The past few years have witnessed an increasing use of machine learning (ML) systems in science. Paul Humphreys has argued that, because of specific characteristics of ML systems, human scientists are pushed out of the loop of science. In this chapter, I investigate to what extent this is true. First, I express these concerns in terms of what I call epistemic control. I identify two conditions for epistemic control, called tracking and tracing, drawing on works in philosophy of technology. With this new understanding of the problem, I then argue against Humphreys pessimistic view. Finally, I construct a more nuanced view of epistemic control in ML-based science.