# Introduction to Non-Genetic Darwinism/Immune System Darwinism
## Immune System Darwinism
### Aims

* To Introduce information on the Nature of the Immune System
* To Explain How the Immune System works
* To Underscore the Problems the Immune system has to overcome
* To Introduce Dr. Edelman's Contribution

## Lesson
### Over view of the Immune System

The Immune system is the way a multi-cellular animal
* becomes aware that it has been invaded by pathogens
* Marshals resources to fight the invading pathogens
* Remembers most pathogens so that their invasion again is dealt with faster the second time.

#### The problem of Identifying Pathogens

The body is full of chemicals in many different states in the process of forming reactions. Some of these chemicals are benign and some are toxic to the body. Some of these chemicals are parts of invading organisms or viruses, which will attempt to colonize the body, in their own search for survival. The immune system must somehow detect which chemicals are benign, and which are toxic, which belong to its own body, and which come from some other organism, and get it right enough that most of the time, the organism will be able to fight off toxins and invaders.
This problem can be broken down into two parts, recognition of alien chemicals, that are not part of the body, and recognition of benign chemicals that are, or at least could be part of the body, or used by the body, in some way.

##### Creating Antibodies

One way that body recognizes pathogens, is to attach specialized proteins called anti-bodies to the invading pathogens, and not attach them to the benign chemicals. But first, the body needs to know which are which.

##### Propagation of antibodies

Once a pathogen has been discovered the next step, is to propagate the antibodies for that pathogen, so that all the instances of the pathogen get tagged. Special helper cells called lymphocytes, detect active anti-bodies and reproduce them. Populating the blood system with more copies of the antibodies.

##### Activating Cell Defenses

Once the body knows which pathogens are alien, and therefore might be harmful to the body, it can marshal it's defenses at the cellular level, and deal with the pathogens. Methods of dealing with pathogens include absorbing them within disposable cells, ejecting them out of affected cells, so that they can be absorbed within a disposable cell, and if they can't be ejected, killing off the cell, which they have invaded, so that it can't spread them.

##### Killer Cells

One type of cell for instance, called a T cell, can inject a cellular poison into a cell, in essence killing it, so that it can be removed from the body, it's pathogens included. One reason that AIDS is so deadly, is because it infects these killer cells, so that they spread the infection instead of killing the infected cells.

#### The problem of Identifying the Self

If the body is full of benign chemicals and pathogens sometimes contain or produce benign chemicals as well as toxins, then identifying the pathogen, means that we also have to identify the body, and the benign chemicals so that we can keep from creating antibodies to parts of our body, and thus killing our own body instead of the pathogen. Pathogens being evolved themselves, have sometimes learned to camoflauge themselves as parts of the body, thus limiting the effect of the immune system. One reason why AIDS is so hard to build a vaccine for, is that it has developed a strategy of sloppy copying of the DNA that encodes for its surface chemicals so that instead of having to detect one strain of AIDS, the body has to detect hundreds some of which mimic benign chemicals at the same location that others have their identifiable pathogenic chemicals.

##### The Major Histocompatibility Complex

With invaders that are cellular in nature, the body has developed a security badge called the Major Histocompatibility Complex that is different for every body. Any cell that has a different MHC might be an invader, and thus should be isolated and killed. It is for this reason that organ transplants often involve the injection of immune depressant chemicals. The chemicals keep the bodies immune system from attacking the new organ until it is recognized as being part of the body.

##### The Spleen

An organ that is very important to the immune system is the spleen, where antibodies are tested against the templates for benign chemicals, and removed from the blood when they are found to attach to the wrong template. An interesting aspect of the immune system is that the body has to learn to recognize its own benign nature, and as a result the immune system is not fully in place until about 2 to 3 years after the birth of a human baby for instance. Partly this is to keep the baby from reacting to it's mothers cells which pass to it through the placenta, and mothers milk, and partly this is because the spleen takes a while to grow. Some people are against the injection of vaccines early in the life of the baby, because it is thought that if the injection comes before the baby's immune system is ready for it, pathogens might be incorporated in the self-image the immunne system has of the body, or alternately, the premature activation of the immune system might affect growth factors needed for the baby to fully develop. The spleen in known for its higher concentration of B type helper cells.

##### Auto-Immune Diseases

There are two types of immune diseases, diseases where the immune system mistakes a benign chemical for a pathogen and creates antibodies to it, thus attacking the body, or some chemical needed for its health, and diseases where the immune system fails to recognize a pathogen, and therefore does not create antibodies that marshal the defenses of the body against it. Most illness involving an infection involves either this, or a disease that propagates faster then the defenses can be activated and thus colonizes the body, despite the immune system.

#### The Nobel Prize and the Natural Selection of Antibodies

The reason Dr. Edelman received the Nobel prize, was for his work in understanding antibody structure, which indicated that certain theories of antibody generation were more likely. What he revealed was a pattern of behavior that defined a Darwinistic system that generated antibodies by propagating anitbodies that were most likely to be related to pathogens and suppressed the generation of antibodies that were most likely to be related to benign chemicals.
This system depended on the competition among lymphocytes for the chance to attach to the pathogen, and thus trigger lymphocyte reproduction. Since each lymphocyte had a different combination of antibodies, the lymphocyte that won, would clone the active antibodies increasing the population of that type of antibody.
It is important to realize that while we are talking about a system of natural selection, it works by reproduction of antibodies not by reproduction of cells even though the cloning is done at the cellular level and involves the growth of new cells.

## Assignment

* Does Anti-body Selection involve GENES? Write a short essay on what you think
* If Anti-body Selection does not involve GENES, what is the "Selection" mechanism by which one generation of antibodies is different from the next? Does this actually result in a form of Natural Selection that could be called Darwinism?
* Why do you think that the immune system attacks pancreatic cells in Diabetes patients? Would drinking formula based on Cows milk be a possible problem? Or weaning from expensive formula to inexpensive Cows milk too early? Would Soyabean products cause the same effect?
* Some diseases like Tuberculosis encyst themselves in inert materials. Why would this make immune reaction to them difficult?
* Why do you think that some auto-immune diseases are thought to be the result of pathogens that mimic benign chemicals? Does this suggest that the spleen might be ineffective sometimes? or does it suggest when in the life of the organism it became infected with the disease?
* Which do you think would be more effective at killing and managing disease, chemicals like penicillin that kill off germs, or an immune system that can react to a wider range of pathogens?
* Which do you think would be more effective at stopping a major infection involving a germ? An immune system or the right antibiotic? Why?
* Allergies are thought to be an immune disease that reacts to toxins in the blood. What possible reason would the body have for flooding the surface of the nose with mucus? Dripping mucus down the back of the throat? Causing the inside surface of the lungs to swell? Causing a rash? making pimples? causing the surface of the skin to swell? Making the skin itch? Causing you to sneeze?
Are these valid immune reactions? Does taking antihistamines increase or decrease the chance that you will get sick? Or does it depend on why you are reacting?
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