Or [the state of a disbeliever] is like the darkness in a vast deep sea, overwhelmed with a great wave topped by a great wave, topped by dark clouds, darkness upon darkness: if a man stretches out his hand, he can hardly see it! And he for whom Allâh has not appointed light, for him there is no light- 24:40
Most of the seas are covered with thick cumulus cloud that block a great portion of sunlight. In the deep seas, internal waves are formed in the upper portion of the sea and the deep sea. When the rays of sunlight strike, the cloud absorb some of them and this is one kind of shade or darkness. When the rays strike the surface waves, the waves also reflect some of the light, and when the rays strike the internal waves more of the light is reflected back. This is another kind of darkness.
The Miraculous aspect:
The miraculous aspect of this Qur’anic Verse is that it clearly states that there exist “darknesses” in the depth of the sea that are piled one on top of the other, and there are internal waves in the deep seas and oceans, and that the seas and oceans are usually covered by thick clouds which block a considerable amount of the sun’s ray.
In the twienth century, scientist discovered a strange phenomenon that occurs only in the “vast deep sea”, which is that when light reaches a depth of five metres, the red color disappears. When it reaches thirty metres, the orange light disappears. At a depth of fifty metres, yellow light begins to disappear. At a depth of hundred metres, green light disappears. At two hundred metres, blue light disappears: “(layers of)darkness upon darkness”. At a depth of five hundred metres, everything appears black and the diver can only see what looks like moving shadows: “if a man stretches out his hand, he can hardly see it!” The Qur’anic description is very precise. It does not say that he cannot see it; rather it says that he “can hardly see it”. There is still some vision, but everything looks black.
The Verse does not stop here, rather Allah, the Exalted, says:”overwhelmed with a great wave topped by a great wave”. Is there more than one type of wave? Yes, the internal waves which were discovered in 1990.The fish at a depth of thousand metres have no eyes; rather they are equipped with bioluminescence. This is what meant when Allah, the Almighty, says: “And he for whom Allâh has not appointed light, for him there is no light”.
These astonishing scientific facts are mentioned in the Noble Qur’an which came down to Arabs in the desert who did not know how to swim or sail in the seas and oceans. The discovery was made after hundreds of sea stations were set up and pictures were taken by satellite.
Professor Schroeder, one of the greatest oceanographers in West Germany used to say, “When science progresses, religion must inevitably retreat”. But when he heard the translation of the Qur’an he was stunned and said, “These cannot be the words of a human being”
source: http://requestaquran.com/2012/01/14/the-darkness-of-the-sea/