PHILIPPIANS 2:12-13 - The Making of a Saint

Introduction

It is our custom every Sunday to conclude the first half of our worship service (as we just did) by singing the Doxology (literally, “word of glory”). This is part of our order of worship as a way for us to sort of “wrap up” everything that we have done and said and sang and read and prayed since the start of the service—offering all of it to God for His praise and glory, and calling on all creatures here below and the heavenly host above to join us in the praise of our Triune God that we have offered up in our worship, as we prepare our hearts for Him to speak to us from His Word.

The last line of the Doxology is probably the only place where God the Holy Spirit is called by the old archaic name “The Holy Ghost”. In the 17th century when the King James Bible was translated, the Old English word gast was the literal equivalent of the Latin word spiritus—in this context it meant an immaterial or non-physical being. So that’s why you will see the words “ghost” and “spirit” used interchangeably in the King James Version. Our modern connotations of the word “ghost” make it less appropriate to use to describe God the Holy Spirit, and so we use the Latin-based word instead of Old English.

But “Ghost” versus “Spirit” aside, have you ever considered why we refer to the Third Person of the Trinity as the Holy Spirit? Now, we affirm that all three members of the Trinity are equal in every way, so it isn’t because the Spirit is more holy than the Father or the Son. (After all, we don’t say God the Holy Father, God the Holy Son—though they certainly are equal in holiness to the Holy Spirit.)

In his pamphlet Who Is The Holy Spirit, R. C. Sproul offers an explanation:

“...the term holy is attached to His title because of the particular task the Spirit performs in our redemption. Among the persons of the Trinity, the Spirit is the principal actor who works for our sanctification, enabling the process by which we are conformed to the image of Christ and made holy. (Sproul, R. C. (2012). Who Is the Holy Spirit? (Vol. 13, p. 36). Reformation Trust.)

Yes, Father, Son and Spirit are all holy, but it is the Spirit’s work to make you holy. So I want to search the Scriptures with you this morning to see together that

It is the PARTICULAR work of the Holy Spirit to MAKE you into a SAINT

We looked last week at the role of the Holy Spirit in our spiritual regeneration from death to life; and we learned there that He alone is the One Who brought us from spiritual death to life, from being dead in our trespasses and sins to a new life by which we can hear and respond to and please and obey Him.

But the Holy Spirit’s work of regenerating us solely by His own power is not the only work that He does in us—and unlike His work of regeneration, we are commanded by Scripture to participate in His work of making us holy. The passage we read a few moments ago from 1 Peter is a clear command to be holy as the One Who called you out of death to life (the Spirit) is holy. In Paul’s letter to the Philippians, he exhorts his readers to work out in their lives what God is working into their lives:

Philippians 2:12–13 (ESV)

12 Therefore, my beloved, as you have always obeyed, so now, not only as in my presence but much more in my absence, work out your own salvation with fear and trembling, 13 for it is God who works in you, both to will and to work for his good pleasure.

The Holy Spirit is working in you, Christian, so that you may desire to please Him and work to please Him. And so I want us to consider together at least four different means by which the Holy Spirit is making you holy:

The first is found in Romans 8:9 (p. 944 of the pew Bible):

Romans 8:9 (ESV)

9 You, however, are not in the flesh but in the Spirit, if in fact the Spirit of God dwells in you. Anyone who does not have the Spirit of Christ does not belong to him.

Here we find the first means by which the Spirit is making you holy:

I. He DWELLS in you (Romans 8:9)

It has been noted before that the Holy Spirit’s relationship to believers in the New Testament is fundamentally different from the Old Testament. In the Old Testament, there would be times when the Holy Spirit would “rest” upon someone, or “come upon” them in some way. And so we see the Spirit “came upon” the prophet Azariah in 2 Chronicles 15 when he went out to meet King Asa to prophesy to him, and the Spirit “resting upon” the seventy elders that Moses set apart for leadership in the wilderness:

Numbers 11:24–25 (ESV)

24 So Moses went out and told the people the words of the Lord. And he gathered seventy men of the elders of the people and placed them around the tent. 25 Then the Lord came down in the cloud and spoke to him, and took some of the Spirit that was on him and put it on the seventy elders. And as soon as the Spirit rested on them, they prophesied. But they did not continue doing it.

