Monday, October 31, 2011

The Short Attention Span Segment #4

Ok, here we go, this week's top five for those who don't want to pay attention for too long:

1. NASA Astronomy image of the day, for absolutely breathtaking images of the universe, I can stare at these for hours: Today's Image (31st October)

2. Getting into the spirit of Halloween, with some amazing pumpkin carving: Halloween Pumpkin-Palooza

3. Because Ezio is the ultimate assassin: Penny Arcade

4. The Atheist Experience, a fab radio/web streaming show: Atheist Experience Homepage

5. Australian scientists Mike Lee and Trevor Worthy argue the case for Archaeopteryx being a primitive bird (and not a raptor as argued by Chinese researchers in July 2011): Cosmos Magazine News and Original Publication

Tuesday, October 18, 2011

Picture of the Week: The Bedside of Awesome

My bedside to-be-read pile of recent purchases/borrowings. From top to bottom: "Cosmos" by Carl Sagan, "Pandora's Seed" by Spencer Wells, "The Magic of Reality" by Richard Dawkins, "Arguably" Essays by Christopher Hitchens and last, but by no means least "The Philosopher's Breakfast Club" by Laura J. Snyder.

Absent is "Warm Bodies" by Isaac Marion, my latest purchase for the zombie fiction collection. It's was absent as it's currently on my desk.

Some epic reading ahead - I cannot wait to get stuck in, trouble is, I don't know which one to go for first! Too bad I can't have a week off work with bad weather.

Monday, October 17, 2011


2012 Global Atheist Convention

The Short Attention Span Segment #3

This week’s top five:


1. Richard Dawkins’ new book “The Magic of Reality”. Aimed at all ages, and it is one of the most beautifully illustrated books I’ve ever seen. A gorgeous book which shows that true magic is really all around us: The Magic of Reality at RD.net


2. After a few months absence, Hitch back on his feet – still full of sharp wit and all kinds of awesome. He was at the Texas Freethought Convention receiving the Dawkins Award from Richard himself: Geoff Bang's Blogpost on the event and Videos : Part 1 and Part 2


3. The Dropkick Murphys are in town (and yes, I’ve got tickets): State of Massachusetts


4. T-Rex just got even more scary: Science Daily


5. I somehow don’t think this will mean we can give up the gym: Cosmos Magazine

Monday, October 10, 2011

From The Phd Files: You can't always get what you want....

Last Friday I attended the opening of the Adelaide Festival Ideas. As well getting to see a personal hero in the flesh, it also sparked much discussion and thought amongst the attendees. In case you are wondering, my personal hero who was in attendance is Professor Peter Doherty, Nobel Laureate, immunologist and champion of science communication. Alongside Peter was Phillip Adams (another fave of mine), Barbara Hardy and Professor Penny Sackett, the former Chief Scientist of Australia. Penny gave the keynote address of the festival entitled "Science and Uncertainty", in which she talked about the uncertainty of the measurements of science, the importance of a transparent scientific process, and just how perfection is impossible. She also argued we really need to use the evidence we have on which to base our actions, and as the wheels of science keep turning, we can build and improve on the evidence in the never ending process of research and understanding. What followed was a great discussion between the audience, Phillip, Peter, Penny and Barbara, and I walked away feeling honoured that I'm part of the machinery which furthers our understanding of the world, and how science and knowledge and knowledge in all its amazing forms make me feel inspired to be part of humanity.

On a personal level, the concept of uncertainty really hit hard in the last few weeks. Whilst the evening at the festival of ideas made me feel inspired, of late I've been feeling anything but. It's a well known fact that the process of obtaining a PhD is like a rollercoaster - full of the highest of the highs, and the lowest of the lows. The moment of elation when that experiment works cannot be compared to anything else, but the drudgery it can take to get there can just about break the strongest of wills. And PhDs are full of uncertainty - uncertainty about how the research will pan out, where the money will come from, whether you'll get the paperwork done in time, if you'll have a job next year or whether tomorrow you'll log in to your email to find someone has just beat you to the punch and published your scoop, thus downgrading your hard work and revelationary findings to a much lesser journal. This is the nature of the beast that is science, and a PhD is a the baptism of fire into probably one of the most uncertain, but most rewarding careers.

Anyway, a case in point happened to me recently. I went away for a bit over a week - an escape from the lab to refresh, get my head around some statistical analyses I needed to master, and catch up with the family - a working holiday of sorts. Three days in, and just as I'm undoing all the stress and craziness of the last few months, and getting into the swing of country pace, I get a email and a phone call. Turns out, the contractors the university employ are incapable of reading - they shut down the power to the cleanroom, which involved entering said cleanroom in their dirty work gear, pulling all the plugs and leaving. No power for a weekend means no fridge and no freezer keeping things chilled. I got the phone call when my colleague rang me - they had arrived Monday morning to a lab which was akin to a swimming pool. As for the reagents? Written off - enzymes don't like room temp! And even so, it's often not worth bothering with sub-par reagents. If things don't work how does one know that it's the experiment or the thawed out dodgy enzymes?

It turns out the university had forgotten to notify us of the power outage, as they had forgotten we had a laboratory in the building. But they did have insurance - now comes the painstaking task of reordering all the ruined stock and waiting, and dealing with a new ordering system to boot makes this not the most pleasant of tasks. The kicker of the situation was that some of my reagents had just been bought prior to going away, they were unopened, and ready and waiting for the flurry of productivity I was going to launch into when I got back....but as my title tells, you can't always get what you want. Very rarely in science do things go the way you want or plan, but as the song goes, you sometimes get what you need, and in the process you get more interesting results and learn a few lessons which will make you a better scientist.

