Earlier this year, we looked at a story about Washington State University chemistry professor Aurora Clark who claimed to have adapted Google’s PageRank algorithm for use in moleculaRnetworks, which is designed to enable scientists to determine molecular shapes and chemical reactions “without the expense, logistics and occasional danger of lab experiments.”

In fact, we also interviewed her:

More recently, a study, published in the Public Library of Science journal Computational Biology, looked at improving outcome prediction for cancer patients by network-based ranking of marker genes, using Google’s PageRank concept. The abstract for the study says:

Predicting the clinical outcome of cancer patients based on the expression of marker genes in their tumors has received increasing interest in the past decade. Accurate predictors of outcome and response to therapy could be used to personalize and thereby improve therapy. However, state of the art methods used so far often found marker genes with limited prediction accuracy, limited reproducibility, and unclear biological relevance. To address this problem, we developed a novel computational approach to identify genes prognostic for outcome that couples gene expression measurements from primary tumor samples with a network of known relationships between the genes. Our approach ranks genes according to their prognostic relevance using both expression and network information in a manner similar to Google’s PageRank. We applied this method to gene expression profiles which we obtained from 30 patients with pancreatic cancer, and identified seven candidate marker genes prognostic for outcome. Compared to genes found with state of the art methods, such as Pearson correlation of gene expression with survival time, we improve the prediction accuracy by up to 7%. Accuracies were assessed using support vector machine classifiers and Monte Carlo cross-validation. We then validated the prognostic value of our seven candidate markers using immunohistochemistry on an independent set of 412 pancreatic cancer samples. Notably, signatures derived from our candidate markers were independently predictive of outcome and superior to established clinical prognostic factors such as grade, tumor size, and nodal status. As the amount of genomic data of individual tumors grows rapidly, our algorithm meets the need for powerful computational approaches that are key to exploit these data for personalized cancer therapies in clinical practice.

The Author Summrary says:

Why do some people with the same type of cancer die early and some live long? Apart from influences from the environment and personal lifestyle, we believe that differences in the individual tumor genome account for different survival times. Recently, powerful methods have become available to systematically read genomic information of patient samples. The major remaining challenge is how to spot, among the thousands of changes, those few that are relevant for tumor aggressiveness and thereby affecting patient survival. Here, we make use of the fact that genes and proteins in a cell never act alone, but form a network of interactions. Finding the relevant information in big networks of web documents and hyperlinks has been mastered by Google with their PageRank algorithm. Similar to PageRank, we have developed an algorithm that can identify genes that are better indicators for survival than genes found by traditional algorithms. Our method can aid the clinician in deciding if a patient should receive chemotherapy or not. Reliable prediction of survival and response to therapy based on molecular markers bears a great potential to improve and personalize patient therapies in the future.

I’m not going to pretend like I understand the ins and outs of this complex study, and try to dissect it here, but if you want to dig through it, you can do so here.

(via txchnologist)

The thread begins with a post from user Sunnyujjawal, who says:

While checking some sites links I found 50% free submission directories are out of G now. Will Google count such links in negative SEO or unnatural linking?

Schwartz concurs that about 50% of the ones he searched for did not have listings.

He points to one example: global-web-directory.org. Indeed, I’m getting no results for that site:

I’m not sure about the 50% thing though. I’ve looked at a number of others, and haven’t come across many that were not showing listings (though I have no doubt that there are more out there). Either way, there are still a lot of these sites that are still in Google’s index. We do know, however, that quite a few of them recently received PageRank reductions with the recent update.

This discussion happens to come at a time when we’ve been analyzing Google’s quality guidelines, and its treatment of a certain directory, Best Of The Web, which sells reviews for potential listings, which appear with links that pass PageRank.

Other directories that follow a similar model, may be experiencing similar treatment from Google. In that same WebmasterWorld thread, user Rasputin writes:

I have a paid directory that I haven’t touched for about 3 years, only gets about 25 submissions ($10) a year – strange thing is, I just looked and not only is it well indexed but all the internal pages are now showing page rank – for a very long time they were all ‘greyed out’ after the google clamp-down on directories a couple of years ago.

No idea when it came back, certainly nothing I’ve changed and pretty unlikely it’s attracted natural links.

That’s pretty interesting.

