Responding to an inquiry from a Ministry Assistant at Calvary Chapel, Mark Bonocore shares the Catholic understanding of transubstantiation.
Please allow me to introduce myself to you.  My name is Dan Hickling and I serve here at Calvary Chapel as Pastor Bob Coy's Ministry Assistant.  Here are a couple of actual quotes taken from the 1994 English edition of the Catechism of the Catholic Church.
Article #1374. In the most blessed sacrament of the Eucharist "the body and blood, together with the soul and divinity, of our Lord Jesus Christ and, therefore, the whole Christ is truly, really and substantially contained…It is a substantial presence by which Christ, God and man, makes himself wholly and entirely present."
Article #1374. By the consecration of the bread and wine there takes place a change in the whole substance of the bread into the substance of the body of Christ our Lord and of the whole substance of the wine into the substance of his blood.
This change the holy Catholic Church has fittingly called transubstantiation.  Notice the words chosen by the Vatican to define transubstantiation: Substantially: of a corporeal or material nature, pertaining to the substance, matter, or material of a thing.  Wholly: entirety, totality, the whole amount, extent, to involve all.  Entirely: fully and completely (above definitions taken from Webster's Encyclopedic Unabridged Dictionary).  It's very clear what the Roman Catholic Church is saying.  The elements actually become on every level (including the physical) the body and blood of Jesus Christ.
es, you are correct that we Catholics do believe that Jesus is truly, wholly, entirely, and substantially present in the Eucharist.  However, the mistake that you are making is that you are not using the word "substantially" in the sense that the Catholic Church uses it – that is, how it is used in the context of medieval Scholastic / Aristotelian philosophy (i.e., the systematic language in which "Transubstantiation" was dogmatically defined by the Catholic Church in the year 1215 A.D.).  In essence, there is a MAJOR difference between "transSUBSTANTiation" and "transFORMation".  In "transFORMAation", the actual physical properties of a thing are changed into something else.  This would include, not only the thing's shape and size, but the very molecular structure of the thing itself.  However, when it comes to the Eucharist, Catholics obviously don't believe that the little fragment of what is apparently "bread" in the priest's hand takes on the "form" or "structure" of Jesus Christ – a 6-foot, living and breathing Individual.  We also do not believe that, if one placed a Eucharistic host (the wafer of consecrated "bread") under a microscope that one would be able to see the cells of a Divine Jewish Carpenter, etc.
No.  We do not believe that the form of bread or the form of wine changes at all.  Rather, what we believe is that the substance of bread and wine changes into something (Someone) else.  And here, "substance" is a specific metaphysical term used in the language of Scholastic / Aristotelian philosophy – the language which was used to define our dogmatic doctrine.  And what it refers to is the **essence** of the very thing itself.  For example, if I have an ordinary piece of bread, that piece of bread possesses both a physical reality and a metaphysical reality.  It is both something I can see, touch, and taste (its physical properties) and it is something that exists as a reality beyond the perception of my senses (its metaphysical reality).  For, if I were to leave the room, the bread would still objectively be there.  Our Catholic belief is not that the physical properties of bread and wine change.  Rather, we specifically teach (as stated in the Catechism sections that you quote from above) that Christ is substantially present "UNDER THE SPECIES of bread and wine", meaning that the "species" (the "physical properties" also called "accidents" in the language of Aristotelian / Scholastic philosophy) remain the same.  And so our senses (sight, taste, touch, etc.) only perceive bread and wine.  However, the metaphysical properties of the bread and wine (that is, the substances of the bread and wine) do change in a miraculous act of God which we call "Transubstantiation".  In other words, Jesus is truly, wholly, entirely, and substantially present in the Eucharist in a metaphysical sense, whereas the physical "species" (i.e., the physical properties – everything that can be perceived by our senses) of bread and wine remain the same.
And non-Catholic Christians, like yourself, believe is something very close to this in terms of our justification before God through Christ Jesus.  For, as St. Paul says in Scripture, "In Christ, we are made into a 'new creation'."  Now, clearly, this does not apply to our form – our "physical properties", since we don't look any different; and the world does not see any obvious physical change in a person when he or she becomes a believer in Christ.  However, according to the words of Scripture, we know that a metaphysical change HAS taken place – that the former sinner has been re-created in the image and likeness of Jesus, and is now a new creation.  Ergo, the metaphysical substance has changed.  Truly, wholly, entirely, and substantially.  And this is all we believe when it comes to the nature of the Lord's Supper (the Eucharist).
