One of the common arguments against naturalism is that it forces us to conclude that we are nothing more than bundles of protons and electrons bouncing about without any purpose.
The problem with such reductionist arguments is that they throw the baby out with the bathwater.
To see this, consider the donkey and the dandelion. Both are comprised of mostly four elements: carbon, hydrogen, oxygen, and nitrogen. (After these, there is a smattering of other elements such as sulfur, phosphorus, and a variety of metals.) According to the reductionist argument, then, donkeys are indistinguishable from dandelions: they are both mindless, purposeless conglomerations of the above elements.
But this is, of course, absurd. There is simply no denying that donkeys are very different from dandelions. Yet it is also true that both things are made of carbon, hydrogen, oxygen, and nitrogen. To distinguish between them, then, we have to look at how those atoms are arranged, and how they interact.
For starters, dandelions are composed of large numbers of plant cells whose walls are mostly cellulose, a large molecule made up of many glucose units linked by glycosidic bonds. Glucose itself is a ring of five carbon atoms and one oxygen atom, with various side groups.
Donkeys, on the other hand, are composed of large numbers of animal cells, which are bounded not by cellulose but by cell membranes made up mostly by triglycerides, which in turn have a glycerol back bone and three fatty acids, at least one of which is unsaturated.
And of course the differences extend far beyond the microscopic level of cells. The macroscopic physiologies of the two organisms are as different as night and day. Their behaviors, too, are extremely different (if you ever hear a dandelion bray, let me know).
Clearly, the reductionist description of donkeys and dandelions comes nowhere close to properly describing these organisms. Even if you give to reductionism almost all of the higher order arrangement of atoms (donkeys are just lumps of meat!, dandelions are just stalks and leaves blowing in the wind!), these descriptions fail to capture the full definition of donkeys and dandelions, because not all lumps of meat are the same, and not all stalks and leaves are the same.
Reductionism, then, is a straw man. Even from a strictly scientific point of view, no one is just a lump of meat, and no one is just a ball of atoms.
Those who wish to attack naturalism must therefore realize they’re attacking a worldview that acknowledges – indeed, is scientifically obliged to acknowledge – all the complexities of life, including thought and emotion and purpose. These things are very real. Indeed, that’s the very foundation of naturalism.