More thoughts:
What are you going to do about sleep? The 9:30P - 5A schedule the US Army uses? A 3A-12N schedule? Will you schedule night owls and morning larks differently, or force everyone to be one type?
One of the intentions of boot camp is shared suffering. The last line of the parent comment was sort of a joke, but the more I think about it the more serious it is. Hazing actually increases group strength, and one of basic's functions is as a giant hazing program. Drill sergeants are trained to be hateable in a precise way. Is shared suffering one of your goals? Are you skilled at controlling how you make other people suffer?
Suffering is a big part of being a soldier and being physically active, but not necessarily part of being a rationalist and being mentally active. Will you keep that for the group effects, or try and make the process as pleasant as possible? Is rationality training something that goes better when you force it, like physical training or unit cohesion, or something that goes worse when you force it? Will you try to manage/preserve the curiosity of students, and how? How skilled are you at detecting and manipulating the bounds of human endurance?
Is there a reason you picked boot camp (training to become a soldier) as a model instead of novice or postulant in the Bayesian Order (training to become a monk)? Monks do the things you mention, and tend to have a more recognizably mental focus than soldiers, and seem much like a much more obvious model.
I've gone twice to IHS seminars (applications close in a week!), and greatly enjoyed the experience. They're week-long, with 4 105 minute lectures a day, lots of discussion time, and a nightly social that supposedly ends at midnight, before (optional) breakfast the next morning at 8. The other students are great, and I still keep up with several that I've met there, but the professors are the real draw. The slogan is "sleep less and think more," and it's clear by the end of the week that the pace isn't sustainable (the middle day has a free afternoon which I use to catch up on sleep, so I tend to be better off than most).
I still can't get over the time. 10 weeks is basic combat training. 10 weeks is Y Combinator (and they're the same 10 weeks). 10 weeks is two summer sessions at college, or almost a full long semester. 660 hours at California's minimum wage is $5,280. A 10-week communal experience is a good format for many things, but I don't yet see why it's a good format for rationality training, and risking that much time on something under someone else's control seems risky at best.
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I'll just start off by saying that the latter "problem" will never happen outside of college. People simply do not have the time, effort, or motivation to do other people's work when they have their own job they're supposed to be doing. As rwallace astutely pointed out, college projects are way too small. When you are working, you will find that you (and everyone else) will always have more work to do than time to do it, so you (and everyone else) will not do others's work.
Your problem with the first group seems to boil down to the problem that people have different motivations. The sad truth is that this is going to be true in every setting, throughout your whole life. People always have different expectations of what they need to put in, and what they want to get out of a project.. What you need to do is learn to acknowledge that fact, and work with it. There are several ways of doing this. One of the easiest, though perhaps least fair, is (as was already suggested) to assign the work based on how much each person is likely to do. The problem with this is twofold: how much motivation someone has is is fairly hard to judge accurately, and it can foster feelings of resentment in those who have to do most of the work towards those who are (relatively) coasting.
One thing I liked to do with groups in college, which admittedly is not for everyone, was to have periodic meetings. At the end of each meeting we would decide what we wanted done by the end of the next meeting. We would then partition the work that remained (not just that which we wanted done by the next meeting) among the group members. Everyone was encouraged to do as much of their assigned work as they had time to, but there was no penalty except the ire of the rest of the group if they didn't.
So far this sound like how almost everyone does projects, but here's the catch: we made a deal that no one could leave a meeting until the work that was expected to be done by the end of that meeting was done. If everyone did their assigned work, then meetings were short. If no one did it (as happened sometimes) meetings would go into the wee hours of the morning.
This system worked well for us for a few reasons.
1) Everyone got to do as much work (individually) as they wanted. 2) Everyone ended up doing a portion of the work. Those who had difficulty motivating themselves to work on their own got to do their work with others there to goad them into getting it done. 3) Since everyone ended up working together on large portions of the project, no one felt like anyone else was free-loading, as we all saw everyone else doing at least some work. 4) It was very easy to consult with other group members if there was a part you didn't understand, or had difficulty with. This also lent our documents some flow, as they ended up being done mostly in the same style. 5) Most importantly, the work always ended up getting done.
I'm not saying I've solved the problem, that this is the be-all end-all solution to how every group should work. The point of this post (if there is one) is to say that every group needs to acknowledge the fact that motivations differ among group members, and to find a system to deal with that. If my solution is the one you feel would work best for your team feel free to use it, but if not, get to work developing your own. If you and your team acknowledge and work around the problem, your teamwork will be much more harmonious, and will produce results of much higher quality.