Wednesday, December 23, 2009

Get that Pfizer out of my CIHR

I was surprised to have been so much out of the loop when I learned on the CBC radio show "The Current" that one of the Pfizer VPs had been appointed to the governing council of CIHR (our main health funding agency). Now I love to hate on Pfizer as much as the next guy, especially since one of my good friends works there, and I'm not a huge fan of off-label uses of drugs. But this really made me raise an eyebrow. The thinking behind the decision to appoint Dr Prigent was to bring "much needed" commercialization expertise to CIHR and to help "align the interests of CIHR with those of the pharmaceutical industry". This is not my interpretation of the facts but a direct quote from Dr. Prigent. Now I was under the impression that the mandate of CIHR was to improve the health of Canadians by promoting scientific discovery, not to commercialize products or post better quarterly results. I fully understand that discoveries need to be turned into products in order to reach patients, but I'm not sure that this is the imperative of CIHR. Now most people sitting on the governing council have a conflict of interest, because they stand to gain from getting more funding to their home institution, but I'm afraid this is the beginning of a shift towards more corporate regency over funding focus. Even our neighbours to the south don't allow that. I'd love to hear arguments for increased focus on commercialization in the comments, but If like me you think there is too much potential for conflicts of interest you can sign this petition...


Tuesday, December 22, 2009

Mosquito laser death

Quick bayblab link to an article about geniuses who utilized the awesome power of lasers to combat the most annoying insect. (I don't know how I missed this, it's old news.).
Could you imagine if these things become consumer grade!?! I hope it comes with a smoke machine to enhance the lasertastic spectacle of burning mosquitoes.


Monday, December 21, 2009

Death from the Skies!

We're all going to die. Not in 2012. Not any time soon for most of us. But eventually something catastrophic will happen and life, indeed the Earth, as we know it cease to exist. Luckily, since nobody reading this will likely be around to witness it, we have bad astronomer Phil Plait to explain how it will all go down.

Plait walks us through several doomsday scenarios from extinction-causing impacts to being cooked by cosmic rays to encounters with alien life. In each case, the reader is given the basics to understand the disaster being explored, a detailed explanation of how it might happen, how the human race might prepare for or prevent the particular destruction (if at all) and odds of it happening.

This is first and foremost a science book, and Plait delves into the physics and astronomy with vigor. What exactly is happening at the centre of a star? How is a black hole formed, and what would happen if we fell into one? While some of it might be daunting, it's all written in an easy-to-read and engaging style, that at times feels more like reading good science fiction than science fact. Each scenario is prefaced with a vignette of how it might look if you were caught in the middle of it, and even the cover evokes warm memories of old sci-fi B-movies.

Death from the Skies! may be one of the best science books I've read. Educational and entertaining, it's a must read if you have any interest in astronomy and astrophysics - and possibly even if you don't.

The universe is a harsh and violent place, and sooner or later it will get us. Phil Plait teaches how it will happen, and somehow makes you wish you'll still be around to witness it.

Death from the Skies! by Philip Plait


Thursday, December 17, 2009

It's beginning to look a lot like Christmas...

... but only if you look very, very closely.

Scientists in the UK have made a tiny snowman, one-fifth the width of a human hair.

The micro man is more Tin Man than Frosty though, built with two tiny tin beads, a platinum nose and ion beam etched features.

See here for the story.

[h/t: a loyal FoB]


Wednesday, December 16, 2009

The Geeks' Guide to World Domination

While not actually giving tips for world domination, The Geeks' Guide... by Garth Sundem is an interesting book for the trivially minded. Within its pages, it contains 314(.1516?) short entries about pop-culture, science, brain teasers and other geekery ranging from useful Klingon phrases to how to balance a chemical equation. It's essentially a bathroom book - something you can grab and open up to find an interest fact or list.

The downside (there's always a downside) is that over the course of reading it I caught at least 3 factual errors. Granted, one I wouldn't have noticed if it hadn't come up in a recent round of pub trivia, but another was an obviously imbalanced chemical equation and the third was something any self-respecting geek should know.
And mistakes are pretty much a fatal flaw for what is essentially a trivia book.