But unlike the Old Testament, where the Holy Spirit would merely rest upon or visit God’s people, here in the New Testament we are told that the Holy Spirit dwells in us.

And the fact of His dwelling in us should drive us to holiness in at least two ways—first, it should cause you to

Grow in your HATRED for SIN (1 Corinthians 6:18-20)

The Apostle Paul uses the fact of the Holy Spirit dwelling in believers as a powerful argument against temptation to sexual sin:

1 Corinthians 6:18–20 (ESV)

18 Flee from sexual immorality. Every other sin a person commits is outside the body, but the sexually immoral person sins against his own body. 19 Or do you not know that your body is a temple of the Holy Spirit within you, whom you have from God? You are not your own, 20 for you were bought with a price. So glorify God in your body.

Why do you fight sin, Christian? Why do you grow in your hatred for it? Because you are the dwelling of the Holy Spirit of God Himself!

The Holy Spirit’s dwelling in you not only drives your hatred for sin, but His presence in you causes you to

Grow in your DELIGHT for RIGHTEOUSNESS (Philippians 4:8)

Philippians 4:8 instructs us on what sorts of things should fill our minds as believers:

Philippians 4:8 (ESV)

8 Finally, brothers, whatever is true, whatever is honorable, whatever is just, whatever is pure, whatever is lovely, whatever is commendable, if there is any excellence, if there is anything worthy of praise, think about these things.

The world we inhabit now hates the righteousness of God so passionately that it hates everything that points to Him: Honor and courage and duty and sacrifice are ridiculed and maligned; the stores we tell each other are full of misunderstood and sympathetic villains and hypocritical or incompetent heroes who are revealed in the end to be no better than the antagonist they oppose. The narratives of our culture want to slop everything over with a grey moral relativism; there is no real good or honor or nobility; that which was once called wicked or sinful or evil is either misunderstood or is deliberately being maligned by some bigoted majority that wants to suppress it.

But Christian, you are called to be free from that amoralistic sludge—the Holy Spirit’s dwelling in you means that you have a new affection for righteousness that you did not have before. There is no more room in your heart for the moral ambiguity of our times; no more sympathetic villains and disappointing heroes; you delight to feed your soul on nobility and purity and wisdom and excellence.

As the Holy Spirit dwells in you, He causes you to grow in your hatred for sin and grow in your delight in righteousness. This is another way of saying that

II. He CULTIVATES you (Galatians 5:16-24)

This is the way that Paul describes the work of the Holy Spirit in Galatians. Turn with me to Galatians 5 for a few moments (page 975). The Scriptures tell us here that the work of the Holy Spirit Who dwells in you

Severs the POISONOUS root of SIN (vv. 16-21)

Galatians 5:16–21 (ESV)

16 But I say, walk by the Spirit, and you will not gratify the desires of the flesh. 17 For the desires of the flesh are against the Spirit, and the desires of the Spirit are against the flesh, for these are opposed to each other, to keep you from doing the things you want to do. 18 But if you are led by the Spirit, you are not under the law. 19 Now the works of the flesh are evident: sexual immorality, impurity, sensuality, 20 idolatry, sorcery, enmity, strife, jealousy, fits of anger, rivalries, dissensions, divisions, 21 envy, drunkenness, orgies, and things like these. I warn you, as I warned you before, that those who do such things will not inherit the kingdom of God.

Christian, the promise of the Holy Spirit’s dwelling in you means that you have a new power to resist sin in your life! To “walk by the Spirit” has at least two implications. First, “walking” by definition means a continuous action, right? At the risk of sounding silly, you can’t walk if you’re standing still! Walking by the Spirit means that you are continuously reckoning on His presence in you; you are always thinking and meditating on the holiness He is calling you to. The second implication of the idea of “walking” by the Spirit is that when you are walking, you are GETTING SOMEWHERE! Walking by the Spirit isn’t like walking on a treadmill; walking by the Spirit means that you are advancing in holiness—you are arriving in a new place of freedom from the poisonous root of immorality, impurity, enmity, strife, jealousy, anger, envy, drunkenness and all the rest. As you walk day by day by the Spirit of God as He speaks to you from His Word, you will begin to see those old passions shrivel and wither as you seek to honor Him and fill your mind with His righteousness and goodness and beauty.

