The explanation below may only make sense to you if you read this from an RSS reader. If you don’t please skip it.

Have you ever sent an email to the wrong person? Did wish you could pull it back? I just did this, but for our blog (!).

I was feeding a WP install of what will be our company blog, and then I did something nasty…

I was about to post from my desktop tool (word 2010, used to be live writer), and I hit ‘post’ on the wrong doc, and ‘about’ page, ‘google-translated’ from German; prose as horrible as one can get. The blog selected was academicproductivity.com, not our own. I immediately went to the admin page and removed it, so ap.com’s readers won’t see it. But the RSS feed… is another story. For a blog that was dead for a year, we still have >4000 followers. This was the first post to break a long silent stretch. I’d hate if you, the reader, think we resurrected, just to find out a nonsensical blog post.

Since we use feedburner, removing the post locally didn’t help. I had to log in at feedburner, and try to remove it from there. They have a ‘nuke’ option that should force a refresh. But it just didn’t work. I tried a few times, the nonsensical blog post was still there. The only option I could think of was to delete the feed from feedburner, in the hope that they do not broadcast it. But it was too late; all people who subscribe to ap.com’s RSS feed have received the post.

I apologize for kidnapping your attention without a good reason. I’m sorry you got involved in this, but silly mistakes do occur. I will be more careful in the future.

Since the feedburner feed is now gone, if you want to continue receiving updates from ap.com you’d need to resubscribe. Simply click again on the RSS icon on the address bar, and follow the steps there. In any case, we are not dead, and will continue writing for ap.com whenever we find something worth writing about.

Scott Aaronson uses an analogy to the game industry to describe the predicament academics are in:

I have an ingenious idea for a company. My company will be in the business of selling computer games.

But, unlike other computer game companies, mine will never have to hire a single programmer, game designer, or graphic artist. Instead I’ll simply find people who know how to make games, and ask them to donate their games to me. Naturally, anyone generous enough to donate a game will immediately relinquish all further rights to it. From then on, I alone will be the copyright-holder, distributor, and collector of royalties.

This is not to say, however, that I’ll provide no “value-added.” My company will be the one that packages the games in 25-cent cardboard boxes, then resells the boxes for up to $300 apiece.

But why would developers donate their games to me? Because they’ll need my seal of approval. I’ll convince developers that, if a game isn’t distributed by my company, then the game doesn’t “count”—indeed, barely even exists—and all their labor on it has been in vain.

As crazy as it sounds, this is exactly the situation with academic publishers. The ‘status quo’ is such that young researchers must publish on established journals (to gain the “seal of approval”). For older researchers, switching to open access publishing doesn’t pay off either: it’d show they don’t believe in the value the journals bring, and they are often editors of those (!).

And this is how the current academic publishing industry survives without adding much value. Survival is not the right word, because the leading firms still carry themselves around with arrogance. At the 2010 Semantic Web conference in Shanghai Jay Katzen, a keynote speaker from Elsevier, announced a big project on using the data on papers to create widgets. The API would allow people to do mashups with scientific data, that could be displayed on the publisher’s page. It was sold as “a new paradigm in the way research information is discovered, used, shared and re-used to accelerate science.” The reaction from the audience was instantaneous: “are you telling us that, not happy with monetizing the data and content we freely give you, you want us to build applications using that content for you to sell?”. The answer was honest: “… huh… yes.”

Today, many journal articles are online. In fact, the papers are often on the author’s homepage, and a simple query on google scholar or MS research search will find them. It is hard to imagine what value a publisher adds here.

However, the alternative is not clear. Open access publishing finds it difficult to obtain sustainable sources of financing. PLoS, the Public Library of Science, is financially sustainable, but ArXiv is struggling.

“Now it’s up to the rest of us to supply the anger.” Says Scott. Now more than 800 researchers have declared a boycott against Elsevier, up from 500 yesterday afternoon. Looks like the anger is there.

(An apology for the lack of posting. Dario has moved on to a position as senior researcher at Wikimedia, and I will be working on my startup full-time in a month. Often, I’ve seen blogpost-worthy issues, but I just didn’t have the mental bandwidth to follow up).

Using HTML5 features, this is the kind of obvious tool that makes symbol lookup faster than doing it by hand.

Just draw the symbol in the box and up comes the LaTeX code, and the package name that contains it.

I just found this presentation, and thought it’s worth bringing it to the attention of ap.com readers:

Anita de Waard is the director of Disruptive Technologies at Elsevier. A company that has a position with such a name has my sympathy. Looks like publishers are slowly realizing that they can have a huge impact on how science is done, and how fast it moves, if they simply paid more attention to modern trends.

Only habit prevents us researchers from realizing that the media we use the most, a paper article with a review cycle of years, is woefully wrong in this day and age.

