In discussing the stockyards of Chicago, he compared how the talk of glory, honor, and patriotism in war conceals the trueness and suffering that war promotes, just as the stockyards of Chicago conceals the slaughter of cattle they promote.
We can arrive at this answer because:
To establish this thought, he states that "I had seen nothing sacred, and the things that were glorious, had in the glory and the sacrifices were like the stockyards at Chicago if nothing was done with the meat except to bury it."
This shows that just like the war, the stockyards at Chicago hid the slaughter of cattle and the suffering it caused, exposing only the meat so appreciated by all.
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