The Spirit’s presence in you kills the poisonous root of sin, and in verses 22-24 we see that the Holy Spirit dwelling in you

Feeds the GLORIOUS fruit of RIGHTEOUSNESS (vv. 22-24)

Not only does the Holy Spirit sever the root of your delight in sin, but His presence in you grows the fruits of righteousness in you!

Galatians 5:22–24 (ESV)

22 But the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, 23 gentleness, self-control; against such things there is no law. 24 And those who belong to Christ Jesus have crucified the flesh with its passions and desires.

When you read through the book of Exodus you see how hard and how meticulously those skilled craftsmen worked to adorn and beautify the Tabernacle, the Old Testament dwelling place of God. And later in 1 Kings 6, how many years and how many millions of dollars worth of gold and silver and precious stones and cedar Solomon put into adorning the dwelling place of God in the Temple.

And consider that those were just temporary dwellings of God—you are His permanent dwelling! How much more are you eager, Christian, to fill your life with the beautiful and glorious fruit of love and joy and peace and patience and kindness and goodness and faithfulness and gentleness and self-control! And the beauty of it is that His dwelling in you not only makes it fitting for you to adorn your life this way, His dwelling in you makes it POSSIBLE! He is the reason that you want to adorn your life with the fruits of righteousness, and He is also the source of the power for that righteousness!

The Holy Spirit’s particular work in your life is to make you into a saint—He dwells in you to grow you in your hatred for sin and love for righteousness, severing the root of sin and feeding the glorious fruit of righteousness in you as you walk day by day in His power.

And not only do you have the promise of His presence dwelling in you and cultivating you, the Scriptures promise you that the God the Holy Spirit does even more--

III. He INTERCEDES for you (Romans 8:26-27)

Look with me at Romans 8—page 944. In every moment of your journey here on this earth, as you strive to follow Him and walk with Him and work out the salvation that He has worked into you and make your calling and election sure—He is praying for you!

Romans 8:26–27 (ESV)

26 Likewise the Spirit helps us in our weakness. For we do not know what to pray for as we ought, but the Spirit himself intercedes for us with groanings too deep for words. 27 And he who searches hearts knows what is the mind of the Spirit, because the Spirit intercedes for the saints according to the will of God.

What a promise! God the Holy Spirit is praying for you

When you don’t know WHAT to pray (v. 26)

On those days when you are so overwhelmed by the brokenness of the world around you; when you are so overcome by your own weakness and frailty; when you are weighed down with the disappointment and frustration with your small progress in overcoming sin and cultivating righteousness and you don’t even know what to say to Him in prayer—He helps you in that weakness! He takes all those wordless groanings of your heart and perfectly represents them to the Father!

And what’s more, God the Holy Spirit is interceding for you

When you don’t know HOW to pray (v. 27)

As long as we live here on this earth we will always be fighting the remaining corruption that still resides in us. But the problem with fighting that indwelling sin is that it gets into everything, even our prayers. Because we are still in the midst of the fight, there are times when we pray like the Pharisee “thank God I am not like that Gentile” (Luke 18:11) or in James when “You ask and do not receive, because you ask wrongly, to spend it on your passions” (James 4:3). How often our prayers are selfish or prideful, when we pray in boredom or rote repetition, when we pray in unbelief, that God will not or cannot answer our prayers.

But see the wonderful promise we have at the end of verse 27—that the Spirit “intercedes for the saints according to the will of God.” In his book All Things For Good, the Puritan author Thomas Watson writes about the intercessory ministry of Christ for us in a way that can just as equally be applied to the way the Spirit prays for us:

Christ’s prayer takes away the sins of our prayers. As a child... that is willing to present his father with a posy, goes into the garden, and there gathers some flowers and some weeds together, but coming to his mother, she picks out the weeds and binds the flowers, and so it is presented to the father: thus when we have put up our prayers, Christ comes, and picks away the weeds, the sin of our prayer, and presents nothing but flowers to His Father, which are a sweet smelling savour. (Thomas Watson, All Things for Good)

As you come to God in prayer—weak or stained by sin or unbelief as your prayers may be—the Holy Spirit who dwells in you is picking out the weeds of your sin and presenting your prayer as a sweet-smelling bouquet to a loving Heavenly Father Who hears and answers!

