The Trinitarian Nature of Prayer: Part 3

The Trinitarian Nature of Prayer: Part 3

Apr 27, 2014

By: Emilio Ramos

Series: The Valley of Vision

The Valley of Vision, The Trinitarian Nature of Prayer, Pt. 3

The Spirit’s role is so extensive that I felt the need to continue looking at the Trinitarian nature of prayer by devoting this entire section to the Spirit. It may serve our purpose best to look at the Spirit’s role in prayer by asking who the Spirit is and what precisely is the Spirit’s role in Scripture and in the life of the believer.  We should start then, by remembering the Spirit’s connection to the Trinity.  The Spirit is not to be separated from the role and activity of the Father or the Son.  They are at the most fundamental level one with each other (cf. 1 Cor. 2.10).  They are the same in essence and purpose (Acts 5.3; John 16.12-15).  This is why the Spirit is called the “Spirit of God” (Mt. 3.16; 12.28; Rom. 8.9, 14; 1 Cor. 2.11, 14; 3.16; 7.40; 12.3; Phil. 3.3; 1 John 4.2).  The Spirit represents the Father as much as He represents the Son, He knows what is in the Father (1 Cor. 2.12) just as much as He knows what is in the Son (John 16.14).  That is to say, He knows the thoughts of God, the mind of God, the will of God, the wisdom of God, the decrees of God, and the nature of God perfectly and with equal ultimacy as the rest of the members of the Godhead.

The Holy Spirit is also Christ-centered.  The Spirit is the called the “Spirit of Christ” (Rom. 8.9; 1 Pet. 1.11), “the Spirit of Jesus” (Acts 16.7), and “the Sprit of Jesus Christ” (Phil. 1.19). This is why when Paul spoke of our adoption he identifies the Spirit as the Spirit of God’s “Son” (Gal. 4.6). He is the Spirit sent by Jesus to further the purpose of Jesus among His people.  He is the divine Emissary of Christ that is sent to represent Christ, stand in the place of Christ (John 14.16-17; 16.7), and speak for Christ (1 Pet. 1.11), speak about Christ (John 15.26), and ultimately glorify Christ (John 16.14).  The Spirit is a Christ-centered Spirit because He brings more of Christ to the believer.

Through prayer we have our communion with God the Spirit.  We commune with Him and He with us.  We see this communion and fellowship in three very important ways: Indwelling, Illumination, and Intimacy.  Our communion with God is first and foremost a spiritual communion it is a spiritual fellowship.  We do not see Jesus Christ here and now, physically and visibly; yet, we have fellowship with Him through His Spirit (1 Pet. 1.8; 2 Cor. 13.14; Gal. 4.6). The first thing that this means is that the operations of the Spirit of God have come to us through His indwelling presence.

The Indwelling of the Holy Spirit

In order for the Spirit to assist us in our prayer life, it first means that He must be in our lives that is, He must dwell within us and give us life through salvation.  As we look at the Spirit’s work in our lives, we should be careful to observe the extent of the Spirit’s work in salvation.  The Spirit brings us to Christ, purifies us in Christ, and keep us for Christ.  From our calling to fellowship with Christ to our final glorification with Christ and everything in between, the Spirit is at work in our lives.

The Spirit makes us alive to make us His home

This is one way of looking at regeneration.  It means that the Spirit was involved in your regeneration.  This is why the Spirit is called God’s breath.  Job said, “The Spirit of God has made me, and the breath of the Almighty gives me life” (Job 33.4), Jesus breathes the Spirit on His disciples (John 20.22). He is the sovereign breath of God that makes things alive (Ezek. 37.1-14).  The Spirit of God is totally sovereign in calling whom He wills through regeneration:

John 3:5–8 5 Jesus answered, “Truly, truly, I say to you, unless one is born of water and the Spirit he cannot enter into the kingdom of God. 6 “That which is born of the flesh is flesh, and that which is born of the Spirit is spirit. 7 “Do not be amazed that I said to you, ‘You must be born again.’ 8 “The wind blows where it wishes and you hear the sound of it, but do not know where it comes from and where it is going; so is everyone who is born of the Spirit.”

The Spirit of God is explicitly the Spirit of regeneration and of effectual calling:

Titus 3:4–6 4 But when the kindness of God our Savior and His love for mankind appeared, 5 He saved us, not on the basis of deeds which we have done in righteousness, but according to His mercy, by the washing of regeneration and renewing by the Holy Spirit, 6 whom He poured out upon us richly through Jesus Christ our Savior,

Prayer is something totally new in the believer’s life.  And although people may have grown up praying, growing up in a Christian home, and around religious things like prayer; regeneration is the actualization of a real and new conversation with God. Prayer is a new form of communication that we did not have before, it is communicating with God. 

