A new study published recently is bound to get some serious attention. Spanish researchers looked at over 500 studies that documented the effects of asthma drugs called inhaled corticosteroids: 275 studies weer funded by pharmaceutical companies (they called this group the PF studies; PF stands for Pharmaceutical Funding) and 229 were funded by other sources, such as government agencies and non-profit organizations (they called this group NoPF).

What they found was that 65.1% of the NoPF group found adverse effects of the drugs under study compared to only 34.5% of the studies in the PF group. This is a significant difference that is very worrying.

So the researchers dug a little bit deeper and found that the real difference between the PF and NoPF studies was how the studies were designed. This means that PF-type studies were more able to discern adverse outcomes.

Still, this is a correlation and definitely not a causation at the moment. What this means in reality is that many studies need to be done to be sure of the true effects of a drug. And when you hear the results of a study, always double check who funded the study. The authors called for the strengthening of disclosure of conflicts of interest, which should help.

This post is part of Blog Action Day which I signed up to recently. More details at the Blog Action Day blog announcement.

While many people continue to completely ignore the evidence that climate change is real, and continue to think that humans have nothing to do it with it, a lot of other people are working hard to fix it and minimize the damage us humans are doing to the environment. A survey of all the good work being done is impossible - there is simply a lot of activity. So in this post, I would like to pick out a few high profile and a few virtually unknown examples of what people are doing to fix and mitigate environmental damage.

The examples I've chosen are meant to be diverse, each attacking the problem in a different angle or fixing one small piece at a time. The idea here is to demonstrate to everyone just how amenable the problem is. There simply is no excuse not to minimize our damage. And by "our", I mean you and me, I mean companies, I mean governments and countries. And, perhaps surprsingly, a lot of these examples actually save a lot of money!

So in no particular order...

• I want to start with Climate Care, an Oxford, UK based organization. Climate Care sells carbon offsets. Briefly, every human activity, from travel, to heating houses, to cooking, even food, requires energy, which in turn means everything we do generates carbon dioxide emissions; the emissions are called the carbon footprint of the activity. Some activities have a much larger carbon footprint than others and so it would be useful to be able to calculate the footprint accurately, reduce it as much as possible, and compensate for whatever footprint is left.

  Calculating carbon footprints is a bit of an art and a bit of a science but there are ways to roughly gauge the footprint. The Climate Care website has several carbon footprint calculators that tell you what's the footprint of your activities. What Climate Care does is much more though: the website has guidance on how to lower you carbon footprint and also helps you compensate for whatever carbon impact you have that you cannot change. The compensation is called carbon offsetting and simply put, you pay Climate Care to fund projects that avoid, reduce, or absorb greenhouse gases like carbon dioxide. Projects range from simply planting more trees that absorb carbon dioxide to using alternative fuels that have a lower carbon footprint.

  So how much does this cost? I recently did a return trip from London Heathrow to Boston, so I plugged this into the Climate Care flights calculator and it told me that the resulting emissions are 1.45 tonnes of CO₂ and the cost to offset this will be £10.85. How much is that as a percentage of the ticket price? 3%. That's it.

• Next up is an organization called Less Watts back by Intel Corp. Less Watts is a forum where Linux developers, end users, and IT managers talk and develop solutions to make Linux more power-friendly. What could an operating system do for the environment? A lot actually.

  Think about a laptop you're using to type up a letter or a blog post. You really only need the screen, the keyboard, some processing power to run the software, and occasionally, internet access. What about all the other hardware? A clever operating system sends unused hardware to sleep, waking it up only when it's needed. Also, as the processor is idle, the operating system can wait in many ways, and some use more power than others. I mentioned laptops as they're easy to measure in terms of battery life: a clever system can maximize battery life by consuming less power. Scaled to all computer users world-wide, the power savings, and thus carbon footprint of computing, can be greatly reduced!

• Next up are companies like Google and Microsoft. Granted Google has some very questionable practices, it, Microsoft, and many others are installing solar panels to power their campuses. At the time of writing, Google's solar initiative has generated over 500000 kW-hours while at the time of building Microsofts's was claimed to be the largest in Silicon Valley.