Now saying one wrong thing (or three) doesn't make everything in the book wrong. However trivia, whether in a book or contest form, attracts people (myself included) who get caught up in the details and pride themselves on getting them right. I've been to more than a few trivia contests that have featured heated debates, either amongst teammates or with the quizmaster, over minutia. (The irony being that that trivia is, well, trivial and not worth heated argument) The attitude is summed up in a quote notably missing from The Geeks' Guide's quotable Futurama: "[Y]ou are technically correct – the best kind of correct!"

So if you're one of those people who will be bothered finding one or two errors in a bathroom reader (or not finding them, but knowing they're there) it's probably best to skip this one. But if you can overlook some minor mistakes to find out how to load a pair of dice, learn tongue twisters in foreign languages or discover a quick trick for dividing by 7 then it might be worth checking out - at least for those moments when you're on the can.

The Geeks' Guide to World Domination by Garth Sundem

Some of the entries, and some not in the book, can be read at the author's blog.


Monday, December 14, 2009

Help Contribute to a Scent-free Workplace

I was lamenting the nightmare that is Christmas shopping when I was sent a link to a great potential gift: Flat-D or flatulence deodorizer. It's as though it was designed specifically for my family! The Flat-D is piece of cloth worn inside your undergarment containing activated charcoal. From the website:
Activated charcoal cloth was originally developed by the British Chemical Defense Establishment as a highly efficient filter medium for protection against nerve gas and other highly toxic vapors that might be used in chemical warfare.
Protection against toxic vapors? Sounds like the perfect solution to flatus odor. But does it work? The gasses responsible for malodorous farts are mainly - but not exclusively - sulfur compounds, which should readily adsorb to the activated charcoal, but it's been shown that ingesting charcoal is ineffective (and probably doesn't taste great either). Charcoal textiles, on the other hand, can reduce the escape of sulfur compounds significantly - full briefs capturing virtually all of it, and pads like the Flat-D up to 77% effective (charcoal seat cushions don't help at all). The best part is the Flat-D, like other charcoal textiles, is washable and reusable.

If roasted chestnuts, egg nog and other holiday cheer threaten to turn your holiday festivities into the eleven pipers piping, this may be for you.

"Remember you can hide the sound of a fart by making a louder noise, but you cannot hide the odor of flatulence."


In an Octopus's Garden, In the Shade

Octopuses (apparently not octopi) are smart and have been shown to be able to complete problem solving tasks. Recently they have even been shown to potentially use tools - with one species carrying coconut shells to use as a makeshift shelter should the need arise. Check out this cool video of the behaviour:

Read more about it here.


Tuesday, December 08, 2009

Speaking of food...

Check out these awesome science-themed cookies, including some recipes and instructions.

These cookies look great, and now you can finally eat that delicious looking agar.

[h/t: Pharyngula]


In Defense of Food

I've enjoyed the writing of Michael Pollan in the past, mainly his column in the New York Times Magazine. He writes eloquently and interestingly about food. In Defense of Food is my first experience with his book-length writing.

The book itself is summarized succinctly on the cover: "Eat food. Not too much. Mostly plants." It sounds like reasonable advice, and inside he makes the case for the pithy slogan. He argues that much of what we eat is not food and attacks the Western Diet and the nutritionism movement that focuses on individual compounds and not on whole foods. He describes what he calls "The American paradox": despite a preoccupation with health and nutrition, the US increasingly unhealthy, and proposes some dietary changes to address that fact, elaborating on the cover's mantra. (There's no reason to think this doesn't apply to Canadians as well)

Unfortunately, this book got under my skin right from the start. From the beginning, there is an anti-science tone, even putting the word in scare quotes, "advising you to reject the advice of science and industry" and arguing that current limitations of scientific understanding mean it's not enough to go by when deciding what to eat. Well, if not science then what? "Tradition and common sense" is the answer. That sounds good, and may even be a reasonable starting point but outside scientific rationalism, tradition and common sense can lead down the path to pseudoscience. And we see this fairly often with unproven traditional medicines that "have been used for thousands of years!"

