The distinguishing feature of one's boss is that this person has certain kinds of (formally recognized) power over you within your organization's hierarchy

You're considering just the word "boss". Consider the phrase "real boss". Regardless of the meanings of the constituent words, the phrase itself can often be replaced with "the one with the real power", or "the one who actually makes the decisions." For example, "The king may have nominal power, but he's really only a figurehead, his vizier is the real boss."

Now, we still find something lacking in that the mice don't actually make decisions, the people observing the mice do. However, if the people observing the mice care about doing good research, then decisions about what course of action to take in the future must take into account what happens with the mice. What happens with the mice provides evidence which forces the researchers to update their models, possibly changing the optimal course of action, or fail. The literal meaning "The mice provide evidence, forcing us to update our models, making us, in order to do our job correctly, change our decisions." may be expressed metaphorically as "The mice make decisions on how to do our job correctly" or "The mice are the real boss."

From the context of the article, in which he uses this as an argument for not coming up with certain specific goals before beginning research, this is likely what the author meant.