Jansenius said, “Though Philip did not mean it, yet the Holy Ghost, by his mouth, designed here to teach us that the satisfaction and happiness of a soul consist in the vision and fruition of God.”

Getting to “see” God, to know Him more completely and intimately, brings a great deal of satisfaction (Psalms 16:11; 17:15), for there truly is a God-shaped vacuum in the heart of man that only God can fill (Pascal).

Psalms 16:11  You have made known to me the path of life; you will fill me with joy in your presence, with eternal pleasures at your right hand.

Psalms 17:15  And I—in righteousness I shall see your face; when I awake, I shall be satisfied with seeing your likeness.

But Philip is not thinking of a spiritual vision of God; He wants a physical manifestation of God, or theophany, much as in the Old Testament (Ex 24:9-10, 33:17-23, Isa 6:1). He thinks that if they can only see a physical manifestation of God, that will be all they need for their faith to be made perfect and their doubts to be solved.

Exodus 24:9-10  Moses and Aaron, Nadab and Abihu, and the seventy elders of Israel went up  and saw the God of Israel. Under his feet was something like a pavement made of sapphire, clear as the sky itself.

Exodus 33:17-23  And the LORD said to Moses, “I will do the very thing you have asked, because I am pleased with you and I know you by name.”
  Then Moses said, “Now show me your glory.”  And the LORD said, “I will cause all my goodness to pass in front of you, and I will proclaim my name, the LORD, in your presence. I will have mercy on whom I will have mercy, and I will have compassion on whom I will have compassion.  But,” he said, “you cannot see my face, for no-one may see me and live.”  Then the LORD said, “There is a place near me where you may stand on a rock.  When my glory passes by, I will put you in a cleft in the rock and cover you with my hand until I have passed by.  Then I will remove my hand and you will see my back; but my face must not be seen.”

Isaiah 6:1  In the year that King Uzziah died, I saw the Lord seated on a throne, high and exalted, and the train of his robe filled the temple.

The truth is that a physical revelation of God would have been of little or no benefit to the disciples. All the physical demonstrations at Mount Sinai didn’t keep the Israelites from making and worshipping a golden calf (Ex 19:16-20, 20:18-19, 32:1-8).

Exodus 19:16-20  On the morning of the third day there was thunder and lightning, with a thick cloud over the mountain, and a very loud trumpet blast. Everyone in the camp trembled.  Then Moses led the people out of the camp to meet with God, and they stood at the foot of the mountain.  Mount Sinai was covered with smoke, because the LORD descended on it in fire. The smoke billowed up from it like smoke from a furnace, the whole mountain trembled violently,  and the sound of the trumpet grew louder and louder. Then Moses spoke and the voice of God answered him.  The LORD descended to the top of Mount Sinai and called Moses to the top of the mountain. So Moses went up

Exodus 20:18-19  When the people saw the thunder and lightning and heard the trumpet and saw the mountain in smoke, they trembled with fear. They stayed at a distance  and said to Moses, “Speak to us yourself and we will listen. But do not have God speak to us or we will die.”

Exodus 32:1-8  When the people saw that Moses was so long in coming down from the mountain, they gathered round Aaron and said, “Come, make us gods who will go before us. As for this fellow Moses who brought us up out of Egypt, we don’t know what has happened to him.”  Aaron answered them, “Take off the gold ear-rings that your wives, your sons and your daughters are wearing, and bring them to me.”  So all the people took off their ear-rings and brought them to Aaron.  He took what they handed him and made it into an idol cast in the shape of a calf, fashioning it with a tool. Then they said, “These are your gods, O Israel, who brought you up out of Egypt.”  When Aaron saw this, he built an altar in front of the calf and announced, “Tomorrow there will be a festival to the LORD.”  So the next day the people rose early and sacrificed burnt offerings and presented fellowship offerings. Afterwards they sat down to eat and drink and got up to indulge in revelry.  Then the LORD said to Moses, “Go down, because your people, whom you brought up out of Egypt, have become corrupt.  They have been quick to turn away from what I commanded them and have made themselves an idol cast in the shape of a calf. They have bowed down to it and sacrificed to it and have said, ‘These are your gods, O Israel, who brought you up out of Egypt.’

Unfortunately, man hasn’t changed much over the centuries and we are just like that today. We sometimes believe that if only God would speak to me in this time of doubt or need, if only He would give me a sign, or remove whatever is bothering me, then everything would be perfect. But God doesn’t work that way. Faith is an essential ingredient in our walk with Him (Heb 11:6). We live in the physical realm and expect, or at least desire, for God to meet us there; but God lives in the spiritual realm and desires for us to find Him there (Col 3:1-3).

Hebrews 11:6  And without faith it is impossible to please God, because anyone who comes to him must believe that he exists and that he rewards those who earnestly seek him.

Colossians 3:1-3  Since, then, you have been raised with Christ, set your hearts on things above, where Christ is seated at the right hand of God.  Set your minds on things above, not on earthly things.  For you died, and your life is now hidden with Christ in God.

We may not know exactly what experience Jesus was referring to, but Nathanael certainly did.  Jesus possessed knowledge which no man could have apart from God.  This miracle accomplished its purpose: notice the result in the following verse.

Calvin points out that “We should also gather from this passage a useful lesson, that when we are not even thinking of Christ we are observed by Him; and this must needs be so, that He may bring us back when we have withdrawn from Him.”

Jesus is always interested in what we are doing. Why? Because He loves us so. It should comfort us to know that He knows us completely and yet loves us unconditionally.

From “On Another’s Sorrow” by William Blake:

            Think not thou canst sigh a sigh,
And thy Saviour is not by;
Think not thou canst weep a tear,
And thy Saviour is not near.