The latest issue is all about Science Commons, and since some of the articles are republished from the SC blog, I’m even quoted in it (much to my surprise).

From John Wilbanks’ introduction:

One of the reasons I believe so deeply in the commons approach (by which i mean: contractually constructed regimes that tilt the field towards sharing and reuse, technological enablements that make public knowledge easy to find and use, and default policy rules that create incentives to share and reuse) is that I think it is one of the only non-miraculous ways to defeat complexity. If we can get more people working on individual issues — which are each alone not so complex — and the outputs of research snap together, and smart people can work on the compiled output as well — then it stands to reason that the odds of meaningful discoveries increase in spite of overall systemic complexity

The newsletter is a 37 page PDF, and you can download it here.

I’m a strong believer in the power of good figures.  Everyone knows the tired phrase “a picture says a thousand words”.  In scientific papers, where page charges and editors place restrictions on the amount of text and a color figure might run you $1000, it’s critical to make sure that your figures are absolutely as good as they can be.

One of the best programs for generating images of 3D objects is POV-Ray.  This is a raytracing program - it simulates rays of light and their interactions with a scene.  It’s an incredibly powerful program (just take a look at some of the results in the Hall of Fame), but also fairly complex and not user-friendly.  Some molecular graphics packages have built-in simplified POV-Ray interfaces (pymol and VMD are two that I’m aware of), however the renders produced by these programs just don’t look good enough for me most of the time.

I’m going to try to work out a more “realistic” rendering scene geared mainly towards the visualization of protein structures.  I’ll say from the outset that as of now I’m sort of inspired by the work of David Goodsell, and I’m going to try to incorporate some of that simplicity into the render.

There are a few things that many POV-Ray renders of molecules get “wrong” in my opinion, with the main two being lighting and texture.  This usually leads to sort of plastic-looking things with very harsh lighting and shadows.  Let’s see if we can work on a model system first to try and improve this.
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One of the major metrics scientists use to rank journals is the “Impact Factor“.  This is a real number calculated in mysterious ways by the Thomson Corporation.  The problem with it is twofold: first of all, it’s not accurate; secondly, it’s held in far too high of a position of importance (especially given point one).

This came up in my thoughts because of a comment from Sciencewoman in response to my recommendation that she look into publishing her latest paper in an OA journal:

PA: I looked at the directory [of open access journals] and the only appropriate OA journal had a significantly lower impact factor. Again, as a pre-tenured person, I need to be aware of those things.

This disheartens me because I think that it is precisely amongst the young faculty that a preference for OA publishing can take hold.

So, what is wrong with impact factors?  I hardly know where to start… Indeed the subject has been covered extensively elsewhere, and I’ll refer the reader to papers from Nature, Seglen, & Postma.

Let’s look at this case specifically.  Sciencewoman is worried that publishing her work in a journal with a low impact factor will reflect negatively on the paper - the tenure committee won’t think that it’s “prestigious”.  First of all, this is a fallcious argument.  Impact factors are an aggregate of citation counts for that journal (more or less), and therefore reflect only on the journal as a whole, not individual papers within it.  For instance, let’s say I wrote a really smashing paper in the Journal I Just Made Up, which was cited by every scientist twice.  Since all the other papers in JIJMU were random scraps I found in rubbish bins, they weren’t cited at all.  Just because JIJMU would have a fantastic impact factor (hauled up by my honestly brilliant paper) that doesn’t mean that my neighbor’s grocery list is also groundbreaking research.  This is an extreme example, but I think you get my point.

There are more specific problems with impact factors as they relate to OA journals.  These journals tend to be younger, and therefore are inherently shortchanged when it comes to impact factors which are tallied over several years.  They often serve niche fields, in which the overall impact factor might be lower (the numbers across fields cannot really be directly compared, because of different audience sizes and referencing traditions).  To be fair, there are certain ways that OA journals have an advantage when it comes to impact factors - it’s been shown that OA papers tend to be referenced more often than their closed counterparts.

The fact is that the impact factor as a metric of research quality is embarassingly bad, and I’d be happy if we could just do away with the notion altogether.  I definitely think that a young faculty member up for tenure should be able to make a convincing argument that the committee should look past a flawed number and appreciate the desire to make the work accessible to the largest community possible, by publishing it openly.

anything is hilarious when paired with the proper track from the discography of Queen

I tend to talk a lot about Open Access science because it’s the field I work in and the place I feel like I personally can make the most difference. To be fair, however, I really want *everything* to be open.

That’s why I also like the sort of simmering groundswell of musical artists taking their work into more liberal copyright regimes. The ones who “get it” realize that they can’t fight their fans tooth and nail and still get those same fans to spend money on their work. Radiohead got a lot of press for releasing “In Rainbows” as a digital download with an opt-in price, but unfortunately it seems like this may have been more of a marketing maneuver than a real embrace of copyright freedom.

I discovered Jonathan Coulton some time back, sort of because his name kept popping up around other things that I liked. Something about his DIY nature - running his own website, writing and recording the music in his apartment - really make him a likable guy. It helps that his music is catchy and fun. He puts all of his songs up for sale on his website (as well as a few other places around the web, but buy from him and pass along all the profits why don’t you) as 192 kbps MP3s (oh and he has FLAC now as well) with no DRM at all.

Of course I have heard about Trent Reznor (of Nine Inch Nails) and his bile towards the traditional labels. I also knew that they released their latest album, Ghosts, as a $5 download without DRM under a Creative Commons license. What I hadn’t done until today was actually listen to it. I remembered the NIN from my high school days and assumed that it would be the same sort of stuff. I was wrong. Check some of this stuff out:

It’s sort of ambient instrumental, but with a good mix of sounds and beats that keeps it from getting dull.  I’m really loving what I’ve heard so far, and I’ll be buying this as soon as I’m sitting in front of my media machine.

Comment time (please, so far there are a whopping zero comments here): What is your favorite source of DRM free music? Amazon MP3 store? eMusic? Direct from artists? Other (indie) websites?