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

Dan Dennett: Can we know our own minds?

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.

Nigerian Cat-woman

The fear surrounding this event is not only palpable, but downright disturbing.

I feel as if I should write something more about this, but I think it speaks for itself. From the Nigerian Tribune:

This woman was reported to have earlier been seen as a cat before she reportedly turned into a woman in Port Harcourt, Rivers State, on Thursday. Photo: Bolaji Ogundele.WHAT could be described as a fairy tale turned real on Wednesday in Port Harcourt, Rivers State, as a cat allegedly turned into a middle-aged woman after being hit by a commercial motorcycle (Okada) on Aba/Port Harcourt Expressway.

…Nigerian Tribune learnt that three cats were crossing the busy road when the okada ran over one of them which immediately turned into a woman. This strange occurrence quickly attracted people around who descended on the animals. One of them, it was learnt, was able to escape while the third one was beaten to death, still as a cat though.

…Another witness…said the woman started faking when she saw that many people were gathering around her. “I have never seen anything like this in my life. I saw a woman lying on the road instead of a cat. Blood did not come out of her body at that time. When people gathered and started asking her questions, she pretended that she did not know what had happened,” he said.

…[The woman] was later taken to a hospital for medical attention. It took the intervention of policemen to prevent the mob from killing her. [Bolaji Ogundele, Nigerian Tribune, Cat turns into Woman in P/Harcourt, Port Harcourt, 22nd May 2008].

A new kind of death toll

We’ve all heard about the death toll in Iraq (~4,100 dead at the time of this writing), seen the footage of memorial services, the news reports about hidden casualties and the perceived unreality of what’s happening in the Middle East. But there’s a subset of war casualties we don’t hear much about—those returned soldiers who commit suicide, who attempt suicide, who suffer from post traumatic stress disorder, who suffer from any number of other mental illnesses exacerbated by the war.

Kevin and Joyce Lucey, a couple who lost their son to suicide in 2004, marked this Memorial Day differently, attending a new kind of rally.

Organizers of the waterfront rally, including Veterans for Peace and Iraq Veterans Against the War, said they wanted an alternative way to mark Memorial Day from traditional “militaristic” parades and speeches that glorify war. For instance, President Bush yesterday talked about soldiers in Iraq who died “doing what they loved most: defending the United States of America.” The reality, said Memorial Day for Peace organizers, is that troops and civilians alike are dying for Bush’s foreign policy mistakes.

Yet, despite opinion polls over the last two years that consistently show the majority of Americans oppose the five-year-old war, many protests draw small crowds. Only about 100 people, mostly veterans and veteran activists, turned up at the waterfront, drawing a few barbs from the speakers about all the people who view Memorial Day as little more than a day off from work. [Boston Globe, Rally's veterans, activists seek to avoid glorifying war, Scott Allen, May 27th, 2008.]

But what about those who are still with us, struggling with depression, PTSD, and urges to commit suicide? Well, there’s some hope in a new private practice programme. As this article from the AP tells us,

WASHINGTON—Thousands of private counselors are offering free services to troops returning from Iraq and Afghanistan with mental health problems, jumping in to help because the military is short on therapists.

On this Memorial Day, America’s armed forces and its veterans are coping with depression, suicide, family, marital and job problems on a scale not seen since Vietnam. The government has been in beg-borrow-and-steal mode, trying to hire psychiatrists and other professionals, recruit them with incentives or borrow them from other agencies.

Among those volunteering an hour a week to help is Brenna Chirby, a psychologist with a private practice in McLean, Va.

“It’s only an hour of your time,” said Chirby, who counsels a family member of a man deployed multiple times. “How can you not give that to these men and women that … are going oversees and fighting for us?”

There are only 1,431 mental health professionals among the nation’s 1.4 million active-duty military personnel, said Terry Jones, a Pentagon spokesman on health issues.

About 20,000 more full- and part-time professionals provide health care services for the Veterans Administration and the Pentagon. They include psychiatrists, psychologists, psychiatric nurses, social workers and substance abuse counselors. [Pauline Jelinek, AP, May 25th, 2008.]