User Netmeg adds:

I don’t think free or paid makes anywhere near as much of a difference as to whether or not the directory is actually curated for quality. Because if it isn’t, what other reason is there for it to exist other than to create links?

That’s a very relevant point, and that seems to be Google’s reasoning, based on this video from Matt Cutts from several years ago:

“Standard directory listings remain in our editors complete editorial control, and as such do not need the nofollow tag,” Best Of The Web President Greg Hartnett told WebProNews. “An editor looked at those listings (pay for review or not) and decided that they meet editorial guidelines and as such merit a listing. We vouch for that listing, so why would we nofollow it?”

If you go to global-web-directory.org,’s submission page, it would appear that they violate Google’s quality guidelines. There is a pricing structure as follows:

Express Reviews – $2
Regular Reviews – Free
Regular Reviews with reciprocal – Free

While they advertise a paid review process, it’s clearly much different than how Best Of The Web operates. The only payment is for speeding up the review process, from the looks of it. Otherwise it’s free, and they’ll even throw in a reciprocal link for free. That could be the part that Google has a problem with. If sites are really being “reviewed” for quality, perhaps that is one thing, but if your’e saying flat out that you’ll give a link back, that might fall under Google’s “link schemes” criteria, discussed in the quality guidelines.

It does list “links intended to manipulate PageRank” as the first example, and it does look like the site attempts to show the listings’ PageRank right with the listings.:

If you really look around the site, however, you’ll find many category pages without listings, just displaying ads. It’s not hard to see why Google wouldn’t want this site in its index.

Update: There’s an interesting post about this issue at Search News Central, from Terry Van Horne. Terry writes:

Directories that would be candidates for this kind of “draconian” action were as good as de-indexed ages ago. We sent out our super staffer Mike, with our vetted list of directories to see what he could find. From that (top end list) we found 65 no change, 2 domains parked and 1 de-indexed site; roughly 1.3% were de-indexed.

Next we went to our friends at Steam Driven Media for the last 100 (based on TBPR) from a list of 1500. From this group we found 1 with low indexation and 9 deindexed/gone – roughly 10% affected. Keep in mind, we have no idea how long these sites were out of the Google index.

Van Horne questions whether directories are really “getting nuked or not”.

So far, we’ve not really seen anything indicating it’s as big a change as made out to be by the original poster in the WebmasterWorld thread.

Have you seen paid directories rising in Google? Free ones disappearing? Let us know what you’re seeing.

Hat tip to Barry Schwartz for spotting discussion about this on the forums and Twitter. Here’s some of the Twitter excitement:

If your PR dropped, here’s a video from Google’s Matt Cutts explaining why this may have happened:

“The information that you get from the Google Toolbar is updated about 3 or 4 times a year, and the reason we don’t provide it every single day is because we don’t want webmasters to get obsessed with the green in the Google Toolbar, and not pay the attention that should be spent on titles and accessibility, and good content, and all those kinds of things,” he said in the video (from last year). “A lot of people, if you show them just the PageRank and update it every day, they’re just going to focus on that. So we didn’t want that kind of obsession or backlink obsession to take hold where people would only pay attention to the PageRank in the toolbar.”

“Then, the question of ‘how can I identify the causes of a PageRank drop’ – well, if the only PageRank that you had, for example, was from one very reputable link, and that site stopped linking to you, that could lead to a drop in PageRank,” he continues. “If you’ve done something really weird with your internal linking, and you canonicalization is very strange, so we don’t know – maybe there’s a completely different site on www vs non-www – so you know, those kinds of canonicalization issues, that can also lead to a PageRank drop.”

According to Schwartz, the last update was in February.

“In response, the webspam team has taken manual action to demote www.google.com/chrome for at least 60 days,” Google’s Matt Cutts said at the time. “After that, someone on the Chrome side can submit a reconsideration request documenting their clean-up just like any other company would. During the 60 days, the PageRank of www.google.com/chrome will also be lowered to reflect the fact that we also won’t trust outgoing links from that page.”

This was Google’s effort to show others that it would treat its own properties the same as others’. It looked like this had a direct impact on Chrome’s market share, at a time when Microsoft’s Internet Explorer was showing signs of improvement.

The penalty has now been lifted, as the 60-day mark has come. Barry Schwartz reports that Google has confirmed this.

