Sunday, June 29, 2008

TED, no bill

If you've ever wondered what a conference is like, or even if you know and no longer want anything to do with them, go to this site now.

The TED (Technology, Entertainment, Design) Conference is an amazing gathering of some of the brightest thinkers and doers in almost all realms of human effort. Some of the brightest people in the world are challenged to give "the talk of their lives" in 18 minutes. They have a large number of the presentations given at these conferences on their site available free - streaming or download.

These are the best videos I have ever seen. I've been watching them for hours. They're engaging, educational, inspiring and frequently funny. I guarantee it will be the smartest thing you've done all day. Thanks to BoingBoing for pointing me there.

Sir Ken Robinson on how education kills creativity

Hans Rosling with the best statistics you've ever seen

Genius VS Ramachandran on your brain

Saturday, June 28, 2008

Hockey exchange

So I say my blog is sometimes not about science. Just because that hasn't been true so far doesn't mean it will never be true. Like today for example.

Last year, as the Canadian dollar began to soar, I started wondering what this would mean for NHL teams north of the border, particularly my beloved Habs. NHL teams operating in Canada have certain economic disadvantages that aren't immediately apparent, such as higher tax rates that discourage players from wanting to maintain a residence here, and the recently eliminated problem that they had to pay ridiculous exchange rates to convert their income to pay salaries in US dollars.

Our newly-equalized currencies are changing the face of hockey (and the Toronto Raptors and Blue Jays franchises). Combined with a skyrocketing salary cap, and good performances from most of the Canadian teams since the lockout, teams north of the border are effectively rolling in money and opportunities to sign big-name talent - look at Edmonton's offers last summer for Vanek and then Dustin Penner; Montreal's recent acquisition of Alex Tanguay and current negotiations with Mats Sundin. And bet that the Maple Leafs, once they finish gutting their entire organization (Wellwood on waivers? Really?), will have a lot of money for big contract with a young gunner they can groom as the next captain.

Despite the damage to our tourism and export industries, our current exchange rate might be pointing us to a renaissance of Canadian hockey, where Canadian teams can expect to win a Cup every so often (if they can beat Detroit) , to sell out every game (as Montreal has done since the lockout) , and to have top talent knocking on their doors. Then maybe Jim Balsillie can finally have an NHL franchise in Hamilton, and maybe Winnipeg could attract a team back there.

Go Jets.

Thursday, June 26, 2008

Ethical Facelifts

Bit of a change in style. Now accepting applications for cool logos.

It's been a long time since I saw so many articles about scientific ethics in the news in so short a period. Well, since Vioxx, anyways. Not long ago, I alluded to the Swiss as having gone "bugf#$k nuts," by which I meant totally crazy. Since 2004, they have enforced a Gene Technology Law, which stipulates that in Swiss experiments, the dignity of [living things] needs to be considered in research. They are in the press these days because they have upheld the decision as it applies to plants, which of course made everyone go "wuh?"

The first effect of this law is to make science even less feasible economically - a Swiss study involving maternal separation in monkeys is going to court now to find out whether it can proceed or not. Making your scientists go to court is only diverting more funds from the state to fight these legal battles, making science that much more expensive to carry out. This is not a good thing for a country's biotech industry, or their "intellectual economy".

Another thing, as pointed out in this Nature editorial, is that dignity is a slippery concept. They cite an American governmental inquiry on dignity in bioethics, which the boys at Nature seem to think is self-contradictory. And they're probably right, but I don't have the time nor the inclination to go wallowing through a 577-page .pdf file written by various and sundry higly respected thinkers to find out that dignity is tough to talk about meaningfully, because it's tough to define, but nonetheless vitally important.

Don't get me wrong - I'm not getting down on dignity. I'm just saying if you ask a dozen people what it is, you'll get 12 different answers, and that this translates to an important point about how advances in the sciences are going to have to force progress in humanities. Development in science is outstripping the development of laws and ethics to control them.

As a direct result of this, you get what we have in California right now, which I also alluded to in an earlier post. California recently issued cease-and-desist letters to various companies that engage in direct-to-consumer genetic testing. Several companies now will sequence your genome (for a small fee) and compare it to known bits of code that predispose you to heart disease, Alzheimer's, whatever. California's decision to require a physician's consent for the tests seems to be an oddly reactionary biotech policy from a state that is known for creating $100 million funds for stem cell research under the nose of the Bush administration.

