In the Talmud (Sanhedrin 91b) we find:
Antoninus said to Rebbe At what point is the soul given to a human? Is it from the moment of decree [that such a child will exist], or from the moment of formation? He responded: "from the moment of formation." He replied, "is it possible that a piece of meat can last for three days without salt, and yet not become rotten? Rather it must be from the moment of decree." Rebbe said: "This thing that I learned from Antoninus, and there is a supporting verse: [Job 10] Your Providence has guarded my soul."
Within these words we find the purpose and function of the soul. It guards the physical system of which it is attached. We find similarly in Chullin 93b where a body part, although not in operation, is considered to have life to the extent that it doesn't rot.
The physical biological systems are obviously built to do their job. If it wouldn't work it would be a futile, complex design. But indeed, the physical design is necessary and responsible for the success of the organism. However, the more complex something is the more delicate it is. We know all to well how delicate the human being is, for example. This is where the outside influence comes in. The soul is a field, or a bias, nudging things to continue and head in the right direction. We find this expressed in the Medrash Bereishis Rabbah (10:6)
Rebbi Simon taught: There isn't a blade of grass which doesn't have a Mazal (angel) in the heaven hitting it and commanding it, "Grow!" As it says in Iyov, "Knowest thou the ordinances of the heavens? Canst thou establish the dominion thereof in the earth?"
In Etz Chaim of Sifrei Arizal it attributes some form of soul even to inanimate objects. This further points to fact that it is not about making it work.
The idea behind all this is that although God created a closed-system universe (for the most part), He still left it open to influence from above. Randomness is a part of the fabric of the universe. I recall hearing in the name of the Vilna Gaon that God kept weather out of the hands of predictable laws of nanture, and left that in His control. The physical world is not cut off completely but it is surely its own domain. This ratio of physical to spiritual is found in other scenarios as well. The human is mostly desire-driven, but governed by thought, controlled by the conscious self.