To say that the organism is nothing but its atomic constituents – taking “atom” in its original Democritean sense, as the most basic and indisintegrable component of all corporeal objects – is to say that in itself it is nothing. It is to say that there is in fact no organism at all, but rather only atoms.
For anyone trying to understand anything more complex than atoms, this is obviously an unsatisfactory result. It eliminates all such complexities ontologically. If everything is nothing but atoms, then there are no such things as organisms, or societies, or ecologies, or watersheds, or even vortices, winds, currents, crystals – or, indeed, atoms in the modern, Rutherfordian sense, or for that matter protons on the one hand, or molecules on the other. What’s worse, there are then no such things as the minds and thoughts of organisms such as we. In that case, there is no such thing as the system of thoughts that constitutes materialist reduction. Having devoured all science, the doctrine devours itself.
Like all evil ideas, materialist reduction reduces in the end, and logically, to the ultimate absurdity: nothingness.