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Towards the end of Mark 14, Jesus warns Peter to keep watch lest he fall into temptation:

Then he returned to his disciples and found them sleeping. "Simon," he said to Peter, "are you asleep? Couldn’t you keep watch for one hour? Watch and pray so that you will not fall into temptation. The spirit is willing, but the flesh is weak."

Mark 14:37-38 NIV

Most translations don't seem to capitalize spirit in the phrase "the spirit is willing", indicating that they take this in reference to Peter's spirit. Witherington (SRC), however, interprets this as the Holy Spirit, citing Isaiah 31:3 and Psalm 51:11-12 as possible support. This also seems to fit will with the encouragement towards prayer.

Beyond this are there good reasons to think this refers to the Holy Spirit vs Peter's (a person's) spirit?

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I am not sure it makes sense to see "spirit" and "Spirit" in an either/or sense. If we understand the "spirit" part of man that Paul refers to in his Epistle to the Thessalonians (1 Th 2:3) to be that Spirit which God breathed into man that brought life to his soul (Gen 2:7 LXX), then the two are intimately coupled. Man's spirit is always in synchrony with the Holy Spirit, but life's struggle is to heed the spirit (and hence, the Spirit) over flesh.

The 19th century Russian monk and theologian, Theophan the Recluse, wrote:

The spirit as a force proceeding from God, knows God, seeks after God and only in Him finds its rest. By means of some kind of hidden spiritual sensitivity, the spirit is convinced of its origin in God. The spirit feels its total dependency on Him and acknowledges that it is obliged to please God in every way and live in Him and for Him.

The Spiritual Life and How to Be Attuned to It (St. Paisius Serbian Orthodox Monastery, 2003), p. 46-47

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This is one of those passages that you have to read all of the gospels and look at everything that was going on within the 24 hr period in question. For each gospel tells us something a little different. In Luke's account, we do not hear the bit about the spirit being weak. It does however, tell us that Satan had asked to sift Peter. And furthermore, Jesus tells Peter he needed to pray in order to not give into temptation. What we see then is that Jesus is specifically speaking to Peter. The temptation that Peter needed to pray for was the coming temptation where he lies about knowing Jesus. Jesus even warns Peter that he would betray him. Paul also gives some help in clarifying the meaning. For he describes doing the things he does not want to do, and not doing the things he wants to do. The notion of the spirit and the flesh (carnal nature) being at odds with one another is taught all throughout scripture and is separate from the the Holy Spirit's involvement. And it is these two natures that Jesus is referring to.

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In Mark 14:38, it is written,

38 Watch and pray so that you do not enter temptation. The spirit is ready, but the flesh is weak.

ΛΗʹ γρηγορεῖτε καὶ προσεύχεσθε ἵνα μὴ εἰσέλθητε εἰς πειρασμόν τὸ μὲν πνεῦμα πρόθυμον ἡ δὲ σὰρξ ἀσθενής TR, 1550

According to John 7:39, those who believed in Jesus (which would have included his apostles) were not given the Holy Spirit until the Lord Jesus Christ was glorified, referring to his ascension.1

The Lord Jesus Christ commands the apostles to “watch and pray” because they fell asleep during their watch. After his command, he informs the apostles, “The spirit is ready, but the flesh is weak.” At the least, he is obviously referring to their flesh being weak. After all, it was they who fell asleep. Whether he includes himself by his statement is uncertain, but possible.

Because his apostles did not have the Holy Spirit, informing the apostles that “the [Holy] Spirit is ready” would have been a moot point. They didn’t have the Holy Spirit, so what did that matter? Rather, it seems that the Lord Jesus Christ was referring to their own human spirit as being ready.

