A simple Turing machine, in each step, takes as input its own state and the state of its environment. Output is its next state, how to change the environment, and how to move to a different environment.
Or: the input to a Turing machine is the tape and its starting position. The output of the turing machine is the tape when it's done.
We can look at the Turing machine at these two levels as input->output. The aggregate input-output is easier to see. The each-step input-output explains how it works.
When we're looking at biological computation, do we ever get to see the individual steps? We're lucky to get a view of the aggregate input/output. How do you debug a cell?
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