So in light of Friday's lecture and discussion, it got me thinking - we have scientific uncertainty in the form of the experimental measure, we have uncertainty about where the next paycheck is coming from, we have uncertainty about whether we can get that publication accepted, uncertainty about the results, and to add to all this uncertainty, whether we can do our experiments at all. Day in and day out, there's uncertainty on all levels in science, and it can drag you down. When I read a paper, I can now appreciate not only the data collection, the analysis but the day to day dealings that have had to be overcome to enabled that paper to get to publication. There's a lot of blood, sweat and tears in a few pages of scientific results, and now I'm living it day to day I've got a another whole level of respect for those authors.

So would I trade the roller coaster of research for some sort of certainty? Never! The thrill of not knowing what results will reveal, of not knowing what each day will bring, or what the next challenge is, that mystery is part of what makes science so great, and why I love what I do. In spite of losing all my reagents, and of the delays, the payoffs in spite all those types of scientific uncertainty are immense - the potential to contribute to the understanding of the world around us, to be part of the scientific machinery, to feel that elation when your paper is published or you see those bands on a gel far out ways the failures, the stress, the tedious moments and the downers. After all, how boring would life be if everything was certain?

Tuesday, October 4, 2011

Citizen Science: How People Power Is Helping to Solve Scientific Riddles


Science was once seen as off limits to the average person, to be only to be conducted by nerdy types in white coats, who speak in strange terms and don’t have much of a life. Well, that stereotype is well and truly toppled with the recent news regarding the use of a program called FoldIt, a group of gamers and the unravelling of a protein which is found in virus family known as retroviruses, which include the likes of HIV.

With recent technological developments, scientists are producing an ever-increasing amount of data, more data they can possibly hope to analyse in their lifetimes. On the opposite side of the spectrum, many people have computers, Xboxes and Playstations that don’t utilise their full processing power. In 2008, a group of Washington University researchers saw the potential to harness people’s technology in its downtime and FoldIt was the result.


FoldIt is just one example of a program that utilises either people or their technology (or in some cases both) to further scientific research. In the case of FoldIt, participants download the program, and then set about playing a ‘game’ against one another to determine a folding pattern for a particular protein. However in this case, this game doesn’t result in a high score, it results in contributing to scientific knowledge. Humans still outdo computers when it comes to complex pattern recognition and FoldIt harnesses our inner problem-solving capabilities to elucidate structures within a competitive gaming environment which makes the science fun! In regards to the protein mentioned earlier, FoldIt participants solved the structure of a protease whose structure had been baffling researchers for 15 years. Proteases are cutting enzymes and are important in the complex formation of retroviruses such as HIV. According to the FoldIt website, it took gamers just 3 weeks to sort out the predicted structure for the protein.


The results were published in the journal Nature Structural and Molecular Biology with both researchers and gamers listed as authors. And the implications? A 3D structure is vital for scientists not only to study a protein and its interactions, but for finding new drug targets and designing new therapies. The combination of the citizen scientist and experts may mean the development of new drugs not only for HIV, but the likes of Alzheimer’s disease, cancer and other diseases.

From the smallest of viruses to the largest of the galaxies, the involvement of volunteers in science is making a big impact.


But the involvement of the community does not end there. Whilst one computer’s processing power may not seem like much, the combination of thousands of participant’s computers certainly adds up, and enables a lifetime’s worth of searching and analysis to be performed in a matter of days. A number of other research groups have applied people (and computing) power including in the field of astronomy. In August 2010, a paper was published in the prestigious journal Science, and was co-authored by a couple who were credited with discovering a new radio pulsar named PSR J2007+2722-. Radio pulsars are a signal of a neutron star. The couple were not researchers, but had downloaded Einstein@Home, a program which analyses gravitational wave sources, in the search for neutron stars, and were using their spare computing power to analyse masses of astronomical data. Neutron stars are what is left after a supernova, and thus can provide information about not only the lifecycle of a star but improve understanding about the workings of the universe.


The most famous use of voluntary computing resources is probably SETI@Home, which is the use of processing power to search for radio signals that may indicate the presence of intelligent life in the universe (aside from us, of course!). Established in 1999 by researchers the University of California Berkley, SETI@Home was the first use of home computer users, and currently there are over 5.2 million participants worldwide, who have logged over two million years worth of computing time – a massive feat, which may not have turned up ET but has demonstrated the need for people-power and how citizen scientists are turning up some great discoveries, which otherwise would just not be possible.


For further information on how you can get involved through your CPU to unravel HIV, search for neutron stars or search for extra-terrestrial life check out the homepages of the programs:

FoldIt

Einstein@Home

SETI@Home

Rosetta@Home

Folding@Home


And you never know, it may be your Playstation or computer which provides the next big discovery and helps scientists understand the world around us. Science is no longer just in the hands of the folk in white coats, it is in the hands of anyone who wants to get involved.


References:

Scientific American, September 20 2011 - Foldit Gamers Solve Riddle of HIV Enzyme within 3 Weeks

Science Daily, August 12 2010 - Citizen Scientists Discover Rotating Pulsar