Blind mole rats and my first citation

I published part of my MSc research last April. It was my first and only paper, and had taken about an extra year or two after my MSc finished to wrap up all the revisions, run new experiments, write and revise again. I remember being in a hotel room in China during my time on a cleft-lip surgical mission, writing scripts and starting programs on Brian’s computers back at Mac. It passed through three rounds of reviewing and on the final round, one of the reviewers still didn’t agree that the findings made sense but s/he also didn’t seem to understand the experiments. Thankfully, the editor of the journal stepped in and told us it was accepted anyway. It’s tough writing about population genetics and computational biology. It’s like explaining math without using numbers.

So once in a while, I like to look at how many times the paper has been downloaded. Ya, nerdy and kind of self-absorbed, but you’d do it too. After all, many people google themselves (I do that too, but thanks to a Singaporean pop star it doesn’t satisfy my ego), and many others start personal blogs (ahem). Good thing there’s such a fuss about stopping internet censorship because how else would we find out so much stuff about ourselves?

Instead of studying Pharm, I checked on my paper’s views again. And my paper has been cited! The paper citing me is called “Is Evolution of Blind Mole Rats Determined by Climate Oscillations?”. Oh academia. Bonus points for it being a paper about climate change (my paper had nothing to do with climate change).

Swearing in the House of Commons is news

Environment Minister Peter Kent chides the other parties for not having been in Durban at the recent UN Climate Conference.

This is despite the fact that he is directly responsible for their absence, as he banned them from attending as part of the Canadian contingent (it is not unusual for opposition parties to be included, allowed to attend).

Justin Trudeau swears at Environment Minister Peter Kent then later apologizes.

“And I think the opposition has its back against the wall and doesn’t know what to do,” [University of Ottawa political science expert Michael Behiels] said. “Not a single opposition amendment has been accepted. Everything they try to do is basically laughed at, dismissed. So the opposition MPs have had it, and it’s just pouring out.”

Frustration all around.

Read more here.

Are the tar sands “ethical oil”?

Quotes from David Suzuki’s thoughts on the question: “Can oil be ethical?”

Two days after he was appointed federal environment minister, Peter Kent […] trumpe[d] Alberta’s tar sands as “ethical oil“. We rightly criticize oil-producing countries that support or indulge in violence, murder, oppression of minority groups and women, and so on. But because Canada does not overtly support or indulge in such practices, does that mean our oil is more ethical? Levant acknowledges that exploiting and using fossil fuels has environmental impacts. Does that mean there is a hierarchy of ethical practices or that one ethical practice cancels out other unethical activities?

The application of ethical standards in our purchase and use of products should be applied universally and not selectively. Canada signed the Kyoto Protocol, which became international law. When Jean Chrétien signed the document, he did so not as a Liberal but as the prime minister of Canada. This meant that, as a nation, we were committed to achieving the targets set by the agreement. On becoming leader of a minority government, Harper declared his intention to ignore Canada’s commitment. Is it ethical to ignore an internationally binding legal commitment? This is even more astonishing in light of Prime Minister Harper’s outspoken commitment to law and order.

Canada is one of the highest per capita emitters of greenhouse gases. Our rapidly melting permafrost releases massive amounts of the potent greenhouse gas methane, amplifying our contribution to the global crisis of climate change. Alberta’s tar sands require enormous amounts of energy and water to extract, further compounding Canada’s already excessive emissions. Is there not an ethical component to our demand for a greater share of the Earth’s atmosphere than most other nations? Rapid exploitation of Canada’s tar sands — by companies from countries including theU.S., Korea, and China — is not crucial for our nation’s survival or even well-being, yet we ignore the impact on the rest of the world. If that isn’t unethical, I don’t know what is.

Stop The Tar Sands

Not surprising but still ultimately sad. The guardian’s take here, which nicely sums up the (non)-repercussions of backing out of Kyoto at this point, and what it would have taken to meet Kyoto (it’s true that by now it was way too late).

From PostNoBills:

The Canadian government currently lead by Prime-Minister Stephen Harper is not gambling with our future, gambling implies that we are unsure of the result, Stephen Harper, his governement and the governemnt of Alberta lead by current premier Alison Redford as well as the various vested buisness interests are plainly and simply destroying our environment. Here are a couple of quick facts: About 90% of the water used to process the Tar Sands ends up in acutely toxic tailing ponds that line the Athabaska River and threaten the health of the whole river basin. For every barrel of oil extracted, six barrels of tailings are produced.  [Steph: For every 1 barrel of oil extracted, 3 barrels of water are used.] According to a recent Environmental Defense report, the ponds are already leaking over 11 million litres a day of contaminated water into the environment. Should proposed projects proceed on schedule, 2012 would see a five-fold increase, to over 25 billion litres a year.

