From: Mathias Ganter (mganter@u.washington.edu)
Date: Tue Nov 30 2004 - 23:05:17 PST
Authors and Title
Richard E. Lenski, Charles Ofria, Robert T. Pennock, Christoph Adami: The
evolutionary origin of complex features. Nature 423, 139 - 144 (08 May
2003); doi:10.1038/nature01568
<http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v423/n6936/
abs/nature01568_fs.html>
http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v423/n6936/a
bs/nature01568_fs.html
Remarks
As the title suggests this paper by Lenski et al. simulates the evolution of
higher organisms from rudimentary ones by the implementation of an
artificial digital life form that is able to mutate, replicate and compete
thus following the Darwinian evolution, i.e. natural selection and survival
of the fittest. The whole digital life is built on computer programs that
have the ability to perform complex logic functions each of which can be
used to gain energy.
The main two subjects of this article are mutations and selection of
superior life forms of digital life.
Mutations can have various effects (beneficial, neutral, and deleterious).
Forms of mutations are point mutations, deletions and insertions. They can
cause damage in the short term, but on the other hand they can ultimately
become a positive force in the genealogy of a complex organism. The
complexity results from simplicity, i.e. simple components may yield to more
extensive ones by the modification existing structures and functions (while
some are more important than others; in nature, functions can often be
derived from structure - protein structure predictions to answer functional
questions). They also mention that the development from simple to more
complex functions is only possible by using a pre-assigned reward simulating
Darwinian evolution.
They also mention that various different mutations can result in various
solutions for a specific problem, although they represent a different path
to the goal.
A great advantage of this digital life implementation compared to real
evolutionary studies with missing links is the fact that the whole
evolutionary process including all intermediate states can be analyzed
easily: replication efficiency and computational merit. There is no lack of
missing links which makes the analysis easier than using various coalescent
programs inferring about a whole bunch of unknown parameters like mutation
rate, branch length, effective population size,.
There is not a real independent evolutionary process because of the fixed
rewards in form of computational merits.
In addition, the outcome of the experiment is clearly pre-assigned in form
of the logical function with the highest reward- in nature, nothing is
pre-assigned. Are these rewards reasonable or is this prior knowledge biased
towards the outcome they want.
Furthermore, the experiment does not represent a higher organism because one
considers asexual replication, a fixed population size and no recombination
or migration.
Their studies could be extended by
- having a population with a varying size,
- taking several populations into account with migration events,
- dropping the idea of asexual reproduction and replacing it by sexual
replication,
- assigning different rewards,
- starting with a different set of functions,
- taking different, more complex logical functions into account.
This problem can be considered as a search problem because one searches for
the optimal solution in a finite state space (the number of all possible
genome sequences). It uses a heuristic in form of the rewards.
It can also be considered as a more or less random walk in a finite state
space finding the most promising individuals (highest fitness) where each
individual only depends on its direct ancestor (Markov chain).
This archive was generated by hypermail 2.1.6 : Tue Nov 30 2004 - 23:05:25 PST