Synchronizing Rhythms of Logic

A proof in quantum theory made twenty years ago prompts interrelated developments in physics, biology, graph theory, and the philosophy of science. The proof shows an ineradicable need for guesswork, beyond logic, to link physical evidence to any theoretical explanation. In physics and in biology, recognizing guesswork reveals a kind of synchronization, found in digital computer hardware but overlooked in theoretical physics, with implications for a biological basis to the concepts of time and distance in physics. By refuting the assumption that "physical" implies "eventually entirely explicable," the proof inspires renewed attention to experimental practice. Pervasive in the practice of modern science, digital computation and communications depends on physically distinct conditions and transitions among them. Organizing these conditions and transitions depends on a form of synchronization unlike that usual in physics. As shown here, this logical synchronization: (1) is essential to computing and digital communications networks, and (2) requires guesswork for its maintenance, whether directly or in the design of automated maintenance. By abstracting digital hardware, we model human thinking as logically synchronized computation, punctuated by unforeseeable changes. We adapt marked graphs to sharpen understandings of computation, whether it is electronic or takes place in living organisms. The marked graphs reveal a logical substructure to spatial and temporal navigation, with implications across physics and its applications to other sciences. By limiting our model to thelogical aspect of communications and computations -- leaving out energy, weight, shape, etc. -- we reveal logical structure applicable not just in electronics but also to the functioning of living organisms.