Exploring the early development of an area of medical literature can inform contemporary medical debates. Different methods of inference include deduction, induction, abduction, and inference to the best explanation. I argue that early shaken baby research is best understood as using abduction to tentatively suggest that infants with unexplained intracranial and ocular bleeding have been assaulted. However, this tentative conclusion was quickly interpreted, by some at least, as a general rule that infants with these pathological signs were certainly cases of (...) abuse. Rather than focusing on inductive arguments, researchers today may be better off focusing on making a compelling inference to the best explanation. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...) research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)