The legality of this question, assuming a class-action suit against the State by the companies involved, will hinge upon the legislature in this article. Essentially, the decision should be predicated on whether these tests are diagnostic or not. As the lawyers for the defense know, they are not. Diagnostic tools are predictive - a positive result indicates a medical condition and informs the appropriate treatment. What these companies do is associational - they can look at your bits of DNA code and then say "ooh, people with that bit have a 6-fold increased risk of getting the hoobajabbies after their 65th birthday! You'd better start taking antioxidants!" Which is why I agreed with the CEO of one of these companies in my last post when he implied that their industry was entertainment more than anything else.

I think that ethics would be better served by allowing the tests, and providing an option for subjects to make their anonymous genomes publicly available for research purposes. And instead of requiring a doctor's approval, send a Ph.D. to explain what the test results really mean - three studies found that people with this polymorphism have an increased risk of the hoobajabbies, but this more recent study found no association, and the effect size in the meta-analysis is weak; plus there's this editorial in Archives that just came out saying the stats in all these studies are bullcrap anyways. So it's inconclusive.

Tuesday, June 24, 2008

Basic Biological Change

Some excellent (as per usual) articles today at Wired magazine provide excellent illustrations of the changing nature of the way we do biology. Not content with the "Information Age," Wired editors are calling this the "Petabyte Age," and boldly proclaim that "More isn't just more - more is different."

When it comes to biology, they couldn't be more right. The scientific method starts with observations. It was accepted early on that no person could observe everything, and a big part of scientific study and training is learning where (and how) to make observations. In biology, for example, it's only been roughly 50 years since we figured out what gene expression was. 30 years ago, you could look at one gene at a time - but it had better be highly active. 15 years ago you could do loads of genes from the same sample, but they had to be done one at a time. Today, we are close to being able to looking at the expression patterns of every single gene in a given sample - whether we know what the gene is/does or not - simultaneously.

These tremendously powerful approaches, which are becoming more commonplace all the time, generate these massive datasets that humans simply can't deal with. Not that brains don't have the computing power to do it, but they're usually busy with things like sensory input and breathing. The development of new methods for generating and analyzing "big" data will trump traditional scientific approaches for a number of important reasons.

First of these is the simple volume of data. No longer shall we have to pick and choose endpoints to examine or the means to analyze them. Where possible, we measure everything. Which is a bit frightening. Then feed it all to a system that starts doing correlations and cluster analyses and crazy matrix algebra and tells us what's important. Which is the second thing - a total lack of bias in the interpretation.

Bias has been an important tool in science in the sense that hypotheses and models bring you to look at certain things and not at others. This "framing," as it is called in the artificial intelligence community, is very difficult for computers. But maybe they don't have to bother, and we can take advantage of this to see things that we would never have looked for (or even considered), no thanks to the tunnel vision of so-called scientific expertise. If we could work out a way to normalize the data from experiments across labs, we could then make the datasets public - like I talked about GlaxoSmithKline doing last week - preferably into a common, searchable resource, and produce more information than any single scientist could create in their careers. And we'll find out that more isn't just more, it is qualitatively different. Of course, this difference means there will be a whole new set of problems to solve as these analyses evolve.

The irony is that mathematicians and computer scientists will be able to do PhDs in biology from their armchairs in their spare time, and risk being more successful at it than the biologists.

* * *

Quote of the month: "The 23andMes of the world are more in the entertainment realm..." This is Andy Gores, CEO of HairDX, commenting on why he was disappointed about the company's recent decision to stop selling genetic tests without a doctor's approval in California and New York. 23andMe will sequence your genome for about a thousand dollars, and tell you whether you have elevated risk for a given condition based on your DNA. HairDX, one presumes, does something similar for genetically testing your chances for hair loss. People would do well remember this.

Sunday, June 22, 2008

Whistles can't feed your cat.

From around the web: Finally some big press for astrocytes, one of the "other kinds" of brain cell. In addition to neurons, there are also glial cells in the brain that are at least as important to normal function as their more glamorous counterparts. Astrocytes are highly active in brains, involved in immune response, regulation of the environment around neurons, regulation of blood flow, and even synaptic activity. This study concentrates on how they regulate blood flow, and provides an important caveat for future studies using brain scans like fMRI - neuronal activation measured using blood flow is also measuring astrocytic activation.

