This website shows how a good understanding of the design principles that underly Life is crucial in understanding its Evolution. It gives concrete examples how designs can be applied to Evolution in the same way an engineer uses designs in creating an architecture, or a software engineer designs programs that can evolve. If we apply the notion of a design for Evolution and see that it is in its basis an evolving system of molecular machines, we can start to reverse engineer Evolution. This website shows scenario's for the origin of Life, the eukaryotic cell and evolution to multicellular organisms.
The scenarios that can be deduced following a design framework are drastically different from the theories that have been proposed so far. The design framework and the resulting new insight in the path of evolution can therefore present a new set of paradigms for new evolutionary theories.
Evolution can be modeled on a design framework
The design framework on which the new theory was built can be best described using the design-by-contract methodology from software development. It represents an object-oriented programming where systems can expand as long as existing interfaces must remain intact. Such a system can only expand by refining existing interfaces and implementing new interfaces. Dependencies in the system on interfaces prevents modification of functionality and lead to legacy systems. From the dependencies in the system, one can deduce the evolution of the system.
Life evolved inside-out
It proposes that the first entity of Life was the replicating of DNA, representing also the first life cycle. This replicating (cycling) DNA that started to produce ribozymes including ribosomes subunits and later proteins organized in a nucleolus. The nucleosus wrapped itself in a protein matrix and was surrounded by the nuclear lamina. On this nuclear lamina, the nuclear envelope evolved giving rise to the nucleus as the first cell. Outside of the nucleus, again a protein matrix, the cytoskeleton was formed onto which an additional membrane fused, the plasma membrane.
Ontology reflects phylogeny
The eukaryote cell acquired the capability to fuse with another cell which duplicated its DNA content, resulting in a life cycle that contained both a haploid and a diploid stage. In higher eukaryotes multicellularity evolves in the diploid stage by a progressive mitosis of the fertilized egg and a postponement of the sexual maturity of the germ cells. Early decisions in egg division decide the fate map of the mature organism and represent strong branching point in evolution. Overall, evolution is seen as the addition over time of extra functionality on top of the original life cycle of replicating DNA.