It will be very interesting to see how Chrome’s market share numbers look after being out of the penalty box for a while.

So far, we’ve taken a closer look at the increased sensitivity of the Panda update, some location-based changes to YouTube suggestions, and the increased importance of image search optimization. Another very interesting entry to Google’s list is:

Link evaluation. We often use characteristics of links to help us figure out the topic of a linked page. We have changed the way in which we evaluate links; in particular, we are turning off a method of link analysis that we used for several years. We often rearchitect or turn off parts of our scoring in order to keep our system maintainable, clean and understandable.

It would, of course, be helpful to know some more specifics about this method of link analysis, but that’s probably one of those things that Google would rather play a bit closer to their chest than some of their other signals. Google can’t have people going out and exploiting that information and gaming the results, now could they? That could be a big “bug” that could end up hurting that search quality they’re trying so hard to maintain.

I’m sure there will be plenty of theories and speculation regarding how Google is analyzing links, just as there has been since the dawn of PageRank.

I doubt this new change will bring about any major findings in SEO, but it’s interesting to know that such a change was made – one that removes something that Google has been using for “several years”. One has to wonder if this will have a major impact on the PageRank of sites around the web.

When asked about the whole thing, Google Fellow Amit Singhal told WebProNews, “Our goal in search is to help people expand their knowledge of the world, and we’re delighted to see that our PageRank algorithm is being used to do just that with this innovative and efficient molecular research method.”

As explained in the original announcement about this initiative:

In living things, water can perform key functions like helping proteins fold or organizing itself around the things it dissolves so molecules stay apart in a fluid state. But the processes are dazzlingly complex, changing in fractions of a second and in myriad possible forms.

Google’s PageRank software, developed by its founders at Stanford University, uses an algorithm—a set of mathematical formulas—to measure and prioritize the relevance of various Web pages to a user’s search. Clark and her colleagues realized that the interactions between molecules are a lot like links between Web pages. Some links between some molecules will be stronger and more likely than others.

In the video above, Clark shares a bit about the inspiration and process in which PageRank is being applied to chemistry.

Pretty interesting. What do you think?

“What’s most cool about this work is we can take technology from a totally separate realm of science, computer science, and apply it to understanding our natural world,” says Clark.

The software focuses on hydrogen bonds in water. “From a biological or chemical standpoint, water is where it’s at,” says Clark.

An interesting passage from the announcement about the project:

In living things, water can perform key functions like helping proteins fold or organizing itself around the things it dissolves so molecules stay apart in a fluid state. But the processes are dazzlingly complex, changing in fractions of a second and in myriad possible forms.

Google’s PageRank software, developed by its founders at Stanford University, uses an algorithm—a set of mathematical formulas—to measure and prioritize the relevance of various Web pages to a user’s search. Clark and her colleagues realized that the interactions between molecules are a lot like links between Web pages. Some links between some molecules will be stronger and more likely than others.

“So the same algorithm that is used to understand how Web pages are connected can be used to understand how molecules interact,” says Clark.

The work is being funded by the U.S. Department of Energy’s Basic Energy Sciences program.

Are the search engines headed in the right direction? Tell us what you think in the comments.

Cutts on Why Your PageRank Would Drop

While not exactly an announcement, Google’s head of web spam Matt Cutts did post a video discussing reasons why Google Toolbar PageRank would drop. We talked about this a little bit more here, but you can hear exactly what he had to say in this video:

There is a part in there where he mentions that if you were caught selling links, but have stopped and want to earn Google’s trust back, you should submit a reconsideration request. On that note, Google announced that it is getting “more transparent” with its reconsideration requests.

Better Communication

“Now, if your site is affected by a manual spam action, we may let you know if we were able to revoke that manual action based on your reconsideration request,” explain Tiffany Oberoi and Michael Wyszomierski of Google’s Search Quality team in a joint blog post. “Or, we could tell you if your site is still in violation of our guidelines. This might be a discouraging thing to hear, but once you know that there is still a problem, it will help you diagnose the issue.”

“If your site is not actually affected by any manual action (this is the most common scenario), we may let you know that as well,” they add. “Perhaps your site isn’t being ranked highly by our algorithms, in which case our systems will respond to improvements on the site as changes are made, without your needing to submit a reconsideration request. Or maybe your site has access issues that are preventing Googlebot from crawling and indexing it.”

