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Shaddows: Improving the ranking of good sites is their bread-and-butter. That's the main algo.
The negative scoring* parts target the people who "fake" quality.
Other point, maybe google is getting better at discerning and ranking higher quality pages without depending so much on link equity.
thats why Panda is maybe 85% of what a user does on your site with a google tool activated
Click trails played a big part in the way they were doing things