Design Versus Naturalism

I am reading William Dembski's book "The Design Revolution." The book is well written and I am sure that I will have continuing thoughts on the content of the book. Currently I have noticed that design theorists do not attempt to attach any specific attributes with the presupposed designing intelligence. They merely presuppose design based upon the first step of the scientific method: observation. Observation leads design theorists to propose that there are possible explanations of existing biological structures that give evidence of design. In contemplating their methods it is clear to me that they must presuppose design. However I realize also that the adverse is true when it comes to naturalists. They predispose that there is no design and that the biological structures that exist today do not arise out of design. In essence they predispose that life is undesigned. Therefore design theorists presuppose that the biological structures arise because of design while the naturalists presuppose that biological structures are undesigned. Richard Dawkins wrote a book called "The Blind Watchmaker" which explains that the apparent design is only apparent and actually an illusion. This however admits that there is at least on the surface level an indication of design. He is able to justify his dissent with this belief by proposing that there are blind forces that can account for the apparent complexity of biological systems. But I would like to ask what makes him presuppose this in the first place. This type of thinking seems to undercut the basis of the scientific method. If the most basic observation leads the observer to infer design than why is design not hypothesized as an explanation of biological systems. Why do scientists ignore what seems apparent? If they had first dealt with the issue of design by examining biological structures to see if they had the hallmarks of design would they still insist that they are undesigned?