Drug giant GlaxoSmithKline put massive amounts of their own biological data online for free - hopefully something we can look forward to seeing more of. This somewhat innovative move makes a ton of sense. They cannot possibly follow up on everything they have in these enormous datasets, and independent researchers might be able to use findings from these studies at starting points to help advance cancer research in general. Count on more and more datasets like this to crop up online over the next couple of years.

Lastly, a comment on an important piece of news about the abundance of scientific fraud. A broad survey of American scientists found that between 6 and 9 percent of students and faculty knew of peers who had either falsified or plagiarized data. Almost half knew of other examples of misconduct (holding back data from competitors, for example). An overwhelming 94% of faculty said they have some responsibility for the conduct of their peers, but only 13% report actually doing anything about perceived examples of misconduct.

The problem is endemic to the structure of the scientific community. When you are working on a doctorate, or a fellowship, there is little or no motivation to report on scientific misconduct in your lab. If you do, papers from your lab might have to be retracted, granting agencies could withdraw your funding, your project might get shut down (or lose the data it was started from), and your boss may be able to make life very, very difficult for you in the long run. As a student, there is absolutely no reward - and huge consequences - for being a whistleblower, unless you count sleeping at night. Which doesn't pay the bills.

Thursday, June 19, 2008

What's "beaver" in Spanish?

Nature reports this week on how the beloved Canadian beaver has outworn its welcome in Tierra del Fuego, where 50 of the things introduced in the 1940s bred like rodents will, and now number about 100 000. As intended, it it did provide a substantial fur market for the indigenous people, but had devastating consequences for the local flora and fauna. They are now looking into ways of "eradicating" the beavers. One hopes they don't import a pile of foxes or something.

While traveling in New Zealand a couple years ago, I met a guy at the hostel who had been touring through Australia. He told a story about some guys he met in a small town up in the northeast. When asked what they did fun for fun, these guys said they "go on a catshoot," by which they meant they would drive around (perhaps in varying states of intoxication) and shoot at cats with BB guns. While this sounds cruel and appalling at first, I later learned that cats were a huge problem in the rainforests there. Escaped domestic cats bred over time have become fearsome predators and unbalanced the already wonky ecosystem (what with all the cane toads, pigs, foxes, rabbits and whatnot). Which just goes to show that country people know what's good for the country everywhere you go, even if they sometimes seem like freaky rednecks.

* * *

Small bits of news: Nature reports that biotech giant Invitrogen (who have just finished buying Millipore, Upstate, Chemicon, and maybe several other firms) have offered about US$6.7 billion for Applied Biosystems, another giant in the industry. One is reminded of beer companies, or Microsoft. Canada will partner with California in a $100 million investment into research on cancer stem cells, which will cement our positions as world leaders in this field; strategically it looks like a smart investment, and says that cancer is back in vogue with funding agencies. Scientific American reports on another important step in killing the nature vs. nurture worldview, and what one of the study's authors very cleverly refers to as "genetic nihilism."

This kind of thinking, in which one assumes that genes dictate our lives and there's nothing we can do about, is reminiscent of destiny (or divine purpose) vs. free will debates that have raged through history (and to my admittedly primitive understanding of such things, there's still no conclusive winner). Genes don't change in their sequences over the course of life, but the ways they are structured, "read," regulated, and affect our lives is very much open to input from a surprisingly wide variety of sources. Trust me, I'm doing a whole doctoral thesis on it. Not to say that every gene can be turned up or down so easily, but very good evidence is accumulating that simple things like proper diet and regular exercise can push gene expression in certain directions, which are usually considered good for the animals involved in terms of any number of health indicators.

So what we're saying as biologists, just to make it absolutely clear: Genetics rule our lives. Genetics do not rule our lives. Any questions?

Monday, June 16, 2008

The more things change...

A round of the science news reveals an equally brilliant follow-up to last week's article about drinking during pregnancy: Scotsmen show that pregnant women shouldn't be smoking pot either. What's a poor girl to do? Doctors complain about a bottle of pills called "Placebo" on sale in the US for $6/bottle (50 pills). They're right - Smarties would be way cheaper, equally damaging to your child's psyche, and, hey, if you're going to be a crap parent then you might as well go all out.

The story that most catches my eye is this one about differences seen in brain scans of homo- and heterosexual subjects. The first question I always think to myself when I read about research like this is "Why do people want to get themselves embroiled in this?" The research I do involves rats and cell cultures, not people and highly-charged issues like homosexuality and sexual arousal. I'd be scared of running a lab with so much emotional impact on people, not to mention counting on a Conservative government for funding.

