This thesis discusses the development of software architecture to support the computational investigation of random polygons in 3 space. The random polygons themselves are a simple model of long polymer chains. (A DNA molecule is one example of a polymer.) This software architecture includes "building blocks" which specify the actual manipulations and computations to be performed, and a structural framework which allows the user to specify which manipulations/computations to perform, in which order and with how many repetitions. The overall framework is designed in such a way that new building blocks can easily be added in the future. The development of three different building blocks to be used in this architecture which are entitled: Reducer, Lengthener and OutsideInLengthener are also discussed in this thesis. These building blocks manipulate the existing polygons - increasing or decreasing their size.

Watson and Crick’s double-helical model of DNA is considered to be one of the great discoveries in biology. However, in 1976, two groups of scientists, one in New Zealand, the other in India, independently published essentially the same radical alternative to the double helix. The alternative, Side-By-Side (SBS) or ‘warped zipper’ conformation for DNA is not helical. Rather than intertwine, as do Watson and Crick’s helices, its two exoskeletal strands are topologically independent. Thus, unlike the double helix, they may separated during replication without unwinding. This dissertation presents, but does not arbitrate among scientific arguments. Its concerns are meta-scientific; in particular, why and how the individuals who invented the & ‘warped zipper’ came to do so. Against Popper and most recent philosophers of science, it is taken to be “the business of epistemology to produce what has been called a ‘rational reconstruction’ of the steps that have led the scientist to a discovery [Popper (1972), p.31, emphasis in the original].” On the received view, the invention of the ‘warped zipper’ must be irrational or, at best, non-rational thereby excluding from philosophical investigation. I establish that this philosophical dogma is not true a priori, as is usually supposed, and, in the case of the SBS structure of DNA, false a posteriori. The motivation for, and development of the SBS structure for DNA reveals a process best characterized as significantly, though not entirely, rational.

Watson and Crick’s double-helical model of DNA is considered to be one of the great discoveries in biology. However, in 1976, two groups of scientists, one in New Zealand, the other in India, independently published essentially the same radical alternative to the double helix. The alternative, Side-By-Side (SBS) or ‘warped zipper’ conformation for DNA is not helical. Rather than intertwine, as do Watson and Crick’s helices, its two exoskeletal strands are topologically independent. Thus, unlike the double helix, they may separated during replication without unwinding. This dissertation presents, but does not arbitrate among scientific arguments. Its concerns are meta-scientific; in particular, why and how the individuals who invented the & ‘warped zipper’ came to do so. Against Popper and most recent philosophers of science, it is taken to be “the business of epistemology to produce what has been called a ‘rational reconstruction’ of the steps that have led the scientist to a discovery [Popper (1972), p.31, emphasis in the original].” On the received view, the invention of the ‘warped zipper’ must be irrational or, at best, non-rational thereby excluding from philosophical investigation. I establish that this philosophical dogma is not true a priori, as is usually supposed, and, in the case of the SBS structure of DNA, false a posteriori. The motivation for, and development of the SBS structure for DNA reveals a process best characterized as significantly, though not entirely, rational.