There is indeed a distinct difference between the meaning of "soul" and "spirit." This emerges quite clearly in Genesis 2:7, "…then the Lord God formed the man of dust from the ground and breathed into his nostrils the breath of life, and the man became a living creature" (ESV). In the original Hebrew what God breathed into his nostrils was "spirit" (Hebrew: ruach), resulting in man becoming a living-soul (or literally a living soul which is the Hebrew word: nephesh). From this text alone I conclude that strictly speaking the Hebrew word soul (nephesh) means a living-union of dust (or body) and spirit. And, indeed, the book of Ecclesiastes 12:7 says that when we die "the dust returns to the earth as it was, and the spirit returns to God who gave it." From this I understand that in some instances in the O.T. the word soul (nephesh) is used to refer to people as composite beings (body and soul in living unity). See Genesis 46:26 for example which says (in the ESV) "All the persons belonging to Jacob who came into Egypt … were 66 persons." The word translated as persons is the Hebrew plural for "souls."
The problem arises from the fact that in common usage the words soul and spirit are often taken as virtually synonymous. Jesus himself, for example, said: "Do not fear those who kill the body but cannot kill the soul. Rather fear him who can destroy both soul and body in hell" (Matt. 10:28). In this instance I believe Jesus was using the common, everyday way of speaking. He was not being technical but using terms to convey to everyone who heard him the simple fact that there is something much worse than physical death. Similarly in the book of Revelation John uses the term "souls" to refer to those he saw there who had been killed because they were serving Christ (6:9 and 20:4). But in Hebrews we read of "the spirits of the righteous made perfect" as a description of those who are in heaven with Jesus. So we should not be surprised that the Westminster Standards also speak of "the souls of believers" who are at their death made perfect in holiness and do immediately pass into glory. Everyone knows that, in these instances, it is the spiritual aspect of man (rather than the physical) that is intended.
Man, as created by God, is a composite being (dust + spirit = soul). It is for this reason that John can speak of two resurrections! Revelation 20:6 says "blessed and holy is the one who shares in the first resurrection! Over such the second death has no power …" The Reformed have always (as far as I know) taken this to refer to what Jesus said as recorded in John 5:25: "Truly, truly, I say to you, an hour is coming, and is now here, when the dead will hear the voice of the Son of God, and those who hear will live." For this reason John can say in 1 John 5:24, "Truly, truly, I say to you, whoever hears my word and believes him who sent me has eternal life. He does not come into judgment, but has passed from death to life."
Clearly, then, the first resurrection has to do with man's spirit. And this means that there is a certain priority of the spiritual aspect of man over the physical. This does not mean, as the ancient Greeks and many modern Americans thought, that the body is worthlessa kind of throw-away thing like a paper cup at MacDonalds. Not at all. But it does indicate that already those who are in union with Christ have part in the life which is eternal as to their spirit. They don't have it all yet but they do have it. And because they do have it they can apply to themselves what Jesus said to Martha (John 11:25b), "Whoever believes in me, though he die, yet shall he live, and everyone who lives and believes in me shall never die."
Now it would be possible to think this simply means that only our spirits are now, already, united to Christ, partaking in the blessings of his resurrection. But the Westminster Catechism (Q/A 37) wisely reminds us that our body tooeven though it be buried in a tombis still united to Christ. That is why the Scriptures say that believers (and they only) "sleep" (2 Thess. 5:13-18) until the second coming of Jesus. And this means that our bodies too already receive blessed benefits from the resurrection of Jesus. So taking the word "soul" in its original sense as a union of dust and spirit, it is not hard to see why, in common usage, we speak of our souls (ourselves as living beings) passing into glory.
This understanding has enabled me to see that there really is no conflict and that there is no reason to object to "common usage" as long as the intended meaning is clear. In other words, we need to benefit by the more precise distinctions without being too critical of the common usage.
And the bottom line is that you can almost always tell, from the context in which the word "soul" is used as a virtual synonym for "spirit", that this is what is intended.
Thank you for asking an important and interesting question.
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