I don't do brain scans, so I can't comment on this paper to the depth I could on something way less interesting (but I will inevitably end up talking about on day). But it all looks legit - there's a whole body a of research showing that men have asymmetrical brains (enlarged right hemisphere) compared to women, and these guys show differences in resting activity patterns and connectivity. However, we'll all be lot more impressed when researchers can look at a brain scan without seeing the patient and be able to predict whether they were looking at a straight or gay representative of a given sex. And why not? A group published last month on a study where they successfully predicted nouns the subjects were thinking about by their brain scans.

One of the most interesting things about the study was that subjects asked to sit and rest in a PET scanner to measure brain activity. They saw plenty in an area called the amygdala, which tends to go active in times of emotional arousal. Which is nice, because maybe it means that gay or straight, men and women are more alike than we like to think sometimes - scientific evidence suggests that either a) everyone gets nervous around doctors whilst in a brain scanner, or my preferred explanation b) left to our own devices, we all think about sex.

Friday, June 13, 2008

The Mirror of the Terminator is Still Bad News.

I don't mean to keep ragging on the English, but who was the genius that decided to name the British Military's new communication satellite network "Skynet?" We can only hope that, actually no, they've never seen Terminator 2, what an unusual coincidence that is... (uncomfortable laugh). Otherwise officers in the British Army have a worryingly dark sense of humour.

* * *

Wired reported yesterday on the fruits of a relatively new "drug" discovery processes that might lead to new migraine meds. What is most interesting about the story is the "drugs" in question, which aren't like drugs at all. The problem with most drugs, particularly in neuropharmacology, is that they are "dirty," as we call them - they bind to many biological targets, which can make their mechanisms of action difficult to understand. This technique sidesteps that difficulty in a very innovative fashion.

Proteins do the work of cells, which is to say absolutely everything you do, and their structures are what is being coded for within our so-called "genetic code" that lies along DNA strands. Genes are "read," and transcribed to an intermediary between DNA and protein known as "messenger" RNA. This mRNA takes the message to another region, where it is translated into a protein. Another kind of RNA - RNAi - was discovered fairly recently and the subject for which the Nobel Prize in Medicine was given to Mello & Fire in 2006. In theory, they are used by cells to shut down the mRNAs of one or many specific gene(s) so they are never translated, providing a potentially much more selective and rational approach to drug design compared to pharmacology.

The neatest thing that these guys did was their homework - trust me when I tell you that mRNA is a bitch to work with. In the body, it seems to be a very dynamically regulated process, and things called RNase can break the mRNA down quickly. RNase is everywhere outside of cells, and if you're not careful when doing work with mRNA, you will find it's all been eaten at the end of your experiment. This is why we convict killers on DNA rather than RNA evidence.

This company, however, took advantage of a strange property of molecules - stereoisometry - and designed mirror-image molecules of the sugar backbones of our RNA molecules. Think of it this way - your left hand is a mirror-image of your right hand. While they are identical, you can't make them overlap. Our bodies can't digest these mirror-image sugars, but they should still bind to their target mRNAs. Which, in theory, would make them a brilliant medium for drug discovery and could provide much-needed new insight into understanding human mental health and disorders thereof.

If I had money, I would probably invest in these guys, assuming they have stock available. They just got a pile of money from Eli-Lilly to do this, too...

Wednesday, June 11, 2008

Keith Chen rules. Bumblebee women less so.

I was going to blog about something else, but something really stupid piqued my interest instead.

First, a tour of the science news - British researchers prove once again that size isn't everything - unsurprisingly to us neuroscientists, intelligence seems to have a better correlation to synapse number (the connections between brain cells) and complexity than simple brain size. Leading journal Nature shows it's behind the times (the New York Times, at least) by reporting that an Italian group has shown that monkeys can understand money; Keith Chen has been doing this for years as reported here. Finally, the Swiss have gone bugf#$k nuts, as evidenced by a new law prohibiting the use of research techniques that may sacrifice the dignity of creatures, which apparently includes the dignity of plants.

So on to the stupid part. I was fortunate enough to travel to England in April on the boss' tab, where I spent a couple days with friends before I headed on to a conference. England had some minor culture shock associated with it - but I enjoy drinking in public, arguments, sarcasm, cask ales and so forth. What I don't like, and call me sexist if you will, is women drinking like blue-collar alcoholic middle-aged men (particularly if they have a beer gut to match).

