One of the things that rekindled my interest in bible study was the realization that there is a correlation between the bible and the so called "supernatural occurences".  For example, many patients on their death bed talk of floating outside of their body and having "out of body experiences".  Some have spoken of a silver rope that attached their floating self to their physical body.  They didn't know what this rope was, but got a feeling that if this rope broke that they would be dead and seperated from their body forever. Ecclesiastics 12:6-7 speaks of this silver rope as well; it states that if the silver chord is  ever broken that the body will return to the dust from which it came and the spirit will return to Heaven.

The study of spirit and soul is sometimes complicated by the fact that both words are used figuratively in many passages.   If you don't have an understanding of what the words mean you won't be able to determine which usage is figurative and which is literal.

As an example as to how this can lead to confuse, suppose I wanted to understand the meaning of the word dead in English.  If I ran across the expression that someone was dead wrong that would cause confusion if I didn't understand that it was just a figure of speech that meant the person was very wrong and didn't actually have anything to do with the actual meaning of the work dead. 
 

One must also keep in mind that the Old Testament was written (primarily) in Hebrew and the New Testament was written in Greek.  The Hebrews and the Greeks had different concepts of what the spirit and the soul are.  There was really no equivalent for the term as we currently understand it in the ancient Hebrew language because the ancient Hebrew's didn't truly differentiate the spirit from the soul.

Both words are also used to indicate a living being.  Spirit is generally used in relation with God.

The Body

Our flesh bodies are the center of our 5 senses--sight, smell, sound, taste, and touch.  These are all attributes of our body.  Additionally, our bodies are also the center for lust, hunger, and everything else that is described as our "animal nature" or "animalistic behaviour".  These are the qualities that we share with animals since both our human bodies and animal bodies are all flesh created from the earth.  This is why all men sin because it is in the nature of our bodily makeup. 

When certain situations arise or certain stimuli are introduced we instinctively want to behave in a certain way.  For example, nature causes some species to become sexually aroused near the period of time when they're bodies are physically able to conceive children.  This is how our bodies encourage us to reproduce.

What seperates us from animals is that we have a conscious will and thus have more control over our actions.  There is a stimulus and there is a response to the stimulus.  Steven Covey talks about the fact that for humans there is a small gap between stimulus and response where we choose our response.  During this gap we have the ability to override our natural/anamalistic behaviour.  When threatened, some animals will automatically begin to attack or fight.  For humans, we have a natural response, but we can consciously choose whether to act out that natural response. 

The term "overcoming the flesh" refers to the act of behaving differently than your body encourages you to behave because you decide that you should behave differently.  Humans have this "gap", or ability to make a conscious choice because we have a human soul.  This is what is refered to as "free will".  We have the ability to consciously control our behaviour and even (to some extent) our emotions.
 

The Soul

When you are in your mothers womb, your soul is put into your body.  This can be seen in Luke 1:41 when Mary was pregnant with Christ and her sister Elizabeth was pregnant with John The Baptist.  When Mary came near Elizabeth, John jumped in Elizabeth's stomach because he could feel the presence of Christ.  This shows that both souls were in the bodies before they were born. 

The word soul is used in the Bible to mean: "soul," "living being," "life," "self," "person," "desire," "appetite," "emotion" and "passion" (Brown-Driver-Briggs, Hebrew-English Lexicon, s.v.)

Many bible verses referring to "your heart" or "your mind" are refering to your soul.  The heart is often refered to as the seat of your emotions.  It is linked to love and other emotions as in the  expressions "my heart goes out to you", and "I could feel it in my heart".  1 John 5:8 refers to the soul as "the blood".  If we understand that the purpose of the heart is to pump blood throughout the body, and that our emotions are in our soul, we can somewhat see why John would make this reference.  The mind is the seat of your rational thought.  When blood no longer flows to your brain, you are clinically dead.

Although the soul is closely linked to your physical body, the existance of the soul is not tied to the life of the body. The soul existed before we obtained a body and will exist after our body is dead.  In Jer 1:4-5   God states that he knew Jeremiah before he was in his mother's womb.  This shows that the soul exists before your physical body is formed.   Rev 6:9, and Rev 20:4 speak of the soul existing after the death of the body.
 

The Spirit

Satan influences your body; God influences your spirit.

Some would say that the so called "6th sense" is your spirit's influence on your mind.

Some mistakenly believe that references to the spirit are all refering to God's spirit, but Romans 8:16 is one of many places that show that we have our own spirit, and that it's not just God's Spirit that is within us.  Aside from the figurative uses of the word spirit, spirit is used in three distinct ways in the bible: 1) The Holy Spirit which is God's spirit, 2) the spirits of angels, 3) the spirit of human beings.  Although God, angels and man are three different levels of beings, the concept of what a spirit is the same for all three.  In the same manner that "a hand" would have the same function for all three beings, "the spirit" has the same function for all three. 

