Category Archives: Writing

Writing

PRISM Bullshit and Hypocrisy

I’m not the only one harping on about open access to scientific journals. I’ve linked to at least two other blogs discussing the issue, and I’m sure there are hundreds more.

I wrote in January about an article in Nature that highlighted the PR offensive being launched by the major science publishers.

That effort has apparently borne fruit. The issue is well-covered by John Dupuis. A sad but interesting twist, which made the front page of Slashdot, is that these organizations bent on protecting their copyright lock-in stole images from Getty Images for their web site. As the post in that last link notes, the onslaught of complaints subsequent to hitting the Slashdot front page convinced them to go buy the images properly from Getty.

Just as Microsoft started the FUD machine as Linux gained prominence, watch for a truckload of FUD from PRISM in the days to come.

ADDENDUM: There’s a good summary post that quotes my statement just above (and those of many other science bloggers) here.

Google Notebook

I mentioned my newfound love for Google Docs the other day.  I’m also rapidly becoming a fan of Google Notebook.  It allows you to set up any number of notebooks, and with a browser extension makes it easy to add any highlighted bit of text from your browser to the notebook.

This isn’t a big deal, as it’s relatively easy to copy and paste text into an editor. It has three key advantages over that method:

1. It automatically includes the title and URL of the page from which the clip was taken.

2. It is accessible from anywhere and …

3. It’s possible to add comments on to any of the clips.

If you’re a Google Docs user, another benefit is that you can send entire notebooks to Google Docs. Thus, researching a personal reference page might go something like this:

1. Search for whatever it is you’re looking for. Your search could include web search engines, books, electronics, various other items, even library searches.

2. As you find things you’re interested in, just paste them into the google notebook (usually one dedicated to the topic).  This is the search equivalent of brainstorming. You might add notes on clips indicating why you chose them.

3. When you’ve exhausted your search, go back to the notebook. Trim down the list to get rid of stuff that ultimately you don’t need. Add further comments if you have them. Drag and drop clips to reorder them. When done, export to Google Docs. From there you can edit all of your clips and comments, merge them into a cohesive whole, whatever. You can then export to something else, like PDF, post to your blog, or publish to the web.

I know it’s been around for a little while, but I didn’t really grasp how powerful it was when it first came it. It’s definitely worth a try. I’ve used it as described above at least three times in the last two days.

Follow-up on PLoS ONE Ratings, from PLoS

I mentioned yesterday the new rating system/software launched by PLoS one. This was precipitated by an announcement on the software/technical side. Today they have an article on the PLoS blog about the new rating system, encouraging people to rate articles.

Here’s the intro from the post:

I’ve been waiting to write this Blog posting for a while and now I can. As from today PLoS ONE has a user rating system for its articles. All users can now rate articles in three subjective categories: Insight, Reliability and Style. We have made the tool, now we need you to come and use it.

User rating is a very common feature of websites these days, be it for movies, books, blog posts, pretty much anything. What user rating allows is a quick and easy survey of a communities opinion. Despite the obvious advantages to hard pressed scientists trying to get to grips with a vast literature this simple system hasn’t been much applied to scientific papers up to this point.

The major exception to this is probably Faculty of 1000, which has been providing ratings for papers for many years, but that is not based on the opinion of a whole community but only the thoughts of a select few.

So what will this new rating system look like? Well, if you go to any of the six hundred or so papers that PLoS ONE has so far published and look in the right had column you will see a little box containing five small stars. Those indicate the overall aggregate rating of the paper based on individual ‘votes’ from individual users.

What’s interesting about this is that it’s a little different from a citation index, the main way that articles are scored. You see, normally scientific articles are given a ranking or score based on how much they are cited in other articles. This is a pretty good idea, but it neglects sort of “terminal” articles — that is, articles that mark the end of most investigation into a particular niche. These articles may nonetheless be extremely interesting or useful, but never garner a large citation index. Furthermore, articles of interest to people in other fields, or even the general public, will never garner any indication of said interest or popularity under the conventional system. The occasional exception might be popular science articles inspired by new publications in Nature or Science.

With the emergence of an article rating system, that may change. People can read and rate articles without having to write an entire manuscript. People can leave comments on articles without drafting (and having accepted) an “official” editorial or response in a major academic journal. Things are getting a lot more interesting, and quickly.

As the title of the article suggests, Rate Early, Rate Often.

More open academics: Manuscriptorium

Historians have a bit of an advantage when it comes to open access to research material — so much of what they’re interested in is well out of copyright. To that end, Manuscriptorium is assembling digitized manuscripts and other research materials in a convenient and open-access library.

Their about page is very informative, describing the origins of the project. It seems to be run by the Czech government, and includes not only digital resources but metadata on meatspace records and artifacts as well.

I saw a sign on a reference librarian’s door the other day about spending hours of aimless internet searching versus 10 minutes with a reference librarian. It’s a decent point, and I was in the library that day to look at reference materials better than anything I could find online, but more and more of the resources and catalogs (real-world pointers) that we need to do research are becoming available online, and to everyone.

More on open science: PLoS ONE

I wrote last month about my desire for more open access in science, and how PLoS was leading the way. I also said I had some ideas about what more could be done.

It looks like PLoS ONE stole them.

Of course, I jest.

Obviously they’ve been working on this for a while, and I missed it. I only know about it because I’m now subscribed to their RSS feed. This is the framework upon which the future of science publishing will be built. There are many PLoS (Public Library of Science, by the way) journals — PLoS ONE seems to aim to be the open-access equivalent of Science or Nature.

Anyone is allowed to register and comment on or rate articles (with some caveats). They even have guidelines for rating articles. The initial review they mention by an editor and perhaps a few reviewers keeps out the quacks, but anyone is allowed to point out weaknesses in the article or make suggestions on it. It reverses my original idea a bit, in which the article would not be “published” until it had passed a vote by public reviewers, but it is perhaps a more functional model.

I am planning to register and see about reviewing and commenting on some articles. Are you?