In fairness, he's mostly speaking about science in a narrower sense and uses some science to back his arguments, but the opening tone feels otherwise. The real science he's attacking is reductionist nutritionism, the kind of thinking that gives us 'trans-fats are bad', 'eat more omega-3s', etc., distilling food down into more basic elements. It's not hard to be frustrated by reports of what's good or bad for you changing seemingly daily, and he makes a reasonable case for rethinking that approach. Unfortunately, this poses another problem for Pollan. He attempts to debunk nutritional science but at the same time depends on it to support his own arguments about what kind of food we should be eating. The inconsistency is obvious, and Pollan himself is aware of it. He does attempt to address this problem, but never really succeeds at doing it satisfactorily (at least for me).

This isn't the only logical flaw in his thesis. He appeals to tradition, but what gets traditions started? How did our ancestors know what works and what doesn't? How do we figure it out to start new traditions? Trial and error is one way, and historically possibly the main way, these things have been worked out. For example, one complaint is that our bodies aren't used to the new Western diet and its manufactured foods, we get sicker because of it (eg. increased rates of obesity and diabetes) and we should move back to eating "real" food. This may well be true, but as he also notes, the same thing happened when cow (and other animal) milk was introduced to the human diet. Now, milk seems as natural and wholesome a food as any other, but would Pollan have argued against milk as a food if he were around back then? "We've adapted!" seems like a probable defense, but how do you adapt or learn or improve without trying new things?

While this all seems quite negative, the book was interesting and easy-to-read, even if some of the support for the thesis had holes. Despite some flawed argumentation, In Defense of Food does offer some food for thought regarding our philosophy towards food - what it is and how to think about it - even if you walk away not agreeing.

In Defense of Food by Michael Pollan


Saturday, December 05, 2009

Really bad trips

There some pretty obvious consequences of recreational drug use, including physically debilitating consequences. Typical consequences are usually thought to be the result of chronic use, addiction and/or overdose. (Check out "Faces of Meth.") There are, however, less typical examples of the consequences of drug use.

The first example that I found quite interesting is hallucinogen persisting perception disorder (HPPD), which sounds like it could be extremely inconvenient. After as little as a single dose of LSD, psilocybin or related hallucinogenic drugs, symptoms of visual aberrations persist. Hallucinating for the rest of your life takes the fun out hallucinations. Sufferers of HPPD also can distinguish what is a hallucination and what is real ie. they have pseudohallucinations, which sounds even less fun.

The second example involves a illicit synthetic opiate drug called (1-methyl-4-phenylpiperidin-4-yl) propanoate (MPPP).
From an article in TIME magazine:
When George Carillo arrived at the Santa Clara Valley Medical Center in San Jose one steamy July day in 1982, he seemed more a mannequin than a man. The 42-year-old heroin addict was bent over and twisted, drooling and unable to speak; almost every muscle was immobilized. No one knew what to make of his condition, so a call went out for Dr. J. William Langston, the hospital's chief neurologist. Langston took one look and was amazed. Carillo's symptoms suggested that he had been suffering for at least a decade from Parkinson's disease, a nervous system disorder that causes tremors and a gradual loss of mobility. But that hardly seemed plausible: Parkinson's rarely strikes anyone under the age of 50.

Using stiffened fingers to scrawl answers to doctors' questions, Carillo managed to provide a few clues. The symptoms had come on suddenly after he and his girlfriend, Juanita Lopez, 3l, had tried a new synthetic heroin. Though the drug had caused an odd burning sensation when injected and hallucinations, they continued to use it for three days; two days later both had frozen into living statues.

During the manufacture of MPPP the related MPTP can be accidentally produced. MPTP in the body is converted to a neurotoxin which is selectively causes neuronal death in dopaminergic cells. This selective toxicity causes the hallmark Parkinson's symptoms. This drug has been now used extensively to study Parkinson's and create animals models of this terrible disease. It also hints that an environmental toxin may contribute strongly to early onset Parkinson's. The possible causes of Parkinson's is extremely interesting and warrants a separate post.