Google says it’s not able to reply to individual requests with specific feedback, but that now webmasters will be able to find out if their site has been affected by a manual action and will know the outcome of the reconsideration review.

Google Using Blocked Site Data in Algorithm

Earlier this year, Google announced some new domain blocking features, which included a browser extension, and a link next to search results, which allow users to block sites that they don’t like. This was part of Google’s big quality clean up initiative, which also includes the Panda update and the +1 button. Initially, the sites blocked were on a personalized basis, but that is no longer completely the case. Google search quality engineer Johannes Henkel is quoted as saying, “We’ve also started incorporating data about sites people have blocked into our general search ranking algorithms to help users find more high quality sites.”

Pagination and View-All in Search Results

Google is “making a larger effort” to return single-page versions of content in search results, when the content is broken up among multiple pages. Think multiple page articles and content slideshows. Google says users tend to prefer single page versions of content, but sometimes these can load slowly, so there are also times when the multiple pages work better.

“So while a view-all page is commonly desired, as a webmaster it’s important to balance this preference with the page’s load time and overall user experience,” Google indexing team software engineers Benjia Li & Joachim Kupke say in a joint blog post on the Webmaster Central blog.

You can read more about the technical specs here. They summarize it all nicely: “Because users generally prefer the view-all option in search results, we’re making more of an effort to properly detect and serve this version to searchers. If you have a series of content, there’s nothing more you need to do.”

To better optimize your view-all page, you can use rel=”canonical” from component pages to the single-page version; otherwise, if a view-all page doesn’t provide a good user experience for your site, you can use the rel=”next” and rel=”prev” attributes as a strong hint for Google to identify the series of pages and still surface a component page in results.

They talk even more about the specs of using rel=”next” and rel=”rev” in this post.

Rich Snippets for Apps

Google is also showing rich snippets for apps in search results now. They’re getting info for these from various places including: Android Market, Apple iTunes and CNET.

“Before you install a software application, you may want to check out what others think about it and how much it costs,” says product manager Alejandro Goyen. “Starting today, you’ll be able to get information about the applications, including review and price information, right in your search results.”

That’s something to consider if your business has an app. It’s a reputation factor.

Editing in YouTube

This isn’t exactly a search feature, but when you consider how big a role video can play in search marketing and that YouTube is the second largest search engine, it’s certainly worth your attention. YouTube has launched new editing tools that allow you to easy edit videos right from YouTube itself.

This should help you improve your videos, which are not only searchable on the second largest search engine and embeddable across the web, but often appear right in the results of regular Google searches. This new editing functionality will make it easier to try new things with less successful videos and potentially make them more viral.

Bing Adaptive Search

Ok, getting away from Google, Bing has launched adaptive search, which is essentially its version of personalized search. The company says it “helps decipher the intent and context of each search you conduct based on your search history.”

“The concept of personalized search is not a new idea, but Bing continues to focus on it and drive progress as the search space evolves,” a representative for Bing tells WebProNews. “In fact, Bing views personalized search as less of a ‘feature’ and more of what to expect from search.”
 
“Ultimately, the goal is to reduce ambiguity and help people find what they’re looking for more quickly,” he adds. “The personalization can be pretty subtle to the naked eye, but the more Bing learns about your intent the more personal it will become. And Bing also wants to be sure a diverse set of results still show up so people aren’t locked in a ‘filter bubble’. We think this provides a good balance.”

You’ve been dealing with this kind of thing with Google for quite some time, but it does throw in another SEO factor to consider for Bing, which as previously mentioned continues to gain market share.

WebProNews is interviewing Bing’s Stefan Weitz as I write this, so check back at WebProNews for more on this soon.

New Analytics Tool from Blekko

Finally, alternative search engine Blekko has released an interesting search analytics tool, which some of you might find useful. It’s called “Web Grepper”.

“The Web Grepper searches for unique data information and trends that are embedded in code and cannot be found on any other search engine,” a spokesperson for the company tells WebProNews. “For example, you could search to see how many pages request your user information when you visit, the types of  targeting information the site collecting, or how many sites have ‘Like’ vs ‘+1′ buttons, etc.”

Users can submit questions to the tool and the Blekko community votes on a daily basis on which questions will be analyzed.

