There are two definitions of science which are in operation.
The first definition of science is "observation, theorization, experimentation, collection of data, and making inferences and explanations with impartiality." This is a standard definition of science (though not the only one) and the process it represents is one from which, in a modern-context, we gain an understanding of the material world that allows us to produce cars, washing-machines, airplanes, medicine and so on and it includes investigating causes and effects and the special properties of things. This "scientific method" has been applied and harnessed to allow the beneficial interests of humankind to be realized and safeguarded through a gradual understanding of the system of interconnected causes and effects. The first definition of science presupposes and affirms order, regularity and rationality in the universe. The natural disposition of humans is imprinted with this affirmation. (Read "Humans May Be Primed to Believe in Creation" see here).
The second definition is "the explanation of all phenomena through natural, materialistic causes only." This is really a philosophical assertion, that only natural causes exist (because the universe is considered to be a closed system of material causes and effects without outside influence). Providing material explanations (of causes and effects) in the study of the world is not really an issue and does not clash with the Islamic understanding of how the universe or life operates, since affirmation of the ways and means and causes and effects and of the inherent properties in things that collectively comprise the "natural causes" is established in the revealed texts and is agreed by the majority of Muslims (see here, and here). So up until this point, we can accept such materialistic explanations. This is not even in dispute. However, the real intent behind this second definition of science goes beyond what we have just mentioned. It is to credit nature (physical law and random events acting upon matter) with an illusion of design that we allegedly observe when we explore and study life and the universe, and then to consider this the only "rational explanation" that must underpin all scientific enquiry. From here arises Dawkins' "blind-watchmaker", "mountain of improbability" and Hawkin's "nothing" (which is really "a law of gravity") from which "the universe can and will create itself" and so on, where we move away from empirical science and instead to "metaphysical belief." These explanations arise and are demanded by the prior commitment to naturalism which is concealed in this second definition of science.
The intent behind mentioning this - and it is something to always keep in mind - is that when these atheist materialists claim science and adherence to the scientific method, we have to make this distinction so as to clearly understand the reality of where they are coming from, and not be fooled by their claim that they are following the scientific method when it comes to origin of the universe and origin of life. Rather, they are holding a prior belief in naturalism, then using that to generate theories and then attempting to use the scientific method to validate those theories instead of using the scientific method upon a clean slate to lead to unbiased conclusions. Consider this: Using the scientific method (the first definition) establishes empirically, according to them, that the universe began. Pay attention here, this is known to them through the first definition of science. But, prior commitment to naturalism forces theories which try to undermine this view and its implications. This is what atheist scientists and Philosophers have been attempting and they have to bring stories dictated to them by their naturalism. Stories of oscillating universes, multiverses, self-creation and so on to make this universe insignificant or eternal. Here we have the second definition of science in operation and we are deceived into thinking that this is "true science" when in reality its just a back-door for a metaphysical naturalistic belief to tinker with the actual hard science which to them has established something atheists are troubled by. At the same time these naturalistic beliefs they propose cannot be considered scientific by the first definition of science, since they cannot directly put the core elements of these metaphysical beliefs through the scientific method upon that definition. The same can be said about origins of life, and that can be illustrated separately in other articles. The key thing here is to understand how things are running. This is just one element of many that needs to be understood to deconstruct the naturalistic religion parading as objective scientific inquiry. Regarding naturalistic causes it is important to understand that Muslims affirm them and they create no issues at all, refer to these two articles for more on the subject: Ibn Taymiyyah on the Affirmation of Natural (Material) Causes and the creed of the Naturalists (see here) and Ibn Al-Qayyim on the Affirmation of Material Causes, Forces, and Inherent Properties of Things (see here).
Written by Abū ʿIyād on 23/12/1434H (28/10/2013CE)