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The first part of verse 16 speaks of a matter-the mystery of godliness. Hence, we would expect Paul to use the relative pronoun “which” to refer to the mystery of godliness as a matter. However, the fact that he uses the relative pronoun “Who” implies that the mystery of godliness is a person and not merely a matter. As we shall see, this person is Christ as the Head with His Body.

Through incarnation and human living (John 1:1, 14), God was manifested in the flesh. “In the flesh” means in the likeness, in the fashion, of man (Rom. 8:3; Phil. 2:7-8). In the form of man Christ appeared to people (2 Cor. 5:16), yet He was God manifested in a man.

Christ was also “vindicated in the Spirit.” The Greek word also means justified. The incarnated Christ in His human living was not only vindicated as the Son of God by the Spirit (Matt. 3:16-17; Rom. 1:3-4), but was also justified, proved, and approved as right and righteous by the Spirit (Matt. 3:15-16; 4:1). He was manifested in the flesh, but vindicated and justified in the Spirit. He appeared in the flesh, but He lived in the Spirit (Luke 4:1, 14; Matt. 12:28) and offered Himself to God through the Spirit (Heb. 9:14). His transfiguration (Matt. 17:2) and His resurrection are all vindications of the Spirit. Furthermore, in resurrection He even became the life-giving Spirit (1 Cor. 15:45; 2 Cor. 3:17) to dwell and live in us (Rom. 8:9-10) for the manifestation of God in the flesh as the mystery of godliness. Hence, now we know Him and His members no longer according to the flesh, but according to the Spirit (2 Cor. 5:16). Since the manifestation of God in the flesh is vindicated in the Spirit, and the Spirit is one with our spirit (Rom. 8:16), we must live and behave in our spirit that this vindication may be accomplished.

Paul also says “seen by angels.” Angels saw the incarnation, human living, and ascension of Christ (Luke 2:9-14; Matt. 4:11; Acts 1:10-11; Rev. 5:6, 11-12).

Christ was also preached among the nations. Christ as God’s manifestation in the flesh has been preached as the gospel among the nations, including the nation of Israel, from the day of Pentecost (Rom. 16:26; Eph. 3:8).

Furthermore, Christ has been “believed on in the world.” Christ as the embodiment of God in the flesh has been believed on, received as Savior and life, by people in the world (Acts 13:48).

Paul concludes verse 16 with the phrase “taken up in glory.” This refers to Christ’s ascension into glory (Mark 16:19; Acts 1:9-11; 2:33; Phil. 2:9). According to the sequence of historical events, Christ’s ascension preceded His being preached among the nations. However, it is listed here as the last event of Christ being the manifestation of God in the flesh. This seems to indicate the church taken up in glory. Hence, it implies that not only Christ Himself as the Head, but also the church as the Body, is the manifestation of God in the flesh. When a church is well taken care of according to the instructions given in the first two chapters, with the oversight of the elders and the service of the deacons fully established, as revealed in chapter three, the church will function as the house and household of the living God for His move on the earth and as the supporting pillar and holding base of the truth, bearing the divine reality of Christ and His Body as a testimony to the world. Then the church becomes the continuation of Christ’s manifestation of God in the flesh. This is the great mystery of godliness-Christ lived out of the church as the manifestation of God in the flesh!

I wish to emphasize the fact that although Christ was taken up in glory (Acts 1) before the preaching of Him began in Acts 2, Paul mentions this last, not only after the preaching, but even after being believed on in the world. This indicates that “taken up in glory” may include not only the ascension of Christ, but also the rapture of the church. The Head, Christ, was taken up before the preaching of Him began; however, the Body, the church, will be taken up only after Christ has been preached and believed on in the world. Therefore, in verse 16 there is a definite indication that this verse refers not only to the Head as the manifestation of God in the flesh, but also to the Body as the continuation of this manifestation. This is indeed logical, for how can a person’s head function in isolation from his body? The Head, Christ, has been taken up in glory, and the Body, the church, will also be taken up in glory. Both the Head and the Body are the mystery of godliness. This is the manifestation of God in the flesh.
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Life-Study of 1 & 2 Timothy, Titus and Philemon   pg 26