Machines All the Way Up and Cognition All the Way Down: Updating the machine metaphor in biology

Cell and developmental biology offer numerous remarkable examples of collective intelligence and adaptive plasticity to novel circumstances, as cells implement large-scale form and function. Many of these capabilities seem different from the behavior of machines or the results of computations. And yet, they are implemented by biochemical, biophysical, and bioelectrical events which are often interpreted with the machine metaphor that dominates molecular and cell biology. The seeming incongruity between molecular mechanisms and the emergence of self-constructing and goal-driven intentional living agents has driven a perennial debate between mechanist and organicist thinkers. Here, we discuss the inadequacies of, on the one hand, the (unminded) mechanist and computationalist frameworks, and on the other, dualistic conceptions of machine vs. mind. Both fail to provide an integration of agential and mechanistic aspects evident in biology. We propose that a new kind of cognitivism, cognition all the way down, provides the necessary unification of ‘bottom-up’ and ‘top-down’ causal flows evident in living systems. We illustrate how the organizational layers between genotype and phenotype provide problem-solving intelligence, not merely complexity, and discuss the benefits and inadequacies of specific machine metaphors in this context. By taking a pragmatist approach to the hypothesis that life and mind are fundamentally the same problem, formalisms are emerging that embrace the unique quality of the agential material of life while fully benefitting from the advances of modern machine science. New ways to map formal concepts of machine and data to biology provide a route toward unifying evolutionary and developmental biology, and rich substrates for the use of truly bio-inspired principles to advance engineering and computer science.