Your flowchart for lacZ expression already presents the danger of
being interpreted in a linear fashion. The "decisions" made by
lacI (repressor) and CRP are made in parallel. You probably have
not made the mistake, but your diagram would suggest that CRP acts
first and lacI second.
I think you'll find such diagrams will suffer from such problems
increasingly as you try to model a significantly complex system.
Flowcharts are inherently linear beasts, ill-suited for parallel
processes, especially biological ones with many non-linearly combined
Department of Cellular and Developmental Biology
Department of Genetics / HHMI
robison at mito.harvard.edu