A somewhat related idea are the 5 stars of open linked data:

★ make your stuff available on the web (whatever format)

★★ make it available as structured data (e.g. excel instead of image scan of a table)

★★★ non-proprietary format (e.g. csv instead of excel)

★★★★ use URLs to identify things, so that people can point at your stuff

★★★★★ link your data to other people’s data to provide context

If scientists and publishers have opendata in mind (and the trend is there!) doing research becomes more fun immediately (no more mails to the authors asking for data that get no response). Seeing that the academic publishing industry has at least one person (Anita) that gets it makes me feel good. Looks like Elsevier has a head-start.

Imagine a world where real-time search is the norm. You will get just the information you seek landing on your lap the exact minute it becomes available, without you having to explicitly search for it. Will this change the way you do science? SciSurfer thinks it will.

The release cycle of scientific knowledge is slow. It may take up to 2 years for a paper to get accepted in a journal. The publishing process in itself will add a buffer of a few months (arguably because of the time cost of having a paper edition, even though most people will never use it). So, for some of us, it doesn’t feel like we are missing much if we do not get the latest updates on our field the very same minute they are published. Just going to conferences yearly feels like more than enough. But there is a portion of the academia that needs constant updates on their field, as close to real-time as possible. If you are in the life sciences, getting the latest paper about a molecule or a gene you work on before your competitor does may make or break your career.

For those academics, sciSurfer may be a very valuable tool. The basic idea of sciSurfer is to integrate all journal feeds and search over them. Note that they do not archive RSS, so only the latest articles are available. This is a different way to think about search, closer to twitter’s than to Google’s.

In use

If you are used to RSS feed readers, the interface will look familiar. Left side there’s a list of journals and searches. Every time there’s a new unread item the containing ‘folder’ turns bold. On the right side there’s a list of articles (title, authors, and abstract). The journal it comes from is shown in green. The interface resembles Google reader (in fact, sciSurfer is built on app engine, so it may share code with reader).

What is the advantage of scisurfer over simply subscribing to the RSS feed of the journals? Search. Scisurfer does searches over all the journals they are indexing. This is pretty impressive, because I don’t know of any search engine that works on RSS feeds. Using an RSS reader, the equivalent to scisurfer would be to subscribe to the RSS of all journals, and apply searches over those. This is beyond the capabilities of most destop RSS readers. Implementing search by author, abstract, etc is also beyond the feature set of a normal RSS reader. In fact, it’s not that easy to deal with author names. We all have had the experience of getting papers by people with the same lastname and initials as our intended query term that are NOT the person we are looking for. Thomson Reuters has a solution: researcher ID. Researcher ID is based on the simple idea that each individual would get a unique identification (ID) number acting as a digital “calling card” that the researcher can place anywhere, such as a personal home page, a CV, or a university page. It has been out for more than two years now, so it’s still too early to say whether it has been adopted successfully.

Apart from the reader, there are two other tools, news and journals. Searching journals by name integrates the RSS feeds of otherwise disperse journals. Still, I haven’t found a good use for this tool.

Navigating trends

The main use I can think of for sciSurfer is monitoring Trending topics. We are getting used to explosions in popularity thanks to twitter and Facebook updates. Good twitter clients show you ‘what’s hot’ together with an explanation on why. Even Mendeley is getting status updates these days, making it look more and more like ‘facebook for scientists’.

There are several things to like about sciSurfer.  It integrates with your Google account, so it’s one less login to remember. The devs show that they are on top of things and the result is a fast turnaround when I requested changes. They are very open about feature requests. In my experience, when a journal was not in sciSurfer’s list, the devs added it within hours.

But by far the best result of using sciSurfer is that it makes you aware of what is going on in your field in a way that feels different and pleasant. The most similar feeling that I got online is when I found a neat Phd. student tagging articles in citeUlike that are relevant for me (it’s like finding a gold mine).

Mendeley uses a similar real-time approach in their statistics. For example, they show what are the most read papers per discipline at a given point in time.

I’m not sure one can do searches according to popularity just yet on any of these tools, implementing a real-time soft peer review.

How does sciSurfer plan to make money? The free tool is limited to ten saved searches. They will charge for extra functionality. There’s an iPhone version coming, which may well be another source of funds.

Conclusion

As the number of publications grows, it becomes more and more difficult to follow the latest scientific trends. The approach that sciSurfer takes is that if you know your keywords then it should be trivial to filter the fire hose of information, by doing a trivial keyword match. While keyword match could go a long way, I’m skeptical that the future of search lies in dumb matching. The way I currently filter information is very social, that is, I’m surrounded by people I respect and I ‘feel’ what they believe is good research. If I’m like most researchers, then social filtering would be a natural fit. However, I rarely get value from social networks online (science-wise; no matter how hard social networks try to capture my attention!). It may well be that to form a reputation, scientists need to do far more than posting interesting updates in their microblogging feeds. And for us to follow their recommendations…

I’m not sure how big of a problem selecting classes is for students, and how much it can be automated, but now there’s a tool specifically solving this problem. CourseRank tracks scheduling conflicts, together with some other Interesting features. For example, it gathers course/professor reviews, workload estimations and aggregates questions and answers.