Until a chance encounter over coffee the other day, this new death toll had not occurred to me—sure, I knew troops had issues with PTSD and the like, I even know a couple. But the idea of suicide as a result of war, although immediately understandable, was not on my personal radar. And how true is that for the public in general? Mental illness carries a stigma—a lesser stigma in the US than some other parts of the world, but a stigma all the same. Which is why it’s important, imperative even, that we talk about it, today.

For more information, help, and non-judgemental discussion about suicide and depression, contact The Samaritans at http://www.samaritanshope.org and 877-870-HOPE (4673).

Memorial Day – a time to consider national priorities?

Food for thought: two months’ worth of the military budget would wipe out the student loan debt of every current student in America and then some.

Four months’ worth would send every student academically eligible to attend college to school for free.

Three months’ worth would pay for the entire reconstruction of the Gulf Coast, erasing Katrina’s damage.

Friend of Pensive, Chris Penn has posted a short article on where the US military budget could go, and a reminder that we can help make policies in the voting booth this November (well, those of us that are US citizens, so not me -but the point stands).

Food for Thought on Memorial Day

Should there be a Muslim school in a predominantly Anglican, Australian town?

With its lace curtain bungalows and steepled Anglican church, the once tranquil town of Camden in New South Wales seems the most improbable of settings for a row that combines race and religion.

…

Now the town, which lies on south-west fringes of Sydney, is confronting a very 21st Century issue: the proposal to construct an Islamic school for some 1,200 Muslim pupils.

This is definitely a touchy subject, inflaming a lot of passions:

“Everywhere is being destroyed. Why don’t we tell the truth. They’re wrecking Australia. They’re taking us over,” she said.

“Why hasn’t anyone got any guts? They’ve got terrorists amongst ‘em… They want to be here so they can go and hide in all the farm houses… This town has every nationality… but Muslims do not fit in this town. We are Aussies, OK.”

I won’t shy away from calling this what it is – xenophobic racism. Stopping a religious school because it is not your religion is wrong.

But…

There is a valid objection to the school – “planning”: a 1200 student school in an area that has, (in my rough guess) about 500 Muslim students means a lot of students are going to be bussed or driven in. In an age where carbon should be a critical factor in every decision, I think this should more than enough to quash the school.

Beyond that, I have a fundamental objection to religious schools of any sort. Religion has no place in education – the notion of received or revealed wisdom is a direct contradiction of how the world works – in science, in mathematics, in history. Truth is found through thought and investigation. Not through reading one or two books of dubious veracity.

Religion stunts the development of the human mind – it is a meme that once served a purpose (of a sort) but has survived long past the point where it did anyone any real good. In a very real way, it is like an appendix of the psyche – a vestigial organ that dates back to long ago and now just consumes resources and endangers our lives by eventually becoming inflamed and bursting.

No-one should be exposed to religion, least of all children who haven’t the experience to tell dogma, superstition and wishful thinking from truth. No religious groups should be allowed to run schools, period. If religion must exist in this world, it should be treated the way pornography is – kept away from children by law, made hard to find, the users ostracized and condemned. All religions have an agenda – even if it is a relatively innocent agenda of self-propagation – and education coming from an agenda is bound to be substandard.

BBC – Town moves against Islamic school

Video: Karen Armstrong: Charter for Compassion

As she accepts her 2008 TED Prize, author and scholar Karen Armstrong talks about how the Abrahamic religions — Islam, Judaism, Christianity — have been diverted from the moral purpose they share to foster compassion. But Armstrong has seen a yearning to change this fact. People want to be religious, she says; we should act to help make religion a force for harmony. She asks the TED community to help her build a Charter for Compassion — to help restore the Golden Rule as the central global religious doctrine.

I find the idea that humanity needs religion to encourage or justify compassion incredibly insulting. Religion has contributed to many of the great evils perpetrated over the entire span of human history. We can learn to be nice to each other without some sort of cosmic judge looking over our shoulders. And then it is real compassion – an act of love and respect for our fellows – not an act of fear.

