In the comments under the IT article is this:-

John Robinson

One problem with this question being viewed as a shibboleth is that most people misunderstand what the doctrine means. It is based on Aristotelian categories which distinguish the substance of something (its essence independent of all physical properties) from its accidents (all its physical properties). Transubstantiation means that the substance of the bread and wine are changed into the substance (spiritual presence is probably the best way to put this in contemporary terms) of Christ but the accidents remain the same i.e the physical properties of bread and wine remain the same and the physical properties of the body and blood of Christ are not involved, but Christ's essence i.e spiritual presence is.

I was wondering how the Aristotelian hypothesis fitted into the atomic theory of matter? Perhaps the great Aristotle was talking complete bollocks on this subject, and the RCC are maintaining his hypothesis well past its sell-by date?