In Kurze Erklärung der Evangeliums Matthäi, regarding Matt. 26:41 (the synoptic parallel of Mark 14:38), Wilhelm Martin Lebrecht De Wette wrote,2

De Wette, p. 224, Matt. 26:41

which may be translated as,

They were in need of watching for themselves, the corporal and the spiritual [watching], and the prayer. ἵνα - πειρασμόν (“so that...temptation”)] so that you do not enter temptation, cp. Matt. 6:13. τὸ μὲν πνεῦμα κτλ. (“the spirit,” etc.)] πνεῦμα (“spirit”) = νοῦς (“mind”), ὁ ἔσω ἄνθρωπος (“the inner man”) Rom. 7:22, the spiritual, moral drive; σάρξ (“flesh”) is the sensual will, Rom. 7:18, 7:25), cp. LB. d. Sittenl. §. 11. 15. This had become especially true of Peter.

To answer your question: the main point contrary to the assertion that the Lord Jesus Christ was referring to the Holy Spirit is that the apostles did not have the Holy Spirit, and had he been referring to the Holy Spirit, it would have been a moot point. If one supposes that the Lord Jesus Christ was referring to the Holy Spirit, then one must endeavor to prove the apostles possessed the Holy Spirit before the Lord Jesus Christ was glorified, contrary to his own statement that it would not be given until thereafter.


Footnotes

1 cp. John 16:7
2 p. 224

References

De Wette, Wilhelm Martin Lebrecht. Kurze Erklärung der Evangeliums Matthäi. Leipzig: Weidmannsche Buchhandlung, 1836.

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Whose spirit is willing in Mark 14:38?

Mark 14:38 (NASB)

38 Keep watching and praying that you may not come into temptation; the spirit is willing, but the flesh is weak.

IT REFERS TO A PERSON'S INDIVIDUAL SPIRIT-- SEE CATEGORY B, BELOW.

SPIRIT.

The Greek word translated as “spirit” is “pneuma”,(from the Greek verb “pneo” =breath or blow) the basic meaning is of which is “wind” the movement of air. Wind is a force that we can feel but cannot be touched or seen In the scriptures the writers used it in a variety of ways and translators have recognized the multiple use of "spirit." It is used to mean wind, breath, spirit, one's own spirit, spirit persons, and Holy Spirit.

A The breath , or life force which animates the body.

James 2:26 (NLT)

26 "Just as the body is dead without spirit (breath). so also faith is dead without good works"

John 19:30 (NLT)

30 "When Jesus had tasted it, he said, “It is finished!” Then he bowed his head and gave up his spirit. (last breath)

B/ A person’s individual spirit , the emotions ,thoughts , feelings and actions that emanate from a person’s figurative heart

Mark 14:38 (NASB)

38 "Keep watching and praying that you may not come into temptation; the spirit is willing, but the flesh is weak.”

John 13:21 (NASB)

21 "When Jesus had said this, He became troubled in spirit, and testified and said,

“Luke 1:80 (NASB)

"And the child continued to grow and to become strong in spirit, Truly, truly, I say to you, that one of you will betray Me.”

 ,  C The spiritual person

1 Corinthians 3:1 (NASB)

3 "And I, brethren, could not speak to you as to spiritual men, but as to men of flesh, as to infants in Christ."

Ephesians 4:23-24 (NASB)

23 "And that you be renewed in the spirit of your mind, 24 and put on the new self, which in the likeness of God has been created in righteousness and holiness of the truth."

1 Corinthians 2:14-16 (NASB)

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."

D Spirit Persons,

John 4:24 (NASB)

24 God is spirit, and those who worship Him must worship in spirit and truth.”

1 Corinthians 15:45 (MEV)

45 "So it is written, “The first man Adam was made a living soul.” The last Adam was made a life-giving spirit."

1 Peter 3:19 (NASB)

19 "In which also He went and made proclamation to the spirits now in prison."

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Peter's spiritual state

Were the disciples regenerate? Oddly it doesn't appear they were. It doesn't appear so, though they are said to "believe in Jesus":

Joh_2:11 This beginning of miracles did Jesus in Cana of Galilee, and manifested forth his glory; and his disciples believed on him.

But they did not yet seem to believe that Jesus would be resurrected:

Joh_2:22 When therefore he was risen from the dead, his disciples remembered that he had said this unto them; and they believed the scripture, and the word which Jesus had said.

