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Scientific Journals and SOPA

There is some good news and not so good news on the scientific journals front.

First, the good news.  For those of us in STEM jobs who are laid off, we face a double whammy.  In order for us to stay current in our fields we *must* keep up with new literature.  Future employers won’t want to hire someone who doesn’t know what’s been going on in this rapidly changing research environment.  Watching NOVA is no substitute. The problem is that when you get laid off, you lose access to the licenses you need to search and retrieve literature, patents, methods, etc.  You can still get papers but you either need to subscribe to the journals, which could cost hundreds of dollars a year, or you need to buy the paper outright.  Prices for a *single* paper from journals like Journal of Medicinal Chemistry or Science cost $30.00.  On new projects, it is not uncommon to read a dozen papers to start.

There are some other subscription services like Deep Dyve that offer packages of a certain number of papers per month.   The problem with this is that you may need to go back to that paper sometime in the future and with Deep Dyve, that’s impossible.  You are only renting that copy and within days, it disappears, never to be accessed again without forking over the cash.  The best option is to go to a library where you can read as many papers as you like for free but then you have to go to the library.  You can’t just do it from home.  And that becomes a problem when you’re in the middle of reading a paper at home and you see a citation for a paper you need for background.  Then you have to haul your sorry ass down to the library.   I’m close enough to Princeton’s scientific library so access is not a problem but it’s not exactly convenient.

Let’s just say that it adds insult to injury for the journal aggregators to charge an unemployed person so bloody much for a digital copy of a paper, especially when those papers are important to our future employment.  I brought this up to a representative of the American Chemical Society (ACS) last May and got the impression that the old dude was really living in a different century.  The ACS had no intention of lowering the cost or allowing us to buy papers ala an iTunes model.  So, I was surprised to see that the ACS is relenting somewhat and is making their SciFinder application available to unemployed chemists who previously had an account at their former workplace.  They must have gotten a lot of desperate and angry pleas for access.  SciFinder licenses are difficult enough to get when you are employed.  In fact, I finally got one about two weeks before I was laid off so I don’t think I ever had an opportunity to use it.  But if you’re looking for a way to search the literature/patents through SciFinder, and you previously had access, you might want to check it out.

The bad news is that SOPA might make all that access impossible.  That’s because when scientists write papers, they liberally filch methods, pictures and other details from previously published papers from other authors.  That’s just the nature of science.  Everyone is standing on the shoulders of someone else and the reason authors publish is so they can share that information and to keep their jobs.  Publish or perish.  SOPA will interfere with that process for scientific literature in digital form, which is everything these days.  From the TechDirt article on the issue:

These kinds of “violations” are inevitable, because science is about sharing – it’s what you are supposed to do in order to spread knowledge. And thus drawing on standard materials in this way is a habit that pervades all of academic publishing to such a degree that few scientists are even aware they are doing it – or that there might be legal issues. That will make policing this kind of “accepted” infringement extremely difficult, if not impossible.

If SOPA is passed, Neylon points out an interesting consequence:

“So if someone, purely as a thought experiment you understand, crowd-sourced the identification of copyright violations in papers published by supporters of SOPA, then they could legitimately take down journal websites, like Science Direct and Nature.com. That’s right, just find the plagiarised papers, raise them as a copyright violation, and you can have the journal website shut down.”Scientific publishers that are represented by the Association of American Publishers, which appears in the “List of Supporters” (pdf) for SOPA, could therefore find their own Web sites shut down repeatedly thanks to this law they are currently backing by default, since none has yet come out against SOPA. Looks like US politicans aren’t the only ones who haven’t really thought this through.

I’m not surprised that publishers like the ACS haven’t thought this through carefully.  They are just trying to cash in by soaking companies, academic institutions and the unemployed for as much as they possibly can.  That’s why they charge $30.00/copy.  Of course they want SOPA so they can make sure that no one gives out copies of papers that they didn’t authorize.  But they’re really not thinking about the copyright violations in each paper.

I don’t know how they’re proposing to get around this.  There could be a lot of pharmaceutical company tit for tat.  Maybe Glaxo doesn’t want Merck scientists lifting their methods and throws a flag, while some little company wants to publish based on multiple companies published citations and gets flagged multiple times.  The end result is that nothing would get published and we’d all be cut off from one another, scared silly that our internet access could be terminated over some unintentional violation.  Not that you’d use the internet much because everything would be off limits.  It could open up a whole new field of employment in companies.  You could have copyright MBAs sitting in their cubes, heartlessly penalizing everyone they are competing with, damaging the spirit of sharing among the science community.  It wouldn’t be the first time they’ve thoughtlessly ruined research.

So, those of you out there who care about keeping science literature sharable, contact your congressman and senators.  SOPA is going to make an already bad situation so much worse.

Field testing the iPad

Long time, no see, guys.  My work life has gotten interesting lately and I find myself back in the lab after 20 years.  And I just have to say that all in all, this has been a very good move for me.  I recommend it to any former lab rat who has found themselves behind a monitor for too long.  Technology has changed a great deal in two decades and learning and relearning new things makes work challenging and fun.  It’s the best of both worlds, really.  I still get to park my fat ass behind the computer for part of the day to play with models but my ass is getting smaller from running around the bench.  So, two thumbs up for the lab.

