In evolutionary informatics, two paramaters are needed for evolutionary algorithms. Heritability and Selection.

Heritability implies the following:

1) "Parents" give rise to "offspring".
2) Traits from "parents" are passed on to "offspring".
3) Each "offspring" from a "parent" signifies a new generation.
4) Variation between generations may or may not occur.

Selection implies that certain traits that are not on a fitness landscape will not be selected.

Let's look at Autodock as an example and how it relates to evolutionary informatics.

Read the rest of this entry »

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.

The quantum teleportation experiments have demonstrated that information can be viewed as a fundamental irreducible property of physics (informationalism). Systems biology is moving in that same direction, as viewing cells as computers with machinery and software makes it possible to view information as a fundamental category of nature and all future developments of systems biology can include this concept when looking at cells.

There are many interesting passages in this article. A few of these are going to be highlighted for discussion.

Read the rest of this entry »