Very cool. I have dreamed of building something similar. I would be interested in these modifications:

1. Change living/non-living distinction of food to two different dimensions, shared by living and non living food alike: * Composition - arbitrary bits to match against a consuming organism's diet * Defense - arbitrary bits to match against consuming organism's capabilities, might be a function of energy level for living food

2. Organisms leave behind waste as part of eating and/or moving. Waste left behind is food for other organisms

This might allow for the rise of symbiosis and multicellular organisms