Monday, July 28, 2008

Wasted money, but not time

Busy week, what with the astronaut cover letter and pumping out data like Conservatives pump out dough. Big pumping, that's what we call it. Somehow, we have gone from running a $2.8 billion surplus over April and May last year to running a $517 million deficit over the same time this year. $3.3 billion seems like a lot of money to me, and so does the $1.1 billion we didn't collect from corporate revenues. Particularly with all this stuff about Liechtenstein in the press.

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Again, like you needed a reason not to eat it, boys - soy foods such as tofu may decimate your sperm count. A scary-but-true fact you might not have known: in every species tested so far, halving normal caloric intake leads to drastic prolongation of lifespan (kind of counter-intuitive, right?). Scientists may have packed part of this into pill form by activating gene expression using what is hoped to be the first generation of anti-aging drugs, resveratrol. Neurosurgery may prove to be an effective last-chance measure against highly resistant chronic depression, although it will be a long time before we know what relapse rates are like. Lastly, an interesting finding from London - a mutation in an obesity-linked gene is associated with increased appetite. This may sound like a no-brainer, but it's the first mutation we've seen that does this. Of course, our catalog of mutants is still pretty limited...

Sunday, July 20, 2008

McCartney - Scary Bacteria - Internet vs. Science?

I have railed before on rock stars for being idiots, and Sir Paul McCartney has definitely done that in the past - only 2 years ago joining his then-wife Heather Mills in a damning crusade against the Canadian seal hunt. Now he's playing a free show for the 400th anniversary of Quebec city and some Parti Québecois members are protesting that a performance by a Brit on the Plains of Abraham (where Wolfe and Montcalm fought in 1759 and Britain conquered the forces of France) is a dreadful insult. Which I guess is sort of understandable, and if nothing else predictable.

The following from Sir Paul in response to the criticisms from the PQ was neither: "They won," he said, apparently referring to the war. "What are they moaning about? They won... I wouldn't have minded if they lost. It's me that should be moaning, right?" He pauses for several seconds. "I'm only kidding you know."

Wow. Kidding about what, exactly? Kidding that you're that ignorant about the history of this country (and a significant battle in the history of Britain)? Or kidding around about an event that essentially represents the instant the Québecois came under British rule, which is a bit of a sensitive issue. Even significantly more so than the seal hunt.

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Science has an excellent piece this week on antibiotic resistant bacteria. Some infections (C. difficile, for example) are just impossible to fight with most of the antibiotics we've invented so far. The bacteria have evolved to resist the drugs we have, and as a result are extremely difficult to kill. And we don't seem to have any blockbuster antibiotic drugs on the horizon, which is actually quite frightening - about the only things in biology scarier than these things are prions. Which I won't get into here.

But it does bring me to a personal pet peeve - I have a big problem with antibacterial soaps. First of all, some bacteria are quite useful, for example, mice raised in a sterile environment have seriously compromised immune systems. Secondly, you are a human-bacteria hybrid - bacterial cells in our bodies outnumber our own human cells by a factor of 10 to one. Accepting that evolution exists (and failing that, antibiotic-resistant bacteria indeed exist), using antibacterial soaps is just going help you grow resistant strains of bacteria in your house, which may or may not be good for your immune system - or your own bacterial cells...

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This Wired blog brought an interesting article from Science to my attention - surely it's changed science for the better, but has the Internet changed scientists for the better? The author of the article has some interesting data that as Internet resources have risen in size and accessibility, authors are citing more recent and more high-impact journals, and less journals overall. This implies that their breadth of scholarship is declining somehow, and allegedly relates to the fact that scientists no longer browse through paper-based journals.

I don't think this is the right interpretation of the data. I would say that this means that the pace of science is quickening. We're doing things quicker and better than ever before: 15 and 20 years ago, some of today's fairly major fields simply didn't exist. For example, stem cells weren't an issue in biology 20 years ago. Now, there are thousands (possibly tens of thousands) of people working in the field. What literature from 20 years ago are they going to cite, exactly?

Personally, I think the Internet can be of great benefit to the breadth of a science education. But it's a bit of a double-edged sword. You can be an academic viking, pillaging the literature to get support for the assertions and/or hypothesis you want to make (and trust me, you can find stuff to support almost any argument). But you can also use it to make other fields more accessible, to browse journals and sometimes doctoral theses, and have search tools email you articles from backwater journals you've never even heard of.

