Archive for the ‘Science’ Category

Man Vs Machine

We all know of the SETI@home project, where since 1999 we have been able to donate our computers unused resources to download and analyzes radio telescope data to assist in the search for aliens. Biologists got in on distributed computing too and launched Folding@home and rosetta@home where computers and next generation consoles (PS3s) are used to try and predict protein folding.

However due to the nature of proteins and the complex interactions which they undergo, writing accurate algorithms to try and determine the correct structure is difficult, so since May researches at the University of Washington have decided to harness the power of online gamers and scientist who spend too much time on their computers, oh and possibly the bored graduate student who wants to look like they are doing work.

Foldit presents an unfolded protein and the user then has to wiggle, shake and move the protein into the optimal configuration, as you move towards the optimal structure you are awarded points. So far 60 proteins have been released for competition, and around 600 people registered to fold, in less than 2 months, it seems to have captured the interest of a lot of people.

For players without a biochemistry background the learning curve is step, but biochemistry is not a prerequisite for success, because it is possible to fold the proteins after going through the tutorial. Most of the online players are from non science backgrounds, showing that this tool really is harnessing the power of gamers.

Whether it folds proteins more accurately, and faster than computer based methods is yet to be seen


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Courtesy of TED, Philosopher Dan Dennett makes a compelling argument that not only don’t we understand our own consciousness, but that half the time our brains are actively fooling us, arguing that human consciousness and free will are the result of physical processes and are not what we traditionally think they are. See more of his fascinating talks here.

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Publish or Perish. If you’ve ever worked in research, you’ve heard it. Publications, author number (am I first, second, or last?), references, reviews—they’re all lifeblood to the career researcher.

Now, I am just starting out on my academic career. I haven’t quite got my pesky PhD out of the way yet—though it should all be finalised soon—at the moment my focus is on generating some publications so people will read what I’m working on and want to employ me or work with me in the future. Publish or perish, remember?

Having a unique name in science is much more of a benefit than a hindrance; provided someone finds your first paper finding the rest is easy. On the other hand if you are Mary Smith, someone had to sift through all the M. Smiths and try and find out which of the 6500 papers are actually yours (and that was just from a PubMed search [1]). In an attempt to make life easier people it is common for find people using their middle initials when publishing to ensure they can be found easily. There’s just one thing—what happens to my publications if I change my name when I get married?

As you look around the world, there are many traditions about keeping your name, changing your name, and even hyphenating or combining surnames to create something new [2]. I don’t have a strong attachment to my surname—sure I’ve had it for 26 years, but I don’t really care about it. I let people mispronounce it and spell it incorrectly, something I would never consider letting someone do with my first name. Growing up I always just thought I would simply take my husband’s name when I was married.

Life being what it is, by the time I got around to getting married I had a mortgage, a few degrees, and had moved half way around the world to a smallish town with no Australian embassy nearby. If I wanted to try and officially change my name I would have to change a lot of documents—something that’s not easy in your country of citizenship, and even harder when you live on the other side of the world. How do I change the name on my work visa, when I haven’t change the name on my passport or where I work? All in all it seemed a little bit too hard so I’ve put that final decision on hold ’til I get back to Australia or my passport runs out – whichever comes first.

So, back to science and publishing. So far, I’ve had two papers published, one in Physiology and one in Virology, and I expect most of my publications will end up in PubMed at some point [1] .

The first article I had my name on was from my honours year. I did a fair bit of work on it, but I was way down in the author list by the time it was published. My second paper was my first publication from my thesis—and I was first author. It takes a bit of time to get a paper polished, submitted, and accepted, so I wasn’t really worried about my surname when we sent it in. Until I got the notification that (paper title) would be published just two days before I was married, that is.

I wasn’t too sure what to do. I wanted to somehow acknowledge that I was married, even moved into a new stage in my life. Besides, I’d always assumed I’d just take my husband’s name, right? But what if my earlier work didn’t come up when people searched for me in the database? Eventually, I decided the easiest way to keep all my options open was to use a hyphenated name for any future publications, thinking that would allow people who know me by either name to find my work. I think this is what’s called “wishful thinking”.

So I did a couple of quick searches to confirm that hyphenating my name would still allow my articles to be found. Everything looked okay, so I went ahead with Sheryl Maher-Sturgess.

Not long after my second article was published, I was playing around on PubMed trying to find it. Maher brought up nothing. Sturgess brought up nothing. Why? Because PubMed will only return search results for an exact name match, I.e. if you search for smith you will only find papers by Smith, and no results for Smith-Chang will appear. I decided I would ask the curators of PubMed what I could do to get my names linked, the reply:

Unfortunately we cannot link variations of one person’s name in PubMed records. If you are able to get your name changed in the actual journal then we will make the change in PubMed.

In this case, contact the publisher to report the error and ask that they publish an erratum. An erratum in the journal must be on a numbered page, not “tipped” in or unbound. The NLM does not make changes in the database until the erratum is published.

It seems a little strange to me that I should ask a journal I published in 5 years ago to publish and erratum just so I can have my papers linked and it also seems a little deceitful, since I wasn’t Maher-Strugess back then.

Still, I thought, since I can Google myself with my married name, my maiden name, or my hyphenated name and find my second article, Google Scholar should work okay, right? Wrong. Google hasn’t outfitted their new Scholar application with the same comprehensive capabilities as their original search engine. I’ve recently alerted Google to this issue—and it is now on their list of things to do. Who knows they might decide to implement it in the future.

By changing my name, I’ve lost one publication, and in the grand scheme of things it isn’t going to be an important one I’m a middle author on a paper which I spend a year working on, it was a big deal till I started doing my own research and writing paper I’m going to be first author on. For someone who had a well established career before deciding to change their name it (because they’ve got married or divorced) would be a much bigger problem. When you apply for grants they ask you to list all your publications. What happens when the sleep deprived assessor who has been reading these huge applications for the last 4 days gets to yours and cannot find the applicants name on any of the publications included – they may not make the connection, and most forms don’t give you an opportunity to list other names you’ve been known as. At least with a hyphen both names are there so finding me in the author list shouldn’t be too hard (there is that wishful thinking again).

Until then I’ll just have to spell my name for everyone I work with, and hope that future employers pay more attention to my supplied list of publications that database search results.


[1] www.pubmed.com is a service provided by the US National Library of Medicine and The National Institute of Health which maintains an online open access database of health related publication. For most people in working on human health this is the primary source for finding relevant research.

[2] Formally in Commonwealth countries it is common for the wife to go from being Miss Jane Smith before to marriage to Mrs Peter Brown after her marriage, although it is also common (although not traditionally correct) for the wife to be known as Mrs Jane Brown after her marriage. In Asian cultures it is also common for the wife to take her husband’s surname. In many European countries the wife will keep her surname but go from Miss to Mrs (or the local equivalent).

[3] http://scholar.google.ca/schhp?hl=env

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