There is a book available, "Case of the Frozen Addicts" and a NOVA documentary of the same name about MPTP victims. There are at least 3o0 people in California who have used this drug. I can't find a download or streaming of the NOVA episode unfortunately.
Of course, medically prescribed drugs can have some extremely bad permanent effects, but hopefully in that case there is a professional who knows the drugs and what to look out for. Also recreational drugs are done on a self dosing schedule and, especially in the case of addition and/or dependence, one might loose perspective on symptoms of damage and subsequently an appropriate dose.


Friday, December 04, 2009

Cancer Carnival #28

Welcome to the Cancer Research Blog Carnival #28, and the final edition of 2009. We have a full slate of editions open for hosting in the new year, so send us an email at bayblab@gmail or leave a note in the comments.

First up LabRat has some nice research blogging on the motility of cancer cells.
In order to break away from the neoplasm and spread the disease cancer cells must gain motility. Studying how cancer cells move can be difficult in vivo because the conventional method of immuno-histology (which involves taking slices out of a tumour during development then fixing and staining them) prevent movement all together. Newer work has been done using Intravital imaging [...], where a fluorescently-labelled tumour is generated in an animal and then observed while the animal is anaesthetised.
Lab Rat discusses some of the findings, and the difference between single cell and group motility.

Next our friend Alexey at Hematopoiesis has a review of a couple of papers that discuss the stem-like qualities of T-cells. How does this relate to cancer? He explains:
Because adult stem cells, cancer stem cells and self-renewing T-cells share common features (chemoresistance, quiescence…) chasing for efficient killing of the cancer we can also kill memory T-cells and shut down long-lasting immunity after therapy. Bad news.
Bad news indeed. But it is followed up by good news, so head there to read it.

Cancer screening - always an interesting topic as detection techniques get more sensitive - was discussed over at Scienceblogs recently, spurred on by new recommendations for breast cancer screening. Orac at Respectful Insolence kicked things off:
No, I wasn't surprised that recommendations to scale back mammographic screening were released. I saw it coming, based on a series of studies, some of which I've discussed right here on this very blog. What surprised me is how much of a departure from current mammography guidelines the USPSTF recommendations were and, even more so, that they were released this year.
It is a lengthy post, and worth the read for the details of the changes and the reaction of an oncologist. The recommendations call for a reduction in mammography (and self-examination) based in part on potential harms such as overdiagnosis and unnecessary biopsy. Greg Laden has a different point of view
It seems to me that the solution being recommended is this: Let's have less information at hand so that we don't fuck up our use of that information. If we don't have information that we can misuse, then we can't misuse it.
Finally, Mike the Mad Biologist discusses what happens when woo-ism meets cancer prevention wherein he discusses clinical trials of drugs which halve the risk of breast cancer. Yet they aren't embraced with enthusiasm.
I could understand if you tried the medication, and you felt lousy. Somehow, I don't think "a spiritual element" is going to halve the probability of breast cancer. (Before anyone thinks I'm picking on women, men seem just as idiotic regarding prostate cancer prevention--which has a much lower survival rate). But people who are frightened will engage in activities that lend the illusion of control (there is little conclusive evidence that diet can significantly lower breast cancer rates in older women*). The terror of knowing that there's is a one-in-five chance of getting cancer, combined with the knowledge that, even with medication, there is still a one-in-ten chance of getting cancer has to be terrifying.
That's it for this month's Cancer Research Blog Carnival. For older editions, visit the Carnival Homepage. Don't forget, the CRBC has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.


Thursday, December 03, 2009

Brain, Thinly Sliced

This is a long day in the lab:
We are slicing the brain of the amnesic patient H.M. into giant histological sections. The whole brain specimen has been successfully frozen to -40C and will be sectioned during one continuous session that we expect will last approximately 30 hours (+ some breaks and some sleep in between). The procedure was designed for the safe collection of all tissue slices of the brain and for the acquisition of blockface images throughout the entire block.
Live video of the brain sectioning can be seen here. The brain in question is that of Henry Molaison who had parts of his brain removed to control epileptic seizures, and ended up not being able to form new memories.


