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Evolution - Combinations

Combinatorial changes

Recombination of existing designs can be an efficient way to explore new designs. It is an effective evolutionary strategy. There are a number of interesting elaborations of the basic strategy in nature.
  • LIFO Plasmids - Plasmids are small loops of DNA that help to recombine designs in bacteria.
  • Recombination Advantages - Recombination of existing units has several advantages over evolving new units.
  • Dominance - In computer models, variations in the dominance of genes can promote spread of beneficial genes.
  • Nematodes - These organisms show that in an unstable environment the rate of change and recombination can be increased.
  • Gene fusion - There seem to be streamlined mechanisms for formation of new proteins from components of old ones.

Index3.2 Combinatorial Change

LIFO Plasmids

Even 'asexual' bacteria recombine designs. Small circular DNA elements called plasmids carry extrachromosomal information which can migrate even between different species of bacteria and which on occasion can integrate into the genome.

Plasmids can carry such properties as resistance to Penicillin.

These plasmids obey an interesting Last-In-First-Out (LIFO) rule. A sick cell may eject plasmids - it makes evolutionary sense to eject the most recently acquired ones first.

Index3.2 Combinatorial Change

3.2.2 Recombination Advantages

Recombination of working designs as in sexual reproduction has advantages from many perspectives:
  1. It increases 'variance' in designs without decreasing the average quality. This is an advantage because the 'best' designs will be better than in a lower variance population.
  2. It makes possible efficient error correction - for the chances of both parents having the same damaged genes is low.
  3. It allows new designs to be tried out in parallel rather than in serial. In an asexual population if two different individuals have useful innovations no descendant will end up with both.
  4. In diploid or polyploid organisms, the recombination process if coupled with additional copies of the genes during life. This allows for safer experimentation with changes in genes, for a functional gene can often to some extent compensate for a defective one.

Index3.2 Combinatorial Change

3.2.3 Dominance

If one is writing software that uses a 'genetic algorithm' optimisation technique, recombination is demonstrably a useful property to add. It is also worth considering whether 'dominance' of genes is useful.

It is possible to devise relatively simple rules for dominance that have the indirect effect that damaging genes tend to become recessive and beneficial ones tend to become dominant. Put more provocatively, with the right mechanism, a genome would evolve to put 'dominance' on its best characteristics.

The model that shows the advantages of dominance is closely analogous to the model for variable variability. In each case the models work because genomes which make 'the wrong' choices about their meta genes do less well.

Index3.2 Combinatorial Change

3.2.4 Nematodes

Nematodes (C.Elegans) provide an interesting hybrid between sexual and asexual reproduction.

Nematodes are hermaphrodite and normally self fertilising. However when conditions change or when there is damage due to ionising radiation, an increased percentage of nematodes lose their female characteristics and are male. They behave differently and fertilise other nematodes. This means that in response to damage a greater use of the genetic repair mechanism is made; also in response to change, changes in the genome are explored more rapidly.

Index3.2 Combinatorial Change

3.2.5 Gene fusion

Recombination of designs is also evident at the level of proteins.

Proteins are made up from 'domains' which can often be found in different combinations in other proteins. It seems that there are mechanisms that promote distinct units that work closely together being brought together, possibly eventually becoming one protein.

In single cell organisms genes needed at much the same time are close on the genome. Two genes may even share the same promoter.

In higher organisms the existence of introns (non coding regions between domain like sections of proteins) point to the importance of mechanisms that rearrange the functional units from which proteins are constructed.

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"Evolution - Combinations" page last updated 5-July-2003