The term "evil spirits" is often used to refer to angels that have turned against God (see Fallen Angels).  All of these beings are composed of soul, body, and spirit; although, their bodies are not made of the same flesh as ours.  Angels do not have flesh bodies; they have spiritual bodies.  These are bodies made of a different type of matter.  These are the types of bodies we will have when we get to Heaven because "flesh and blood will never inherit the kindom of God".   Because angels are in spiritual bodies they are often refered to as spirits.

Many theologins argue over the meaning of 1 John 5:6-8, and the phrase that Jesus came to the earth "not only by water, but by water and blood".   This phrase has been interpreted to mean (1) the baptism and death of Christ; (2) the water and blood which flowed from Christ's side on the cross; (3) purification and redemption; and (4) the sacraments of baptism and the Lord's Supper.   None of these are accurate since John states that Jesus "came to the earth by water and blood".  The only interpretation that would fit would be one that relates to how Jesus came to the earth. 

With the above explanations of the body, spirit, and soul we can now clearly see that this verse means that  Jesus Christ came to the earth not only in the flesh, but as flesh and soul.

Since Jesus came in a flesh body he had all of the limitations, frailties and temptation of a flesh body.  The only reason that Jesus' life was worthy of being a sacrifice for all of our sins was because He was able to "overcome the flesh".  He was able to proove that a flesh being could live without sin.  Living a life without sin in a flesh body was the act that earned eternal life.  Only after Jesus earned eternal life was he able to be a sacrafice for our sins and give us all the chance at eternal life.

See also:  Trinity, Angels, Fallen Angels, Where Are The Dead, Christ

Gen 3:19-23
19 In the sweat of your face you shall eat bread Till you return to the ground,
For out of it you were taken; For dust you are, And to dust you shall return." 
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1 Kings 17:17-24
17 Now it happened after these things that the son of the woman who owned the house became sick. And his sickness was so serious that there was no breath left in him. 18 So she said to Elijah, "What have I to do with you, O man of God? Have you come to me to bring my sin to remembrance, and to kill my son?" 19 And he said to her, "Give me your son." So he took him out of her arms and carried him to the upper room where he was staying, and laid him on his own bed. 20 Then he cried out to the LORD and said, "O LORD my God, have You also brought tragedy on the widow with whom I lodge, by killing her son?" 21 And he stretched himself out on the child three times, and cried out to the LORD and said, "O LORD my God, I pray, let this child's soul come back to him." 22 Then the LORD heard the voice of Elijah; and the soul of the child came back to him, and he revived. 23 And Elijah took the child and brought him down from the upper room into the house, and gave him to his mother. And Elijah said, "See, your son lives!" 24 Then the woman said to Elijah, "Now by this I know that you are a man of God, and that the word of the LORD in your mouth is the truth." 
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Ps 16:8-11
8 I have set the LORD always before me;
Because He is at my right hand I shall not be moved. 

