Re: [asa] PSCF article on immune system

From: Bill Powers <wjp@swcp.com>
Date: Fri Dec 04 2009 - 16:58:35 EST

Don:

Either the system isn't as wonderful as I would like to believe, or what
you say is inadequate.

If, as you say, there are really "many" adequate antibodies for any
given pathogen, then there aren't really 10^10 possible "solutions."
What this suggests is that the number of real defensive antibodies is
significantly lower than 10^10. In this case, random search methods can
be adequate, given the time required for finding the "solution." But if
this is the case, do we really need the variety provided by the random
aspect of the process.

It seems to me more likely that, while there may be many adequate
antibodies for a given pathogen, this number is not large (e.g, say on
the order of 100). I suggest this is the case because otherwise I fear
that antibodies will not be able to keep up with pathogen mutation and
variety. What I think is happening (and hope also) is that B cells
are a kind of mutational factory. In order to keep up with natural
mutation the speed of this mutational factory (dare I say designed
machine) must be significantly more rapid than the rate of natural
mutation. This is so not only to handle the rate of individual
mutation, but also with the rates represented by the great host of all
pathogens. It seems that this is possible by a frequent sampling of the
pathogen environment, keeping a library of antibody experience. Under
the assumption that pathogen mutation will be "incremental," the saved
library will serve as starting points in the random, but small changes
made in the library of antibodies. This library serves as a history of
pathogen contact. I would expect that there would be at least two
search methods. One, the incremental search suggested above, but also
another that searches more widely and randomly over the antibody space
of possibilities.

bill

On Sat, 5 Dec 2009, Don Nield wrote:

> Bill Powers wrote:
>> I have read the recent article by Craig Story on immunology, and I have a
>> few comments.
>>
>> 1) The main thrust of the piece is to persuade us that "random" processes
>> are essential in the vital functioning of the creation of antibodies. There
>> are, he says, some 10^10 different antibody formations possible. This vast
>> number of possibilities is accomplished with from only about 500 gene
>> segments. It is possible to generate such a large number of possibilities
>> from so small a number of gene segments because the joining of these
>> segments is imprecise and influenced by random processes.
>>
>> In this way Craig wants us to understand what a marvelous chemical machine
>> is the antibody mechanism, and the essential necessary use of randomness to
>> protect from a wide host of unseen pathogens.
>>
>> So here is my question, one Craig devotes very little time to, since it is
>> not the primary focus of the article.
>>
>> With 10^10 possible antibodies, it would seem impossible for a random
>> system to work. We would all die long before the appropriate antibodies
>> were found in this haystack. This means that, while randomness may very
>> well be a crucial part of the system, it cannot be the central governing
>> process.
>>
>>
> This is not a problem. One does not need the absolute optimum over the 10^10
> possibilities. Anything that works sufficiently well will do. Thus
> optimizing over a reasonably large subset of the possibilities is useful.
> Don
>
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Received on Fri Dec 4 16:59:12 2009

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