The Holy Spirit’s particular work in you is to make you into a saint—to make you holy, to grow your love for righteousness and hatred for sin, to guide you and nourish you in bearing righteous fruit, praying and interceding for you as you seek to walk day by day in obedience to Him.

And as He ministers in all of these ways, Christian, you find that you are more and more able to discern His leading in your life, to hear His voice and understand what He is calling you to do. He dwells in you, cultivates you, intercedes for you and the Scripture says

IV. He ILLUMINES you (1 Corinthians 2:10-13)

Turn with me to 1 Corinthians 2—page 953. See here how the Spirit works to enlighten you and bring you more and more into line with His own mind:

1 Corinthians 2:10–13 (ESV)

10 these things God has revealed to us through the Spirit. For the Spirit searches everything, even the depths of God. 11 For who knows a person’s thoughts except the spirit of that person, which is in him? So also no one comprehends the thoughts of God except the Spirit of God. 12 Now we have received not the spirit of the world, but the Spirit who is from God, that we might understand the things freely given us by God. 13 And we impart this in words not taught by human wisdom but taught by the Spirit, interpreting spiritual truths to those who are spiritual.

But what does it mean to “understand the things freely given to us by God”? What does it mean to be “taught by the Spirit, interpreting spiritual truths to those who are spiritual?” If we are not careful here, we may stray off into dangerous territory, believing that the Spirit will immediately and directly communicate with us.

But as we saw a couple weeks back, the Holy Spirit has written a Book. A complete, authoritative and living Book that contains everything that we need for life and godliness. So the illumination that He promises here comes completely and sufficiently from this Book. The Holy Spirit taught the writers of the Scriptures what to say, and now He illumines our minds to understand what He wrote through them. The Holy Spirit illumines you, Christian--

He RENEWS your MIND through His WORD (Romans 12:2; Psalm 119)

Romans 12:2 tells us

Romans 12:2 (ESV)

2 Do not be conformed to this world, but be transformed by the renewal of your mind, that by testing you may discern what is the will of God, what is good and acceptable and perfect.

As you fill your mind with His Word, you are filling your mind with the Holy Spirit. And as the Holy Spirit fills your mind by His Word, He transforms your whole way of thinking! This is what the Psalmist sang throughout Psalm 119--

Psalm 119:11–12 (ESV)

11 I have stored up your word in my heart, that I might not sin against you. 12 Blessed are you, O Lord; teach me your statutes.

Psalm 119:33–34 (ESV)

33 Teach me, O Lord, the way of your statutes; and I will keep it to the end. 34 Give me understanding, that I may keep your law and observe it with my whole heart.

Psalm 119:99–100 (ESV)

99 I have more understanding than all my teachers, for your testimonies are my meditation. 100 I understand more than the aged, for I keep your precepts.

And as you are daily filling your mind with the Holy Spirit’s inspired Word, He goes to work renewing and transforming your mind so that you grow in discerning His will—what is good, and acceptable and perfect. The illumination of the Holy Spirit means that

You GROW into MATURITY in DISCERNMENT (Hebrews 5:11-14)

The writer of Hebrews grappled with the immaturity and lack of discernment among his readers—he upbraided them for their lack of maturity in understanding the mind of God:

Hebrews 5:11–12 (ESV)

11 About this we have much to say, and it is hard to explain, since you have become dull of hearing. 12 For though by this time you ought to be teachers, you need someone to teach you again the basic principles of the oracles of God. You need milk, not solid food,

They had not been in the constant practice of filling their minds with God’s Word, they had allowed their minds to become dull and their appetite for God’s Word had wasted away. And so they were weak and childish in their faith, unable to grasp the kind of wisdom that comes from a renewed mind:

Hebrews 5:14 (ESV)

14 But solid food is for the mature, for those who have their powers of discernment trained by constant practice to distinguish good from evil.

