Naturalism as a working principle

Sometimes we can test a hypothesis by direct observation, but more often we do not see processes or causes directly (for example, electrons, atoms, hydrogen bonds, molecules, and genes are not directly visible, and we cannot watch the occurrence of mutation during DNA replication). Rather we infer such processes by comparing the outcome of observations or experiments with predictions made from competing hypotheses. In order to make such inferences, we must assume that the processes obey natural laws. D. Futuyma, Evolution (Sinaur 2005),  526.

One problem with his stipulation is that his characterization is anthropomorphic: "processes obey natural laws." That conjures up the image of one agent giving orders to another agent, and enforcing his order at gunpoint. "I command you! Obey–or else!"

Is he consciously using a metaphor? If so, what's his literal substitution?

On the face of it, aren't natural laws just inductive generalizations? They don't make things happen. 

In order to make such inferences, we must assume that the processes obey natural laws: statements that certain patterns of events will always occur in certain conditions hold…Because supernatural events or agents are supposed to suspend or violate natural laws, science cannot infer anything about them, and indeed, cannot judge the validity of any hypotheses that involve them.
Science must therefore adopt the position that natural causes are responsible for whatever we wish to explain about the natural world…it is a commitment to methodological naturalism (the working principle that we can entertain only natural causes when we seek scientific explanations), ibid. 526-27.

The way he defines methodological naturalism leaves things open to supernatural causation. He says "certain patterns of events will always occur in certain conditions hold." But on that definition, fiat creationism, progressive creationism, and intelligent design theory are all compatible with methodological naturalism. None of them denies that the same types of causes yield the same types of effects. If, instead of automatic processes, God directly causes something to happen, or "loads the dice," you have a different outcome because the initial condition is different. Divine agency introduces a different initial condition. It's not same cause, different effect–or different cause, same effect. Rather, it's different cause, different effect. 

Likewise, God can work through natural causes. He can prearrange events to yield a particular outcome at a particular time and place. In principle, the destruction of Sodom and Gomorrah could employ purely natural mechanisms.