Why did Jesus asked his disciples to collect the fragments of bread in baskets?
As per scripture Jesus ask is disciples to collect only the bread fragments only, but not the bones or flesh of the fish....
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While the synoptic gospels (Matthew, Mark and Luke) are not clear as to whether the fragments were of bread alone (they only mention 12 baskets of leftovers), the gospel of John indicates that the fragments were indeed of bread.
Quoting John 6:13 from NASB translation:
So they gathered them up, and filled twelve baskets with fragments from the five barley loaves which were left over by those who had eaten.
It is the same with KJV and NIV translations. See parallel view of all three translations.
And the reason why Jesus asked the disciples to gather the leftovers is found in the previous verse, John 6:12
When they were filled, He said to His disciples, “Gather up the leftover fragments so that nothing will be lost.”
Jesus wanted all the leftover fragments to be gathered, but the leftover fragments in this case only happened to be fragments of bread. (The crowd must have really loved the fish!)
And note that the bread and the fish were given by a lad (John 6:9) and Jesus gave thanks to the Father for them (John 6:11), blessed them (Matthew 14:19), broke them (Luke 9:16) and asked the disciples to distribute them.
The message Jesus wanted to convey was that: What is given to Him will be received with thanks, blessed, broken and be used to bless others. Nothing of what is given to Him will be wasted.
Another thing we learn from this is indicative of the principle we find in the life of Jesus: He was not wasteful. And He wanted His disciples also to learn this principle from Him.
One apparent reason for their gathering of the food which remained(besides what Jesus said in John 6:12 - 'that nothing be lost') might be according to a related speech he gave to his disciples later on the ship(Mat 16:5-12, Mark 8:13-21). That is, when he was exhorting them not to worry about their lack of supplies, he brought up the previous incidents of the miracles of the loaves as proof(Matthew 14:15-21, Mark 6:35-44), and asked whether they at those times had had lack, to which question they answered with silence. Therefore, it is deduced that their gathering of the leftovers had something to do with proving before all that all had been filled, which fact later proved useful in addressing the concerns of his disciples. Also, Mark informs, that, besides the fragments of bread that remained, they retrieved the fish that remained - Mark 6:43.