head of Tyrannosaurus Rex

Does the information always increase in Ev runs?

INTRODUCTION

Richard Wein asked:

"I would like to know roughly what proportion of the time your program ... produces a high-information result. I would guess it's every time, but I'd be grateful if you would confirm that please."

MATERIALS AND METHODS

The cleanest way to test this is to use the standard example from the ev paper. According to my notes in the ev program documentation 'see also' section, this is the "Parameter file for selective phase in the paper: evp.selection".

I want to look further out than 1000 generations, so I set the parameters to run to 2000 generations where things should have stabilized. Then I ran the evp program changing the random seed from 0.00 to 0.99.

RESULTS

CONCLUSION

The ev program was run repeatedly to 2000 generations starting with 100 different random seeds. The lowest observed final information content was 2.3 bits and the highest was 5.2 bits, with a mean of 3.8 +/- 0.5 bits. Duplicate runs occured 7% of the time. These duplicates do not affect any conclusions, but they do suggest that the random number generator is not the best. Despite this, the program invariably gave a significant information increase. From the observed values, we can determine that the probability of a return to zero information is 1.5 x 10-14 (7.6 standard deviations).

2003 July 7

Are the Logos Different in Different Runs?

Pim van Meurs asked:
... even with the same initial conditions for the genome, the final evolved binding sites/recognizers will vary?
Yes, the sites and their recognizer are different. For every point in the graph above, I captured the corresponding logos

color bar Small icon for Theory of Molecular Machines: physics,
chemistry, biology, molecular biology, evolutionary theory,
genetic engineering, sequence logos, information theory,
electrical engineering, thermodynamics, statistical
mechanics, hypersphere packing, gumball machines, Maxwell's
Daemon, limits of computers


Schneider Lab

origin: 2002 February 22
updated: 2003 July 7
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