Quite simply, they weren’t. Negatives were put between a light source and photographic paper. When exposed to light, and then chemically processed, areas of the paper that were exposed to light turned dark, while unexposed areas remained light. Intensity of the darkness depends on exposure time.
So a dark shadow in real-life, appears white (transparent) in the negative, but admits the passage of light which exposes the dark shadow in the final photograph.
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