These aren’t the only things going on in search this week, but these are some of the more noteworthy things that are likely to have a bigger impact on most site owners, than say things like Flight Search and Baseball scores.

Do any of these items concern you? Make your life easier? Let us know in the comments.

There is so much content out there, it’s impossible not to miss some things, so hopefully this can help prevent you from missing some good videos. If you like the compilation, or any of the videos within, why not share it with others? And certainly, feel free to comment on any subject mentioned in any of them.

Update: Don’t miss the videos from day two and day three.

We ran an article about this yesterday, but it’s still getting a lot of attention today. The Winklevoss twins have appeared in a Wonderful Pistachios ad.

Next Media Animation, the Taiwanese animation firm, which parodies many tech news topics, has a new video out about Ron Paul:

This follows one they recently release about Rick Perry:

Cisco has a marketing campaign bashing Juniper Networks for “not keeping its promises to customers” as the company puts it. There is a whole site dedicated to this campaign, which includes the following video:

Vitamin Water is running an ad campaign where it is calling upon consumers to upload videos showing how they embody “Nash-ness” – as in Steve Nash-ness:

Robert Scoble shared a video where he sat down with TechCrunch Disrupt finalist Shaker, which he says will be “an important company in the social world”. What do you think?

This trailer for the film Connected has been making the rounds. It’s about how technology is changing us and “what it means to be connected in the 21st century”:

We broke this down a bit in another article, but Google’s Matt Cutts put out this video talking about why webmasters may see a decline in their PageRank, and what they can do about it in some cases:

Speaking of Google, their Johnny Cash Project campaign is also getting a lot of attention:

Typically in these videos, Cutts is responding to a user-submitted question, and that is the case here. The question was: “I use the Google Toolbar to monitor PageRank. I read on the Internet that it gives old and quite unreliable data. Can I have reliable realtime PageRank information about the sites I administer? And how can I idenity causes of a PageRank drop?”

“The information that you get from the Google Toolbar is updated about 3 or 4 times a year, and the reason we don’t provide it every single day is because we don’t want webmasters to get obsessed with the green in the Google Toolbar, and not pay the attention that should be spent on titles and accessibility, and good content, and all those kinds of things,” says Cutts. “A lot of people, if you show them just the PageRank and update it every day, they’re just going to focus on that. So we didn’t want that kind of obsession or backlink obsession to take hold where people would only pay attention to the PageRank in the toolbar.”

This is not the first time we’ve seen Google de-emphasize the need for webmasters to focus on PageRank. Ultimately, while it may be a strong signal used by Google in determining search result ranking, there are over 200 other ones, and the formula changes every single day. Social and location factors have certainly played bigger roles in recent memory. You can bet that Google’s +1s are going to continue to play a strong role.

“The question that it’s ‘quite unreliable’ – it’s not unreliable, it’s just rounded to a zero to ten sort of scale, so there’s nothing unreliable about that necessarily,” says Cutts.

“Then, the question of ‘how can I identify the causes of a PageRank drop’ – well, if the only PageRank that you had, for example, was from one very reputable link, and that site stopped linking to you, that could lead to a drop in PageRank,” he continues. “If you’ve done something really weird with your internal linking, and you canonicalization is very strange, so we don’t know – maybe there’s a completely different site on www vs non-www – so you know, those kinds of canonicalization issues, that can also lead to a PageRank drop.”

“But one of the most common reasons we see for a PageRank drop, at least in the Google Toolbar, is if a site is selling links, and so if your PageRank dropped 30% all of a sudden, and you were selling links that passed PageRank, the reason for that is selling links that pass PageRank violates our quality guidelines,” he says. “And if you think about it, it’s a pretty understandable thing. It’s a lot like payola, in the sense that you pay somebody money and that you get a mention, and it’s not adequately disclosed to the search engine. If some site is doing that, that can account for a drop in the Toolbar PageRank.”

“So if that’s what might have happened, all you have to do is remove the links that you were selling, and then do a reconsideration request, and say, ‘Hey, I was selling links, they passed PageRank, I saw my PageRank dropped, and so I’ve removed those links, you can verify it, and please let me regain my trust with Google.’ And so if we see that things look good, and it looks like there’s a good faith effort there, and we’re reasonably convinced the selling of PageRank won’t happen again for example, then often times your PageRank will return.”

You can find the reconsideration request form here.