A typical explanation (or "explaining away") of human religion is that we tend to see intentionality everywhere, since we are so familiar with the concept from our own thought processes. In other words, since our own actions can typically be explained by our own purposes, it is natural to explain events in nature according to some purpose--the storm has come because the gods are angry, there is no rain because the gods are punishing us, we won the war because the gods were on our side, and so on. We know better now, the argument goes, than to impose our anthropocentric reasoning on the world around us. Nature doesn't follow any purpose; it follows laws.
I don't have a problem with the idea that intentionality is a concept we impose on our vision of reality in order to understand it. What I would like people to call into question is whether there's any other way to understand reality. Cartesian coordinates are not inherent to space; they are a conceptual framework which aids spatial reasoning. Mathematical laws are likewise not inherently "there;" we filter our experience through them in order to understand some particular feature of what's going on. Seeing our favorite conceptual framework as the way things "really are" is normally not a problem in science. In fact, coming up with a conceptual framework to "impose" on reality is one of the most important roles of a scientist.
The question is, of course, whether the concept of intentionality helps us understand anything, whether it ought to be replaced by a better framework, and whether it can be refined to give better understanding. I submit that most complex systems really need to be understood in intentional terms. When we observe the behavior of animals, for example, there is really no substitute for saying they want or don't want food. It is no triumph of modern science to "reduce" living things down to mere machines, because there simply is no mechanical language that significantly captures desire as a state of being. Desire and intention are fundamental concepts. They can be applied to plenty of other complex systems, too, which may not traditionally be considered beings with "souls." The market, for example, clearly wants things. If there is too much of a good, its price will go down. If there is too much uncertainty in financial markets, there will be large price volatility. It is vain to continually "remind" ourselves that the market does not "really" want things, because after all it is not a human being. So what? It is not a human being, but like human beings, it clearly moves in such a way as to pursue discernible goals.
One day computers may become intelligent enough to have intentions. Certainly computers are machines. If even they can have intentions, why can't we just admit that intentionality is a much more general concept than just some "anthropocentric" rendering of the world around us? Perhaps, on the contrary, we experience intentionality because we are part of a universe where it is abundant, and somehow we satisfy the criteria necessary to experience it.
The universe itself is, by definition, the most complex thing that exists. It only seems natural that it should have intentions. Perhaps this sounds more like pantheism than monotheism. Yet one thing that is still unclear, no matter how many people assert that it is clear, is what relationship exists between being and intention. Does my intention drive my being, or does my being drive my intention? In many ways this is an extremely practical concern. Do the ugly things I say result from hunger or a lack of sleep? Or am I responsible for those words in a way that transcends my physical existence? Well, the same question could be asked of the universe. Does all the complexity of the universe arise from a promordial physical state, thus allowing intentionality to emerge? Or is the universe intended to exist?
As much as scientists these days seem increasingly successful at showing that complex phenomena can emerge out of simpler ones, I don't think this question is any more decided by science than whether human beings have free will. It is of course entirely reasonable to explain human life in terms of simpler physical processes. That gives rise to modern medicine and improvements in physical well-being. Yet it doesn't help anyone decide whether life is really worth living or not. It doesn't tell anyone whether there's something wonderful about the world we live in. And ultimtely it doesn't really explain how we do anything. I have no doubt in my mind that, whatever difficulties might be there on account of my physical limitations, I make decisions that determine my behavior. If, indeed, this experience of free will is only an illusion, who, exactly, is performing it?
The grand irony is that we jettison the concept of intentionality more vigorously precisely when we wish all the more to control things. We wish to control how long we live, so clearly the human body is nothing but physical processes. We wish to control nature, so clearly there is no meaning to nature other than physical laws. Thus in seeking to control life, we render it totally unintelligible. Life cannot truly be life unless it has that spontaneous force we call intention. Living longer is certainly an understandable goal, but if in order to do so we must view ourselves as machines rather than as living things, is it truly life that is prolonged?
The concept of intentionality is robust and can be refined. We need not believe the gods are angry when there is a storm. But it is not at all unreasonable to talk about nature "seeking" a kind of equilibrium, so that weather can indeed be seen as a result of nature's intentions. And why wouldn't it be reasonable to extend this more broadly, to see broad connections between all the processes in the universe, and to find common purpose behind them? For example, we know that through a cycle of birth and death living things evolve and branch out into many different organisms of increasing complexity. Why shouldn't that be part of the purpose of the universe? In dying, we give life. Through suffering, we are purified. Perhaps this process can continue indefinitely, and one day the universe will see the will of God done on earth as it is in heaven. Who knows? Such questions may be beyond the scope of any one scientific discipline, but there is no reason why intelligent human beings should find such questions ridiculous.