The “charitable works” of the religious are akin to those of people on court ordered public service – no matter what face they try to put upon it, we all know that they are only there because a higher power that they fear has made them. This is distinct from true volunteers who sacrifice their own time, resources, and/or comfort for the greater good of what ever group they identify with – a society, a nation, a race, a species or the “Greater Terran Group of Life Forms” (As far as I know, no-one on Earth is working consciously to help out a group larger than all life on Earth).

We can be nice to each other with worrying about what Yahweh or Zeus or Kwan-yin tell us to do. Listen to your own conscience. Act rationally. Compassion is the end result of rationality. Don’t apologize for religion, just join the rest of us that can see that we have outgrown it.

Science and Surnames

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

Imagine

Imagine if only 12 out of 6,000 churches, synagogues or mosques were left standing in the place where you live. Imagine if over a million plus of your people were killed.

Imagine thousands and thousand and thousands of strangers being sent to your home and taking up residence, swamping/overwhelming you and your remaining family members so that you are lost in the swarm, your voice is drowned out by the noise of a huge throng, and you are crushed by the weight of so many bodies pressing against you.

Imagine that you are, for the most part, a peaceful person whose only wish is to live peacefully in your home. You have no desire to go to someone else’s home and take it over, let alone take what they have and make it yours. For the most part, you simply want to work, practice your faith, take care of your family, and be friends with you neighbors. But you can’t, you aren’t allowed to. Instead, the things you love are destroyed, and even your voice, which you would like to raise in song and prayer, is taken from you.

This is life for the average Tibetan.

The cultural genocide that has been occurring in Tibet for the past 50 plus years is appalling. It has also been largely ignored by certain world powers—and by us in our safe comfortable homes.

It seems likely the only reason Tibet is in the news is because of the Summer Olympics soon to be held in China.

I’d like to see the U. S. boycott the Olympics in Beijing. If we could boycott the Moscow games in 1980 over the Soviet invasion of Afghanistan, why not boycott over China’s invasion of Tibet?

Perhaps Tibet is too small, too isolated, too insignificant for us to bother about.

What would you do if your home were being invaded? I would like to imagine I would be like those brave monks who recently stood strong in the face of impossible odds. But I don’t know if I am that strong because, from where I sit, I can’t even begin to imagine what it would be like to lose what I have, to lose my way of life, to have my beliefs denied me, to have my culture stripped from me, to have my family killed right there in front of my face.

But maybe, just maybe, Tibetan voices are finally been heard above the noise of those imported masses.

There have been protests as the Olympic torch has made its way around the world and meetings between the Dalai Lama and China seem possible.

One can only hope.

My concern is that China is only contemplating talks with the Dalai Lama because of the Olympics.

My concern is, like much of what I’ve seen about China, (mostly on CCTV) that these talks will just be for show. I can almost hear those in power saying, “if we can just get through the Olympics….”

My concern is once the Olympics is over certain world powers will again sweep Tibet under their proverbial rugs, pretending the dirt isn’t really there.

My concern is, things will return to how they were before.

Except of course for the Tibetans–their lives will only get worse.

Imagine.

The Road, by Cormac McCarthy

When Oprah speaks, everyone reads—or so the bookstores would have us think, with their gold “Oprah’s Bookclub” stickers and “Recommended Reading” lists. I usually avoid the frilled up, racked tables at the front of the store, but every now and then, something with the “Oprah’s Bookclub” sticker looks like it could be good. “The Road“, by Cormac McCarthy (No Country for Old Men), was one of those: a literary Mad Max according to those in the know. Now, it looks like The Road may even be coming to the big screen, with Charlize Theron and Guy Pearce (or maybe Viggo Mortensen).

McCarthy evokes a bleak, meaningless end to the world in this story set within the final whimper – fields of ash and snow, dead plants, the detritus of riots, fleeing refugees, and burning cities. The only other living things on the barren landscape are the cannibalistic groups, feeding off the weak and the dead.