bkoep Staff Lv 1
I'll chime in with a few thoughts from the "scientific" perspective:
Re: bonuses vs. penalties
I absolutely understand the preference for filters that effect bonuses instead of penalties (i.e. carrots instead of sticks), and we could probably adjust some of our "discouraging" filters to work on this principle with minimal disruptions. In many cases, unfortunately, the "penalty model" better reflects the intention of the filter, and restructuring the filter would make it (even more) incomprehensible.
With the Ideal Loops filter, for example, we don't want players to design additional loops into their structures—so we can't simply reward each ideal loop. And one troublesome loop doesn't necessarily doom a good design—so we also don't want an all-or-nothing bonus that only kicks in at 100% satisfaction. The penalty model skirts both of these issues, and behaves in a way that is easy to understand (even if it is discouraging to lose points).
(For what it's worth, we expected the Ideal Loop filter to be extremely restrictive, and we've been very impressed at how many Foldit players have been able to design proteins with 100% ideal loops.)