For such a vast and beautiful country, full of boreal forrests and fresh water it is quite sickening that we are also responsible for one of the largest projects that is causing such catastrophic environmental damage to the entire planet. It comes as no surprise that Canada’s current political leaders would be withdrawing from the Kyoto Protocal. When you’re running one of the largest sources of greenhouse gas emisions it makes no business sense to have to pay for it, does it? The fight is not about Kyoto now, it is about stopping the tar sands. How much more of the future are we willing to forsake to run the present day. We should be talking about sustainability not profitabilty.

postnobillz

“It’s in the way we live our lives exactly like the double-edge of a cold familiar knife and supremacy weighs heavy on the day it’s never really what you own but what you threw away and how much did you pay?”
Greg Graffin

Today it was announced that Canada will be withdrawing from the Kyoto Protocol. It’s not too hard to see why, all one has to do is look towards Alberta and the Oil Sands. “The Alberta Oil Sands Operation are the largest single point source of greenhouse gas emissions in Canada” Source, desmogblog.com If current development plans proceed, by 2020 the Tar Sands will release twice as many greenhouse gases as are currently produced by all the cars and trucks in Canada.

The Canadian government currently lead by Prime-Minister Stephen Harper is not gambling with our future, gambling implies that we are unsure of the result, Stephen…

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Get It Done: Revived

If you haven’t yet seen this video of Anjali Appadurai addressing the U.N. Climate Change Conference, you should.

Last night I was talking to Frond about a friend of his from the India Fellowship, who had taken ideas from her year in India and was applying it to a new clothing line she was starting, with a business model based on developing the local economy of Detroit.  I thought about my roommate’s sister who went from International Development into Jewelry Making (“metal-smithing” she calls it), and makes amazing pieces that are out of this world.  I thought that it would be nice to have a passion that was more whimsical, that was more creative, and less emotionally draining than some “cause” like Climate Change.  In response, Frond told me about the advice he was given back when he wanted to go into music and philosophy.  Basically, not to do it.  That unless he found an academic position, he’d be another artist working hard in music, pouring their passions in, and having to scrape by.  Or having to accept struggling to find students to teach music to, in order to make a living out of their passions.

I can see how any passion can be draining, just as much as it drives you.  So although Anjali Appadurai is preaching to the choir when it comes to people like me, it is so invigorating to see someone so angrily, eloquently, and – there’s no other word for it – passionately express why you were drawn to this passion in the first place.

The transcript:

CHAIRPERSON: I’d now like to give the floor to Miss Anjali Appadurai with College of the Atlantic, who will speak on behalf of youth non-governmental organizations. Miss Appadurai, you have the floor.

ANJALI APPADURAI: I speak for more than half the world’s population. We are the silent majority. You’ve given us a seat in this hall, but our interests are not on the table. What does it take to get a stake in this game? Lobbyists? Corporate influence? Money? You’ve been negotiating all my life. In that time, you’ve failed to meet pledges, you’ve missed targets, and you’ve broken promises. But you’ve heard this all before.

We’re in Africa, home to communities on the front line of climate change. The world’s poorest countries need funding for adaptation now. The Horn of Africa and those nearby in KwaMashu needed it yesterday. But as 2012 dawns, our Green Climate Fund remains empty. The International Energy Agency tells us we have five years until the window to avoid irreversible climate change closes. The science tells us that we have five years maximum. You’re saying, “Give us 10.”

The most stark betrayal of your generation’s responsibility to ours is that you call this “ambition.” Where is the courage in these rooms? Now is not the time for incremental action. In the long run, these will be seen as the defining moments of an era in which narrow self-interest prevailed over science, reason and common compassion.

There is real ambition in this room, but it’s been dismissed as radical, deemed not politically possible. Stand with Africa. Long-term thinking is not radical. What’s radical is to completely alter the planet’s climate, to betray the future of my generation, and to condemn millions to death by climate change. What’s radical is to write off the fact that change is within our reach. 2011 was the year in which the silent majority found their voice, the year when the bottom shook the top. 2011 was the year when the radical became reality.

Common, but differentiated, and historical responsibility are not up for debate. Respect the foundational principles of this convention. Respect the integral values of humanity. Respect the future of your descendants. Mandela said, “It always seems impossible, until it’s done.” So, distinguished delegates and governments around the world, governments of the developed world, deep cuts now. Get it done.

