by Royal Truman

Abstract—Avida is a computer software platform designed to test neo-Darwinian scenarios including speciation, evolution of novel complex functions, and genetic drift. A large number of parameter settings are available to the researcher. We evaluate here published tests and intrinsic Avida characteristics in an attempt to extrapolate towards real biological organisms. Computer based models and simulations must capture enough realism to facilitate valid decisions. Neglect of key factors or unrealistic parameter settings permit conclusions to be claimed which merely reflect what the decision maker intended a priori.

The long-term effect on genetic systems of random insertions, deletions and point mutations over deep time may be degradation of function and specificity; or the generation of true biological novelty. Competing factors are involved and only detailed quantitative analysis with real world experiments can firm up our opinions in this matter. In Part 1 we examine some of these issues and in Part 2 explore some more quantitative details based on Avida runs.

It was found in this two part series that reports which demonstrate rapid increase in complex, genetically coded novel functions are an artefact intrinsic to how the Avida computer runs are planned and some neglected details constraints found in nature.

Using biologically realistic parameter settings and including neglected factors led to the opposite view, both theoretically and when using Avida experiments. Mutations plus natural selection in rapidly reproducing, asexual, small genomes fails to explain the original of ever increasing cellular functionality, including molecular machines.

Note: The figures and tables from Part 2 of this paper are not embedded in the text. Rather, there is an individual link to each figure and table at the bottom of this page.

Part one of the paper is available below:
Evaluation of neo-Darwinian Theory with Avida Simulations: Part 1

Part two of the paper is available below:
Evaluation of neo-Darwinian Theory with Avida Simulations: Part 2

Figures for Part 2

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

Figure 7

Figure 8

Figure 9

Figure 10

Figure 11

Figure 12

Figure 13

Figure 14

Tables for Part 2

Table 1

Table 2

Table 3

Table 4

Table 5

Table 6

Table 7

Table 8

Table 9

Table 10

Table 11

Table 12

Table 13