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I'm not at all convinced that it's any kind of penalty
After some discussion, I think I should explain this a little more. There is one way we might say Panda is APPLIED like a penalty. You basically have two kinds of affected pages - the primary pages that Panda assessed as low quality, and then the rest of the site that received some kind a site-wide demotion.
The site-wide demotion is applied like a penalty in that a negative factor is consistently applied to rankings across a lot of pages. However, I'm not assuming that rankings will return after a set "time put" period in the penalty box. If Google feels they identified pages that give their users a poor experience, then they would not let those pages rank again just because a certain amount have time has passed.
The site-wide demotion seems to flow backwards through the site's internal linking. This I'm still not totally certain of, but there does seem to be a pattern that says "the negative site-wide factor is strongest for pages that are just one click away from the really bad page and not as strong for pages that are more distant."
Does "idea two" line up with what others see on affected sites?
[edited by: tedster at 3:01 am (utc) on Apr 8, 2011]