Mic check!

PEOPLE’S MIC: Mic check!

ANJALI APPADURAI: Mic check!

PEOPLE’S MIC: Mic check!

ANJALI APPADURAI: Equity now!

PEOPLE’S MIC: Equity now!

ANJALI APPADURAI: Equity now!

PEOPLE’S MIC: Equity now!

ANJALI APPADURAI: You’ve run out of excuses!

PEOPLE’S MIC: You’ve run out of excuses!

ANJALI APPADURAI: We’re running out of time!

PEOPLE’S MIC: We’re running out of time!

ANJALI APPADURAI: Get it done!

PEOPLE’S MIC: Get it done!

ANJALI APPADURAI: Get it done!

PEOPLE’S MIC: Get it done!

ANJALI APPADURAI: Get it done!

PEOPLE’S MIC: Get it done!

CHAIRPERSON: Thank you, Miss Appadurai, who was speaking on behalf of half of the world’s population, I think she said at the beginning. And on a purely personal note, I wonder why we let not speak half of the world’s population first in this conference, but only last.

Increased in-hospital infections with increased temperatures

Knitted bacteria by loxosceles

An 8-year study of infection data from 132 hospitals finds that as outside temperatures rise, in-hospital infections with some of the most problematic pathogens rise also. – Wired.com

What just happened? The researchers looked at blood-samples from 132 US  hospitals (they admit that New England was somewhat lacking in representation) for 8 years, tracking the number of infections diagnosed as due to different kinds of bacteria.  It’s never normal to find bacteria in your blood, even normal flora of our bodies like E.Coli.

What were they looking for? They wanted to see whether the number of bacterial infections changed depending on the temperature outside (i.e. the season).

What’d they find? Well…

Independent of season, monthly humidity, monthly precipitation, and long-term trends, each 5.6°C (10°F) rise in mean monthly temperature corresponded to increases in Gram-negative bacterial BSI frequencies ranging between 3.5% for E. coli (95% CI 2.1–4.9) to 10.8% for Acinetobacter (95% CI 6.9–14.7). The same rise in mean monthly temperature corresponded to an increase of 2.2% in S. aureus BSI frequency (95% CI 1.3–3.2) but no significant change in Enterococcus BSI frequency. – Eber et. al (2011)

For every 5.6°C rise in monthly temperature, they increases in some bacterial infections and not others.

The ones they saw increases for are the Gram-negatives:

– E.Coli, which can cause a range of infections, from meningitis in young people to moderate diarrhea and dehydration, to extreme bloody diarrhea and widespread internal bleeding around your body.

– “Acinetobacter” or Actinobacter, which can cause pneumonia, or pus-filled cavities (abscesses) around your body if it gets systemic (i.e. into your blood).

Both of these bacteria are normally found on or in healthy people.  The trouble starts when it gets to where it shouldn’t get, and/or change so that they are more disease-causing.  That’s called “acquiring increased virulence” and it happens a lot in hospitals where you have lots of sick people and people who are always around sick people, and lots of antibiotic use.  Since there’s so much antibiotic use, bacteria in hospitals can more quickly develop antibiotic resistance which is something they can pass on to other bacteria.  Along with sharing antibiotic resistance, bacteria can share other virulence factors.

One of the more well known potentially antibiotic resistant bacteria, S.aureus, was also found to have increased numbers of infections as outdoor temperatures went up.  S. aureus resistance is pretty common now in both hospitals and out in the communities.  There are still treatments for most, but there are also strains of antibiotic S. aureus that don’t currently have any antibiotic that will consistently work.

No increase was observed for Enterococcus, which are bacteria that can cause GI problems like diarrhea, but can also cause troubles elsewhere once they get into the blood.

The bottom line? Bacteria become more dangerous as temperatures outside go up.  We’ve already seen that as temperatures go up, there are more infections.  The last paragraph of the paper sums the whole thing up (as they always do!):

In conclusion, we reported substantial increases in the frequencies of bloodstream infections due to clinically important Gram-negative organisms in summer months. These increases, as well as variations in infection frequencies within seasons, appear to be associated with elevated monthly outdoor temperatures. The seasonal trends reported may be used to inform infection prevention and should be considered in the design and evaluation of longitudinal quasi-experimental studies of infection prevention interventions. Furthermore, if the underlying mechanisms of the temperature associations are identified, these findings could inform the global climate change debate.

Emphasis mine.  Interesting!