i read to put paper towels down. i've had them for less than a day. the paper towels are a mess. what's the harm in letting them be directly on the litter?
Short answer added after typing way too much information below: If you are convinced that the chicks know what food is and they are all eating out of the feeder consistently, then there is likely no harm at all in letting them be on the litter.
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Sometimes there is no harm. Folks have been raising chicks in all sorts of way for millennia.
For me, I feel better making sure that the chicks learn what feed is before I introduce them to shavings. In fact, the only thing they can eat in my brooder is feed or water.** They could tear the paper towels, I suppose, but it doesn't get that far. I sprinkle the feed all over the paper towels. Chick aren't hatched knowing the difference and so they will peck at everything. The ground is their favorite thing to peck at. Luckily, their droppings don't taste good and they stop pecking at those quite quickly. So if food is on the ground and in the feeders, then they learn what good food tastes like.
If I put them on litter, they could easily get confused, think the litter is food, and eat too much litter. Then they will be at the very least nutritionally harmed because they won't be getting the amount of nutrients they need because the litter will be taking up space in their crop, etc.
I put the paper towels on the bottom of the brooder for about 5 days. Then switch to shavings. Though I guess, I have had them outside in the coop on shavings at 3 or 4 days before. So, I guess I play it by ear sometimes. The good news is that there are a bunch of ways to work the system.
Yes, yes, it gets messy. I end up using a lot (A LOT) of paper towels and have a trash bin right next to the brooder for switching out the dirty towels for the clean.
**I sprinkle play sand on top of the feed in their feeders as if I were putting pepper on their feed. I do this from day two or three. Personal choice. I think it helps develop the gizzard early, but there are studies out there saying it doesn't matter as well as studies that say otherwise. But sometimes the studies are comparing chickens that will never be free ranged. Anyway, I do not give play sand or fine grit "free choice" until they are a lot older in case they mistake the sand/grit for feed and over indulge.