This is a result of the Spirit’s renewal.  The Spirit loves to make things new because God loves to make things new and will one day make all things new (Rev. 21.5). The Spirit is always involved in God’s creative activities.  The Psalmist declared, “By the word of the Lord the heavens were made, And by the breath of His mouth all their host” (Ps. 33.6).  Prayer is evidence that God has a plan to renew and regenerate all things, to make all things new and to redeemed all things (cf. Rom. 8.20; 2 Cor. 5.17).

For this reason the Spirit has decided to take up residence in our heart through faith.  The Spirit dwells in us and this too is evidence that He plans on making all things new.  A new people (Lk. 22.20), a new body (Rom. 12.4-5; 1 Cor. 10.17; Eph. 5.30), a new temple where God may dwell in the midst of His people, we are the temple of God:

1 Corinthians 3:16–17 16 Do you not know that you are a temple of God and that the Spirit of God dwells in you? 17 If any man destroys the temple of God, God will destroy him, for the temple of God is holy, and that is what you are.

The Spirit makes a pledge that He promises to keep

The Spirit is called many things in Scripture and has many functions and operations and ministries. One of the most important ministries that the Spirit has is His ability secure the believer’s hope of glorification.  The way Scripture speaks of this is by referring to the Spirit as God’s guarantee or pledge (ἀρραβών).  As God’s pledge, the Spirit is a promissory Spirit.  He is the Spirit of things to come; namely glorification.  Paul refers to this by talking about our glorification as God getting what He wants:

Ephesians 1:13–14 13 In Him, you also, after listening to the message of truth, the gospel of your salvation—having also believed, you were sealed in Him with the Holy Spirit of promise, 14 who is given as a pledge of our inheritance, with a view to the redemption of God’s own possession, to the praise of His glory.

Two times Paul says that God gave us His Spirit so that we might have a pledge, an installment of things to come, a deposit, a down payment:

2 Corinthians 1:22 22 who also sealed us and gave us the Spirit in our hearts as a pledge.

2 Corinthians 5:5 5 Now He who prepared us for this very purpose is God, who gave to us the Spirit as a pledge.

The Spirit makes a people that He aims to purify

Not only does the Spirit’s role in our lives work to promise us things to come, He also sanctifies us for present purity.  The Spirit is in fact called “the Spirit of holiness” (Rom. 1.4).  The Spirit is totally dedicated not only to calling us, saving us, regenerating us, sealing us, and glorifying us but also sanctifying us as we look forward to our eschatological reward.  Paul brings all these elements together in a single text:

2 Thessalonians 2:13–14 13 But we should always give thanks to God for you, brethren beloved by the Lord, because God has chosen you from the beginning for salvation through sanctification by the Spirit and faith in the truth. 14 It was for this He called you through our gospel, that you may gain the glory of our Lord Jesus Christ.

Thus, by indwelling us, the Spirit makes us alive through regeneration, promises us the guarantee of glorification, and purifies God’s people through sanctification and faith. Ironically, I was recently asked if sanctification is a monergestic or synergistic act. The answer to that question is partially answered here. In fact there are two aspects of sanctification, positional and progressive. Positional sanctification is a monergestic act exclusively accomplished by God in our lives, a once and for all setting apart of the believer by causing a permanent break with sin’s dominion.  Progressive sanctification however is both human and divine, that is, it is a synergistic work where God works through us in our faith to sanctify us more and more (cf. Phil. 2.13).  This is Paul’s focus here in Thessalonians.


The sanctification process continues our whole life and it is primarily accomplished by the Spirit’s application of God’s truth to our lives. Thus, our fellowship with the Spirit is also known through the Spirit’s impartation of spiritual truth or illumination. This work of illumination is so essential to what the Spirit does that on four separate occasions John refers to the Spirit as, “the Spirit of truth” (John 14.17; 15.26; 16.13, 1 John 4.6).  This name was given to the Spirit to highlight His role in the work of redemption that through His illuminating work, the Spirit would impart revelation to the disciples which they did not previously have about Christ. The fact that Jesus would be taken up from the apostles means the Spirit would speak for Christ, that is, in His stead.  He did this with perfect representation and perfect precision and consistency:

John 16:12–15 12 “I have many more things to say to you, but you cannot bear them now. 13 “But when He, the Spirit of truth, comes, He will guide you into all the truth; for He will not speak on His own initiative, but whatever He hears, He will speak; and He will disclose to you what is to come. 14 “He will glorify Me, for He will take of Mine and will disclose it to you. 15 “All things that the Father has are Mine; therefore I said that He takes of Mine and will disclose it to you.

