Basically what these guys did was metaprogramming whereby they developed a computer program (the original robots) that output (randomly "mated" and mutated in this case) other programs (the liar bots).
The art of metaprogramming, Part 1
The art of metaprogramming, Part 2
The art of metaprogramming, Part 3
Funnily enough, the immune system is also a metaprogramming system.
Antibody diversification is crucial in limiting the frequency of environmentally acquired infections and thereby increasing the fitness of the organism. Antibody diversification is achieved by assembling variable (V), diversity (D) and joining (J) gene segments (
V(D)J recombination) by
non-homologous recombination. Further diversification is carried out by somatic hypermutation (
SHM) and
Class Switch Recombination.
So why is it a metaprogramming system?
Well the system is composed of a code and the code has the information for the antibodies. Above that system (the metaprogramming system), is a system that constantly changes the code of the system that produces the antibodies.
How is this carried out...
Cytosine deamination through the cytosine deaminase (AID) protein
AID deaminates cytosine to uracil in single stranded DNA (ssDNA - arising during gene transcription) and is dependent on active gene transcription of the various antibody genes. The induced mutation is resolved by at least 4 pathways (Figure 1):
1) Copying of the base by high-fidelity polymerases during DNA replication.
2) Short-Patch Base Excision Repair (SP-BER) by uracil-DNA glycosylase removal and subsequent repair of the base.
3) Long-Patch Base Excision Repair (LP-BER)
4) Mismatch repair (MMR)
Link to big picture
Figure 1: Activation induced cytosine deamination and the pathways involved in resolving the induced mutation.
1) Normal DNA replication results in a C:G→T:A transition.
2) Successful SP-BER resolves the mutation, however the recruitment of error-prone translesion polymerases results (e.g. REV1) in transversions (REV1; C:G→G:C) and transition.
3) LP-BER can also resolve the mutation, however recruitment of low-fidelity polymerases (e.g. Pol n) also causes transition and transversion mutations.
4) MMR repair can also resolve the mutation, however the recruitment of low-fidelity polymerases through this pathway is a major cause of A:T transitions.
AID causes somatic hypermutation and its activity is limited to the certain genetic regions of the immune system. These induced mutations in turn changes the code that codes for the antibodies. The system is controlled (Figure 2). The activity and gene expression of AID is controlled. The type of error-repair pathway and the subsequent recruitment of various low-fidelity polymerases determine the type of mutations after the repair process and these also seem to be controlled. Current research focuses on the mechanisms of control of downstream repair pathways and why this system is selectively targeted to the small region of antibody genes.
Figure 2: Controlled variability of somatic hypermutation.
But it gets even more interesting. The genetic code is optimal for cytosine deamination in so many ways and actually facilitates the evolution of the immune system. See
here.
E.g.
1) Cytosine deamination does not result in stop codon formation.
2) The code is highly optimal for encoding arbitrary additional information, i.e., information other than the amino acid sequence in protein-coding sequences.
References:
Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF et al. The biochemistry of somatic hypermutation. Annu Rev Immunol. 2008;26:481-511.
Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20.
Goodman MF, Scharff MD, Romesberg FE. Abstract AID-initiated purposeful mutations in immunoglobulin genes. Adv Immunol. 2007;94:127-55.
Basu U, Chaudhuri J, Phan RT, Datta A, Alt FW. Regulation of activation induced deaminase via phosphorylation. Adv Exp Med Biol. 2007;596:129-37