Chapter One may be found here:
CHAPTER TWO: How Faith Changes the Heart
It having been showed hitherto who are true believers: it follows to show how a believer is to behave himself throughout his whole conversation [manner of life]. 1. Wherein is to be laid down, first, the grounds of a godly life, that is, that it is grounded on faith, and proceeds from a pure heart. 2. The parts of it, which is to flee evil, and do good.
Godliness Rests Upon Faith
Unfeigned faith and a godly life are inseparable companions.
First, godliness cannot be without true faith, James 2:18, Hebrews 11:6, Genesis 6:5. The fountain being evil, the rivers which run from it cannot be good. So where faith is not in the heart, there can be no goodness in the life; by which we see how many deceive themselves, thinking they fear love and serve God; and yet have no faith, or constant desire of it.
Second, neither can faith be without godliness, for as no man lives godly which believes not; so no man who believes, can live wickedly; but as he is newborn, so like a new creature [he] follows newness of life and obedience; although this does not appear either at the first beginning of his conversion, nor in the vehemency of temptation, Titus 2:12.
True Faith Transforms the Life
Neither does faith work a bare wandering desire to please God, but it frames also the man onto it [faith shapes one], and teaches him in some true and acceptable measure to go about it; and when it is over matched with fleshly corruption, yet it raises signings and strivings in the heart, till it be subdued.
So that as they are deceived which pass from a little sorrow for sin to newness of life, as they imagine, without faith, the beginning and worker of all new life. So they also are no less deluded but please themselves, thinking they have faith, when their lives are not only filled with offensive actions, but also with custom in common in the same. For he that is honored with the title of a believer, must be known by the livery of an uncorrupt life. The true servants of God dare no otherwise believe their sins to be forgiven them, then they walk humbly before God and man.
Faith Lays Hold to All the Promises of God
When faith is said to be necessary to a godly life, we must not only understand by “faith” to be saved. The godly man must labor to believe all the promises of this life and of life to come (whether the great and principal, as of the graces of the Spirit; or the smaller, as bodily safety and preservation from dangers so far as they shall be good for him) do belong on to him. And besides he must believe that both all the commandments (which teacher obedience) and the threatenings (because they restrain the contrary), are set down for him particularly to bind his conscience thereunto, Romans 15:4.
Thus he must attend upon the whole word of God. Many who have hoped to be saved do not thus. Some sins they make no conscience of; some promises they look not at. [Therefore] they are not so well fenced as they might be; but hold the very promise of salvation itself very weakly. This comes to pass partly because they are not taught these things are right: partly because being taught, they do not digest and work upon them their consciences.
This brings doubting and unsettledness even to good Christians: therefore he that believes to be saved, must believe also that he shall be sanctified, 1 Corinthians 1:30; that he shall receive grace from God to bring forth fruits of amendment of life; and that he shall be enabled to cast off his old conversation. [He must also believe that he will] have grace to go through troubles and deliverance from them.
For assistance and blessing of God, he must depend on God’s Word; this is the obedience of faith, Romans 1:5. , which if we have as a foundation to uphold and encourage us, it will greatly avail for the furthering of us in a godly course; by this we shall sooner wade through doubts, and grow out of fear; whereas otherwise we think and fear often times and be without help.
Many examples we have in the Scripture of such as thus believe, especially set down in the 11th chapter to Hebrews: Hebrews 11:16, 38; Galatians 2:19. When men do not thus walk in the strength of God his word, it causes tedious troubles in them, and indeed the offensive lives of many, and the starting aside of sundry [many persons] come from this want [lack].
Paul Complained of his Flesh – Not of Faith
But it may be objected, that Paul himself seemed to want [lack] to this, for he found no means to perform that which was good, as he complains, Romans 7:18. I answer onto that
He complains not that he had no promise of stremgth, or that he had no faith in the same, for he saith the contrary, Philippians 4:13. He complains that for all the hope of help that he had, yet the rebellion of his flesh did mightily striving resist the spirit. And this must every faithful man look for while he live.
A Godly Life Proceeds from a Pure Heart
Now for the fountain from whence a godly life does proceed, it is from the heart, which therefore must be purged and cleansed.
For this we are to know, that the heart of man, before it be emptied, is a dungeon of iniquity; before it be enlightened, a den of darkness; before it be cleansed, a puddle of filthiness: and that which St. James speaks of the tongue, may much more be said of the heart, that before it be tamed, it is an unruly evil. Now if such a heart be the guide for our life, how monstrous and loathsome must that life needs be? Of necessity then the heart must be purged and changed.
The Spirit Transforms the Heart
This purging of the heart is renewing in holiness and righteousness by little and little of all true believers, they being first delivered and freed from the tyranny of sin and fear of damnation; for then does sin receive a deadly wound, and the power thereof is abated and crucified. [The change] is showed by the hatred of sin and a delighting in goodness.
Although this change [will] be but weakness at first. Yet if it be in truth, and will, and desire, it is an infallible mark of God’s election and love towards them. This grace is dimmed and often choked in many because [they fail to seek God]. God does strengthen and continue this gift of holiness and sanctification, as it is nourished, esteemed, set by, and as men do stir it up for themselves, by asking after it when they do miss it, and provoking themselves to pray for such good affections and cannot be satisfied without them; as David did, Psalm 43:5, 103:1.
