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    • Killing Herd Animals
      One of the great crimes and tragedies of our world is how we treat the animals we eat (or whose milk or eggs or other products we eat and use.) Factory farming keeps them in tiny enclosures, feeds them monotonous foods, and then when they’re slaughtered it’s a terrible experience: they’re terrified and die in […]
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Oil Spill update: “Top Kill” has failed

Supposedly an email was sent from BP saying “Top Kill” has been killed:

Earlier today, BP COO Doug Suttles had no good news for local reporters following the company’s “top kill” effort to plug the oil well in the Gulf of Mexico, telling them that it had not yet worked and he did not know whether it would be successful yet. And now a few moments ago, CNN International Desk Assignment Editor Nick Valencia is reporting on Twitter that Plaquemines President Billy Nungesser has received and email saying Top Kill has officially failed.

A Congressman also gets emotional over the situation.

There is nothing to say and no adequate words to describe how we all feel about this, so make it an open thread.

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.

Ahhhh….

Lazy Saturday Oil News: BP Atlantis and Other Dangerous Gulf Oil Rigs

BP's Atlantis Platform in Gulf of Mexico

Good morning Conflucians!! This morning I’ve been trying to educate myself a little bit about oil drilling in the Gulf of Mexico.


BP ATLANTIS

Did you know that BP has another oil rig in the Gulf of Mexico that is drilling even deeper than the Deepwater Horizon–more than 7,000 feet under water? It’s called Atlantis.

Considered one of BP’s most technically challenging projects ever, the Atlantis platform is currently the deepest moored floating dual oil and gas production facility in the world and weighing in at 58,700t, it is also one of the largest. BP is operator of Atlantis with 56% ownership with its partner in the venture, BHP Billiton, having a 44% working interest.

The platform is located 190 miles south of New Orleans in 7,070ft (2,150m) of water, the field itself occupying five blocks – Green Canyon 699, 700, 742, 743 and 744 – with water depths ranging between 4,400ft and 7,100ft (1,338m and 2,158m)….

Atlantis has a production capacity of 200,000 barrels of oil and 180 million cubic feet of gas a day, with the expectation that it will have reached plateau production by the end of 2008.

The field has an estimated life of 15 years and oil reserves of 635,000 million barrels of oil equivalent.

Like Deepwater Horizon, Atlantis was approved to drill “without critical safety documents,” according to Food and Water Watch (via Democracy Now) If there were an oil spill from Atlantis, it could be far worse than the accident at Deepwater Horizon.

Food and Water Watch has started a new website devoted to convincing the Obama administration to stop BP’s Atlantis operations until the rig is shown to be safe and reliable. Here is a video from the site:

Via Food and Water Watch, on May 16, 60 Minutes ran an interview with a whistleblower, Kenneth Abbott.

Mr. Abbott tried to warn BP executives about missing engineering documents that are critical to the safe operation of Atlantis. It is because of Kenneth Abbott that we have an opportunity to prevent another disaster that could be several times more destructive than the Horizon explosion and bigger than the Exxon Valdez spill in just two days. Atlantis poses an enormous safety risk, one that could seriously endanger its workers and the environment in and around the Gulf of Mexico, including the livelihoods and well being of residents in surrounding communities. BP management has noted that an accident resulting from “catastrophic Operator error” on Atlantis could occur.

You can watch the 60 Minutes segments here.


MORE UNSAFE OIL RIGS
IN THE GULF OF MEXICO

Via Democracy Now, the Center for Biological Diversity has filed a lawsuit to close down 49 more drilling sites in the gulf that were approved by MMS without any environmental review. From the press release:

Just like BP’s Deepwater Horizon drilling plan, all 49 plans in today’s suit state that no environmental review is necessary because there is essentially no chance of a large oil spill, and if a spill were to occur, it would be quickly cleaned up with no lasting damage.

“Secretary Salazar continues to exercise extremely poor judgment in approving these plans without meaningful environmental review,” said Miyoko Sakashita, oceans director at the Center. “He seems to have learned nothing from the oil pouring out into the Gulf of Mexico. Since Salazar is unwilling to shut down the use of environmental waivers that even the president has denounced, we are asking the courts to do so.”

President Obama has “suspended” new drilling projects, but has done nothing yet to make sure that these dangerous oil rigs already operating in the Gulf are reviewed to see if they have sufficient back up plans in case of a blowout.

As you can see, I’m still obsessed with the oil spill, but feel free to post links to any kind of news in the comments. And have a great Saturday and a relaxing Memorial Day weekend.

I’m soothing myself with this after my morning of oil research: