearly accepts it as the best basis for the future development of antibody theory. He stresses the multiplicity of the globulin types that can be present in the blood and is profoundly sceptical of any approach which attempts to “unitarian” an interpretation of antibody. In his view properdin has as much right to be called an antibody as any other globulin.

Before receiving Talmage’s review we had adopted virtually the same approach but had developed it from what might be called a “clonal” point of view. This is simply a recognition that the expendable cells of the body can be regarded as belonging to clones which have arisen as a result of somatic mutation or conceivably other inheritable changes. Each such clone will have some individual characteristic and in a special sense will be subject to an evolutionary process of selective survival within the internal environment of the body.

It is believed that the advantages of Jerne’stheory can be retained and its difficulties overcome if the recognition of foreign pattern is ascribed to clones of lymphocytic cells and not to circulating natural antibody. The resulting formulation may be stated as follows:

The plasma-globulins comprise a wide variety of individually patterned molecules and probably several types of physically distinct structure. Amongst them are molecules with reactive sites which can correspond probably with varying degrees of precision to all, or virtually all, the antigenic determinants that occur in biological material other than that characteristic of the body itself. Each type of pattern is a specific product of a clone of mesenchymal cells and it is the essence of the hypothesis that each cell automatically has available on its surface representative reactive sites equivalent to those of the globulin they produce. For the sake of ease of exposition these cells will be referred to as lymphocytes, it being understood that other mesenchymal types may also be involved. Under appropriate conditions, cells of most clones can either liberate soluble antibody or give rise to descendant cells which can.

It is assumed that when an antigen enters the blood or tissue fluids it will attach to the surface of any lymphocyte carrying reactive sites which correspond to one of its antigenic determinants. The capacity of a circulating lymphocyte to pass to tissue sites and there to initiate
proliferation is now relatively well established (cf. Gowens, 1957; Simonsen, 1957). It is postulated that when antigen-natural antibody contact takes place on the surface of a lymphocyte the cell is activated to settle in an appropriate tissue, spleen, lymph node or local inflammatory accumulation, and there undergo proliferation to produce a variety of descendants. In this way preferential proliferation will be initiated of all those clones whose reactive sites correspond to the antigenic determinants on the antigen used. The descendants will include plasmacytoid forms capable of active liberation of soluble antibody and lymphocytes which can fulfill the same functions as the parental forms. The net result will be a change in the composition of the globulin molecule population to give an excess of molecules capable of reacting with the antigen, in other words the serum will now take on the qualities of specific antibody. The increase in the number of circulating lymphocytes of the clones concerned will also ensure that the response to a subsequent entry of the same antigen will be extensive and rapid, i.e. a secondary type immunological response will occur.

Such a point of view is basically an attempt to apply the concept of population genetics to the clones of mesenchymal cells within the body. It is clear that the internal environment involved is an exceedingly complex one and in all probability many factors will impinge on clones of antibody-producing cells from that environment. It is equally certain that inheritable changes (at the clonal level) will occur as a result of somatic mutation or of the still obscure processes responsible for differentiation during development of regeneration and repair.

It would be inappropriate to elaborate this view much further in a preliminary communication, but it should be immediately evident that it has highly relevant implications for the general function of the lymphocyte, for the fact that sensitization and homograft immunity reactions seem to be mediated by lymphocytes or other mesenchymal cells without liberation of classical antibody, and for recent findings of extremely rapid liberation of antibody from normal cells. A preliminary survey of a variety of pathological conditions which involve anomalous immune reactions also suggests that this cellular approach has greater relevance to the problems than any of the other hypotheses. These aspects will be elaborated in a more extensive contribution now in preparation.

One aspect, however, should be mentioned. The theory requires at some stage in early embryonic development a genetic process for which there is no available precedent. In some way we have to picture a “randomization” of the coding responsible for part of the specification of gamma globulin molecules, so that after several cell generations in early mesenchymal cells there are specifications in the genomes for virtually every variant that can exist as a gamma globulin molecule. This must then be followed by a phase in which the randomly developed specification is stabilized and transferred as such to descendant cells. At this stage, again following Jerne, any clones of cells which carry reactive sites corresponding to body determinants will be eliminated. The necrotic effect of the tuberculin on sensitived fibroblasts might be taken as a crude analogue of the process by which clones with unwanted reactivity can be eliminated in the late embryonic period with the concomitant development of immune tolerance.

The hypothesis has many of the same implications as the Burnet-Fenner and the Jerne theories. Its chief advantage
over the former is its relevance to the nature of normal antibodies including the red cell isoagglutinins and the simpler interpretation of tolerance to potential antigens experienced in embryonic life. Its advantages over Jerne’s theory are its capacity to cover homograft and related types of immunity as well as the production of classical antibody, and to eliminate the very unlikely assumption that entry of a globulin molecule into a cell will stimulate the cell to produce exact replicas of that globulin.

Despite the speculative character of much of the detail of this modification of Jerne’s theory–which might be referred to as the “clonal selection hypothesis”–it has so many implications calling for experimental inquiry that it has been thought justifiable to submit this preliminary account for publication.

DOI:10.3322/canjclin.26.2.119

In Summary:

• Irun Cohen, an immunologist at the Weizmann Institute of Science, Israel, argued that the clonal selection paradigm is no longer a convenient paradigm for organizing thinking about the immune system
• He contended that most immunologists now investigate questions for which the clonal selection paradigm makes no provision and that one of its major tenets is contradicted by the prevalence of natural autoimmunity
• Cohen stated that the results of a diabetes drug trial served as a proof-of-concept in the controversy between contending theories regarding the basic organization of the immune system
• Cohen argued that the tenets of classic clonal selection are not compatible with the findings reported in the paper
• On the contrary, the success of the clinical trial of therapeutic peptide vaccination was compatible with the homunculus concept of autoimmunity, which states:
  1. The aim of the immune system is not to discriminate self from non-self, but to organize inflammation in a way that maintains, heals and, where possible, regenerates damaged cells and tissues; the healthy system is continuously responding to self.
  2. The healthy repertoire includes a high frequency of lymphocytes that recognize key self-antigens: the immunological homunculus.
  3. Autoimmune diseases arise from a failure of normal regulation, and the resulting diseases are predictably associated with collectives of particular self-antigens.
  4. The natural cure to autoimmune disease is to activate and reinstate the regulatory mechanisms built into the homunculus.
• Cohen argued that the immune system is a cognitive system
• In considering the role of autoimmunity in the economy of the body, he suggested that, “Progress in immunology appears to have rendered the clonal selection paradigm incomplete, if not obsolete; true it accounts for the importance of clonal activation, but it fails to encompass, require, or explain most of the subjects being studied by immunologists today …”.
• Polly Matzinger has gone even further: based upon her view that the “danger theory” has negated Burnet’s classical view of self-nonself discrimination, she extends this to suggest that the entire clonal selection paradigm that has ruled immunology for some 35 years has been overthrown
• In his book The Immune Self: Theory or Metaphor?, A. Tauber calls Burnet’s view of tolerance “…a cornerstone of his later immune theory [CST]”, and throughout appears to accept the various challenges to Burnet’s ideas on tolerance and self-nonself as challenges to the central meaning of CST
• Again, in their book The Generation of Diversity, S. Podolsky and A. Tauber discuss the several challenges to Burnet’s idea of self-nonself and conclude that, “Specifically, we must ponder whether CST, as constructed by Burnet, Talmage, and Lederberg [sic!8] … is now being seriously challenged”.
• Between 1930 and the early 1960s, the accepted explanation for the large repertoire of antibody specificities was that antigen somehow acts as a template to transfer information to the globulin-producing mechanism.
• This was termed an “instruction theory” and was advanced in different forms
• At a time when immunology was preoccupied with chemical approaches, and when little was known about how proteins are formed, these instruction theories seemed plausible
• No matter that they could not explain such observations as the persistence of antibody formation
• Niels Jerne suggested that the information for all antibody specificities is inherent in the host and expressed as “natural” antibodies
• Jerne’s idea attracted little support at the time; its surviving claim-to-fame lies in the fact that David Talmage and Macfarlane Burnet independently saw in its selectionist approach the seed of an interesting idea
• Arthur M. Silverstein, immunologist and historian, submitted questions CST must answer:
  1. If a “Landsteiner-size” repertoire arises spontaneously, what is the mechanism for its generation?
  2. If a repertoire is generated randomly and somatically, why are destructive autoantibodies not formed against native antigens to engender immediate autoimmune disease?
  3. Is there more than one type of receptor on a single cell?
  4. If somatic mutation persists after clonal expansion, how can clonal specificity be maintained?
  5. How can interaction of antigen with a surface antibody receptor induce cell proliferation and differentiation?
  6. What determines and regulates which clonal daughters differentiate to form antibody and which survive as memory cells?
• Any valid theory of antibody formation must satisfactorily explain these and other questions
• However, Silverstein suggested that the central theory need not fall just because its promulgator was wrong in proposing a mechanism to answer one of its subsidiary questions
• Some of these questions address the “selection” component of CST, whereas others deal with the “clonal” component; the former might survive the disproof of the latter
• CST has been challenged based upon Burnet’s error in explaining self-nonself discrimination
• In discussing the foundations of CST, Burnet admitted that if immunologists are correct in doubting that “tolerance is wholly a matter of the absence of the immunocyte … an extensive reorientation [of CST] will become necessary”.
• Burnet came close to giving up on CST in 1962, when reports came in of two and even four different antibody specificities produced by a single cell
• Given this wide-open theoretical terrain, it is no wonder that debate continues on such questions such as:
  1. A “big bang” versus the continuous generation of diversity
  2. The relative roles of central versus peripheral mechanisms of tolerance
  3. The number and type of signals required for one or the other response
  4. Whether autoimmunity is dangerous or beneficial (Cohen)
  5. Whether the immune apparatus evolved to recognize infectious pathogens
• In the end it is stated that we must not lose sight of the fact that the CST is only a theory of how antibodies are formed, not a theory of why they are formed

• According to Burnet, there were three (actually four yet Burnet excluded Ehrlich’s Side-chain theory for some reason) theoretical interpretations of antibody production:
  1. The direct template theory
     • The antigen serves as a template against which the specific pattern of the antibody is synthesized
  2. The indirect template theory
     • Postulates a secondary template incorporated into the genetic-synthetic processes of the antibody producing cells
  3. The natural selection theory
     • The antigen acts essentially by selection for excess production of natural antibody molecules of corresponding type
• The two latter theories were devised primarily to account for two sets of phenomena for which the direct template theory seems quite irrelevant:
  1. The first is the absence of immunological response to “self” constituents and the related phenomena of immunological tolerance
  2. The second is the evidence that antibody production can continue in the absence of antigen
• In Burnet’s own Indirect Template theory, a positive recognition of “self” material was ascribed to the presence of “self markers” in all potentially antigenic macromolecules, and corresponding recognition units in the scavenger cells of the body
• At the time it was regarded as inconceivable that a mechanism could exist which would recognise in positive fashion all foreign material and no attempt was made to devise one
• Burnet admitted that they always recognised the clumsy character of the self-marker, self-recognition scheme
• Burnet applauded Jerne’s Natural Selection hypothesis (odd he called it a hypothesis rather than a theory) as it provided an approach to this alternative method of recognising self from not self
• Jerne assumed that amongst the globulin molecules considered “natural antibodies,” there were all the possible patterns needed for specific immunological type reaction with any antigen, except for those patterns corresponding to body antigens which would be eliminated by in vivo absorption
• When a foreign antigen enters the blood it unites, according to Jerne’s scheme, with one of the corresponding natural antibody molecules
• Burnet pondered that if this basis is accepted, most immunological phenomena can be well described in terms of the theory
• However, its major objection is the absence of any precedent for, and the intrinsic unlikelihood of, the suggestion that a molecule of partially denatured antibody could stimulate a cell, into which it had been taken, to produce a series of replicas of the molecule
• Talmage suggested that Jerne’s view is basically an extension of Ehrlich’s side chain theory of antitoxin production and that it would be more satisfactory if the replicating elements essential to any such theory were cellular in character ab initio rather than extracellular protein which can replicate only when taken into an appropriate cell
• Talmage did not elaborate this point of view but clearly accepted it as the best basis for the future development of antibody theory
• He stressed the multiplicity of the globulin types that can be present in the blood and was profoundly sceptical of any approach which attempts to “unitarian” an interpretation of antibody
• In his view properdin had as much right to be called an antibody as any other globulin
• In other words, Talmage didn’t want the unseen antibody to be locked into a definite descriptive box and felt there were many globulin types which could be called antibodies
• Before receiving Talmage’s review, Burnet claimed he had adopted virtually the same approach but had developed it from what might be called a “clonal” point of view
• This was simply a recognition that the expendable cells of the body can be regarded as belonging to clones which have arisen as a result of somatic mutation or conceivably other inheritable changes
• Burnet believed that the advantages of Jerne’s theory (wait…is it a theory or a hypothesis…) could be retained and its difficulties overcome if the recognition of foreign pattern is ascribed to clones of lymphocytic cells and not to circulating natural antibody
• The plasma-globulins comprise a wide variety of individually patterned molecules and probably several types of physically distinct structure
• Amongst them are molecules with reactive sites which can correspond probably with varying degrees of precision to all, or virtually all, the antigenic determinants that occur in biological material other than that characteristic of the body itself
• Each type of pattern is a specific product of a clone of mesenchymal cells and it is the essence of the hypothesis that each cell automatically has available on its surface representative reactive sites equivalent to those of the globulin they produce
• It was assumed that when an antigen enters the blood or tissue fluids it will attach to the surface of any lymphocyte carrying reactive sites which correspond to one of its antigenic determinants
• It was postulated (i.e. suggest or assume the existence, fact, or truth of something as a basis for reasoning, discussion, or belief) that when antigen-natural antibody contact takes place on the surface of a lymphocyte the cell is activated to settle in an appropriate tissue, spleen, lymph node or local inflammatory accumulation, and there undergo proliferation to produce a variety of descendants
• Such a point of view was basically an attempt to apply the concept of population genetics to the clones of mesenchymal cells within the body
• It was clear that the internal environment involved is an exceedingly complex one and in all probability many factors will impinge on clones of antibody-producing cells from that environment
• Burnet felt that it would be inappropriate to elaborate this view much further in a preliminary communication
• A preliminary survey of a variety of pathological conditions which involve anomalous immune reactions suggested that this cellular approach has greater relevance to the problems than any of the other hypotheses (back to hypotheses instead of theories again)
• Burnet stated that his theory required at some stage in early embryonic development a genetic process for which there is no available precedent
• He claimed that they have to, in some way, picture a “randomization” of the coding responsible for part of the specification of gamma globulin molecules, so that after several cell generations in early mesenchymal cells there are specifications in the genomes for virtually every variant that can exist as a gamma globulin molecule
• In other words, one must use ones imagination in order for this “theory” to work
• Burnet claimed that the hypothesis had many of the same implications as the Burnet-Fenner and the Jerne theories (it seems one can switch between hypothesis and theory interchangeably)
• Burnet stated that its chief advantage over his former theory is its relevance to the nature of normal antibodies including the red cell isoagglutinins and the simpler interpretation of tolerance to potential antigens experienced in embryonic life
• Its advantages over Jerne’s theory are its capacity to cover homograft and related types of immunity as well as the production of classical antibody, and to eliminate the very unlikely assumption that entry of a globulin molecule into a cell will stimulate the cell to produce exact replicas of that globulin
• Due to the speculative character of much of the detail of his modification of Jerne’s theory– Burnet referred to his latest as the “clonal selection hypothesis”

In 2007, Arthur M. Silverstein participated with a few other esteemed immunologists in reflecting back on the 50 year impact of the Clonal Selection “theory.” In it, he explained some of the opposition to CST and offered an ominous warning for what had to occur in order for the speculative hypothesis masquerading as a theory to be universally accepted by the immunology community:

Reflections on the clonal-selection theory

“There were two types of opposition to the CST, one early and continued, and the other of more recent vintage. The first was the resistance to this biological theory on the part of the chemically oriented immunologists who had introduced and believed in the instructionist theories of antibody formation that the CST replaced. Many of these immunologists chose to disregard the CST, continuing their physico-chemical studies of antibody and antigen (such as David Pressman, a student of Linus Pauling). Others sought to disprove it (such as Dan Campbell, also a Pauling student, who searched for persisting antigen, and Alain Bussard, who wrote a highly entertaining philosophical challenge to the CST). Some (like Elvin Kabat and Fred Karush) made peace with it. The rest (like Haurowitz and Bussard) never gave in. It was ever thus, as Thomas Kuhn pointed out that the full acceptance of a radically new paradigm occurs only when believers in the old one die out!”

doi: 10.1038/nri2177

According to Silverstein, in order for Frank MacFarlane Burnet’s 1957 Clonal Selection to be universally accepted, the old guard opposing it needs to die out. For whatever reason, Burnet’s storytelling happened to be the last one standing in a long line of theories about the formation and function of antibodies, even though it is still being challenged today. However, calling any of the proposed explanations which came before or after a scientific theory is completely unjustified as not a single one ever used evidence built from the scientific method. In no instance was any natural phenoma ever observed. Combining human and animal blood with various substances in a lab is not a natural phenoma and claiming the resulting effect has significance as to what occurs inside the human body is beyond ridiculous. At no point was a valid independent variable of purified and isolated particles assumed to be antibodies ever observed in order to determine cause and effect nor the form and function of the theorized entities. The idea of antibodies existed first in order to attempt to explain the lab-created effects. Without the direct evidence of these particles in the blood of humans, all of the hypotheses and all of the experimental data used to devise the competing theories amount to nothing but unscientific pseudoscience propping up the imagination of the interpretor. The resulting theories are fictional narratives explaining fictional entities.

If these theories are identified for what they truly are, which is an accumulation of guesswork, hunches, assumptions, and suppositions cobbled together into a fantastical narrative, there would be no problem. If people need to believe in invisible entities belonging to the realm of the imagination in order to have an explanation to justify their belief in a perceived immunity from invading boogeymen, so be it. The problems arise when these exercises in creative writing are presented as the truth rather than the science fiction that they most certainly are. When these stories are used to promote dangerous medical treatments and to determine one either free of or infected with a “deadly pathogen,” that is where the line needs to be drawn. We can not allow the wool to be pulled over our eyes any longer while pseudoscience is being presented as science and fiction is presented as truth. It is far past time to sound the alarm and shine the spotlight on these fraudulent practices before the narrative solidifies further as the truth in the minds of our youth.