In fact, Peter had denied Jesus:

Luk 22:61 And the Lord turned, and looked upon Peter. And Peter remembered the word of the Lord, how he had said unto him, Before the cock crow, thou shalt deny me thrice.

So Peter had failed the test of faith:

Luk_12:9 But he that denieth me before men shall be denied before the angels of God.

But Jesus had spoken of a day, future to his denial when Peter would be "converted":

Luk 22:32 But I have prayed for thee, that thy faith fail not: and when thou art converted, strengthen thy brethren.

And Peter testifies that it was not until Jesus was resurrected that he became converted:

1Pe 1:3 Blessed be the God and Father of our Lord Jesus Christ! According to his great mercy, he has caused us to be born again to a living hope through the resurrection of Jesus Christ from the dead,

At that time Jesus breathed into them the holy breath:

Joh 20:20 When he had said this, he showed them his hands and his side. Then the disciples were glad when they saw the Lord. Joh 20:21 Jesus said to them again, "Peace be with you. As the Father has sent me, even so I am sending you." Joh 20:22 And when he had said this, he breathed on them and said to them, "Receive the Holy Spirit.

So hopefully we can glean from this that Peter's denial of Jesus "didn't count" because he was not yet converted. Like Paul's behavior:

1Ti_1:13 Who was before a blasphemer, and a persecutor, and injurious: but I obtained mercy, because I did it ignorantly in unbelief.

However, had Peter been converted he would have been disqualified from "the kingdom of God":

Luk 9:62 Jesus said to him, "No one who puts his hand to the plow and looks back is fit for the kingdom of God."

So an unregenerate Peter denies the lord, believes with "saving faith" and is forgiven, sets his hand back to the plow and (presumably) never looks back again.

Prayer in Gethsemane

So in the midst of this drama Jesus is in a garden interacting with three of his disciples, including Peter. He tells them to pray for themselves to be :

Mat 26:41 Watch and pray, that ye enter not into temptation: the spirit [breath] indeed is willing, but the flesh is weak.

I take this to mean:

"Pray that you will not cave when tested; talk is cheap but pain (and the fear thereof) is a different story because the flesh is vulnerable [to pain]".

I find this usage of "vulnerable" being echoed here:

1Pe 3:7 Likewise, husbands, live with your wives in an understanding way [in an informed way], showing honor to the woman as the weaker [more vulnerable] vessel, since they are heirs with you of the grace of life, so that your prayers may not be hindered [truncated].

So the disciples, overconfident, fail to apply to God and fall asleep, unprepared for testing.

So there is no "spirit" in view, only the overconfident protestations that escaped like a vapor from Peter's prayerless lips. His "breath" was heroic but his behavior cowardly because of the influence of the fear of pain and death.

The whole concept that Peter might have a "human spirit" is bogus. There is no such thing. According to Moses, man is composed of flesh (the body, from the dirt) and "breath". I recently explained how Substance Dualism became an unimpeachable fixture of Christianity despite its origin in Greek philosophy, scientifically untenable propositions and the testimony of the scriptures. The translation "spirit" in this OP is a symptom of that disease.

What if Peter had been converted when he denied the lord?

So Peter denied the lord in ignorance and was given the charge to place his hands back on the plow of the kingdom. But what if he had been converted? Would he have had a second chance? Many sermons try to comfort the unfaithful by using the example of Peter of "grace". But what does Peter say?

Peter speaks of "the trial of one's faith":

1Pe 1:6 In this you rejoice, though now for a little while, if necessary, you have been grieved by various trials, 1Pe 1:7 so that the tested genuineness of your faith—more precious than gold that perishes though it is tested by fire—may be found to result in praise and glory and honor at the revelation of Jesus Christ. 1Pe 1:8 Though you have not seen him, you love him. Though you do not now see him, you believe in him and rejoice with joy that is inexpressible and filled with glory, 1Pe 1:9 obtaining the outcome of your faith, the salvation of your souls.

