diberry - 6:19 pm on May 4, 2013 (gmt 0)
I'm glad you started this. After one of my sites got Penguined, I made some changes (more for branding than in hopes of winning Google back). My lowered rankings fell further, and then some pages dropped out on certain queries entirely. To this day, the keyphrase I used to rank #1 for will show my page at around 150 one day, 650 another day, 450 another day... no rhyme or reason. Every SEO I've talked to, which includes some reputed people around here, said I had definitely triggered the RMSD penalty in addition to Penguin. The description of that patent just matches so clearly what they're seeing that it seemed unquestionably related.
Cutts does not flat out say, "We're not using that patent." I think his point is more that we should NOT read a patent and decide, "Well, I give up." And fair enough.
We've always talked about how making changes such as moving to a new domain with 301 for branding purposes would cause a temporary drop of something like 20%. Some of it could simply be the algo noticing a big change and kinda... I dunno, it almost feels like it flags the site to be checked more deeply, and then after the deeper checks show there's nothing hinky going on, you get your rankings back. So some of the behavior might relate to that.
But it does seem like in some cases (and maybe "Penguin" and "unnatural links" are two of them), this RMSD thing is happening.