The error here and other places is the simple fact that darkness, physical or otherwise is not ever created. It is the absence of light.
My glass is empty. The emptiness is not made. It is the absence of water (or whatever drink you like).
Using physical light, for the verse tells us that the light was called Day, as an example. Science tells us that light has properties that make it act as though it were particles of matter. To confuse things more, science also tells us that light acts as a wave. (such as "wavelengths" of light) Darkness has no scientific properties. It is simply the absence of light particles or waves.
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