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In comparative theology, I read about the difference with the Protestants, especially in the case of prayer for the dead body, because they reject prayer over the dead body. What I need is to answer this question with the help of verses from the Holy Bible because one Protestant told me that it is meaningless to pray on the dead body at the time of the funeral or on in the church.

The Holy Scripture reveals how precious the temple of God is where He dwells. "The Lord is in His holy temple" (Psalm 11.4).  This statement is only in partial reference to the temple which was built by hands. However, Protestants cannot deny that Christians are also the temple of God which ought to be consecrated to God. "Do you not know that you are the temple of God and that the Spirit of God dwells in you? If anyone defiles the temple of God, God will destroy him. For the temple of God is holy, which temple you are" (1Cor.1 Corinthians 3:16,17). Unfortunately, amongst the Protestant's shortcomings are their neglect to accept how God consecrates an individual to Himself, so that s/he may truly indeed become a holy temple for the Lord's dwelling. This consecration is brought about through the gift of the Holy Spirit in the Holy Sacraments of Baptism and Chrismation (Confirmation). "Most assuredly, I say to you, unless one is born of water and the Spirit, he cannot enter the kingdom of God. That which is born of flesh is flesh, and that which is born of the Spirit is spirit" (John 3:5,6). Thus, this new individual, who becomes the temple of God, becomes a new creation, inseparable with God, unless, even after receiving the Holy Sacraments, s/he rejects the work of the Holy Spirit, which is repentance, "but to him who blasphemes against the Holy spirit, it will not be forgiven" (Luke 12:10; Matthew 12:31,32). The Christian belief is that death is only a departure. With dignity, the body is laid to rest with the customary rituals befitting the believer and that of the temple of God. Yet, the spirit lives on and enters Paradise, just as our Lord clearly confirmed and allowed the admittance of the repented thief, who, as in Holy Baptism, died with Christ (literally) to rise with Christ, and thus, entered into Paradise with the Lord, Himself, "Assuredly, I say to you, today you will be with Me in Paradise" (Luke 23:43), forever inseparable. Thus, prayer on the body of those who repose in the Lord is befitting. "Precious in the sight of the Lord is the death of His saints" (Psalm 116:15).