Now, I have a company lab notebook that’s all legal and stuff that I write things down in but when I was in the lab recently, I found that I wanted a notebook for jotting things down of a more general nature.  It’s mostly reminders, calculations and procedural stuff that could apply to any particular experiment, nothing proprietary.  I recently bought an iPad to semi replace my macbook that’s on it’s last legs so I thought I’d give it a try.  There have been other reviews of the iPad, most recently Anglachel’s.  But I think that the mistake that many people make about the iPad is that they concentrate too much on the hardware.  (If you find the device “too heavy”, you need to hit the gym)  To really understand how the iPad fits into the device spectrum, you have to think out of the box and focus on the apps.  And even though the apps developed for the iPad are still few in number compared to the iPhone, it’s in this area where motivated developers are going to make the iPad a truly revolutionary device.

For my purposes in the lab, the iPad is off to a good start but it could be amazing.  I prop it up using the apple cover in type mode (see pic above) and leave it on the bench, coming back to it now and then to make notations using the Notes app that comes with the iPad.   I can type through my nitrile gloves and my lab is mercifully free from most solvents so I’m not worried about corrosion.  The screen cleans up nicely with a kimwipe.  Nevertheless, a waterproof cover or thin film screen protectent is probably a good idea for people who want to take their iPad into the lab.   There’s an app for making stock solution dilutions and molarity calculations called LabCal.  It’s an iPhone app that runs on the iPad.  Although the iPad doesn’t come with a calculator, there are plenty of cheap calculator apps in the apps store.  I found a nice scientific calculator called Calc XT that has a nifty little scratch pad.  For reading general procedures, I mail the published documents to my email account and access the pdfs using GoodReader.  And for planning my work, I use Todo by Appigo.  These are the main tools I need everyday. I don’t have access to wifi or the 3G network in my area so my scribbles stay on the ipad.  Essentially, what I have is the equivalent of a little steno pad, folder and calculator but the notes are stored by date and everything I need is in one slim device.

But there are a couple of additional apps that I’ve found lurking in the apps store that point the way to the future.  For example, the American Chemical Society has an app that allows the user to select a number of journals to browse.  Highlights and abstracts are delivered to the app and the full journal article can be accessed directly, provided the user has a subscription.  This would be a great way to deliver literature electronically.  Ordinarily, I print papers out from the pdfs because I don’t like reading them on a computer screen.  But on an iPad, literature has the feel of reading a printed document with all of the digital benefits.

Another app, iKinasePro, is a bit pricier but at $9.99 is still a steal.  It gives the user access to a curated database of kinases, along with published inhibitors, links to literature and patents, and a multitouch kinome tree.  But what really drew me to this app is that it features a molecular editor from Chemene that is similar to a ChemDraw widget.  The user can quickly draw a structure and do a

The Chemene Molecular Editor

substructure search of the database to find hits.  The app does require access to a wifi or 3G network, as does the ACS app.  The kinome diagram also doesn’t allow for the finer resolution multitouch, the user can only select certain groups of kinases.  But motivated developers {{hint, hint}} should be paying close attention to that editor because that’s the way we need to go with the electronic notebook app that I’m sure someone is going to make a killing on.

The mobile electronic notebook could be a godsend for labrats.  Imagine one app that does it all: records your steps, has a built in calculator, can calculate dilutions from stock solutions, can calculate the MW from the structure you draw, can fetch the synthetic pathway from the literature, can register your compound, and allow you to search for similar structures and their related activity and ADME data in the database.  Well, that’s just off the top of my head.  And if the lab pages are uploaded to a cloud server, there’s no reason to store anything on the iPad, making loss of proprietary data less likely.

Companies interested in protecting their proprietary information can get an enterprise version of the SDK.  Security of the local wifi and cloud server are out of my scope but where there’s a will, there’s a way.  Ahhhh, there’s the rub.  In many of the companies that I’m familiar with, there is a ginormous bureacracy of Microsoft borgs who will tell you that resistance is useless and that you will be assimilated to the same stupid image that the accountants use.  Mobility, without a mouse or a keyboard?  In. Your. Dreams.  In Microsoft’s holey products, there is a lifetime of employment security for hives full of corporate drones hired to test and patch the version of IE that is already several years out of date and to stamp out proliferating viruses.  Apple products are verboten.  They’re too sleek and simple.  The macbooks run on linux (One helpdesk borg asked me how to spell linux when I needed help with my HP linux workstation.  Yep, it’s that bad.)  The iPad uses an iPhone OS but still, Apple make the borgs antsy.  Which is why we may never get iPads for the labs. I don’t think this is going to change unless the borgs are given ultimatums employment incentives to experiment with other platforms.

Too bad, because I think there is a lot of potential on both the development and the efficiency side of the mobility equation.  It would be a shame to see the modern lab, stripped down and uber frugal, hobbled by a Microsoft mentality.  But whatever the fate of iPad in the lab, it’s a handy device to have around.  Still, if you can’t use it in the lab,  you can go home and use it to rent a movie from Netflix and forget all about work.