Monthly Archives: December 2010

Arsenic Consuming Microbes: Life Not As We Know It.

I was just about to knock off one of the many RSS feeds I had a massive backlog on when I noticed an article about NASA making a pre-announcement about a press conference they were going to have today. Usually this stuff isn’t front page news but this one had just the right combination of words to send us space nuts (and a good chunk of regular people too) into wild speculation about what NASA might have found. Even more interesting was the fact that one of my friends sent me a rabid SMS directing me to the same article. Something told me that whilst this wouldn’t be your run of the mill NASA press conference there was something big on the horizon, leaving my mind to buzz around all the possibilities.

NASA was not one to disappoint on this occasion.

Researchers at NASA’s Astrobiology Institute have discovered a microbe, native to California’s Mono Lake (a highly inhospitable place), that can survive and thrive by replacing one of the essential building blocks of life with an element that’s highly toxic: arsenic. The bacteria, known as GFAJ-1, was known to be arsenic resistant but researchers took it one step further by depriving the microbes of all phosphorus and flooding their environment with arsenic. The result was that not only did the bacteria survive they thrived, continuing to multiply as if nothing had changed in their environment. Further analysis of the bacteria showed that they had incorporated the arsenic into their DNA where the phosphorus should have been. This throws so many things into question and will change the way we search for alien life out in the universe.

The space and science news sites are abuzz with the implications of the discovery and what it means for the future of astrobiology. The news was so big that it even made the morning news here in Australia something that even the shuttle launches struggle to accomplish. Whilst this announcement isn’t as fantastical as some had hoped for (first contact being amongst them) we’re still at a turning point in our understanding about how life formed here on earth and how it can form elsewhere in the universe.

The discovery is interesting as prior to finding these microbes all life on earth has needed to use 6 building blocks in order to survive: carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. Arsenic is just below phosphorus on the periodic table so it shares quite a lot of properties with it and that similarity means it can be substituted into some biological reactions. However arsenic is far more reactive than phosphorous and this means that it is highly toxic to almost every life form on the planet. This bacteria however seems to have developed the ability to use arsenic when it is in a phosphorus poor environment and even has the ability to switch back to phosphorous should it become plentiful again (it actually seems to prefer it).

As with any big discovery this one is not without its critics. Steven Benner, a chemist from the Foundation for Applied Molecular Evolution, makes the point that whilst these bacteria were phosphorus starved there were traces of it available. Enough possibly to sustain these bacteria in the arsenic rich environment. Additionally should these bacteria be incorporating arsenic into their DNA it would be in the form of a arsenate, an ester of arsenic. Such a compound would hydrolyse in water making such arsenate based DNA unstable. He hypothesises that the arsenic is being used in some other fashion, possibly in a way that we do not yet understand. The research is of course continuing and will address these concerns.

We’ve known for a long time that life can develop in places we’d long thought it was impossible to do so but this discovery is something on a whole new level. Showing that a life form, even if it’s a simple one, can replace one of the fundamental building blocks of life with something thought to be toxic means we have to rethink the way in which we look for life here and out in the vastness of space. The prospect of finding life on other planets and moons here in our own solar system just got more possible as our understanding of how life can thrive undergoes a radical paradigm shift. I can’t wait to see how this develops and I’m sure this isn’t the only bacteria out there capable of feats like these. Who knows what kind of alien life we’ll find right here in our own little rock called earth.

Mac OS X: A Veteran Windows User’s Perspective.

I’ve been using the Windows line of operating systems for nigh on 2 decades now for my own personal PC and apart from the occasional tinkering I haven’t bothered trying anything else. My professional life is a different story as with VMware being a heavily modified version of Red Hat Enterprise Linux I’ve had to become more familiar with the open source alternative so that I can troubleshoot the more esoteric problems that it might throw at me. Additionally I had the (mis)fortune of managing one of Apple’s token stab at the enterprise market the Xserve which, whilst didn’t give me any large amount of grief, had its own way of doing things that made most trivial tasks take hours. That was probably the most experience I had had with an Apple OS up until I took my shiny new MacBook Pro (separate review coming soon) with me on my trip around America where I decided I would thoroughly test Mac OS X as my primary operating system.

The initial experience of starting up OS X for the first time is a world away from what I’m used to with Windows installs. You’re greeted with a short video presentation showing the various aspects of the OS which is then followed by the sign up process. I do remember it asking me for my iTunes account name and password during part of this which I thought was a no-no ever since Microsoft got into trouble for trying to get everyone to have a MSN account¹. Less than 5 minutes later I was ready to start bumbling my way through a new OS, and bumble I did.

