ZydoSEO - 4:29 am on Feb 6, 2013 (gmt 0)
I agree with Andy on the following with a slight twist:
have a different view with regards Penguin and links. For one thing, it is extremely difficult to separate out the various algorithmic changes Google makes. Even calendar dates can be problematic since many changes occur concurrently. In a way, it is unhelpful to look at calendar dates and update names, and better to look at symptoms.
In terms of Google's handling of links, my opinion is that certain link activities trigger negative handling of a site, often for specific keywords or specific keyword patterns.
The presence of those negative links is what triggers this problem. However (and it's a big however) there is a side effect of being flagged for those link activities, which is to "taint" other links to a site, even those that could ordinarily be regarded as good links to have. Even if you remove the bad links, you are potentially still left with the 'good links gone bad'. Disavow provides a means to overcome this particular problem.
I have often postulated that such a side effect does exist like Andy mentions where otherwise good links get flagged as bad when problematic linking activities are detected with other inbound links by Penguin. This is similar to Panda where otherwise quality content pages on your site can also be affected by Panda when other lower quality pages trip the Panda Filter.
I see Penguin as more of a "hybrid" between a filter (an algorithmic action taken against a site which when the problem that triggered the filter is corrected, the algo will automatically be lifted) and a penalty (a manual action taken against a site that requires a Reconsideration Request/manual review in order to get it manually lifted). Penguin seems to be like a filter in that Penguin is triggered algorithmically, but more like a penalty in that a Reconsideration Request/manual review is required to get it lifted. This is something new with Google, but enforcing policies by running algo's offline and then applying them through Panda and Penguin updates against their real-time results is also new.
Where Andy and I differ seems to be in what the Disavow Tool achieves. IMO Disavow is logically equivalent to taking down those links. At the moment disavowed links remain in Google's link graph, but essentially get flagged as NOFOLLOW when those links get recrawled over coming weeks after being disavowed.
But whether you take all of the bad links down manually, by using the Disavow Tool, or a combination of both... it's as if the site is STILL flagged as being under the Penguin hybrid filter/penalty. This is why I believe Google is requiring a Reconsideration Request once all questionable links are down (and/or Disavow has had time to process) in order to recover from Penguin. It likely has to be lifted manually (though it was triggered algorithmically).
Many webmasters are afraid to submit a reconsideration request because they know their site will not withstand a manual review, possibly for other reasons. Others don't know how to ID "bad" or "questionable" links so they end up not taking all or enough of the links down that triggered Penguin. So even though they might have removed all questionable links, many sites affected by Penguin never recover. They can't without a Reconsideration Request and passing a manual review of the site (not just for links, but for everything that might be a violation).
It is possible to get Penguin lifted IMO. Some have successfully done so. It's likely that many sites have had it lifted, and don't even know it because they have eliminated a lot of links that made the site rank pre-Penguin. But at least once lifted, the site has a chance of ranking again for those same phrases that they used to assuming good links are acquired in a way acceptable to Google going forward. But as long as your site remains flagged by Penguin, you likely have zero chance of every ranking for those phrases again.