We must accept the fact of Biblical and spiritual enigma, that is, some truths in Scripture are to our minds difficult to reconcile with each other.
"My thoughts are not your thoughts" (Isaiah 55:8).
In God's mind, of course, there are no enigmas. All truth and reality perfectly correlate in His understanding, declared by the Psalmist to be "infinite" (Psalm 147:5). Our Lord never experiences the question sometimes raised in our minds, "Well, if this is true, how can that also be true?" His truth exists in perfect unity, both in the fact of it, and in God's perception thereof. "The darkness and the light are both alike unto Thee" (Psalm 139:12).
This cannot be said of our understanding. The Bible unapologetically presents to us realities that God knows will seem difficult, if not impossible, for us to reconcile. God as one, and yet triune. Eternity and infinity immanent in time and space. Divine sovereignty and human freedom coordinated in a manner that glorifies only God, while nevertheless gracing man with the internal blessing and responsibility of genuine personhood. Salvation freely bestowed by grace through faith, but received with Holy Spirit's witness that works will be the inevitable companion of a genuine experience of God's dynamic presence. Joy and sorrow somehow residing concurrently in the believer's trusting heart. And perhaps the greatest of all mysteries, the Lord Jesus Christ as "God... manifest in the flesh." The list could go on of Scriptural verities that will never be perfectly reconciled in this present lifetime, and which we must accept in peace while often scratching our heads in wonder.
The Bible is a perfectly rational and reasonable document, which to a perfectly rational and reasonable mind (such as its Author) contains no enigmas. To our limited and cloudy understanding, however, Scripture will always present to us rays of light that seem to reveal conflicting landscapes of Truth. This fact itself presents to us perhaps the foundational illumination of our existence, namely, that God is God, and we are not. There are fewer more comforting truths of Scripture because thereby we are called to "lean not unto thine own understanding" (Proverbs 3:5). Certainly we use our understanding, as led and enabled by the Holy Spirit, but we do not trust in it. Thus are we enabled to rest heart and mind in the safe harbor of "O Lord God, Thou knowest" (Ezekiel 37:3).
As the old hymn declares, "We shall understand it better by and by." For now, we understand it as well as possible through the Scriptures, the Holy Spirit, and the mutual insight provided by fellowship with other believers. We rejoice in the light provided, which "shineth more and more unto the perfect day" (Proverbs 4:18). And we rejoice in the mysteries of God and His truth that assure us that God is God and we are not. To the trusting heart in Christ, there is no greater peace.
"I will make darkness light before them."