Knockout CA

The CA on the left (Wild type) has two tails. At t = 2 the CA  was injured, and the tail structure changed (Mutant).

The experiment illustrates some elementary concepts of molecular biology. In the  image below the CA head is magnified. The third row belongs to  a  DNA molecule which extends to both sides of the CA.. The DNA code consists of three letters (A, T, G). A similar arrangement was described before. The code describes the DNA molecule in the third row. {white, white, gray, white, gray, white, white} = {A,A,T,A,T,A,A}.

The wild type  DNA consists of two genes represented by two gray squares. (T = 1).  In the mutant CA the left gene was knocked off . Despite this, both  CA remain somewhat similar. In order to depict their difference, mutant-CA was subtracted from the wild type.  Apparently the left border is more disturbed than the right.

The knockout  technique is an important  tool for studying gene function. The idea seems straight forward.  You destroy a gene and examine the animal (phenotype) for missing functions. These were exerted by the particular gene before its destruction. Unfortunately in most (if not all) experiments,  this logic fails.  It presumes that there exists a simple mapping from genotype to phenotype. Yet the mapping is non linear and extremely complex, since gene function depends on the context in which it exists.

Each CA-state represents such a context and the effect of the knocked off gene varies from state to state. Obviously there is no simple (linear) mapping between the missing gene and the different CA states. The effect of a gene is propagated from state to state in an unpredictable fashion.

Suppressor gene

The experiment illustrates how molecular biology conceives cancer formation. The two (T =1), genes might be two alleles. When both exist, the CA has two normal tails. When one is missing, one tail becomes a tumor. A mutation or loss of a single allele  ends  in a tumor. Since tumor appears when one allele is missing, it appears as if the allele suppresses its formation,, and is called  suppressor gene.  However since  a simple linear mapping between gene and phenotype does not exist, such a logic is wrong. The  missing gene or allele  does not suppress a pathology,  rather it induces a now situation, which is neither normal or abnormal (more on the normal v. Chapter   29

injurytime =2; injuryrange = 2; preva[[1]] = a[[1]]; effect[1, 1, 25];

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