Did they not have the astronauts simulate the mission beforehand, on Earth? Wear the clothing, eat the meals, use the toilet, etc?
It sounds like that would have allowed them to fix the suit before they went?
They must have eaten the meals and such to be sure they could function, make sure they didn't have any intolerance, for example?
Apollo was largely driven with the purpose of achieving the goal rather than obsessing on the details on the way to that goal. In fact during Apollo they even completely scrapped mathematical risk modeling because the results it always gave were basically 'you die.'
So for instance a relevant and famous anecdote is that the original tests for Apollo launches didn't have any sort of urine/fecal disposal systems at all. In one delayed launch during testing Alan Shepard was in the capsule for hours and ended up needing to go pee. He asked for permission to depart the capsule, but that was declined to keep it all on track. So he ended up having to just pee all over himself in the suit.
Another piss poor anecdote is Buzz Aldrin on the Moon! When he departed the lunar lander capsule, the impact ended up breaking the urine collection device inside his suit. So his journey on the Moon involved having a healthy dose of urine sloshing around in his boot where it settled.
Of course there's a balance in all things. It's not like they just YOLO'd their way to the Moon. But things where the worst case outcome would be astronaut discomfort were seen as extremely low priority. In the original design, the capsule didn't even have a window or manual controls. So the astronauts were basically just being treated like human Laikas. They had to fight just to get those 'features.'
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I think a big part of the reason for this is because there are basically infinite things that can go wrong. And so if you obsess on getting every single thing right, you'll end up never doing anything at all. In 1962 Kennedy gave his famous 'to the Moon' speech. At that time, we'd only just barely put the first man in orbit but had never done anything beyond that, at all. Just 7 years later a man would walk on the Moon. In modern times we've been basically trying to recreate what we did in the 60s, and spent decades doing so. And this obsession on the details is certainly a big part of the reason why.
Warning: gross
Of course, but the fundamental problem is that difficulties compound. It starts with: pooping is much harder when gravity isn't there to persistently tug on the turd. Something that is slightly obnoxious on Earth (using a bag, using a suit flap) turns into an absolute trainwreck when you have a bag, a suit flap, and turd separation failure. Now you have to do precise mechanical manipulation of an object you don't want to touch behind your back through a bag and a suit flap, every failure multiplies the work, and now the turds can float away to multiply the work outside your immediate vicinity. Ditto for kneading the antibacterial into the poo: if you fail to do this thoroughly on Earth, bacterial offgassing causes the bag to vent, but in all likelihood that's the end of it because you can arrange for gravity to keep the poo away from the vent. In fact, you would probably do this without even thinking or imagining how it could go wrong. In zero gravity, you can't simply arrange "vent on top, poo on bottom", so the event is likely to launch aerosolized poo into your living environment where you have to put up with it for the next few days.
It's difficult to fully appreciate gravity until it's gone.
Astronauts are heroes for the risks they take, but they are also heroes for dealing with this.