In response to our story on Google confirming a Penguin refresh is needed to recover from Penguin, Google’s John Mueller added more context to his answer in the Google Webmaster Help thread.

In short, he made a few points:

(1) Even when Google runs an algorithm update or refresh, the “changes aren’t immediately visible even after a refresh, that’s normal,” John said.

(2) A single site is “never in a void alone with just a single algorithm,” many algorithms impact a single site.

(3) In “some cases where a site is strongly affected by a single algorithm,” but John added “that doesn’t mean that it won’t see any changes until that algorithm or its data is refreshed.”

(4) “Theoretical void of just your site and a single algorithm,” John said, “you’d need to wait for the algorithm and/or its data to refresh to see any changes based on the new situation.”

In summary, John is explaining that changes in rankings happen to sites impacted by Penguin as well. Because a site impacted by Penguin is also likely impacted by other algorithms. If you clean the Penguin side up, you are likely also cleaning up things with other algorithms that may be negatively or positively impacting your site. Thus you may see changes, slowly, during the Penguin hit, until Google releases the full Penguin update.

Here is the full post by John, I recommend you read it a couple times:

The Google algorithm(s) is one big melting pot of zeros and ones.

Forum discussion at Google Webmaster Help.