My first initial task was to install Windows 7 on it since I know OS X wouldn’t be able to run everything I wanted it to. Getting bootcamp configured was pretty painless with the help of the guide Apple provides so there’s some big props for them there. About 20 minutes later I had a full Windows 7 installation running with all the drivers I needed, although I did update the video card with NVIDIA’s latest offerings. Satisfied that everything was fine on the Windows side I flipped back over to OS X to give it the initial shakedown.

First I tried browsing the web using the inbuilt browser, Safari. It opened up in a not-so-fullscreen manner so I hit what I thought was the maximise button to get it to fill the screen. It didn’t do anything and after researching around a bit I found that OS X doesn’t really have a concept of fullscreen and that button really only serves to switch between window sizes. I could get a close approximation to the maximise button by stretching everything out but that could also end up a window bigger than the screen it was on, especially with the lack of precision granted by the trackpad I was using.

Here is where I feel Apple is let down by its community. Whilst I’m not an easily offended person my searches for a solution to the fullscreen problem brought me to this forum thread in which it takes no less than a single post for a OS X user to abuse someone for trying to find a feature similar to Windows. I’d love to say that it was an isolated incident but time after time when I found myself looking for the answer to some problem I could easily solve in Windows this kind of elitism seems to follow quite closely. Granted I’m not saying all OS X users are like this but there’s enough of them to do a royal disservice to those of us who aren’t complete novices when it comes to computers but are unfamiliar with the world of OS X.

Undeterred from those experiences I went ahead and signed up for the Apple Developer Program and downloaded the latest version of Xcode. Installation was pretty easy and I was able to build a simple program about 10 minutes later with little hassles. Regular readers will know of the trials and tribulations I’ve been through since then but overall I’d count Xcode as a decent IDE but still needing some work to be up to the standard I’ve come to expect. Thankfully most of my questions regarding the IDE (such as deploying code to a real iPhone) were already answered in the online documentation which goes a long way to bridging the gaps.

Not long after using the laptop as a development machine I packed it up and took it with me on a trip around the USA and Canada. Here OS X started to show some of it’s convenience features that I really started to appreciate. The first was it opening up iPhoto when I plugged in my camera, where upon it began walking me through creating events and some of the other features it has. Unfortunately it didn’t like the way my camera stores movies (and iMovie doesn’t like the format) so they had to remain on the camera. Still it was nice to be able to load all the photos on the laptop at the end of the day and have them nicely arranged in a bunch of tiles.

The fun really started when I began trying to do things I had never attempted in another operating system before. Mostly this was troubleshooting things like why my camera wasn’t showing up (needed a reboot) or when I was trying to spoof my MAC address so that I didn’t have to pay the exorbitant price for the hotel Internet connection (why a $50/night place gives me Internet for free and a $400/night place doesn’t is beyond me). It seems in these areas of esoteric OS X issues and chicanery the community is much better than what I had initially encountered with me being able to Google up several solutions without any high and mighty Apple attitudes creeping in.

All the rudimentary programs (Finder, TextEditor, StickyNotes) function as expected and are pretty much identical to their counterparts on Windows. The same can be said for the system settings as once you click on it you’ve basically got a Windows control panel staring back at you. So whilst the visuals might be different the administration of OS X settings isn’t too far removed from what many of us long time Windowers are used to. Of course a bit of familiarity with the *nix terminal won’t go astray when you’re trying to do something really out of left field, but if you’ve used the command prompt or written a script in windows I don’t think you’d have too much trouble.

Overall I found OS X to be quite satisfactory as a desktop OS as it provided all the functionality I required of it whilst providing some value add that I wasn’t expecting. Still the experience wasn’t exactly mind blowing and there are many differences that are there just for differences sake (using the command key instead of control, close/minimise/maximise buttons on wrong side) that don’t do them any favours. I won’t be removing OS X completely as it works extremely well for what I use it for but I won’t be replacing Windows 7 as my current default OS. Would I recommend it for others? Hard to tell and it’s something that I’ll probably explore in a future post.

¹I did this set up over 2 months ago now so I might just be remembering this incorrectly but I did give up my iTunes account info well before I saw the desktop. It may not be required to use OS X but I wouldn’t have put it in unless I thought it was required.