Mega-sites, like http://news.bbc.co.uk have tens or hundreds of editors writing new content – i.e. new pages - all day long! Each one of those pages has rich, worthwile content of its own and a link back to its parent or the home page! That’s why the Home page Toolbar PR of these sites is 9/10 and the rest of us just get pushed lower and lower by comparison…
Should have added in my previous comment that our site has been established since 2000 and all our links have always been followable – including comment links (but all are manually edited to weed out spambots). We have never artificially cultivated backlinks but I have noticed that longstanding backlinks from established sites like government and trade organisations are changing to ‘nofollow’ (and our homepage PR has declined from 7 to 4 over the past 5 years). If webmasters of the established sites are converting to systems which automatically change links to ‘nofollow’ then soon the only followable links will be those that are paid for – and the blackhats win again.

As mentioned above, the two versions of the algorithm do not differ fundamentally from each other. A PageRank which has been calculated by using the second version of the algorithm has to be multiplied by the total number of web pages to get the according PageRank that would have been caculated by using the first version. Even Page and Brin mixed up the two algorithm versions in their most popular paper "The Anatomy of a Large-Scale Hypertextual Web Search Engine", where they claim the first version of the algorithm to form a probability distribution over web pages with the sum of all pages' PageRanks being one.
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I think that removing the link to the sitemap shouldn’t be a big problem for the navigation, but I wonder what happens with the disclaimer and the contact page? If nofollow doesn’t sink the linked page, how can we tell the search engine that these are not content pages. For some websites these are some of the most linked pages. And yes for some the contact page is worth gaining rank, but for my website is not.
Every mechanism or algorithm is good untill someone brake it. In my opinion as people tend to scam the search results, google is getting more and more consevative upon indexing and ranking search results. When I search a word or a phrase I see more wikipedia, amazon, google, youtube, etc. links returning my search, even the page name or headline does not cover the keywords in the phrase. I’m getting afraid that this may lead to an elitist web nature in the future.

A decent article which encourages discussion and healthy debate. Reading some of the comments I see it also highlights some of the misunderstandings some people (including some SEOs) have of Google PageRank. Toolbar PageRank is not the same thing as PageRank. The little green bar (Toolbar PageRank) was never a very accurate metric and told you very little about the value of any particular web page. It may have been officially killed off earlier this year, but the truth is its been dead for many years. Real PageRank on the other hand, is at the core of Google’s algorithm and remains very important.
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All in all, PageRank sculpting (or whatever we should call it) didn’t really rule my world. But, I did think that it was a totally legitimate method to use. Now that we know the ‘weight’ leaks, this will put a totally new (and more damaging) spin on things. Could we not have just left the ‘weight’ with the parent page? This is what I thought would happen most of the time anyway.

And my vital question about Amazon affiliate links. I think many people also wonder about it as well. I have several blogs where I solely write unique content reviews about several Amazon products, nothing more. As you know, all these links are full of tags, affiliate IDs whatsoever (bad in SEO terms). Should I nofollow them all or leave as they are?
@Ronny – At SMX Advanced it was noted by Google that they can, and do follow JavaScript links. They also said that there is a way to provide a nofollow to a JavaScript link but they didn’t go into much detail about it. Vanessa Fox recently wrote a lengthy article about it over on Search Engine Land which will likely address any questions you might have: http://searchengineland.com/google-io-new-advances-in-the-searchability-of-javascript-and-flash-but-is-it-enough-19881
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