Thus we ought to cherish and blow up the sparks within us, which will not ordinarily fail us, especially for any long time — except in time of temptation, [or it result from] our default and folly.
As for the matter how this is done, we are to know what is the proper and wonderful work of God by the power of the Holy Ghost. Acts 15:9; Isaiah 11:2. He that has faith unfeigned and [a] heart sanctified and purified from his natural corruption and wicked disposition; as it is not to accounted being little worth, it being an evident work of the Spirit; so neither is he to stand at this stay in this, it being about the beginning of the work that shall follow it.
Faith is the Instrument Used by the Spirit
Objection: How does God purge our hearts, when faith is said to do it. Acts 15:9, 1 John 3:5.
Answer: Faith is truly said to do it: because those men not yet assured of the happiness of heaven, not knowing, nor feeling any better delights — [those men] seek after those [delights] which their blind and deceitful hearts do dream of here on earth.
But as soon as they are assured of God’s favor through faith, so soon are their hearts changed, and their affections set another way; so that faith may well be said to purify and cleanse the heart, 1 Peter 1:4; but not as the chief and highest cause, for that is the Holy Ghost. [Faith is] but as the instrument.
Thus from faith and a pure heart do arise a good conscience, a sweet peace, and holy security; having received from God a mind to know him, a heart to love him, the will to please him; and strength also in some measure acceptable to obey him.
From hence does proceed that true repentance, which is a purpose of the heart. Acts 11:23; an inclination of the will, Psalm 119:44, 57; and a continuing every in the life, Acts 24:16. [Such a man will] cast off all evil and obey God both inwardly and outwardly, according to the measure of knowledge and everyone.
Only True Heart Change Will Produce a Godly Life
So that this sound of purging of the heart, is that strong foundation upon which only a good life comes to be built. For God will have our whole heart, not a piece of it, for it is neither beseeming his greatness, nor fit for them to [suffer? offer?] or receive so great good blessings at his hands. Many indeed are hardly brought to this, and therefore all their fair shows and colors do vanish away, and come to nothing, for rash and hasty purposes are no sufficient foundation to bear up so great and weighty buildings, as the whole course of their lives to be wholly passed.
But if men at their first embracing of the gospel to give their hearts holy to the Lord, then should God have more honor, and themselves more abiding comfort.
The Progress of Godliness
Now having shown the ground and root of the godly life, that is, faith and a pure heart; it remains to speak of the parts of it, which is a renouncing of all sin, and a care to walk in a new life.
A Continual Hatred of Sin
The party believing is brought to this power and grace, that he is out of love with all ungodliness, but not only with some part or kind, but loathes the whole course of iniquity, which was his only delight pleasure before. Neither does he this in some good mood only, or when some shame or danger approach, than to show some mistake of it. But in good advisement he is resolved to cast off such behavior, as a loathsome ragged garment. Hosea 4:9, Ephesians 4:24, Matthew 16:24.
For want of this settled denying of ourselves, divers [many people] never attain true godliness. Some never conceiving [understanding] the doctrine, others forgetting, and some supporting it, the most receiving a coldly, and going about it preposterously.
Whereas the servants of God leave not sin for a time, nor by constraint, or for company, and fear, etc. But being at utter defiance with it, do abjure it forever. Nehemiah 10:29.
But in all these they trust not to their own strength, but daily considering what cause they have to do so. [First, they are] infinitely bound to God to discharge it [their duty to forsake sin]. [They also] become firmly persuaded that God who has made them willing, will also make them able to do it. Philippians 4:13, Romans 9:31. And therefore, although they see not the help present with their eyes, yet they hope for that which they see not, and therefore wait patiently for, till it be granted [to] them.
Thus both faith and hope being nourished and strengthened in them day-to-day, they do find both the will and desire and strength (though imperfect) to accomplish the peace of their hearts, that which they set upon and attempted. Indeed it is not obtained without striving, but [that] is no just cause of discouragement to us, to take pain for so great a profit, when we are sure of that before we go about it.
Should We Be Discouraged if We are not Perfect?
Objection What if the faithful do not always prevail therein?
Answer: As it is true that in some particulars they are overcome, yet that does not cut off all comfort for them: for howsoever they do not account light of any fall, yet those very falls turn to their gain afterwards; for thereby they come to know themselves better, their prime pride is much assuaged, they have experience of God’is grace toward them, and they cleave more nearer onto him after, and are more circumspect in looking to their ways: Remember always that this belongs only to the true believer, who having the Lord for his teacher, is become both skillful and able to do this; which the natural man (in whom is no dram of goodness) is altogether impossible.
 New life will entail obedience.
 Obedience grows over time. It is as not as great as first as it must become. Moreover, temptation derails obedience.
 A distinctive uniform – usually worn by a servant. See, e.g., 1 Peter 5:5.
