  Templated copying is the central operation by which biology produces complex
molecules. Cells copy sequence information from DNA to RNA and on into
proteins, which are the molecules responsible for the function and regulation
of cellular systems. In the templated copying process the template catalyses
the formation of a second molecule carrying the same sequence. Traditionally,
people have ignored the separation of the template and copy at the end of the
process, but separation is necessary and fundamentally changes the
thermodynamics of the process. In general, creating an accurate polymer costs
free energy. Omitting separation, this cost can be compensated for by the extra
free energy released by "correct" copy/template bonds. Separation requires
these bonds be broken, so true copying requires an input of free energy.
Equally the fact that copy/template bonds are temporary means there is no
thermodynamic bias towards accuracy, instead copying relies only on kinetic
effects to promote accuracy. In general, transducing energy can only happen
reversibly when the transduction process is quasistatic and time varying;
something that cannot be true when you are relying on kinetic discrimination.
  Copying is a far from equilibrium process. This thesis explores the
consequences of this observation. We start in the limit of infinite length
copies where the costs of accuracy represent hard thermodynamic bounds and then
moves to the finite length limit where these same limits can be understood as
kinetic barriers. We then discuss copying systems as non-equilibrium steady
states, which can be analysed as information engines moving free energy between
out-of-equilibrium baths.