Yet, you also write:
Notice that in describing transubstantiation they did not use the words metaphysical, immaterial, or abstract.  In recent years, Catholic apologists have begun to employ this view in defense of this teaching for obvious reasons.  But this doesn't alter the official pronouncement of the Catholic Church that a complete and total change occurs that goes beyond the metaphysical and into the physical (even though such a change is absolutely imperceptible).
But, Dan, your quotes from the Catholic Catechism above do not include the word "physical" either.  Rather, you are unwisely presuming that.  Indeed, given that the dogma of Transubstantiation was formulated using the language of Scholastic theology, it follows that we should understand the term "substance" within that specific context which is precisely what the Catholic Church does.  And, in the language Scholastic / Aristotelian philosophy, "substance" simply refers to the metaphysical essence of a thing, not to its physical properties.  For example, if you care to turn to section 252 of the Catholic Catechism, you will see "substance" defined as follows:
The Church uses (I) the term substance (rendered also at times by "essence" or "nature") to designate the Divine Being in its unity…
Now, granted, this particular passage is speaking about the Blessed Trinity, but it proves the semantic point.  The substance is the underlying metaphysical nature of a thing.  It is not its physical form.  It is not its molecular structure.
I should also point out, contrary to your misconception above, that "metaphysical" is not the same thing as "immaterial" or "abstract".  Rather, "metaphysical" refers to a God-created reality that transcends the physical.  Big difference.  Per my example above, when one becomes a "new creation" in Christ, one is not made into a "new creation" in an "immaterial" or "abstract" way, but rather in a literal, through metaphysical, way.  As Scripture says, the Church is the Body of Christ.  And when Saul of Tarsus persecuted the infant Church, Jesus did not say to him, "Saul, Saul, why are you persecuting my Church?"…or… "Why are you persecuting those who believe my Word?"  Rather, He said, "Saul, Saul, why are you persecuting ME?" – a reference to a **literal**, though metaphysical, reality – the Church as the Body of Christ.  And, in the same way, we do not believe that Christ is "immaterially present" or "abstractly present" in the Eucharist.  This would be a heresy for a Catholic to say.  Rather, we believe that Jesus is really and substantially present in the Eucharist; but we believe that this Presence is metaphysical in nature, not physical in nature.  Something can indeed be metaphysical and still be material.  It is a mistake to assume otherwise.  Or do you deny that the Bible is the inspired Word of God – a metaphysical reality made manifest by the material printed page, but not something which you can physically discern via the physical nature of the printed page itself (e.g. by comparing a printed page of Scripture to a printed page of the phone book)?
Yet, you also write:
If you disagree on this, please show me an actual quote or pronouncement from the Catholic Church, itself, which clearly says that a physical change does not occur within the sphere of transubstantiation.  Thanks for your patience in receiving this response.  I also appreciate you taking the time to explain the intricacies involved with the Catholic concept of transubstantiation.  I still believe that this was a relatively recent distinction that the Catholic Church has been forced to make…and that the majority of Catholics out there are under the impression that a complete transformation of the elements takes place…but what you've shared will be helpful to me in my future studies on this subject.  Thanks again and may the Lord bless you as you follow after Him.  Amen, brother.
