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Let’s put those two verses together and look at them.  John 3:16says, “For God so loved the world, that he gave his only begotten Son, that whosoever believeth in him should not perish, but have everlasting life.”  Now let’s read Ecclesiastes 3:1-2, “For everything there is a season, and a time for very purpose under heaven: a time to be born, and a time to die; a time to plant, and a time to pluck up that which is planted.” 

To put these two verses in perspective, let’s go back to Genesis, at the original sin of man.  Genesis 2:16-17 says, “And the LORD God commanded the man, saying, Of every tree of the garden thou mayest freely eat: But of the tree of the knowledge of good and evil, thou shalt not eat of it: for in the day that thou eatest thereof thou shalt surely die.”  We know that Adam and Eve both ate of this forbidden fruit from the tree of the knowledge of good and evil, but did they die in the day that they ate it?  Yes they did!  While they did not die physically that day, they began the dying process that day.  They lost their ability to live forever physically on the earth.  We read later in Genesis 3:22-24, “And the LORD God said, Behold, the man is become as one of us, to know good and evil: and now, lest he put forth his hand, and take also of the tree of life, and eat, and live for ever: Therefore the LORD God sent him forth from the garden of Eden, to till the ground from whence he was taken. So he drove out the man; and he placed at the east of the garden of Eden Cherubims, and a flaming sword which turned every way, to keep the way of the tree of life.”  The Lord did not want Adam and Eve to partake of the tree of life and live forever in their sinful state, so they were driven from the garden, which in reality, was for their own good.  

On the day that Adam and Eve disobeyed the Lord, they did die spiritually.  Their innocence was lost, their relationship with the Lord was lost, they were now spiritually dead and in need of a savior.  The Lord said to the serpent in Genesis 3:15, “And I will put enmity between thee and the woman, and between thy seed and her seed; it shall bruise thy head, and thou shalt bruise his heel.”  These words foretold of the coming savior who would die for the sins of the people.  Genesis 3:21tells us, “Unto Adam also and to his wife did the LORD God make coats of skins, and clothed them.”  The killing of these animals in order to make skins to cover the nakedness of Adam and Eve is a type of the death of the Lord Jesus that He would accomplish to save us from our sins and give us eternal life.

Now let’s go back to your original question.  John 3:16teaches us that God sent His Son, so that through faith in Him, we might never perish, but have eternal life.  This does not mean that we will not have to go through physical death.  We read of our appointment with death in Hebrews 9:27, “…it is appointed unto men once to die, but after this the judgment.”  Because of sin, we, as believers on the Lord Jesus Christ, are still subject to physical death, even as Adam and Eve eventually died.  However, it is promised to us that we will never perish!  The Lord Jesus repeated the promise of John 3:16in John 10:27-28where He said, “My sheep hear my voice, and I know them, and they follow me: And I give unto them eternal life; and they shall never perish, neither shall any man pluck them out of my hand.”  This speaks to the security of the new life that we have in Christ Jesus.  As a believer on the Lord Jesus, we have the promise that we will live eternally with Him in Glory.  Nothing can change that.  The Lord said in John 10:28that we would “never perish”. 

Of course, it could be that we may never see physical death.  If the Lord should come soon, and I believe He will, all believers on Him will be taken to meet the Lord in the air without seeing death.  1 Corinthians 15:51-52 says, “Behold, I shew you a mystery; We shall not all sleep, but we shall all be changed, In a moment, in the twinkling of an eye, at the last trump: for the trumpet shall sound, and the dead shall be raised incorruptible, and we shall be changed.”  May our prayer be as the one we read in Revelation 22:20, “Even so, come, Lord Jesus.”  (138.5)