Degradation of Design and Anti-Patterns

Since the fall of creation, it has been in a state of decay. The beauty of the creation is ever present; however, it is diminished by multiple generations of adaptation to a sin cursed world. The prevalence of “evil” in the creation has led some to conclude that living systems are not designed, but are the result of random processes. The challenge for a creationist is to demonstrate good design by a creator in the context of a fallen world. One means of recognizing good design is through the use of design patterns. Design patterns are best practice solutions to particular computer programming tasks. Although design patterns originated in the context of object-oriented programming, the design goals of modularity, reusability, and robustness are applicable to any complex system of objects that inter-operate in a reliable fashion. Design patterns accomplish these goals by encapsulating behavior, which is most likely to change, into loosely coupled objects. These objects have prescribed interactions, which makes it easier to anticipate behavior when the environment of the object changes. Although computer programs control the interaction of objects through sequential operations, well-defined interfaces, and message passing, the encapsulation of behavior in biological systems is not as easily achieved. However, encapsulation is prevalent in biology as illustrated by the variety of organs and tissues of an organism and the organelles and metabolic pathways in a cell. If design patterns embody good design practices for complex systems, then anti-patterns embody design practices that fight against the goals of modularity, reusability, and robustness. One way an anti-pattern can arise is from the repeated use of a single solution to solve a variety of problems (aka. To a hammer, everything is a nail syndrome.) Also monolithic systems that can not be easily decomposed into simpler objects manifest another anti-pattern structure. When these two anti-patterns, as well as others, are present in a complex system, the system can manifest unpredictable behavior when changes are made. The goal of this paper is to identify the presence of design patterns and anti-patterns in biochemical systems. Beginning with a portion of the carbon-utilization regulon in Saccharomyces cerevisiae, a search is made for matches to design patterns. With each match, an evaluation is made to determine the completeness of the pattern implementation. In the case of incomplete implementation, a conjecture is made as to possible complete implementations, which infer that the current implementation is a degraded form of a design pattern. When enough data are gathered, a comparison will be made between potential degraded design patterns and anti-patterns to determine any differences and similarities. The observed differences between these patterns will provide a framework for distinguishing between inherent bad design and good design in a fallen world. In addition, with knowledge on how good design is degraded, it may be possible to anticipate how good design can possibly be restored