If one takes water from a container with water, he has picked the water up from its (water's) natural resting place. That is an honest "picking up", and for that he will be liable on Shabbat.
If one picks up a nut (I am thinking walnut) that is floating on the surface of the water, then he has not violated Shabbat because this is not the nut's natural resting place.
What is that nut is floating on the water that is in a box, and the box is floating on the water in its turn? The nut is at rest in the vessel, and he is liable? Or maybe we look at the box and see it floating on the water, and he is not liable?
The answer is "silence" or "teiku." Some say that the four letters of teiku stand for "Tishby iteretz kushiot veibayot", that is, "Eliyahu will explain all hard places and questions."
Art: Still Life of Fruit and Nuts by Giuseppe Ruoppolo






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