Last Call for Cancer Posts

The Cancer Research Blog Carnival will be here tomorrow, so this is your last chance to send in any of your cancer writing from the past month. You can use the form here.


Wednesday, December 02, 2009

Scientific peer review


Tuesday, December 01, 2009

Good Head

Go to the pub, and you'll undoubtedly find people gingerly pouring from a pitcher trying to minimize foam and acheive a headless beer. This despite the fact that many beer glasses, particularly special glasses for premium beers, have a volume marking that allows for half an inch or more of frothy goodness. Which way is better - thick head or no - is a matter of taste, quite literally.

Beer is a delicious glass of chemistry and biology, and the bubbles can be natural or artificial. For the most part, the bubble forming gas is carbon dioxide, which causes bigger bubbles and a 'fizzier' beer. CO2 can be artificially introduced by dissolving it under pressure, or it can be naturally formed as a byproduct of fermentation by the yeast.
Some beers, like the Guinness family of brews, use nitrogen or a CO2-nitrogen mix either as a widget in the pacakged product or to draw the liquid from a keg. These bubbles are smaller and result in a denser head, less effervescent beer and the distinctive 'creamy' texture. Even without foam, the gas involved influences a beer's flavour. Dissolved carbon dioxide forms the weak carbonic acid, affecting the acidity of beer and therefore its taste.

Obviously the bubbles at the top of the beer aren't just gas - there's something holding them together. Lasting bubble formation requires a surfactant, a molecule with both hydrophilic and hydrophobic parts, like the lipids in soap. Ironically, even trace amounts of soap residue in your beer glass can kill the head. As the gas bubbles in your beer rise, they pick up a number of molecules. One of the more important molecules is lipid transfer protein-1 (LTP1) (pictured). This protein is present in barley, but is not surface active until denatured by the boiling of the unfermented liquid (or wort). This protein is so important for foam stability - and foam stability is so important for the beer drinking experience - that German scientists (and who knows beer better than the Germans? The Czechs and the Irish, that's who) have engineered yeast expressing LTP1 to improve the foaminess of your draught. Potential brewmasters should also know that the temperature and duration of boiling your wort affects the extent and degree of LTP1 denaturation, and therefore the quality of your head. But LTP1 isn't the only molecule involved in a frothy mug, and not the only one subject to engineering. Japanese researchers have discovered that another barley protein, lipoxygenase-1 (LOX), has the opposite effect, reducing foam and flavour stability. LOX-less barley has been developed and tested for brewing by Sapporo.

So why go to all the trouble to increase the amount and stability of beer head - something many drinkers go out of their way to avoid? For one thing, a foamy pour reduces carbonation. This has two effects: First - and this is important to any drinker and the bartenders they're tipping - it means you can drink more. On average, a pint of beer contains 2.5 pints of carbon dioxide. A still pour keeps the CO2 dissolved in the beverage, where it ends up in your stomach, contributing to a bloated feeling. Secondly, less dissolved CO2 means a less acidic flavour. A bubbly pour releases the gas, affecting the taste. Acidity is also associated with a less thirst-quenching beer. Yes, research has been done into what factors determine how refreshing that beer is on a hot summer day. Strangely, while acidity - which can be caused by carbonation - along with foam and flavourfulness, negatively affect thirst-quenching properties, bubble density and carbonation have a positive correlation. Which is why your refreshing summer beer tends to be a fizzy, flavourless drink.

As the bubbles rise in your glass, they pick up more than just LTP1. Alpha-acids from the hops are also accumulated, and create a longer lasting foam. More importantly, these are also flavour compounds. Like wine - or just about anything - flavour is as much a play in the nose as on the palate. And while you won't find many beer drinkers discussing 'bouquet', it's there and it's important. The white cap in your glass concentrates these scents and flavours, enhancing the drinking experience.

Next time one of your friends gives you a foamless beer, ask them to pour it right. Not only is it visually appealing (and a clue that the beer you're drinking isn't flat) but it results in a more drinkable pint that engages your tactile, olfactory and gustatory senses. There's a lot of science in there too.