Is that a bad thing? Nobel-winner Eric Kandel is reviving a comparitively ancient (1970s) animal model of safety, and investigating possible antidepressant targets based on differences in gene expression in safe, happy rats compared to anxious, shocked rats. Those at the forefront of science right now still remember the old days, and some of those scientists were much more inventive than you might give them credit for. However, I remain convinced that scientists will continue to be clever in the future, and we probably shouldn't worry about whether the Internet is good or not. Science seems to be doing just fine on it's own...

Wednesday, July 16, 2008

Astronaut application

So, as you may or may not be aware, Canada is hiring two astronauts this year. My friends and I joked that the only way the government would agree to paying the $83, 300 - $162, 700 salary would be by holding a reality show competition - Canada's Next Astronaut, perhaps.

But it's less funny now, seeing as how I applied for the job and have now made it to the second round of selection (all told, not exactly a remarkable feat). Which begs the question - what's in the job application for "astronaut?" Well, I'm here to tell you that it's mostly just normal stuff, like Social Insurance Numbers, marital status, and your CV. Oh, and a cover letter. Stupid @$%&ing cover letter that happens the best (and really only) opportunity I have to make myself appear to be a unique candidate and really market myself.

The cover letter they want you to write is 11, 000 characters long, equivalent to around 1500 words, or about 2 pages. When I write a cover letter, it is generally 4-5 paragraphs and NEVER exceeds a page. Hence, "cover" letter. So I'm a bit of a loss, and here I sit staring at 5, 000 characters and I feel like the Canadian Space Agency will already know my entire life's story.

Which leads me to ask all of my loyal readers - both of you - for advice. What do you put in a cover letter to sell yourself as an astronaut? Do I tell them I'm a big science fiction buff? That I have a science blog? My top scores for StarCraft and/or StarFox? That I don't have strong menu preferences and am generally easy to get along with? That I've always wanted to do it in zero-gravity? Should I mention my acerbic wit and oh-so-funny sarcastic attitude?

Honestly, suggestions are welcome. Really. I think I have the obvious stuff down, but I'm going to need to come up with something both interesting and marketable to nail one of the 40 interviews they're giving for the over 5, 000 applicants...

Thursday, July 10, 2008

Evil Tofu

News roundup (the BBC wins this week) - continued craziness in Britain as two leading sexual health charities have announced the sex lessons should begin at age 4; they conclude with a quote from a 16-year old mother who seems to have been unaware that sex might lead to pregnancy. As if you needed a reason not to eat a lot of it, researchers have shown a correlation between tofu consumption and dementia risk. Those eating tofu at least once per day seem to have increased memory loss by their late 60s. Lastly, according to our Prime Minister's reckoning, it is a "mathematical certainty" that the developing world will have to shoulder most of the world's carbon emission reductions by 2050, which is a relatively original take on the situation. I'd like to see those calculations.

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An interesting question in science, ethics and health was discussed this week (as well on the BBC) by Sir John Sulston, a Nobel-winning biologist and advocate for freedom of information in biology. It is his studied opinion, and my lesser one, that we should not be able to do things like patent genes or genomes, that we are allowing drug companies to become "disease mongerers," and that we are allowing the health of our citizenries be eclipsed in importance by intellectual property law. I think these are irresponsible things for a society to do - the tools by which knowledge is produced can be patented, but I am not sure about the knowledge itself. However, I am sure that health isn't an economic indicator like GDP and shouldn't be overlooked in favour of it because it's more difficult to measure.

I am reminded of what Brazil did a couple of years ago with regard to AIDS medications. Brazil, a developing nation currently straddling the gap between the third and first worlds, has some 620 000 people infected with HIV according to AIDS Alliance. Brazil took the rather noble viewpoint that everyone who had AIDS in their country should be medicated. This was a rather expensive proposition in 1998; the cost of treatment in the developed world is about US$10 000 per patient per year. Even after significant reductions by the pharma companies, the total was still around US$5 000, which runs to a grand total of roughly US$3.1 billion per year of treatment. Rather than let prohibitive costs hold them back, Brazil - which has a remarkably enlightened stance on intellectual property in general - broke the patents and started producing the drugs locally.

