First of
all, the logo tells about the name of the generic system, Isabelle, or
of its concrete instantiations, e.g. Isabelle/HOL. It also expresses
some essentials of the overall Isabelle design philosophy: Composition
of several small well understood building blocks, grouped together or
arranged in layers. The markings on the cubes illustrate this general principle by example of the core meta-logic (which is minimal higher-order logic on top of naively polymorphic simply typed lambda calculus). Thus red cubes symbolize the type system with function spaces (->) and type variables (alpha); violet ones represent the lambda term language with beta conversion etc.; yellow cubes constitute the actual logical parts, namely meta-implication or entailment (|-) and meta-level universal quantification.