Snark is snark but…

Put Down The Fucking Crack Pipe [DrugMonkey]:
[Via ScienceBlogs : Combined Feed]

Editors of scientific journals play a very important role in the scientific enterprise. When scientists begin to develop cutting-edge new ideas, it is key that scientific editors find appropriate peer reviewers to review such new work. However, the recent kerfuffle over the Nature editorial open access smear piece has provided a context in which some journal editors and other closed access buffs are revealing an absolutely staggering level of self-delusion about the real role of editors in the scientific enterprise.

Read the rest of this post… | Read the comments on this post…

Some people like to be provocateurs. This can be a useful approach, as it often deconstructs a question and permits it to be attacked from a different direction. If one can get beyond the snarky things said.

Are editors useful? You bet. Are all editors useful. No but then neither are all scientists. I think the question that is getting booted around here is who do the editors serve: the authors, the readers, the subscribers or the publishers. Any others?

Each of the groups have different needs, requirements and points of view. The best editors have always been the ones that balance these needs best (nice tautology but it scans well). But what happens when there is a conflict in the groups being served? And are there alternate ways for them to be served?

Part of the conflicts coming from Open Access arise from the different needs of say the authors and the publishers. One wants to maximize their reputation and the reach of their science. The other wants to maximize revenue to sustain publication. Readers and subscribers are also becoming more divergent.

Open access provides an alternative and is being drawn along by these different viewpoints. But in this period of flux, the different viewpoints often get heated.

Perhaps good editors will specialize more, focussing on simply the author, for example. Who knows but I am sure something will shake out, what with all the discussion going on.

Technorati Tags: Open Access

Great talking points

by Snap®
Origin of life [Pharyngula]:
[Via ScienceBlogs : Combined Feed]

Nick Matzke has a fine summary of progress in research into abiogenesis. He chastises those people who try to argue that abiogenesis is independent of evolution, or that you can get out of trying to answer the question of where life came from by simply saying that that isn’t evolution. It is! I’ve said it myself, and I really wish people would stop trying weasel out of that question by punting it off to some other discipline.

Read the comments on this post…

The article by Matzke is well worth the read. The level of knowledge about the origins of life on Earth has increased tremendously in recent years. Being able to maintain a cogent argument with someone about this topic compels one to learn what the current level of knowledge is. Like the analysis of the Big Bang, we are continually moving backwards in time, getting closer to the first life.

We have moved back past one celled organisms to an RNA world, unlike ours in many ways but forming the basis for today’s life. And we have also moved forward, gaining an understanding of the organic molecules present in the early Solar System and how they may have contributed to the origins of life.

Just as we do not need to recreate a black hole in the lab to understand how it came into existence, we do not need to create life in the lab to understand its origins. The difference between science and pseudo-science is that science is amenable to examination, trials and experiments.

All of these are continuing to be done with the examination of evolution. not so much for special creation.

Technorati Tags: Biology, Science

Citing references correctly

by Hiro Sheridan
Back off, man. I’m a scientist.:
[Via Unqualified Offerings]

By Thoreau

A recent study finds that scholars are incredibly diligent about properly citing sources and making sure that they understand the contents of a paper before citing it.

Sometimes references are cut and pasted from previous papers, so if there is a mistake in the citation, it will continue. Reference manager software makes this less likely.

The greater problem is that often the citation given does not actually provide the information needed. To save space, articles will often reference a protocol that is described in another article. But sometimes, this article does not actually provide the complete details, necessitating a further search. This sort of serial citation happens all the time.

While the science can be self-correcting, since it has to be verified, the citations often are never really verified. Perhaps this can be fixed.

Technorati Tags: Open Access, Science, Web 2.0

Now we have article 2.0

by luisvilla*
[Crossposted at SpreadingScience]
I will participate in the Elsevier Article 2.0 Contest:
[Via Gobbledygook]

We have been talking a lot about Web 2.0 approaches for scientific papers. Now Elsevier announced an Article 2.0 Contest:

Demonstrate your best ideas for how scientific research articles should be presented on the web and compete to win great prizes!

The contest runs from September 1st until December 31st. Elsevier will provide 7.500 full text articles in XML format (through a REST API). The contestants that creates the best article presentation (creativity, value-add, ease of use and quality) will win prizes.

This is a very interesting contest, and I plan to participate. I do know enough about programming web pages that I can create something useful in four months. My development platform of choice is Ruby on Rails and Rails has great REST support. I will use the next two months before the contest starts to think about the features I want to implement.

I’m sure that other people are also considering to participate in this contest or would like to make suggestions for features. Please contact me by commenting or via Email or FriendFeed. A great opportunity to not only talk about Science 2.0, but actually do something about it.

While there are not any real rules up yet, this is intriguing. Reformatting a science paper for the Internet. All the information should be there to demonstrate how this new medium can change the way we read articles and disperse information.

We have already seen a little of this in the way journals published by Highwire Press are able to also contain links to papers published more recently, that cite the relevant paper. Take for example this paper by a friend of mine ULBPs, human ligands of the NKG2D receptor, stimulate tumor immunity with enhancement by IL-15.

Scroll to the bottom and there are not only links in the references, which look backwards from the paper, but also citations that look forward, to relevant papers published after this one.

So Elsevier has an interesting idea. Just a couple of hang-ups, as brought out in the comments to Martin’s post. Who owns the application afterwards? What sorts of rights do the creators have? This could be a case where Elsevier only has to pay $2500 but gets the equivalent of hundreds if not thousands of hours of development work done by a large group of people.

This works well for Open Source approaches, since the community ‘owns’ the final result. But in this case, it very likely may be Elsevier that owns everything, making the $2500 a very small price to pay indeed.

This could, in fact, spear an Open Source approach to redefining how papers are presented on the Internet. This is because PLoS presents its papers in downloadable XML format where the same sort of process as Elsevier is attempting could be done by a community for the entire communtiy’s enrichment.

And since all of the PLoS papers are Open Access, instead of the limited number that Elsevier decides to chose, we could get a real view of how this medium could boost the transfer of information for scientific papers.

I wonder what an Open Source approach would look like and how it might differ from a commercial approach?

*I also wonder what the title of the book actually translates to in Japanese?

Technorati Tags: Bioinformatics, Science, Social media, Web 2.0