5 ¶ And the light shineth in darkness; and the darkness comprehended it not.
Whether or not this refers to spiritual darkness as Paul did later;
Ephesians 6:12 For we wrestle not against flesh and blood, but against principalities, against powers, against the rulers of the darkness of this world, against spiritual wickedness in high places.
Galatians 1:4 Who gave himself for our sins, that he might deliver us from this present evil world, according to the will of God and our Father:
…the first reference to darkness comes in the first few verses of the Bible. While that is a literal reference to literal darkness as in distinguished from light a spiritual application can be that there is a spiritual darkness in the universe and Christ, the Word, was that light that was separate from it.
1John 1:5 This then is the message which we have heard of him, and declare unto you, that God is light, and in him is no darkness at all.
In the Bible comprehend means to understand.
Job 37:5 God thundereth marvellously with his voice; great things doeth he, which we cannot comprehend.
Spiritual darkness is ignorant. It neither understands our need for Christ nor does it understand God’s love for us. It cannot. The natural man is blanketed in spiritual darkness and cannot comprehend the things of God.
1Corinthians 2:14 But the natural man receiveth not the things of the Spirit of God: for they are foolishness unto him: neither can he know them, because they are spiritually discerned.
Just so, the carnal Christian does not realize that he or she has cut themselves off from understanding.
1John 2:11 But he that hateth his brother is in darkness, and walketh in darkness, and knoweth not whither he goeth, because that darkness hath blinded his eyes.
The light of Christ is a beacon in a world of shadows and darkness. Unfortunately, for many conservative Christians, fundamentalists, the light is very dim in their fear of man, bigotry, hatred, paranoia, and elevating culture and politics to the level of Bible doctrine.