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One of the central problems in software engineering is the inherent complexity. Since software is the result of human creative activity, cognitive informatics plays an important role in understanding its fundamental characteristics. This paper models one of the fundamental characteristics of software, complexity, by examining the cognitive weights of basic software control structures. Based on this approach a new concept of cognitive functional size of software is developed. Comparative case studies of the cognitive complexity and physical size of 20 programs are reported. The cognitive functional size provides a foundation for cross-platform analysis of complexity, size, and comprehension effort in the design, implementation, and maintenance phases of software engineering.