Perhaps the most dramatic difference between our biological gates and conventional logic gates is the difference in speed. Electrical gates now function with delays of tens of picoseconds. Biological gates constructed using this methodology will have delays governed by the speed of protein manufacturing--perhaps many minutes. Roughly speaking, we should think of this logic family as functioning at frequencies measured in millihertz, rather than at rates measured in Megahertz.
While other biological mechanisms might be constructed which could function (optimistically) at kilohertz rates, such structures will require a degree of engineering finesse which we believe will not be available in the short term. Protein design, and, especially, protein-complex design, required for such high-speed gates, is not sufficiently well understood at the present time. Indeed, the major requirement may be, ironically, better and faster computational tools.