There are two ways Allah creates. Cause and effect, and Be and it is.
Cause and effect itself is a result of Be and it is. The very idea of cause of effect is an original idea that at one point in pre-eternity did not exist and was brought into creation by Allah and it's one of those creations that's completely taken for granted.
Cause and effect is a mercy for human beings by which we can learn what causes what and what doesn't and predict it and then plan accordingly and even manipulate the causes to get what we want.
Be and it is, on the other hand will never be known to us in this world. "I did not let make them witness the creation of the heavens and the earth nor the creation of their own selves, so do not take as helpers those who lead others astray" (18:51 Kahf).
What happened from the time there was mud & water to the moment you had Sayyidna Adam standing, fully clothed and speaking? That exactly is what this verse is talking about. We will never know *how* Allah created Adam. That is the point of Be and it is. Our minds will not comprehend it in this life, and even if it could, Allah chose to veil it from us.
Some people say, well I have to know the cause. I tell them look, on what basis are you taking cause and effect to be some universal given of existence?? It too is a creation that at one point Allah said Be and it became.
And guess what else, like all other creation, it will be given death too. Cause and effect will die and cease to exist in the way we know it now. Only traces of it will exist. In the next life we will be given Be and it is by the permission of Allah. In Jannah there are no processes and there is no production. If you want something you merely think it and it comes to you. So those who have been trained through certain literature to be obsessed with this idea that everything must have a material cause or else I won't accept it...that mentality has to be limited to certain worldly spheres, like medicine where we are ordered by Sharia to use cause and effect. Otherwise, it's not absolute and it itself is subject to the same questioning (of what brought the idea of cause and effect into existence?). Like all other creation, we must by guided to know when to use it and what it's limits are. In contrast, there is no such problem in Islam. The origin of all things is Allah and Allah Himself is wholly different from all things by very definition in that God has no beginning and no end and is not subjected to time, space, materiality or cause and effect. Wallahu wali al-tawfiq.