  Why is this important? Internet data centers consume large amounts of electricity, and the more we depend on internet-based services, the more of a demand there'll be. It's good to see companies noting this fact and trying to work with it.

• There is a startup company working on energy generation from vibrations called Perpetuum. Basically, these tiny generators convert vibrations into a little trickle of electricity. These so-called microgenerators can power measurement devices placed in very hard to reach places, like in monitoring machines in a factory or at the top of buildings, and allow these measurements to be relayed using a wireless connection. Very cool and frankly, this is the kind of creative thinking we need to tackle global warming.

• Finally, I want to talk about Virgin Galactic, especially their proposed Spaceport America design. The architecture of the spaceport is an amazing marriage of design and function that works with its environment. Two things are worth noting here: the spaceport looks like it is part of the surrounding desert, so it's not like the eye-sores that we call airports today. Secondly, notice how the spaceport is heated and cooled (slide 4 in the second link) using the surrounding air. This mechanism will ensure that the energy spent to control the temperature of the spaceport will be minimal. This is called 'sustainable design' and it's a movement that's gaining a lot of traction these days. Watch this space (sorry for the pun ).

So as you can see, tackling global warming and minimizing the human impact on the environment is doable. It doesn't require some magic potion or divine intervention. It is simply a matter of everyone thinking more about how their actions affect the environment and how to minimize those effects. Easier said than done, yes, but it can be done.

Technorati Tags: Blog Action Day

A supernova is the explosion of a star at the end of its life. When this happens, huge amounts of matter and energy are released in the explosion, giving rise to a bright new object in the sky. This start remnant remains visible for a few weeks and then dies away.

Supernova 2005ap shown with four nearby galaxies (A, B, C, and D). The photo on the right was taken two and half months later than the one on the left.

Because they are explosions, you know astronomers will keep a league table of the most powerful explosions. And so it goes that a few days ago, the most powerful supernova explosion was detected. Called SN 2005ap, the paper describes the measurements that put the explosion's peak brightness at more than 100 billion times the brightness of the Sun and placing the supernova at 4.7 billion light-years away from us. To re-phrase the distance measurement, the explosion happened 4.7 billion years ago, but only now are we seeing it because light needs time to travel that distance.

I heard about the news from Bad Astronomy Blog, which also has a lot more details about the science behind supernova explosions and measurements.

The world is gasping after US researchers reported the hot news that the chemical that makes peppers hot is the key to targeted pain killing.

Image showing capsaicin and the new experimental pain killer QX-314.

To understand the significance of this report, we need to step back and understand what makes hot chili peppers hot. Chili pepper have a protein called capsaicin which makes them hot. The amount of capsaicin present is measured using the Scoville scale. Pure capsaicin scores about 15000000 on the Scoville scale while cayenne pepper scores a few tens of thousands. Capsaicin causes a burning sensation of pain by opening a molecular gate found in pain neurons. This gate, called TRPV1, is usually closed and only when it is open do molecules freely enter and leave the cell. Also, TRPV1 is found only in pain neurons and not other neurons, making it a very attractive target we can selectively open up.

Now that we can open a channel into pain neurons, we need the actual pain killer. Enter QX-314. On the face of it, QX-314 is a bad pain killer: add it to nerves and nothing happens. This is because it cannot enter the nerves on its own.

So now we have two nice pieces: we have a pain killer that needs help to enter pain nerves and numb them and we have a way to selectively open up pain nerves. Surely it's not that simple... is it?

Actually, it is! The paper talks about the experiments that demonstrated this. The first test was using isolated nerve cells grown in a dish. The researchers applied capsaicin and QX-314 (separately and in combination) to isolated pain-sensing and other neurons and measured how they responded. What they found was the combination of capsaicin and QX-314 selectively blocked the excitability of pain-sensing neurons, leaving the others unaffected.

Next, the researchers injected capsaicin and QX-314 into the paws of rats and measured their ability to sense pain by placing them on an uncomfortable heat source. With the combination injected, the rates tolerated much more heat than usual. Next, capsaicin and QX-314 were injected near the sciatic nerve of the rats, and a researched pricked their paws with stiff piece of nylon. The animals ignored the provocation. Although the rats seemed immune to pain, they continued to move normally and respond to other stimuli, indicating that QX-314 failed to penetrate their motor neurons.