9 Therefore my heart is glad, and my glory rejoices;
My flesh also will rest in hope. 
10 For You will not leave my soul in Sheol,
Nor will You allow Your Holy One to see corruption. 
11 You will show me the path of life;
In Your presence is fullness of joy;
At Your right hand are pleasures forevermore. 
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Eccl 3:18-22
18 I said in my heart, "Concerning the condition of the sons of men, God tests them, that they may see that they themselves are like animals." 19 For what happens to the sons of men also happens to animals; one thing befalls them: as one dies, so dies the other. Surely, they all have one breath; man has no advantage over animals, for all is vanity. 20 All go to one place: all are from the dust, and all return to dust. 21 Who knows the spirit of the sons of men, which goes upward, and the spirit of the animal, which goes down to the earth? 22 So I perceived that nothing is better than that a man should rejoice in his own works, for that is his heritage. For who can bring him to see what will happen after him? 
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Eccl 8:8
8 No one has power over the spirit to retain the spirit,
And no one has power in the day of death.
There is no release from that war,
And wickedness will not deliver those who are given to it. 
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Eccl 12:6-7
6 Remember your Creator before the silver cord is loosed,
Or the golden bowl is broken,
Or the pitcher shattered at the fountain,
Or the wheel broken at the well. 
7 Then the dust will return to the earth as it was,
And the spirit will return to God who gave it. 
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Isa 42:5
5 Thus says God the LORD,
Who created the heavens and stretched them out,
Who spread forth the earth and that which comes from it,
Who gives breath to the people on it,
And spirit to those who walk on it: 
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Jer 1:4-5
4 Then the word of the LORD came to me, saying: 
5 "Before I formed you in the womb I knew you;
Before you were born I sanctified you;
I ordained you a prophet to the nations." 
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Matt 10:27-29
27 "Whatever I tell you in the dark, speak in the light; and what you hear in the ear, preach on the housetops. 28 And do not fear those who kill the body but cannot kill the soul. But rather fear Him who is able to destroy both soul and body in hell. 
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1 John 5:6-9
6 This is He who came by water and blood--Jesus Christ; not only by water, but by water and blood. And it is the Spirit who bears witness, because the Spirit is truth. 7 For there are three that bear witness in heaven: the Father, the Word, and the Holy Spirit; and these three are one. 8 And there are three that bear witness on earth: the Spirit, the water, and the blood; and these three agree as one. 
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Acts 2:22-35
22 "Men of Israel, hear these words: Jesus of Nazareth, a Man attested by God to you by miracles, wonders, and signs which God did through Him in your midst, as you yourselves also know-- 23 Him, being delivered by the determined purpose and foreknowledge of God, you have taken by lawless hands, have crucified, and put to death; 24 whom God raised up, having loosed the pains of death, because it was not possible that He should be held by it. 25 For David says concerning Him:
'I foresaw the LORD always before my face,For He is at my right hand, that I may not be shaken.  26 Therefore my heart rejoiced, and my tongue was glad;Moreover my flesh also will rest in hope.  27 For You will not leave my soul in Hades,Nor will You allow Your Holy One to see corruption.  28 You have made known to me the ways of life;You will make me full of joy in Your presence.' 
29 "Men and brethren, let me speak freely to you of the patriarch David, that he is both dead and buried, and his tomb is with us to this day. 30 Therefore, being a prophet, and knowing that God had sworn with an oath to him that of the fruit of his body, according to the flesh, He would raise up the Christ to sit on his throne, 31 he, foreseeing this, spoke concerning the resurrection of the Christ, that His soul was not left in Hades, nor did His flesh see corruption. 32 This Jesus God has raised up, of which we are all witnesses. 33 Therefore being exalted to the right hand of God, and having received from the Father the promise of the Holy Spirit, He poured out this which you now see and hear. 34 For David did not ascend into the heavens, but he says himself: 
'The LORD said to my Lord,"Sit at My right hand,  35 Till I make Your enemies Your footstool." ' 
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Rom 8:1-17
8:1 There is therefore now no condemnation to those who are in Christ Jesus, who do not walk according to the flesh, but according to the Spirit. 2 For the law of the Spirit of life in Christ Jesus has made me free from the law of sin and death. 3 For what the law could not do in that it was weak through the flesh, God did by sending His own Son in the likeness of sinful flesh, on account of sin: He condemned sin in the flesh, 4 that the righteous requirement of the law might be fulfilled in us who do not walk according to the flesh but according to the Spirit. 5 For those who live according to the flesh set their minds on the things of the flesh, but those who live according to the Spirit, the things of the Spirit. 6 For to be carnally minded is death, but to be spiritually minded is life and peace. 7 Because the carnal mind is enmity against God; for it is not subject to the law of God, nor indeed can be. 8 So then, those who are in the flesh cannot please God. 9 But you are not in the flesh but in the Spirit, if indeed the Spirit of God dwells in you. Now if anyone does not have the Spirit of Christ, he is not His. 10 And if Christ is in you, the body is dead because of sin, but the Spirit is life because of righteousness. 11 But if the Spirit of Him who raised Jesus from the dead dwells in you, He who raised Christ from the dead will also give life to your mortal bodies through His Spirit who dwells in you. 

12 Therefore, brethren, we are debtors--not to the flesh, to live according to the flesh. 13 For if you live according to the flesh you will die; but if by the Spirit you put to death the deeds of the body, you will live. 14 For as many as are led by the Spirit of God, these are sons of God. 15 For you did not receive the spirit of bondage again to fear, but you received the Spirit of adoption by whom we cry out, "Abba, Father." 16 The Spirit Himself bears witness with our spirit that we are children of God, 17 and if children, then heirs--heirs of God and joint heirs with Christ, if indeed we suffer with Him, that we may also be glorified together. 
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These verses speak to the fact that our body is what makes us sin.  Christ's and God's spirit within us is what makes us do good. 

