Take a look in footnote 59 of an article I wrote two years ago. I cited some studies that may be up the alley you're looking for.
https://startingstrength.com/content...re_butland.pdf
To address the title of the OP: we know that properly performed squats are not only fine for the knees but good for the knees because the experience of hundreds of thousands of people tells us so. We also know that improperly performed squats can damage the knees, for the same reason. These findings have not been published in a peer-reviewed journal of standing, but they remain factual, relevant, and predictable from our analysis.
I see a truck load of reasons why to start this project in a way that is not too hard to follow and jump in if necessary along the way.
Overleaf or GitHub jump to mind.
Or maybe a Jupyter Notebook on github.
If you include software then anyone would be able to reproduce whatever you are doing + maybe generate beautiful images or even clips: very impressive for a wider audience.
There are precedents, e.g. the IAS published an entire book in a year or so with hundreds of contributors in a cutting edge field, the result being here (it would have been impossible otherwise).
It would probably be possible to start alone then maybe a few people around here could jump in provided it's easy enough.
It is also impossible to 'prove squats are safe' using clinical methods. If there was even a way to confirm that the squat was being properly executed in these studies (there's not) and you could do 10 studies with thousands of lifters squatting every rep correctly without knee injury, the conclusion would only be 'found reliable,' and a single disconfirmation would 'disprove' the statement.
This is a case where the less-precise (but still objective and measured) results of coaches around the world in practice will yield greater results than any peer-reviewed literature. Since there aren't thousands of Starting Strength lifters blowing knees out squatting correctly (there's no smoke), we don't go looking for fire.
To really get to the question, you'd have to propose a plausible mechanism by which it would happen, then we could challenge it based on our experience and basic physiology, and every time these arguments come up ("It's the Q-Angle!", etc.), they're found lacking.
A google search:
"deep low bar squats are bad for the knees"
yield nothing saying that low bar squats are bad for the knees (first 10 results).
T Nation wrote a couple of BS:
That's about it.Most people can't squat deep because of one of three problems – lack of mobility, lack of technique, or lack of stability. Regardless, going ass-to-grass isn't really necessary.
Considering the squats I saw, most people do not do low bar squats because they only learned the high-bar squats.
A couple of guys with impressive results (250kg bench press, > 150kg snatch) just told me that they squat the way they squat because it's how to squat.
I convinced one of them to try the low bar squats using the blue book and my own progression and because his squat results were way worse than anyone else.
So talking to a few dozens of guys during the last couple of months about squats indicates to me that they just don't think about it and thus don't even question the fact if it's good or not.
Deep low bar squats never was even an option.
I would be very interested in seeing physics and stuff about the squat, but it's like an answer to a question that no one is asking.
Unless if it's a project just for fun, is it worth months of work?
Writing a good paper is no small feat...
Maybe you coaches have many more data points that would say otherwise, looking forward to it!
Matt: Write it yourself. You're a sharp guy, and you apparently have the time. Get busy.
While we wait: Deep Squats | Mark Rippetoe
Professional soccer clubs spend millions on ACL preventive and rehabilitation technologies and strategies and don't seem to care for any kind of barbell training outside of a 40 kilos High Bar Quarter Squat, instantly shared on Social Media.
I'm using Low Bar Squats with ACL patients on a daily basis and my colleagues don't understand the thinking behind it (they're older than me, I should learn from them, not the other way around) and I can tell they are judging me for putting a barbell on a patient with an ACL graft.
Darin Deaton's video on your Youtube Channel stunned me how early his patients can squat 100 pounds. He's talking about 100 pounds on a female ACL graft patient 7 weeks post-op, are you kidding me? At this stage the patients coming to me can barely walk wihout limping.
I can only get to a bodyweight low bar squat after 5-6 months with male patients... while my colleagues make me think I should only do TRX and Stability Ball wall squats.
The thing is, my patients show outstanding return to their sport after 6-9 months feeling in better shape than before they got their ACL ruptured, and 90% of them fell in love with LBBS.
The "main" Physical Therapist asked me recently "are you even using a BOSU Ball Squat to check if they're in balance on both lower limbs, before considering barbells? Well you should"
IMO using LBS in ACL rehabilitation might be the biggest boost "Deep" Squats can get as publicity, since there is so much money thrown away in this topic in professional clubs, but as you know better than me, won't happen anytime soon.