The problem with the Westminster confession is that while it contains some things that are true, and a good list of references, not everything it claims is actually supported by the verses it cites. It reads in definitions and meanings and philosophies that the verses do not mandate in many cases.
There is a general article on it hear that gets into how it is a mixed bag of good and bad, and the dangers that can crop up if someone or a church group starts treating it as infallible truth or equivalent to scripture.
Christians Together : The Westminster Confession: a critique
More specifically on IX though:
1. God hath endued the will of man with that natural liberty, that it is neither forced, nor, by any absolute necessity of nature, determined to good, or evil (Matthew 17:12; James 1:14; Deuturonomy 30:19; Isaiah 7:11-12†; John 5:40†; James 4:7†).
While what they mean by will and natural liberty is unclear, the verse references given all do support that thought that man can choose to do evil things or choose to do good things. Other verses could be added to this: Josh 24:15, Matt 7:13, Rom 10:10, Acts 17:26-17, Rome 2:13-16, Ezek 33:12-13, etc.
2. Man, in his state of innocency, had freedom, and power to will and to do that which was good and well pleasing to God (Eccl 7:29; Genesis 1:26; Philippians 2:13‡; Colossians 3:10†); but yet, mutably, so that he might fall from it (Genesis 2:16-17; 3:6).
This section suffers from being ambiguous, as it doesn't really describe whether man is mutable by his own actions or God made man imperfect. The scriptures cited, however, make it very clear that God made man in his image and upright but that it was man who went off in 'search of many schemes.' So while man (and angels) were made with the capacity to rebel, this rebellion was not caused or mandated by God.
Phil 2:13 and Col 3:10 are irrelevant support verses for this section as they specifically addressing Christians who have the indwelling Spirit and are made a new creation in Christ, not Adam and Eve at the time of creation. Adam and Eve did not have the indwelling Holy Spirit and were not new creations in Christ.
3. Man, by his fall into a state of sin, hath wholly lost all ability of will to any spiritual good accompanying salvation (Romans 5:6; 8:7; John 6:44, 65†; 15:5): so as, a natural man, being altogether averse from that good (Romans 3:10, 12), and dead in sin (Ephesians 2:1, 5; Colossians 2:13), is not able, by his own strength, to convert himself, or to prepare himself thereunto (John 6:44, 65; 3:3, 5-6†; Ephesians 2:2-5; 1 Corinthians 2:14; Titus 3:3-5).
The section here is not faithful to the scripture text, and makes up philosophical claims whole cloth.
Firstly, the first few support verses do not go so far as to say man can do no spiritual good 'accompanying salvation:'
Rom 5:6 says that when we were powerless Christ died for the ungodly. In the context of the passage it is very clear what we were powerless to do - be justified, reconciled to God, and receive eternal life. It also is very clear when that powerlessness ended - when Christ died! Now we could be justified, reconciled to God, and given eternal life - via faith in Christ! The whole point of the passage is that where there was no hope for us under sin and the law there *is* hope for us under Christ.
Rom 8:7 is, in context, about the mind of unbelievers as contrasted with Christians who have the indwelling Spirit and the mind of Christ. "The mind governed by the flesh is hostile to God; it does not submit to God’s law, nor can it do so." Not being able to submit to God's *law,* which no unbeliever can do, says nothing about being without hope, unable to repent, unable to respond to the gospel in faith, unable to understand that Christ is Saviour and He was sinless and so His blood can cover our sinfulness - etc. We receive the Spirit (Rom 8:14-16) after we have faith (Gal 3:2, Acts 18:15, Gal 3:14) - not before.
John 6:44-45 also doesn't go so far as the Confession. It states man cannot come to Christ without the Father drawing - but the Father draws all by Christ's death (Jn 12:32.) Jn 6:65 also mentions that the Father must grant someone be able to come - i.e. the Father's grace is required. This grace is also given to all through Christ, which is why salvation is 'by grace.' The passage in its context also mentions many things unbelievers must do if they want to do the works of God or come to Christ:
-Believe in the one God sent (Jn 6:28-40)
- Hear the Father and Learn from Him (Jn 6:45)
- Eat Jesus' Flesh/Drink blood i.e. be crucified with Christ and remain in communion with Him (Jn 6:53-59)
So while Jesus points out that they couldn't do anything without the grace of the Father, He specifically puts the choice to come to Him or not, feed on Him or not, and to listen to the Father and learn on their shoulders. This makes a lot of sense considering the Jewish mentality of the era - to them, the Messiah should automatically save them due to their Jewish heritage, and it was an obligation of God's. To them, their personal thoughts on the Messiah and scholars's views on write and wrong were prioritized over humbling themselves and examining scripture.
