higher-level fitness function

[cameronraysmith]

The inverse 2-norm of the distance from the vector of 1s to the sum of individual genomes within a community implemented by

# biofilm.jl
s = reduce((x,y)->x+y, map(x->x.genome, cells))
s = 1./norm(s-0.99)

is degenerate with respect to communities that possess unique individuals whose union provides all possible (biological) functions at the higher level of organization. For example:

julia> 1./(norm([1,1,1]+[0,0,0]+[0,0,0]-0.99))
57.73502691896253

julia> 1./(norm([1,0,0]+[0,1,0]+[0,0,1]-0.99))
57.73502691896253

Other functions that do distinguish these population states may be considered; however, there are conceptual cases for which such degeneracy is desirable.

[cameronraysmith]

The community average normalized cosine similarity distinguishes the states mentioned above afbbaff7f80e3f87a1cd023ca87a89f9fe58e459.