“Truth” means that the Spirit would keep the apostles from theological error as they received and ultimately inscripturated the doctrine of Christ in the New Testament (cf. 2 John 9).  This same principle is extended to the believe who also has the same Spirit of truth though not for reasons of receiving inspired revelation; the Spirit does however illuminate our minds to the already imparted and received revelation of God in His word.  He also keeps us from error as we are given the ability to know the difference between false doctrine and orthodox truth.  John is a consistent theologian on the Spirit because he continues the same theology of the Spirit in all his writings:

1 John 2:26–27 26 These things I have written to you concerning those who are trying to deceive you. 27 As for you, the anointing which you received from Him abides in you, and you have no need for anyone to teach you; but as His anointing teaches you about all things, and is true and is not a lie, and just as it has taught you, you abide in Him.

1 John 4:6 6 We are from God; he who knows God listens to us; he who is not from God does not listen to us. By this we know the spirit of truth and the spirit of error.

The Spirit’s work of illumination is so strong in believers in fact that we are able to discern the deep things of God (1 Cor. 2.10), the mysteries of God (1 Cor. 4.1), mind of God in Christ (1 Cor. 2.16), the hidden wisdom of God which God has revealed in the gospel (1 Cor. 2.7), and the nature of all things in light of God’s counsel (1 Cor. 2.15).  Paul sets the believer and the unbeliever apart specifically because of this distinction:

1 Corinthians 2:14–16 14 But a natural man does not accept the things of the Spirit of God, for they are foolishness to him; and he cannot understand them, because they are spiritually appraised. 15 But he who is spiritual appraises all things, yet he himself is appraised by no one. 16 For who has known the mind of the Lord, that he will instruct Him? But we have the mind of Christ.


Because the Spirit is the Spirit of truth, our fellowship with God does not consist of hidden truths that can only be tapped into by certain individuals who claim to have existential experiences with God that the rest of us do not have. Any experience with the Spirit will ultimately have some basis and grounding in the objective truth of God’s word. Our intimacy with the Spirit therefore is spiritual fellowship that consists of Biblical truth and virtue not mystical ecstasy and contemplative quietism (as with the new age movement or the mystics of monasticism).  This was not Reformed theology and it was not the way the Puritans saw the Spirit’s influence on the believer.  Joel Beeke and Mark Jones sum up the Puritans view of the Spirit this way:

“The Holy Spirit is a divine person in the Godhead...  More specifically, our knowledge of the Spirit’s work in redemption must be understood in connection with the distinctively Reformed Christology of the Puritans. Their Christology was pneumatic, and their pneumatology was christocentric. These elements come together not only in the specific blessings of salvation bestowed upon the elect, but also in terms of the prayer life of believers and the manner in which believers, by the Spirit, appropriate God’s own revelation in His Word. Without the Spirit there is no spiritual life. To put it starkly, the prayers of God’s people apart from the Spirit would be no more efficacious than the prayers of pagans. In similar manner, God’s written Word apart from the Spirit would be as useful or efficacious as the Koran. At the same time, against the Quakers, the Puritans insisted that the Spirit without the Word is also not useful, but leads into false mysticism. The Spirit who has authored the Scriptures works by the Scriptures. God has appointed means to sanctify the members of the church, and those means, such as prayer and God’s Word, are only helpful or effective insofar as they are combined with the Holy Spirit’s work in relation to them.” (Joel R. Beeke and Mark Jones, A Puritan Theology: Doctrine for Life (Grand Rapids, MI: Reformation Heritage Books, 2012), 440–441).

It is in this way, the Spirit working with the Word of God never apart from the Word of God, that He intimately leads us and speaks to us sweet words of assurance, affection, and conviction.  This is how the Spirit becomes “the Spirit of grace and supplication” (Zech. 12.10). 

The Spirit is always closely associated with prayer in Scripture.  We ask the Father in prayer for the Spirit (Mt. 7.11; Lk. 11.13; 18.7), we pray in the sphere and under His influence and with the resources the Spirit has to give us (Eph. 6.18; Jude 20), we pray to God with intimate language that the Spirit inspires and impresses upon us by His indwelling presence (Rom. 8.15-16; Gal. 4.6).  As a pastor, it is my duty to provoke you to pray, help you to pray, join you in prayer and grow you in prayer but it is the Spirit who is able to get the job done:

Romans 8:26–27 26 In the same way the Spirit also helps our weakness; for we do not know how to pray as we should, but the Spirit Himself intercedes for us with groanings too deep for words; 27 and He who searches the hearts knows what the mind of the Spirit is, because He intercedes for the saints according to the will of God.

The Spirit’s great goal in all spiritual influence dealing with prayer is to enlighten us to God’s redemptive work in Christ and the grandeur of our salvation and union in Him until at last we obtain the hope of our calling and see the vindication of God’s Son (cf. Eph. 1.15-21).

Sermon notes are personal pastoral notes and not intended for grammar perfection. If you have questions about certain parts, please contact us.