 Only one who lives like a Christian should believe themselves to be forgiven. Note that he does not say behavior causes God to forgive; nor does he argue that good behavior proves one to be forgiven. Rather, he argues that one who is a Christian (forgiven) will live like a Christian. The manner of life is an evidence – not a cause. Second, it is the Christian himself who looks to his manner of life as proof of forgiveness.
 The object of saving faith is more than just the idea that I will be “saved”. True saving faith lays hold to all the promises – not just one.
 The promises of physical well-being are not absolute: Physical well-being is a good thing – but not the best thing. God will give physical well-being, but only to the extent it will preserve our soul. This concept is well illustrated lines from “O Sacred Head Now Wounded”:
What language shall I borrow to thank Thee, dearest friend,
For this Thy dying sorrow, Thy pity without end?
O make me Thine forever, and should I fainting be,
Lord, let me never, never outlive my love to Thee.
 Although thoroughly evangelical in his theology, Baynes does not think the commands and warnings of the Bible meaningless. God may order the manner of life for his children – even though the conduct of the children is not the basis of their adoption. This is precisely as it is parent-child relationships: Behavior does not make one a child. Imagine a well-behaved boy coming over to play with an ill-behaving boy. The well-behaved boy does not become a son of the household merely by behaving. The ill-behaved boy does not stop being a son because he disobeys.
 Baynes wrote, “by means whereof” rather than “therefore”.
 They are not as protected/safe as they might be.
 The responsibility for weak Christians first rests with the pulpit: The pastor has the primary responsibility of teaching doctrine. A simple read through the pastoral epistles will demonstrate the emphasis which Paul places upon protecting the teaching. Second, the individual has the responsibility for not sufficiently studying, meditating, reading Scripture (Psalm 1:2, “day and night”, that is, continually).
 One who does not believe that he will be changed, that the “old self” (Romans 6:6, ESV) has died with Christ will not see a proper transformation of life. It is a command that we are to “consider ourselves dead to sin but alive to God in Christ Jesus” (Romans 6:11).
 “For the Puritans, conscience is the faculty that God puts in us to be a sounding board for applying His Word to our lives. Our consciences should be weighted with the Word of God; they should be educated by what is taught in Scripture and trained to judge according to Scripture. Then the voice of the conscience will be the voice of God indeed…The Puritans believe that the only cure for a falsely calibrated conscience is for the conscience to be thoroughly educated in Scripture standards” (Joel R. Beeke and Mark Jones, A Puritan Theology: Doctrine for Life (Grand Rapids, Mich.: Reformation Heritage Books, 2012) 920)
 Failure to understand this point has led to much unhappiness among believers: We have a tendency to focus solely upon outward conduct. While conduct does disclose the heart, the relationship between the heart and the hands is not perfect. Moreover, we often fail to rightly consider the Spirit’s work:
The Spirit works in the heart by causing us to see sin as vile and Christ as beautiful. The effect of hating sin and loving Christ will show itself in our conduct.
The common failure of Christians is to seek to amend their behavior rather than seek the work of God’s Spirit in their hearts. Our primary goal is to worship the King. As we seek to worship the Lord, our lives will be transformed. Thus, one who shows no sign of true worship has no good reason to think himself a believer.
 The text is obscure at this point.
 He calls a profession of faith and a public display of piety which does not last as a “fair show and color” – a mere appearance without substance.
 True heart change requires far more than mere change of behavior.
 He does not merely hate certain select sins – usually sins which are no temptation for him.
 To hate a sin which one previously loved is a strong mark of saving faith.
 Augustine wrote in Book 10, Chapter 29 of his Confessions:
And my whole hope is only in Your exceeding great mercy. Give what You command, and command what You will. Thou imposest continency upon us, nevertheless, when I perceived, says one, that I could not otherwise obtain her, except God gave her me; . . . that was a point of wisdom also to know whose gift she was. Wisdom 8:21 For by continency are we bound up and brought into one, whence we were scattered abroad into many. For he loves You too little who loves anything with You, which he loves not for You, O love, who ever burnest, and art never quenched! O charity, my God, kindle me! You command continency; give what You command, and command what You will.
 We must trust God will help – even when we do not see how God can help:
No temptation has overtaken you that is not common to man. God is faithful, and he will not let you be tempted beyond your ability, but with the temptation he will also provide the way of escape, that you may be able to endure it. 1 Corinthians 10:13 (ESV)
And take Christ caution, ye shall not lose your reward. Hold your grip fast. If ye knew the mind of the glorified in heaven, they think heaven come to their hand at an easy market, when they have got it for threescore or fourscore years wrestling with God. When ye are come thither, ye shall think, “All I did, in respect of my rich reward, now enjoyed of free grace, was too little.” Now then, for the love of the Prince of your salvation, who is standing at the end of your way, holding up in His hand the prize and the garland to the race-runners, Forward, forward; faint not.
Samuel Rutherford and Andrew A. Bonar, Letters of Samuel Rutherford: With a Sketch of His Life and Biographical Notices of His Correspondents (Edinburgh; London: Oliphant, Anderson & Ferrier, 1891), 51.
 We must not think any sin a “small sin” — that is account the sin to be “light” (insubstantial, unconsequential).