1 Cor 15:35-51
35 But someone will say, "How are the dead raised up? And with what body do they come?" 36 Foolish one, what you sow is not made alive unless it dies. 37 And what you sow, you do not sow that body that shall be, but mere grain--perhaps wheat or some other grain. 38 But God gives it a body as He pleases, and to each seed its own body. 39 All flesh is not the same flesh, but there is one kind of flesh of men, another flesh of beasts, another of fish, and another of birds. 40 There are also celestial bodies and terrestrial bodies; but the glory of the celestial is one, and the glory of the terrestrial is another. 41 There is one glory of the sun, another glory of the moon, and another glory of the stars; for one star differs from another star in glory. 42 So also is the resurrection of the dead. The body is sown in corruption, it is raised in incorruption. 43 It is sown in dishonor, it is raised in glory. It is sown in weakness, it is raised in power. 44 It is sown a natural body, it is raised a spiritual body. There is a natural body, and there is a spiritual body. 45 And so it is written, "The first man Adam became a living being." The last Adam became a life-giving spirit. 46 However, the spiritual is not first, but the natural, and afterward the spiritual. 47 The first man was of the earth, made of dust; the second Man is the Lord from heaven. 48 As was the man of dust, so also are those who are made of dust; and as is the heavenly Man, so also are those who are heavenly. 49 And as we have borne the image of the man of dust, we shall also bear the image of the heavenly Man. 

50 Now this I say, brethren, that flesh and blood cannot inherit the kingdom of God; nor does corruption inherit incorruption. 
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1 Thess 5:23-24
23 Now may the God of peace Himself sanctify you completely; and may your whole spirit, soul, and body be preserved blameless at the coming of our Lord Jesus Christ. 
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Heb 4:11-12
 12 For the word of God is living and powerful, and sharper than any two-edged sword, piercing even to the division of soul and spirit, and of joints and marrow, and is a discerner of the thoughts and intents of the heart.
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James 2:26
26 For as the body without the spirit is dead, so faith without works is dead also. 
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1 John 5:5-8
5 Who is he who overcomes the world, but he who believes that Jesus is the Son of God? 
6 This is He who came by water and blood--Jesus Christ; not only by water, but by water and blood. And it is the Spirit who bears witness, because the Spirit is truth. 7 For there are three that bear witness in heaven: the Father, the Word, and the Holy Spirit; and these three are one. 8 And there are three that bear witness on earth: the Spirit, the water, and the blood; and these three agree as one.
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Rev 6:9-11
9 When He opened the fifth seal, I saw under the altar the souls of those who had been slain for the word of God and for the testimony which they held. 10 And they cried with a loud voice, saying, "How long, O Lord, holy and true, until You judge and avenge our blood on those who dwell on the earth?" 11 Then a white robe was given to each of them; and it was said to them that they should rest a little while longer, until both the number of their fellow servants and their brethren, who would be killed as they were, was completed. 
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Rev 20:4-5
4 And I saw thrones, and they sat on them, and judgment was committed to them. Then I saw the souls of those who had been beheaded for their witness to Jesus and for the word of God, who had not worshiped the beast or his image, and had not received his mark on their foreheads or on their hands. And they lived and reigned with Christ for a thousand years. 
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15 "And every person who eats what died naturally or what was torn by beasts, whether he is a native of your own country or a stranger, he shall both wash his clothes and bathe in water, and be unclean until evening. Then he shall be clean. 16 But if he does not wash them or bathe his body, then he shall bear his guilt." 
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Deut 12:20-28
20 "When the LORD your God enlarges your border as He has promised you, and you say, 'Let me eat meat,' because you long to eat meat, you may eat as much meat as your heart desires. 21 If the place where the LORD your God chooses to put His name is too far from you, then you may slaughter from your herd and from your flock which the LORD has given you, just as I have commanded you, and you may eat within your gates as much as your heart desires. 22 Just as the gazelle and the deer are eaten, so you may eat them; the unclean and the clean alike may eat them. 23 Only be sure that you do not eat the blood, for the blood is the life; you may not eat the life with the meat. 24 You shall not eat it; you shall pour it on the earth like water. 25 You shall not eat it, that it may go well with you and your children after you, when you do what is right in the sight of the LORD. 26 Only the holy things which you have, and your vowed offerings, you shall take and go to the place which the LORD chooses. 27 And you shall offer your burnt offerings, the meat and the blood, on the altar of the LORD your God; and the blood of your sacrifices shall be poured out on the altar of the LORD your God, and you shall eat the meat. 28 Observe and obey all these words which I command you, that it may go well with you and your children after you forever, when you do what is good and right in the sight of the LORD your God. 
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1 John 5:8
8 And there are three that bear witness on earth: the Spirit, the water, and the blood; and these three agree as one.