Thank you for the blessing and for your charitable and very Christ-like attitude toward me, even though I am a Catholic Christian and, as we know, you at Calvary do not approve of many of our beliefs.  But, the charity of Christ clearly prevails in you, and for that may He be glorified by both of us together.  Also, in regard to Transubstantiation and your belief that the distinction between the "species" (physical properties) of bread and wine and the "substance" (metaphysical reality) of Jesus Christ are, as you say, "recent distinctions"… Well, if you don't mind (and, again, not to win you over to the Catholic position, but merely for the sake of objective truth and also, of course, to show how we Catholics are not trying to deceive anyone), please allow me to illustrate how Transubstantiation has always meant what I described in my previous email.  For example, as I'm sure you already know, St. Thomas Aquinas was one of the leading theological minds that led to the Catholic Church's 13th Century dogmatic definition of Transubstantiation.  In fact, as I previously touched on, it was Aquinas' Scholastic language that was used by the Lateran Council in order to formulate the dogma.  And, writing at that very time (as Transubstantiation was defined by the Church), Thomas Aquinas says many things, such as:
Nothing is more marvelous, for there it comes to pass that the substance of bread and wine is changed into the Body and Blood of Christ.  Here there is perfect God and perfect man, **under the show** of a morsel of bread and a sup of wine.  He is eaten by His faithful, but not mangled.  Nay, when this Sacrament is broken, in each piece He remains entire.  THE APPEARANCE (physical nature) OF BREAD AND WINE REMAINS, but THE THING (substance) IS NOT BREAD AND WINE.  Here is faith's opportunity, faith which takes what is unseen and disguised and keeps THE SENSES from misjudging about the wonted APPEARANCES.  (Thomas Aquinas, Breviary Lessons, Corpus Christi, in Disputations, XXVII de Veritate 4, 336)
and also…
That Christ's true Body and Blood are present in the Sacrament can be perceived neither by sense nor by reason, but by faith alone, which rests on God's authority.  In the text, "This is my Body which is given for you", Cyril comments (i.e., St. Cyril of Jerusalem, c. 360 A.D.) that we must not doubt that this is true, but must take the Savior's word on faith; He is Truth and does not lie.  (Thomas Aquinas, Summa Theologica, 3a, 75, I)
So, as you can see, Dan, these statements by Aquinas (and we can produce countless others from his Summa and from the other writings of the 13th Century Scholastic doctors) are in perfect agreement with the 19th Century quote from Pope Leo XIII, which I presented to you in my previous email.  The Catholic position has not changed between the time that the dogma was defined (in 1215 at the Lateran Council IV) and the time of Pope Leo XIII (1878-1903) or today.  And, indeed, we can trance this back far earlier that Aquinas and far earlier than the defined dogma of Transubstantiation.  For, our Catholic belief is there, and there universally, in the organic Apostolic Tradition of the ancient Church.  For example, writing between 170 and 180 A.D., St. Ireneaus of Lyon, who was the disciple of St. Polycarp, the disciple of the Apostle John himself, writes on the Eucharist (the Lord's Supper) and says:
For just as the bread which comes from the earth, having received the invocation of God, is no longer ordinary bread, but the Eucharist, consisting of TWO REALITIES, EARTHLY AND HEAVENLY, so our bodies, having received the Eucharist, are no longer corruptible, because they have the hope of the resurrection.  (Ireneaus, Five Books on the Unmasking and Refutation of the Falsely named Gnosis, Book 4:18 4-5, circa 180 A.D.)
Now, here, of course, Ireneaus is not speaking in the 13th Century Scholastic (Aristotelian) language that was used to dogmatized Transubstantiation at the Latin-speaking Lateran Council of 1215, but uses the ancient Patristic (neo-Platonic) language of the Greek fathers.  And so, while his use of the term "reality" (i.e., "two realities") is not as precise a term as a Scholastic/Aristotelian like Aquinas would use, the clear meaning remains the same: Catholics do not believe, nor have we ever believed, that a physical change takes place at the Consecration of the Eucharist.  Rather, the change, though absolutely real, is a metaphysical one – a change in substance, not a change in form or physical property.  So, again, Dan, I would seriously urge your Pastor to adjust his view on this.  I am sure that the Pastor has every good intention, and is not trying to misrepresent anything.  And so, for the sake of his own reputation as a student of Christian theology, I simply do not wish to see him embarrass himself by stating something that is clearly, and verifiably, incorrect.
Also, on your point that there are many Catholics out there who are under the impression that a "complete transformation of the elements takes place", you are probably very correct about that.  However, as with Calvary Chapel members who hold opinions that are contrary to your faith, the misunderstanding of such Catholics cannot be applied to the Church itself, since the Church itself clearly teaches otherwise.  We do not teach "transFORMation" (the very word you use above), but "TranSUBSTANtiation", and that word has, and has always had, a specific meaning which, of course, is what I have been trying to convince you of here.
Anyway, dear brother… May the Lord bless and increase you and always hold you close to His Sacred Heart.
Pax et bonum (Peace and blessings)…
Mark Bonocore
June 3, 2009