This last observation is crucial. Pain killers these days are not specific causing general numbness since they affect all nerves. Having a very specific pain killer is very useful indeed!

So what's catch? Well, as we talked about above, capsaicin causes a burning sensation, so the formulation must not cause this kind of pain in humans, perhaps using something else than capsaicin. Also, research is still needed to figure out the best way to make the pain killing effects last as long as possible. Regardless, it's a great first step to a pain free world in a few years time.

We recently talked about Greenland melting in 2007. Along similar lines, the New York Times posted an article yesterday titled Arctic Melt Unnerves the Experts. It's well worth a read if you're into grim factoids about the environment, this time talking about the Arctic polar ice cap. There is also a neat time graphic showing the melting patterns in the past few years. In short: as far as anyone can remember, the Arctic's ice melted the most and is scaring the scientists who can't predict it reliably and who need to figure out the full implications.

The implications of losing this much ice are staggering. A few thoughts:

• The Arctic ice sheet may not recover fully if it loses too much ice in a year.
• Polar ice reflects sunlight and so helps the Earth stay cooler. What happens when it's lost is complex. An excellent introduction to the topic is on NASA's Earth Observatory website.
• A receding ice cap opens up shipping lines. We can already do that during the summer, but the routes may become open for longer and starting earlier in the year in the future.
• The receding ice sheet makes it easier to hunt for resources. Will we be seeing oil rigs at the North Pole in a couple of decades? Do we want to?
• What about wildlife that depends on an icy environment?

As ever, a complex topic with bad news sprinkled in for fun.

Map of melting in Greenland published by NASA. Credit: NASA/Earth Observatory.

NASA is reporting of new data about the melting in Greenland in 2007. In short: areas at high altitudes (over 1.2 miles above sea level) are experiencing record melting, clocking in at a chilling 150% above average. At lower altitudes, the melting is 30% above average. To put this in perspective, the amount of snow that has melted this year over Greenland could cover the U.S. more than twice over.

The melting data came from satellite-based microwave imagery, which was then compared to the average snow melting from 1988-2006. The map on the left shows the melting difference between the past 19 years and this year: the redder it is, the more melting that occured in that area this year. All in all, this puts 2007 as the fifth highest in amount of melting. The top four are, in order: 2005, 2002, 1998 and 2004.

Needless to say, this is scary proof that global warming is really happening and that predicting and modelling how melting occurs is very difficult. And then we have to think about where this melted snow is going, i.e., to the seas, which brings up the thorny issue of rising sea levels. The image above is no longer pretty, is it?

I just came across the UK government's Teachernet's guidance on teaching creationism in UK schools. What's in this document? It's the best write-up I've seen about the evolution debate, along with comment on its place in science teaching in the UK. There is a list of questions, a glossary of terms, a thorough introduction to the topic, and then the guidance. It's written clearly enough for anyone to understand the question and the answer. In short, on teaching ID and creationism in science, the guidance says "don't teach it". Why can't everything be so well explained and clear cut? I love it!

Unfortunately it's not dated, so I can't figure out how new this is. The Word file stats suggest it was created September 2007 (File->Properties then select the Statistics tab). Regardless, it's a very useful document to keep handy for those inevitable times when this discussion comes up.

Starchy diets affected gene copy number.

A new paper published last week looks at diet and the evolution of the human amylase gene copy number. The paper very nicely stacks a pile of evidence that starts to tell another story in human evolution.

Let's start at the top. In humans (and many other animals), the digestion of starch starts in the mouth. The enzyme responsible for starch digestion is called amylase, and specifically, the human salivary α-amylase. Given this genetic component, can we find variation between different human populations? The answer it turns out is yes, and it's correlated with the historical consumption of starch by these different groups of people.

The paper looked at three populations of people that have historically had a diet high in starch and four populations that have historically a diet low in starch. The data they uncovered was that people from high-starch populations tended to have more copies of the amylase genes - in one case 14 copies! - than people from from low-starch populations.

