proceeds by

The word "proceed" is often followed by "to", "with", "against." The meaning would be unclear when it is directly followed by "by" itself:

Context:

(1) Fermentation proceeds by leaving the jars closed and undisturbed in a warm dark place for one month.

(2)The present invention proceeds by deactivating a first port (2) in the blocking state, whereby a second port (1) connected via an inactive link is caused to assume a link-down status.

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Does (1) mean: First, leaving the jars closed and, Second, leaving it undisturbed. In this way, the fermentation will continue for one month in a warm dark place?