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Such suffering was not God's original intent for humanity. The Bible teaches that God created humans in His image to live in unique, sinless fellowship with Him in an earthly paradise. However, God also gave humans the free-will choice to obey Him or to disobey Him, with consequences for disobedience. The root cause of any misfortune experienced by anyone in this life (including tragedies such as childhood illness and death) is the introduction of sin into the world by humanity's original free-will decision to disobey God and thereby to break its fellowship with Him (Genesis 3). The results of this action were a fundamental changing of man's nature that placed humans at enmity with God, and the corruption of all of God's creation, bringing disease, death, and all other forms of misery to mankind. Even children (as innocent as we may regard them as being, and as heartbreaking as it is for us to see them suffer) are not exempted from this condition (Psalm 51:5). However, God also gives humans intelligence to discover the causes of illness and disease, to develop cures for them, and to alleviate human suffering. (Luke, the author of the gospel that bears his name, as well as of the book of Acts, was a physician (Colossians 4:14).) God has also in love and mercy provided the means (the redemption gained by Jesus through His sinless life, atoning death, and resurrection) by which humanity's fellowship with Him can be restored eternally, and all sin, disease, and death can one day be destroyed (Revelation 21:4), as He promised He would do from the moment that humanity first fell into sin (Genesis 3:15).
Many of us forget that God is perfectly impartial, which means that He doesn't take sides in arguments. He treats everyone with perfect fairness based on the exact standard of judgment that we apply to others, (1 Peter 1:17, Matthew 7:1-2). So when an innocent child suffers from a terrible illness, this is because somewhere along the way, someone else's child suffered from a terrible illness caused by the priorities of that society and its people. They made the "judgment" together that this horrible personal experience is acceptable, most likely as part of the definition they had for "social progress" or "human advancement." They see this suffering as the "price" being paid for progress. As long as this price isn't too high, it remains acceptable to the society. Meaning, as long as only a small number of children suffer, this is acceptable. When we begin to outpace each other in knowledge or technology, we end up having a new option called "mitigation." This comes from the Old Testament era. We can effectively use a "scapegoat" to pay the price for us. Unfortunately, this means that we have the option to let someone else's child suffer by making them more vulnerable than ours. Since the "price" is being paid, this works on a practical level, but God doesn't forget the "standard" we are setting. Just as Jesus explains, it will certainly return to us in kind. That is why "mitigation" was never a real solution. It only delays judgment. When this judgment finally does return, it brings commensurate suffering, meaning greatly intensified suffering, just delayed by our mitigation. In our advanced society, this means a small number of children suffer tremendously. We try to "help" them too, but usually by prolonging this suffering while reducing its overall intensity. Ironically, our "compassion" can makes things even worse because God still remembers the original standard of judgment we used when we "judged" someone else's child to suffer so we could avoid this pain or so we could pursue our own dreams of "progress" at their society's expense. So how do we escape from these evil cycles of suffering? We acknowledge that the "full price" has already been paid by the Lord Jesus Christ, not only for sins past and present, but even for human "progress" itself. We should not be tempted by evil into believing that God favors some people over others, and that because our technology is superior and we can find a way to "avoid" or "mitigate" the effects of suffering, we must somehow be God's "favorite." By remembering this, the Holy Spirit will provide us with a genuine "way of escape" (1 Corinthians 10:13). The Lord Jesus Christ is our perpetual "intercessor" before God the Father, (Hebrews 7:25). This role empowers Him to supply us with the real-world wisdom we need to "equalize" things without further suffering. There is ALWAYS a way if we are willing to wait upon Christ for this wisdom. So the next time you see an innocent child suffering, remind yourself that the suffering you are witnessing is part of the suffering already endured fully and completely by Christ, and that there is a very real and practical wisdom available from our Lord that we as Christians can apply to real-world situations that will satisfy the righteous impartiality and justice of God. The simple answer to your question is that God only allows children to suffer because we do. He has already personally paid the price to prevent it from ever happening again. Faith in Him and in this dynamic reality created by Christ is what will allow us to end suffering for all innocent children everywhere, not just the ones we happen to notice or know about personally--all of them equally and fully. That is the precious promise of our impartial God of complete truth and perfect justice. We are here on earth learning to claim this inheritance and we are the ones determining how long this actually takes. We can "hasten the day" by obedience, (2 Peter 3:12).
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