Without going into great detail, there are briefly two philosophical terms necessary to gain a rudimentary understanding of Transubstantiation. They are: Substance and Accident. Accident, as defined by Dr. Joseph Magee, “are the modifications that substance undergo, but that do not change the kind of thing that each substance is. Accidents only exist when they are accidents of some substance. Examples are colors, weight, [and] motion.” Using the example of man, we can say a substantial man remains a substantial man (body and soul) regardless of whether he is fat or skinny, moving or resting, black or white, tall or short, etc.
To my knowledge, the Church has never formally defined whether a man is: 1) a being composed of two incomplete substances (i.e., corporeal and spiritual) which, taken together, form a complete man, or 2) a being composed of a single substance of which a body and soul are included.
Aquinas made the case that it was the latter and Augustine the former. Regardless of which is correct, we can safely say this: if the resurrected Jesus was a complete man (and he is), then his entire substance in the Eucharist would include a corporeal body (though glorified, of course) and a human soul. If any of the two were missing, he would not be a complete man and, therefore, his entire substance would not be present.
This can also be said of his Sacramental Presence in the Eucharist and of his proper species in Heaven (that species that occupies three-dimensional spaces, i.e., his dimensive quality, philosophically categorized as an accident).
STOSS stands or falls on a correct understanding of both the Real Presence and Transubstantiation. It is a basic tenet of STOSS that our body and soul are changed due to becoming one Mystical Body with Jesus through Baptism and a one-flesh nuptial union with him in the Eucharist. In this Appendix, however, we will only be discussing the latter.
. Dr. Joseph M. Magee, “Natural Philosophy - Substance and Accident,” Thomistic Philosophy Page, http://www.aquinasonline.com/Topics/index.html: Joseph M. Magee, Ph.D., 08/27/1999 (accessed 05/02/2013).
. Francis Aveling, “Man,” (2011-10-25). The Catholic Encyclopedia: Complete Vol. 1-15, ed. Charles George Herbermann, (Kindle Locations 426413-426415). Kindle Edition.
. Ibid., Kindle Locations 426402-426404.
. Ibid., Kindle Locations 426398-426399.