This is the result of the Holy Spirit working through His inspired, written word. As Sinclair Ferguson puts it:

“The result of the Spirit working with the Word of God to illumine and transform our thinking is the development of a godly instinct that operates in sometimes surprising ways. The revelation of Scripture becomes, in a well-taught, Spirit-illumined believer, so much a part of his or her mindset that the will of God frequently seems to become instinctively and even immediately clear... It is this kind of spiritual exercise that creates discernment.” (Retrieved from https://www.ligonier.org/learn/articles/holy-spirits-ministry, Accessed 05/19/2023)

We have experience of this kind of instinctive understanding and almost intuitive wisdom in other areas of our lives. My father-in-law Terry knew how to “read” a trout stream, watching the water flow for a few moments and then drop a dry fly right on a seam and pull a fish out. Not because he had some supernatural ability—but because he had fished for trout for sixty years! Dad can go outside and look at the sky for a few minutes and tell you whether it is going to be a good day to cut hay or not—because he has some kind of superpower, but because he has been farming all his life! Taryn can draw her bow over her violin and tell you immediately whether that note is sharp or flat and Pat can strike one key on a piano and tell you the same thing because they have had their discernment trained by constant practice to distinguish sharp from flat, a good note from a bad one.

This is what discernment of the will of God is. This is what it means to know the promptings of the Holy Spirit in your life and understand where He is leading you and what wisdom He gives you for a particular moment. When you, by long practice and diligent devotion and unquenchable desire for the Word of God, have been so transformed in your mind and affections and thoughts and desires, so saturated with the Holy Spirit’s words revealed to you here in the Scriptures that you know good from evil, wisdom from folly, truth from error.

But here we must be careful; for if we allow some modern practices in parts of modern American Christianity to have their say, we will begin to believe that kind of Spirit-cultivated discernment is some sort of “prophecy” or “revelation”. This is where you see the kind of thing where someone will call you up out of the blue (as has happened to me) and say, “The Holy Spirit revealed to me that you needed to hear this “word”—and then they go on to tell me some random thing about how I was feeling or what I was going through. And then I was in the uncomfortable position of having to tell them that I had no idea what they were talking about, that what they were telling me had no connection to where I was or what I was doing. (One fellow responded by saying, “Are you sure?”)

Being led by the Holy Spirit to minister to someone is not a matter of having some random thought about them that you feel “led” to share with them. There have, in fact, been many times in my life when I am convinced that the Holy Spirit led someone to speak to me or do something for me at the moment when I really needed it the most. But none of those people felt the need to start off their comments by informing me that “The Holy Spirit told me to tell you...” In fact, I believe that most of those people who have had that kind of impact on my life didn’t even consciously recognize that they were being led by the Holy Spirit to minister to me. They were just living their lives in Christ.

Christian, do you want that kind of illumination from the Holy Spirit Who dwells in you? Do you want Him operating in you to do His will? Do you want Him to illumine you and direct you by His Word dwelling richly in you to govern those feelings, impressions, convictions, urges, burdens and impulses so that your “powers of discernment are trained by constant practice” to distinguish God’s will?

Then, Christian—fight the sin that still remains in you. The Holy Spirit dwells in you more surely and more powerfully than He ever did in the Old Testament tabernacle—and those who profaned it by their sin were struck dead. How much more, Christian, must you fight to hate sin and live in purity? Don’t make a truce with your lusts, don’t “try to cut down on” your gossip, don’t give yourself a pass on bitterness against your family or envy at your neighbor. If you want the Holy Spirit to do His work in you then you reckon His presence in your life every day. And in that strength you fight to sever the root of sin in your life.

Keep short accounts with God; every gardener knows that their job every morning is to go through the rows and pluck out every weed bigger than their thumbnail. Don’t allow your sin to grow and sink down roots into your life until you need a garden tractor and three friends to come over and root out the giant thistle of sin that you’ve let grow in your heart.

Stop feeding your soul on the amoralistic sludge that comes from a world that hates nobility and truth and honor. Stop entertaining the twisted and inverted attacks of this world’s scorn of what is good—as Isaiah lamented thousands of years ago—Isa 5:20 “Woe to those who call evil good and good evil, who put darkness for light and light for darkness, who put bitter for sweet and sweet for bitter!” Cultivate a delight in the true, the beautiful and the good—and train up those behind you to do the same!

