A major contrast between religious or spiritual thinking and science concerns whether or not physical phenomena can simply be reduced to the sum of their parts. Basic physics, as described by the standard model of elementary particles and forces, is fully reductionist. This notion sticks in the craw of those who see themselves as part of a great, integrated whole.
In the scientific view, evolution reduces to a series of events that are local in space and time -- individual mutations that are passed on to the next generation. In the religious view, every event is part of grand scheme that applies holistically, under divine guidance, to the whole system from bacteria to humans and from billions of years in the past to the present and indefinite future. In the scientific view, physical events also reduce to a series of events local in space and time -- collisions between subatomic particles such as electrons and photons. In the view of quantum spiritualists, subatomic events are part of a grand scheme that applies holistically to every particle from an electron in a french fry at McDonald's to a photon in the cosmic background radiation billions of light-years away and billions of years in the past.
The conventional reductionist picture envisages a series of levels of matter. From elementary particles (or strings, or whatever is the most elementary) we move to the nuclei of atoms, then to the atoms themselves and the molecules that are composed of atoms. While only on the order of a hundred distinguishable atoms exist, the number of molecules is endless -- especially the huge structures built around carbon that form the ingredients of life and our fossil fuels, as well as many synthetic materials from plastics to polyesters.
The objects of our everyday experience are composed of molecules. Living organisms are an important component at this level, at least to us living organisms. How important they are on a cosmic scale is more dubious. Humans organize themselves into societies, so we can regard social systems -- politics, and economics -- as a yet higher level of material existence. Beyond that we have on Earth and its complex environment, the solar system, our galaxy, other galaxies, and whatever else is out there such as black holes, the cosmic background radiation, dark matter, dark energy, and other universes.
Now it should be obvious that an elementary particle physicist cannot take her equations and produce a derivation of every physical property we observe. She cannot calculate the structure of DNA from "first principles" or predict the stock market (though some have tried). At every level of matter from the smallest bodies to the largest we have specialists developing the principles that apply at that level by applying the time-honored methods of science -- observation, model building, and hypothesis testing. These principles are said to "emerge" from the level below. But the fact that we cannot derive everything from particle physics does not mean that the universe still isn't just a collection of particles.
Classical physics was reductionist. While direct proof of the existence of atoms was not found until the twentieth century, Newtonian mechanics was able to describe all of the behavior of macroscopic material systems -- gases, liquids, and solids -- in terms of the motions of their parts. The emergent principles of thermodynamics, which were introduced to describe macroscopic systems such as steam engines and refrigerators, were eventually derived from the submicroscopic atomic theory of matter.
New Age spiritualists and Christian apologists have appropriated quantum mechanics to claim a more holistic picture of nature. However, quantum mechanics and, as mentioned, the standard model of particles and forces, are fully reductionist. The standard model has agreed with all the data gathered at particle accelerators since the 1970s and is only now being seriously tested at the Large Hadron Collider (LHC) in Geneva. Discoveries at the LHC are unlikely to change the general reductionist scheme.
In short, reductionism in physics remains consistent with all the data. It isn't defeated just by the fact that it can't derive everything that happens. It still works. Holism has no evidentiary support. It doesn't work. Holism is nothing more than wishful thinking on the part of those who have the hubris to think that they are an important part of some cosmic plan.