Right now the selection of universities is not that great. It makes sense since the service is specifically tailored to each university, so I can imagine the implementation can take a while.

This is a quick note that may not surprise most people. Amy Bishop, at University of Alabama  Huntsville, just killed three colleagues and injured some more. It seems that this act may be related to having been denied tenure.  A PhD from Harvard, Amy Bishop had grants, and sat in a startup board, which are traces of a successful academic career. She was also a mother of four. Can your academic job environment be so toxic as to motivate murder? She was possibly suffering major depression at the time of the incident, and other mental health issues.

The evidence that an academic career is too stressing is piling up. An academic deals with rejection very often, from both peers and students, gets paid like a boy scout, and works every waking hour. This should be a waking call to all academics that feel tenure is the center of their lives.

A Previous Shooting Death at the Hands of Alabama Suspect – NYTimes.com

UPDATE: removed wrong photo.

Peter Sefton wrote a series of posts on wave. He has published on Scholarly HTML so I read attentively what he has to say. What follows is some highlights of his posts, and my thinking about where things are going. There are at least four things that bother me about wave –as it is today:

1- It’s not really HTML

I thought that waves being XML documents would be a good thing because it’d separate content and formatting. But it seems that they made some strange decisions about how to represent formatting with “very tenuous relationship to HTML”. For example

While there is talk of ‘XML documents’ in the whitepapers etc, a wave document in the current implementation is apparently a series of lines of text. All formatting and what you might think of as structure, such as whether something is a heading or not, is considered an annotation.

This is important right now because the only way to get the resulting doc is to dump the html to a file, or ‘copy-paste’. So, in a way, losing formatting like this would completely incapacitate wave for serious paper writing. I have had some success just copy-pasting and keeping most formatting, but I cannot risk to write a long paper and lose all formatting. Which won’t happen, because…

2- It doesn’t work too well for long, structured documents

Having a large blip for the entire paper with many people editing it seems to perform poorly. And having each person write their own blip-per-paragraph is not very pretty. It’s in fact distracting. I don’t discard wave’s usability to go through the roof once people start making things with it (robots). But it all depends on how well the API is designed. For example, following the mailing list, it seems that there’s no easy way to reorder blips programatically. This sounds like bad design to me.

3- It doesn’t integrate well with citation tools

It may be a matter of time before all the bibliographic tools we like get integrated. For example, Igor does offer some basic integration but this is far from satisfactory.

4-Formatting is simplistic

Wave has no table support. Figures are also not what you would expect, even for a notetaker. Captions are not implemented, nor footnotes. finally, LaTeXy is not the most convenient way to get equations done, I’m afraid, and it doesn’t go both ways.

Clearly, the content/form separation in wave is not designed for academic collaboration, and it shows. The questions is whether we can make this happen by writing robots[1]. Whether wave is the open platform that would make academic writing 2.0 happen.

Wave is just a tool. Why does this matter so much?

You may think that thinking too much about tools is counterproductive. But the way things are, it looks like tools are more and more important. Right now, we are stuck with the paper metaphor. Authors can produce pdfs, and publishers too. A publisher may make a prettier one, but that adds little value. We are equaled in terms of tools. However, publishers such as Elsevier want to get away from the paper metaphor (which is a good thing). As a consequence, authors will not be able to produce HTML as rich as the publisher’s. Here, the difference in tools matter.

In this case, Wave does look like an easy way to craft an interactive experience with little effort. So, even if you discard wave’s usefulness as a collaboration tool, it has quite a lot of value.

But it could very well be that wave doesn’t fulfill its promise. Microsoft Office 2010 offers similar functionality (close to real time edits). And of course, word has unparalleled features such as track changes, integration with endNote, etc. It could be that people adopt this new way of collaborative writing in real time without using wave. What worries me is that openOffice looks seriously left behind now. If it looks like a half-assed implementation of word 2003 features now, imagine when real-time hits mainstream. You need a serious server infrastructure to support that, which is possible for Google or MS, but not for a –smallish- open source foundation. I hope they find a way to jump in the train before it’s too late. Wave has a lot potential, because it is open. If openOffice could support that wave protocol, it could be a big achievement for open source.

If you have had any experience drafting a long doc in wave, please post it in the comments.

[1] For more on this, see my Wave intro for RuPy 2009.

It was a matter of time before someone wrote a robot that grabbed latex  and returned an image after latex processing. LaTeXy does exactly that and has just increased tenfold the usefulness of wave for academics.

Peter Drucker: "There is nothing so useless as doing efficiently that which should not be done at all."