Do you want the Holy Spirit to guide and superintend your thoughts and actions? Do you want to “understand the things freely given to you by God?” Then pray, Christian. Don’t tell yourself, “I’m no good at praying, I don’t know how to do it, I can’t concentrate for more than five minutes...” Don’t you see that the Holy Spirit Who dwells in you takes those stammering, sin-riddled mumblings and half-hearted requests and fumbling confessions of your prayers and turns them into a beautiful bouquet of sweet-smelling incense to rise up before your Heavenly Father? Revelation tells us that the throne room of Heaven is filled with the prayers of the saints—and that includes your prayers! So pray, Christian—He accomplishes more than you know through your prayers!

Do you want to have the mind of God guiding you, Christian? Do you want the Holy Spirit to so illumine and teach and direct you that you instinctively and confidently know His will? Then immerse yourself in His Word. We come back to it over and over again because this is the means by which you hear the voice of God the Holy Spirit. Stop thinking that discernment and spiritual wisdom is defined by Pat Robertson cold reading a broadcast audience on The 700 Club: (“Judy in Montana—your diverticulitis is being healed, praise God!”) That is not the Holy Spirit’s leading. Calling someone out of the blue and telling them some random thing that crossed your mind with no reference to God’s Word and making it sound good by saying “The Holy Spirit told me to tell you...” is a pretty reliable indicator that you’re making crap up. Stop it. Repent. Don’t attribute your own random ideas to God the Holy Spirit.

The Holy Spirit’s particular work is to make you into a saint—as He dwells in you, renews your mind, intercedes for you and illumines you. It all begins (as we saw last week) with His ministry of regeneration—of bringing you from spiritual death to life. If you have trusted in Christ as your Savior, this is God’s will for you—your sanctification! To progressively free you from the power of sin, to grow you in love for His righteousness and hatred for sin, to cultivate His goodness in you and intercede for you and illumine you.

In the Book of Acts, the Apostle Peter is preaching to his countrymen on the Day of Pentecost, when the Holy Spirit manifested His presence in a unique and powerful way—resting on the disciples as a flame of fire just as He rested on the Old Testament tabernacle in a pillar of fire by night, signifying that His dwelling place is now in us. The Scripture tells that as Peter preached to the crowds that day he told them of the guilt that they bore for crucifying Jesus, the Messiah. Acts 2:37 tells us

Acts 2:37 (ESV)

37 Now when they heard this they were cut to the heart, and said to Peter and the rest of the apostles, “Brothers, what shall we do?”

Friend, if you have come here today and the worship of God in this place has cut you to the heart because you realize that your sin and rebellion has brought God’s anger against you; if you are cut to the heart because you realize how far you are from the holiness that God requires—then the Good News for you is the same as it was for those who heard Peter’s message on that day:

Acts 2:38 (ESV)

38 And Peter said to them, “Repent and be baptized every one of you in the name of Jesus Christ for the forgiveness of your sins, and you will receive the gift of the Holy Spirit.

Repent of your sin that has estranged you from God, call on Jesus Christ for the forgiveness that He purchased by shedding His blood on that Cross, and you will receive the gift of the Holy Spirit—to take up His residence in you, to bring you from death to life, to cultivate His holiness in you, to intercede for you and illumine your heart and mind as you fill yourself with His Word. So call on Him today and receive this Gift of being made into the likeness of your Savior, Jesus Christ!

BENEDICTION:

Ephesians 3:20–21 (ESV)

20 Now to him who is able to do far more abundantly than all that we ask or think, according to the power at work within us, 21 to him be glory in the church and in Christ Jesus throughout all generations, forever and ever. Amen.

QUESTIONS FOR REFLECTION:

Why do we particularly refer to the “Holy Spirit” as holy? How is the Spirit’s role particularly concerned with holiness?

Read Exodus 40:34-38. Why was Moses unable to stand in the Tabernacle? Now read 1 Corinthians 6:19. If you are a more permanent dwelling of the Holy Spirit than the Tabernacle was, what does this mean for the way you treat sin in your life?

What are some reasons Christians find it so difficult to pray? How does the way the Bible describes the Holy Spirit’s work in Romans 8:26-27 give you confidence in your practice of prayer?

What are some of the false and dangerous ways some Christians describe being “led by the Spirit”, or having “discernment from the Spirit”? Read Romans 12:2 and Hebrews 5:11-14 again. How do these verses describe the way that we become sensitive to the leading of the Holy Spirit? How can you develop that kind of relationship with the Spirit in your life?