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We've known for a long time now how to "add a new entry to the database," as it were, of immune responses. It's called vaccination, and it's been one of the greatest success stories in the history of medicine.

And yet, allergies and autoimmune disorders, both caused by an immune system gone rogue, are still serious problems today. If it's so easy to add a new immune response, why don't we have any way of deleting one?

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It is an interesting question. The reason for why new immune responses can be launched but the memory of old ones are not deleted is based on the concept of irreversibility of certain chemical reactions.

Launching an immune response involves clonal expansion of cells expressing the epitope sensors such as the immunoglobins and T-cell receptors, accompanied by maturation of these receptors. Some of the reactions involved in this process are irreversible, which include VDJ recombinations, class switching and affinity maturation.

In an overall sense, immune response is analogous to natural selection- in the presence of the antigen the best binders are selected and expanded. Now to make a species extinct you would have to find each individual and kill it. Or you may have to develop a technology that will identify and kill a certain species in an automated manner. This is difficult to implement; how to engineer a mechanism that will precisely seek and destroy all the epitope sensors for a particular antigen. In contrast selection happens spontaneously because it does not proceed with a reason. It just selects the best from available stock.

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Too long for a comment: Because we don't know how to do this. The immune system is an extremely complex and highly regulated function of the human body and it is not easy to shut down single pieces of it without affecting the whole rest. We can completely block immune responses (more or less), which is beneficial for people who got a transplant. These people couldn't survive without this intervention, since their immune system would otherwise turn against their transplant.

The downside for them is, that they are more likely to get severe infections. A friend of mine, which got a kidney transplanted has to be very careful to not get pneumonia, since his immune system can barely fight this.

The other problem with fighting of these immune responses is that they are widely distributed. Lets take allergies as an example: Here you make antibodies which are highly specific for the antigen. This means that you make relative short living plasma cells which actively make large amounts of this antibody and long living memory cells which keep this memory alive. The later are then homing into the bone marrow and wait for another exposure to make them proliferating into more plasma cells and a few memory cells again. This process works for every antigen for which we acquire immunity, including vaccinations.

How should we selectively delete one subgroup of memory cells from the bone marrow without affecting all others? How do we find all versions (one protein, which causes an immune reaction has a lot more than one antigenic peptides) of it? And what else do we mess up, when we try to do so?

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