Displaying articles with tag science

Science Journals and the Blogosphere

Posted by mfenner, Thu May 17 10:52:00 UTC 2007

The latest issue of the journal Cell (May 4, paid access) has an article by Laura Bonetta entitled Scientists enter the Blogosphere. In her article she describes some of the most popular science blogs and the people behind them.

The article is interesting for several reasons. Its main purpose is certainly to introduce the typical reader of the journal Cell (one of the most prestigious journals in the Life Sciences) to the concept of a weblog. Scientists traditionally have been well connected to the internet (remember the days of gopher and usenet?) and have used it for at least 20 years to exchange their ideas with colleagues in different parts of the world. But blogging has been slow to catch on – in sharp contrast to the huge popularity it has quickly gained elsewhere. A few reasons for this obscurity among scientists are obvious, e.g. lack of time, age (most bloggers tend to be younger) and reluctance to talk about unpublished results in public. But blogs are still a fairly new medium and I expect science blogs to become much more widespread over time.

The fact that this article was published in a reputable scientific journal is quite interesting as well. Journals have traditionally been one of the most important sources of information in science (besides scientific meetings and personal communications) and all scientific journals have managed the transition to electronic publishing and online distribution during the past 10-15 years. But the format and business model remained essentially the same. The almost universal access to the internet allows for very different ways of scientific exchange and the traditional journal paper (or talk at a scientific meeting) might not always be the best way of communicating a new scientific finding.

Open Access Publishing is one important driving force behind newer journals that take advantage of the new technical possibilities offered by the internet. PLoS ONE takes the idea of Open Access one step further and adds new features: annotations and discussions. These features were obviously stolen from the blogosphere where online comments are an important part of almost all weblogs. But what is stopping scientist of going the whole way and publish their research findings in their weblog? The answer is peer review: without the critical appraisal of your colleagues (or competitors), your scientific work will not be accepted in the community. Since production and distribution of scientific articles have (almost) become commodities in the age of the internet, peer review became the most important asset of science journals – and nobody knows this better than the editors of Cell. Peer review guaranties that scientific articles are interesting. Interestingness translates into revenue for the journal and scientific reputation (and consequently grant money) for the author. Interestingness of a journal is measured by it’s impact factor, which roughly measures how often it’s articles are cited by other journal articles.

The blogosphere works differently. The interestingness of a blog entry is measured by the number of readers, comments and other blog entries that link to it. Because the cost of setting up a weblog is so low, there is no need for peer review. The blogosphere has shown again and again that for news, politics, culture, information technology and other topics their blog entries can compete with peer-reviewed articles in traditional media. Only time will tell whether this also holds true for science.

0 comments | Filed Under: Science | Tags: science

Papers: iTunes for your Scientific Papers

Posted by mfenner, Tue May 01 08:35:00 UTC 2007

Papers is the new application from the folks that brought us 4Peaks and EnzymeX and other fine Macintosh programs for molecular biologists. Papers again is Macintosh-only (both PowerPC and Intel) and the first of their programs that is not free ($39 or €29 for a single user license).

Before the release of Papers, most scientists had devised their own system of storing the scientific publications most relevant to them. This could be folders with printouts sorted by topic or author or, as practically all papers are now distributed as PDF files, electronic copies stored on a computer in some filing system or another. PDF files could also be stored in reference managers such as Endnote, programs that are needed when you write your own scientific paper. But PDF support in these programs has always been something of an afterthought. For Macintosh users – and many scientists use the Mac – Sente is a wonderful reference manager with good PDF support, e.g. Sente automatically renames imported PDFs to something meaningful, e.g. by first author and publication year.

Papers has taken PDF support to a new level, and the comparison to iTunes is not too far off. It is by far the best application to import all the PDF files of the scientific papers scattered around your hard drive and than match the publication record in the PubMed database. If Papers is like iTunes, than PubMed is like Gracenote, a central database of all scientific papers, maintained by the US National Library of Medicine. The nice integration with PubMed also shows when you want to import the PDF file of a publication you found in PubMed – it just couldn’t be easier.

Once you have your papers in Papers, it is a breeze to find and print out a paper. This is what you will end up doing most of the time, and it is faster and less space-consuming than reaching for that folder with the printouts in your bookshelf. What makes Papers such a pleasure to use is not just the basic idea of handling the PDFs of scientific papers in the best possible way, but do it with the look and feel and attention to detail that we love in a good Macintosh application. One of the features I like in particular is the PubMed search interface. It makes it very easy to use the more advances search features of PubMed.

Papers is at version 1.0.1, so expect a few version 1.0 quircks – from sometimes sluggish behaviour to little interface bugs. What I would like most to see in version 1.1 is a better way of handling the way most scientists look out for new literature. One common approach is to scan new issues of the most important journals in your area of interest for articles relevant to your work. Most journals send out emails with the table of contents (TOC) once a new issue is released. More and more journals are also offering RSS feeds of the same information. In addition to scanning journal TOCs, most people will also regularly search PubMed for particular keywords, either manually or again by email notification or RSS. Papers is trying to help you with both strategies (e.g. by listing the most recent publications of a journal and linking to the table of contents), but the execution is far less elegant than the PDF handling.

Another obvious feature for version 1.1 is library sharing (again think iTunes) so that you can easily exchange references (with or without PDF files) with your coworkers. This of course touches on an aspect which is as bitterly fought in scientific publishing as is the distribution of mp3s in the music world, namely what are you allowed to do with scientific papers as almost all of them are copyrighted material. A growing number of Open Access journals allow you to freely distribute their publications, but most scientific journals don’t, not even when you are the author of the paper.

Papers is not a replacement for Endnote or other reference managers. When it comes to writing your own scientific paper, you still need them to integrate the references into your manuscript. For now, Papers can export to Endnote and other bibliography formats, but we don’t know whether Mek & Tosj have any plans in that direction for Papers 2.0.

0 comments | Filed Under: Reviews | Tags: science