Jn 15:5: This is a very odd support verse to use as it is strictly about Christians, not non-Christians, and the importance of remaining in Christ. 'Apart from me you can do nothing' is very clearly about bearing spiritual fruit, as Jn 15:4 directly states. Faith is how we are grafted into the vine (Rom 11:17-21,) not something we can only get by being in the vine. The fruit we grow adds to our faith as we abide in Christ (II Pet 1:3-11)
Rom 3:10-12: This verse is about all men, Jew and Gentile alike, being under the power of sin (Rom 3:9.) It is a quote from Psalm 14, and shows that mankind has deliberately turned away from God and to sin and are corrupt and perform vile deeds. These fools are deliberately contrasted with God's people in Psalm 14 and concludes with the hope that God's salvation will come from Zion. By quoting this in Romans, Paul shows that salvation has now come, through Christ. The verses do not say anything about man being unable to do anything, such as respond to the gospel in faith, that accompanies salvation. Rather it shows that man can't save himself via the law as all are corrupt. The passage itself clarifies it's own point:
"
Therefore no one will be declared righteous in God’s sight by the works of the law; rather, through the law we become conscious of our sin. But now apart from the law the righteousness of God has been made known, to which the Law and the Prophets testify. This righteousness is given through faith in Jesus Christ to all who believe. There is no difference between Jew and Gentile, for all have sinned and fall short of the glory of God, and all are justified freely by his grace through the redemption that came by Christ Jesus. God presented Christ as a sacrifice of atonement, through the shedding of his blood—to be received by faith." (Rom 3:20-25)
Note the point was not, 'therefore, since you can't be declared righteous by the law, you cannot even receive Christ's sacrifice by faith.' It was not 'Everyone has fallen short, therefore no one can be conscious of their sin and repent.'
The Westminster confession here completely ignores the context in an attempt to prove a point that the passage itself debunks.
Eph 2:1-5, Col 2:13: The confession is correct that these verses show we were dead in sin, but incorrect in any implication that this means we could not respond to the gospel in faith. Eph 2:8 directly clarifies that we are saved through faith - we don't get faith after salvation. Col 2:12 clarifies that our 'dead selves' are buried with Christ in baptism and that we are raised with Christ *through faith,* and that this is how God makes us alive with Christ in Col 2:13. We aren't made alive first so we can 'get faith.'
John 3:3, Jn 3:5-6: These verse states that one can see the kingdom of God unless they are born again." This is true, as we literally cannot enter the kingdom of God in the future until we recieve new spiritual bodies, and we figuratively cannot enter the kingdom of God in the present until we are raised to new life in Christ and have the spirit. But none of that means that a person cannot have faith! Again as Col 2:12-13 shows, faith comes prior to us being raised in Christ (the new birth.)
1 Corinthians 2:14: This is another very odd choice of support verse, as it is specifically speaking of how Christians are given discernment by the indwelling spirit, and how the Spirit guides us in the wisdom of spiritual things. Nothing in the passage supports the idea that 'faith' is something we can only have or learn about once given the spirit - especially as scripture is very clear that faith is a *prerequisite* for receiving the spirit.
Titus 3:3-5: This passage just shows that as unbelievers we were once enslaved to our own pleasures and practiced all manner of malice and hate. But *then* the kindness and love of God appeared! A light in our darkness! God by His mercy saved us through the washing and renewal by the Holy Spirit (which again, as Col 2:12-13 shows, happens *after* faith) and justified us by His grace (which as we know from Rom 5:1 and other passages also happens through faith, not prior to it.) Nothing in the passage says man cannot see the kindness and love of God that appeared in Christ or respond to it. Nothing says man cannot respond in faith.
