Both Uses

fathom
in
Nature, by Emerson
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Literature, poetry, science, are the homage of man to this unfathomed secret, concerning which no sane man can affect an indifference or incuriosity.†
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unfathomed = not understood

standard prefix: The prefix "un-" in unfathomed means not and reverses the meaning of fathomed. This is the same pattern you see in words like unhappy, unknown, and unlucky.
But if, instead of identifying ourselves with the work, we feel that the soul of the workman streams through us, we shall find the peace of the morning dwelling first in our hearts, and the fathomless powers of gravity and chemistry, and, over them, of life preëxisting within us in their highest form.†

fathomless = impossible to understand

standard suffix: The suffix "-less" in fathomless means without and reverses the meaning of fathom. This is the same pattern you see in words like harmless, fearless, and powerless.

Definitions:

(1) (fathom as in: can't fathom)
understand something -- especially when it’s difficult or complex
(2) (meaning too rare to warrant focus)
Fathom can also refer to a unit of measure for water depth (6 feet), or to the act of measuring the depth of water.