I have had a great number of discussions with Roman Catholic apologists on a range of topics.  My experience is that our Catholic friends are guilty of proof texting to a very great extent.  In other words, they take their tradition, which they accept uncritically and then search the scriptures for the best "proof texts" to support what they have already decided to believe, regardless of whether the Bible actually teaches that tradition.  Of course, all of us are tempted to do this, but Catholics are especially guilty in this.  Their use of John 6:55 to prove transubstantiation is a good example of proof texting.  This passage is not about the Lord’s Supper.  Jesus was talking to a group who he fully intended to understand what he was talking about.  These people knew nothing of the Lord’s Supper.  Jesus is talking about the fact that without a relationship with him we will not be saved.  Anyone reading this passage knows that Jesus is not speaking literally.  When Jesus says "my flesh is real food" he is obviously speaking metaphorically.  In any case, there is no evidence he is talking about the bread we eat in the Lord’s Supper.

The early church fathers talked a lot about this subject.  By the fourth century there is evidence that some of the church fathers had begun to believe something like transubstantiation.  For example John Chrysostoam said, 

It is not man that causes the things offered to become the Body and Blood of Christ, but he who was crucified for us, Christ himself. The priest, in the role of Christ, pronounces these words, but their power and grace are God’s. This is my body, he says. This word transforms the things offered.

Earlier (Ignatius, Irenaeus, etc.) church fathers made statements such as the bread and wine are the body and blood of Jesus, which, of course, is quoting the biblical texts.  They were fighting the gnostics who believed that Jesus was not a physical person.  Therefore they emphasized the real body of Jesus, but did not teach what John Chrysostoam taught, which is that a "priest" actually transforms the bread and wine literally into the Body and Blood of Jesus.  For example, Ignatius said that "There is one Eucharist, for there is one flesh of our Lord Jesus Christ who suffered for our sins.  The heretics do not declare that the bread is the flesh of Jesus"    Here you can see no doctrine of transubstantiation.  You also see Ignatius talking about the Lord’s Supper in order to refute the gnostics.

John Oakes