Returning to the topic of science demystifying the universe, I think the inference many take from science's explanations for things is that, once some thing is explained as the product of the interaction of different parts, or as determined and conditioned by external forces, it almost seems as if the thing itself loses reality. When we discover that liquid water changes physical state depending on temperature and pressure, becoming gaseous or solid and crystalline, it seems much less likely to be a fundamental element of the universe, as ancient natural philosophy held it to be, and consequently loses some of its emotional significance for us. Likewise, when we discover that the water molecule is chemically composed of hydrogen and oxygen, elements that occur elsewhere independently, again it no longer seems like a basic element, but an almost accidental juxtaposition of different things. Part of our emotional appreciation of the mystery of Baptism is the idea of such a basic element as water being sanctified for cleansing sins and regenerating human nature. When we know more about the physics and chemistry of water, however, it seems more like an accident that we use Baptism with water, rather than any other substance.
I admit I sometimes get the same feelings about the use of bread and wine in the Eucharist. Surely this is an accidental result of the origin of our faith in the Middle East, where bread and wine are basic foodstuffs. If our faith had originated in northern Europe, we would no doubt be using milk instead of wine; if it had originated in Central America, maize rather than wheat would almost certainly be the element that would become the Body of Christ. It's hard to take seriously the argument that bread and wine are used because they are the best or most basic foods, because what is the best or most basic food is culturally dependent and rather arbitrary.
Of course, if we think in terms of Divine Providence, you could say that, even if water is not a fundamental element, or even if bread and wine are the products of certain cultures, rather than universal to humanity, nevertheless we have to allow that Providence chose this particular compound chemical, water, over others to be the regenerating medium of Baptism, and that Providence chose the basic foodstuffs of a particular culture over that of others to be the elements consecrated by the Holy Spirit as the perfect Sacrifice.