The conclusion that it's definitely evolution still needs more evidence, but the story is starting off to a great start. Why is the conclusion not 100% done and dusted? For each of the populations, we need to check two things:

• Is this variation found only in the amylase gene or is this a typical feature in the populations in question? To answer that, we check variation in other genes in these people and see what's typical and compare the amylase gene variation to the typical rate. The researchers of the paper couldn't do that for all populations, but for one population, a Japanese one, they did find that the amylase variation was significantly more than the most of the rest of the genome, i.e., something is going on and it's not random.
• Which copy number is the base case? One hypothesis that we need to check is that high copy numbers of amylase is the typical state in humans and that populations lost copies when their diets shifted to lower starch content. To fix this, we need to check more people from all over the world to figure out the details.

Still, it's a great first chapter of this story. Watch this space!

Last week, Dave Munger at Cog Daily started a discussion about creating a standard icon for science bloggers to use when reporting on peer-reviewed research. The discussion snow-balled into an idea, and now a new website, Bloggers for Peer-Reviewed Research Reporting, has been launched.

Still, we don't have an icon. This morning I emailed Dave Munger (full email copy posted at BPR3) thinking out loud about the icon and how it fits well with the EasyPg plugin. I've been letting this brew in mind all day, so here are some more thoughts about the icon and the BPR3 initiative.

• The icon should be square as that will allow easier resizing: the same icon can be used at various sizes including 16px by 16px to be used as the favicon of the BPR3 website. Also, it will fit better with the current trend for icons, like the square RSS icon. One exception: the 80x16px 'chicklets' icons/buttons that are also the current trend like the one below (forgive my lack of design skills). This little example shows what we can do: the left hand side of the chicklet can be the BPR3 icon, and we can have text on the right, like simply saying "BPR3". Example uses:
  • 
  • For differentiating peer-review links, something like:

    ...Via CNN: a new paper talks about...

• The icon needs to be accessible, i.e., colour-blind friendly. I'm no expert in this area, so I'll leave it to others.
• Copyright: I think we need an enforceable licence, like a Creative Commons one. I suggest CC Attribution-ShareAlike 3.0 Unported. As long as we have attribution, even if BPR3 fails, the idea will live on.
• The tag line/slogan: Right now it stands as "Report on Peer Reviewed Research". How about '(Yet) Another Peer Review'? We can even go all Web 2.0 on it and call it 'yapr'

The other idea of BPR3 is aggregation of blog posts discussing peer reviewed research. I have a few thoughts on this too:

• It should use HTML markup that can be easily embedded in blog posts. I suggest we use Pg's markup to maintain consistency and avoid creating two 'standards'. Unless, of course, there is something wrong with it, but I can't see any. We can also Technorati tags and pull the data live out of Technorati using their API.
• We should create plugins for the most popular blogging platforms. If we use Pg's markup, my EasyPg plugin would be ready to go. Otherwise, we need to create new plugins to promote usage.

What do you think? Post back here or, better, at BPR3.

In-plane shaking of nanoresonators throws off impurities.

A cool new technology for detection of bacteria, viruses, DNA and other biological molecules has been demonstrated. Resonators (cantilevers) made of narrow strips of silicon a few millionths of a meter long with bound antibodies can be used to detect bacteria suspended in a sample. The bacteria specifically attach to the antibodies and so alter the vibration in a detectable way. The problem is when other impurities in the sample attach non-specifically to the cantilever.

The new paper shows that non-specifically bound material can be shaken off if the resonator vibrates 'in plane', i.e.,side to side. In-plane vibration can be created by hitting the base of the cantilever with a laser beam pulsing at a certain frequency. To measure in-plane motion the researchers shined another laser on the free end of the cantilever and detected the chopping of the beam as the cantilever moved.

So the new technology could work like this: the cantilever is first vibrated up and down to let the sample components attach to it. Then it is made to vibrate sideways to shake of things that didn't attach specifically. What is left are those components you're trying to detect (if they are there) and so you can reliable measure their presence.

Imagine in the future going to a doctor who takes a sample and sends it to the lab. Instead of waiting hours or days to find out if there is an infection and if so what's causing it, the wait could potentially be reduced to minutes. There is a lot work needed to get to that, but we're on our way! Very neat stuff.