Making Sense of AvidaAn attempted gentle introduction to Avida

Bio 481 (Joshua Nahum)

An Avidian

• Self-executing, self-replicating genome– Composed of simple

computer instructions

– Can interact with environment by consuming and producing numbers

– The NAND Instruction

nandnop-BIOnand

1 0 0 11 0 1 1

1 1 0 1

input (food)

output (useful products)

genome

Quick Digression (Logic Functions)

• Logic functions are the operations that can be performed on binary numbers, and yield another binary number.

• Each function can be described by a truth table.

InputA 1 1 0 1 0 0 1

InputB 0 1 0 1 1 0 0

Output 1 0 1 0 1 1 1

Nand Logic

• All other logic functions can be composed solely of connected NAND functions.

• Their complexity is measured by the number of NANDs required.

Input A Output

0 1

1 0

NOT (1 NAND needed)

Multiple NANDs

OR 3 NANDs

EQUAL (5 NANDs)

NOR (4 NANDs)

Adami Nature Reviews Genetics 7, 109–118 (February 2006) | doi:10.1038/nrg1771

Avidian Anatomy

Avidian Physiology • By saving numbers to its memory, and performing

various combination of instructions, an Avidian can output the result of a logic function

• Beneath is the map of the processing of numbers that yields 5 different logic functions.

But why?• Avidian’s fitness is its merit

(aka metabolic rate) divided by its gestation length.

• Two ways to improve fitness• Decrease gestation time

• (less instructions needed to replicate)

• Increase merit• Performing a logic function

can yield merit.• Only if the resource (eg

Notose) is rewarded in the environment.

FitnessMerit

Gestation Length