Where did all matter come from? Answer that first then we can move on to what designs came out of that matter and how it ended up in the current design it's in.
That question goes outside Science. Science can't answer it because Science was not designed to ask it in the first place. I believe that we have an answer in God and His act of Creation, but I believe that because of my Christian heritage, not my scientific one.
Something most Creationists, and even some atheistic scientists either forget or are confused about is that Science is not reality. It is a model of reality (or, more accurately, a collection of models). Reality is too broad to be grasped in both its entirety and in complete detail by any mind lesser than that of God Himself.
In order to understand reality, we have to model it. We have to focus on a specific small portion of reality, and on no more than three or four aspects (variables) within that small portion, and pretend that the influence of anything beyond that tight focus is negligible.
One example of such a model is a map. A map models a portion of the Earth's surface. The larger the area covered by a map, the less accurate it is away from the primary focus, so for whole-Earth maps, there are different projections with different foci. A Mercator projection is focused on the Equator, and becomes distorted at the poles. A polar projection is focused on one of the poles, and is distorted at the equation and totally misleading as one approaches the opposite pole.
In addition, a map can only tell you a few things about the area it models. Depending on the type of map, it can tell you where to find roads, or political boundaries, or elevation, or natural resources, or the weather at a given time, etc. but not all of this information on a single map.
In addition, creating a model is like trying to teach yourself chess without a rulebook. You observe chess in progress and try to classify what you see. Whatever you do not understand, you put aside for the moment. It may turn out to be a rarely used aspect of a rule that is a little more complex than you thought (for example, castling or
en passant capturing of one pawn by another) or it may be an "illegal" move (such as a child might be allowed to make by an indulgent grandparent). You don't know which it is, so you can't include it as one of the rules that you have discovered until you have a chance to investgate more completely.
An example of the former is the bumblebee flying despite apparently failing to meet Bernoulli's principle. An example of the latter (a miracle) is walking on water.
So Science sets aside miracles, and other supernatural influences. (To switch, briefly, to a different metaphor, it's like setting aside a piece of a jigsaw puzzle until you find the pieces it fits with.) Science ignores the actions of God, not because "scientists" have decided that they don't believe in God, but because the very essence of Science is trying to discover the rules, and God does not have to follow the rules.
As I said, Science is a collection of models, each one focused on a very small segment of reality. Evolution is focused on changes in the distribution of traits in a population which improve the animals' fit within the niche that the population has begun to fill. It requires a living population and an environmental niche. It cannot answer questions about the origins of these things, any more than a book of chess rules can answer the question about why Bobby Fisher decided to practice chess instead of football. It takes a different book on a different subject (in this case, a biography) to answer that question.