From this we get the colloquialism "trial" as in "I'm going through a trial" or "a trying situation". The popular idea is that a "trial" is a "difficult time". But in actuality, a "trial" is an "ordeal". In the ancient world an "ordeal" was a legal process. If you survived the ordeal you were deemed to be vindicated by the gods but if you died, well then you were guilty. For more info, see here:

http://ancienthebrewpoetry.typepad.com/ancient_hebrew_poetry/2010/04/trial-by-ordeal-in-the-bible-and-the-ane-tikva-frymerkensky-and-unpublished-manuscripts.html

So for Peter, the "trial by fire" was not just a difficult situation but one designed to separate the gold from the dross. That is, God arranges situations where all the talk ("breath") that is being spouted by people claiming to be faithful to God is put to the test and those who "endure to the end" are saved while those who fail are rejected. Here's a famous example:

Gen 22:1 Sometime later, God tested Abraham. He called out to him, "Abraham!" "Here I am!" he answered. Gen 22:2 God said, "Please take your son, your only unique son whom you love—Isaac—and go to the land of Moriah. Offer him as a burnt offering there on one of the mountains that I will point out to you."

The purpose of this was forensic. That is, since God can't read a person's mind (more on that later) God had devised a test to reveal Abraham's love for Yehovah, or lack thereof. At the end, God says:

Gen 22:12 He said, "Do not lay your hand on the boy or do anything to him, for now I know that you fear God, seeing you have not withheld your son, your only son, from me."

That this decided the validity of Abraham's faith is mentioned by James:

Jas 2:17 So also faith by itself, if it does not have works, is dead.

Jas 2:18 But someone will say, "You have faith and I have works." Show me your faith apart from your works, and I will show you my faith by my works. Jas 2:19 You believe that God is one; you do well. Even the demons believe—and shudder! Jas 2:20 Do you want to be shown, you foolish person, that faith apart from works is useless? Jas 2:21 Was not Abraham our father justified by works when he offered up his son Isaac on the altar? Jas 2:22 You see that faith was active along with his works, and faith was completed by his works; Jas 2:23 and the Scripture was fulfilled that says, "Abraham believed God, and it was counted to him as righteousness"—and he was called a friend of God. Jas 2:24 You see that a person is justified by works and not by faith alone.

David welcomed these trials, as James had suggested:

Jas 1:2 Count it all joy, my brothers, when you meet trials of various kinds,

Psa_7:9 Oh let the wickedness of the wicked come to an end; but establish the just: for the righteous God trieth the hearts and reins.

Psa 17:1 A Prayer of David. Hear a just cause, O LORD; attend to my cry! Give ear to my prayer from lips free of deceit! Psa 17:2 From your presence let my vindication come! Let your eyes behold the right! Psa 17:3 You have tried my heart, you have visited me by night, you have tested me, and you will find nothing; I have purposed that my mouth will not transgress. Psa 17:4 With regard to the works of man, by the word of your lips I have avoided the ways of the violent. Psa 17:5 My steps have held fast to your paths; my feet have not slipped.

Psa_26:2 Examine me, O LORD, and prove me; try my reins and my heart.

Psa_139:23 Search me, O God, and know my heart: try me, and know my thoughts:

So David had passed the tests, proved faithful and he welcomes God's vindication.

Jeremiah knew of this:

Jer_11:20 But, O LORD of hosts, that judgest righteously, that triest the reins and the heart, let me see thy vengeance on them: for unto thee have I revealed my cause.

Jer 17:10 "I the LORD search the heart and test the mind, to give every man according to his ways, according to the fruit of his deeds."

Jer_20:12 But, O LORD of hosts, that triest the righteous, and seest the reins and the heart, let me see thy vengeance on them: for unto thee have I opened my cause.

And so on. It is vain to think that one can fail the trial and yet be vindicated with salvation.

1Ki 20:11 The king of Israel answered, "The saying goes, 'Don't brag about a victory before you have even dressed for battle.'"

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