This had a tremendous effect - it created skilled jobs, saved the Brazilian government billions of dollars, and - most importantly - ensured that they had the capacity to provide the medications required by that portion of their population. Of course, Merck was pretty upset about this, even going so far to say that this might mean it would be no longer profitable to develop drugs for the developing world. Considering we now know that at least one major drug company spends over 50% more on marketing than drug development, I don't think we should be very sympathetic to this sort of reasoning. Allowing profit to trump health is evil, and that's all I have to say about that.

Sunday, July 6, 2008

The 8 glasses of water myth

You've all heard and read - over and over again - that we need to drink 8 glasses of water every day to keep ourselves healthy. Does anyone remember seeing any references for this assertion? Any scientific evidence whatsoever?

No, you don't. Because there aren't any. It's a load of crap.

There was a report from the National Research Council in 1945 that stated that we need about 1 millilitre of water per calorie of food intake, which runs to about 2 - 2.5 litres of water (8-10 8 oz. glasses per day). However, the next sentence states that this amount is already found in prepared food. Humans aren't the only organisms on the planet that are around 95% water.

For the data: here's a short excerpt from the British Medical Journal examining this (along with 9 other science myths, a great read - here's a truncated version from the Globe and Mail if you don't have BMJ access). Here's an article on Dr. Heinz Valtin M.D., kidney specialist, Professor Emeritus, and author of a (fairly) recent invited review on the subject. Finally, there is his exhaustive review of the literature, for which you can see the abstract here on PubMed, and the actual review is to be found here at the American Journal of Physiology.

Among the things he finds in the literature over the course of this review: 1) Caffeinated beverages are not dehydrating to those who take them regularly. Maybe a little if you haven't taken any caffeine in weeks. 2) Feeling thirsty doesn't mean you're dehydrated. It means you're on the road there - thirst occurs when the concentration of dissolved substances of blood has risen 2% due to water loss. Dehydration starts at 5%. 3) Dark urine doesn't mean dehydration. It means orange pee.

Among the things he doesn't find: ANY scientific evidence that you need 8 glasses of water (and only water, not coffee, juice, beer, whatever).

So rejoice, coffee, beer, and cola drinkers. Stop feeling guilty about whether you get enough water. If you're thirsty, drink something. If you're not, don't worry about it. Evolution is smart enough to program organisms to know when they need water.

Wednesday, July 2, 2008

Biological Toolbox Expanded

It's rather shocking that news of this paper hasn't spread like wildfire already (trust Wired to be ahead of the game). However, trust even Wired to get some of the details wrong and evoke some sensationalism out of their readers by proclaiming that anyone could become immune to AIDS. Oh, and keep your eye on Sangamo Biosciences (SGMO), because this could get big.

The first thing to know about this paper is that it is, in fact, awesome. They are working on a gene called CCR5, which produces a protein normally used by immune cells in the body. The HIV virus uses this protein to infiltrate the cells and do its work. A significantly elevated portion of northern Europeans have a curious deletion in the middle of this gene called Δ32, whereas African populations do not.* The deletion results in a non-functional protein and makes the cell more difficult to hijack, but the roughly 10% of northern Europeans that have two copies of this deletion are resistant - not immune - to HIV infection.

What the researchers do is to take some well-defined bits of known proteins, and use them to design their own customized, fully pimped-out protein. For example, some proteins use bits (OK, domains) known as zinc fingers to bind very specific sequences of DNA. So this group designed some zinc fingers that would point their protein to a spot near the Δ32 deletion. Then they use another protein domain to chop both strands of the DNA where the zinc fingers bind, and then just count on the fact that DNA will repair itself imperfectly afterwards (known as nonhomologous end joining, if you're that bored). I wouldn't be telling you this if it hadn't worked, so you have guessed that their deletion confers HIV resistance to immune cells infected with it. Of course, you have to get this protein into the cells first - ironically, you deliver the gene coding it using another type of virus.

But it's all astonishingly cool, when you think about it. This brilliant little addition to the molecular biology toolbox allows the targeting of specific disruptions to literally any part of any gene. This will be used in widespread fashion by researchers looking to mutate specific parts of proteins to better understand their functions (which could potentially expand our protein-pimping garage, so to speak), and may eventually find its way where RNAi has not and find clinical applications not just in AIDS, but in a wide variety of diseases and potentially even in stroke.

* As an aside, some might wonder if the European/African Δ32 divergence was caused by natural selection by other diseases, specifically the Black Plague, but the frequency of the deletion was similar in DNA from Bronze Age samples. So, no.