So that helped to explain to me this gem from the BBC, published March 26 2008(!), declaring that drinking during pregnancy might be a bad idea. You would think this was a no-brainer, but apparently not - this British woman gave birth during a pub crawl (any bets on her alcohol intake?), claiming she didn't even know she was pregnant. Tragically, the baby boy weighs only 2 pounds and has about a 50/50 chance of living. No punch line here, folks, unless you count the fact that she was dressed as a bumblebee at the time, which is significantly more sad than funny, p < 0.05.

My brother and I bitch every year that we haven't come anywhere near as far along as some futurists/sci-fi writers believed we would have by this time (It's 2008! Where's my damn flying car?!), but the Brits are just getting around to banning drinking during pregnancy. I guess it's nice to see the colonials pulling ahead of empire... but I still want my friggin' flying car.

Sunday, June 8, 2008

Win Ben Stein's Esteem? Forget it.

I'm sad today.

One of the things I find most upsetting about living in this modern era is the sheer vacuousness of our role models, who - for reasons completely beyond me - are mostly entertainers. We have pro athletes that can barely string 4 sentences together (and in a post-game interview, they tend to be the same ones in every sport, from every athlete); musicians who will hold court on any subject that comes to mind (third world debt relief and seal "hunting," for example); and actors with IQs somewhere around ground floor levels. We refuse to take our lead from intelligent, educated, or even plain reasonable people.

For this reason, I used to admire Ben Stein. Best known as Ferris Bueller's teacher and host (and usual winner) of Win Ben Stein's Money, Stein is smart, well-spoken and educated. Despite having been a speechwriter for Nixon and Ford, I always had a great respect for him as possibly the only actor able to beat geeks (not just average members of the general public) on a trivia show. I mean, have you ever seen "Celebrity Jeopardy"? These people are downright idiots.

However, Ben Stein has stupidly decided to mire himself in the old creationist debate by starring in a new movie called "Expelled: No Intelligence Allowed." Which is an odd subtitle to any film made in Hollywood - intelligence hasn't been allowed in these films since before I was born. Basically, the film is creationist propaganda, another desperate ploy for enhanced legitimacy of this disturbing movements.

Now, I could send you to Ben's wikipedia article, where a quoted conversation seems to indicate this guy just has a huge hate-on for science: "science leads you to killing people." Or I could send you to his blog posting for said film, full of bizarre assertions like "Some of the greatest scientists of all time, including Galileo, Newton, Einstein, operated under the hypothesis that their work was to understand the principles and phenomena as designed by a creator. Operating under that hypothesis, they discovered the most important laws of motion, gravity... and even economics." Of course economics has a creator, Ben. It's a human phenomenon designed by humans for humans. If God made economics, it might actually work - though probably not. But these are ad hominem arguments, and as such aren't really arguments at all.

Importantly, Ben talks about how Creationists and Creationist ideas are suppressed by Big Science and all the mean, mean men with Ph.D.s and decades of learning behind their belts. Suppression was what the Church did to Galileo when he started talking about Copernican astronomy - and good thing, too, because God knows what a malarkey that turned out to be.

Suppression is possibly the wrong word to use in this context. Scientists, on a whole, demand proof (which is why economics is not so much a science as a complicated way of not understanding certain phenomena). If a group of editors refuses to publish "Creationist" ideas because of a lack of scientific rigour, or a lack of concrete experiments suggesting an underlying theory that will in turn bring out testable hypotheses, Creationists cry "Suppression!" I wish I could do this when my articles get bounced from Nature, and then get all kinds of media attention, grant money, and fame for being a failure in science.

Because that is Creationism, in a nutshell - a failure in science. Or a pseudoscientific success if you will. Science's demands are quite simple: 1) Make observations. 2) Develop testable hypotheses based on these observations. 3) Carry out the tests and revise hypotheses. 4) Repeat until dissertation is finished, or death occurs. Creationism flies through checkpoint 1, but splatters itself against the concrete wall that is number 2. You can't test hypotheses about God, and therefore God has no place in science. You can be a religious scientist - many of these exist, and have their own particular ways of reconciling their faith with their occupation. Anomalous, yes. Suppressed, hardly. But God has no place in the science classroom or its theories.

But this is what we get for looking to celebrities for guidance of any kind instead of people with an actual education and experience in the topic at hand. No, we go for the good-looking ones who can throw a ball REALLY hard. We get the Tom Hankses of the world to endorse our presidential campaigns, and the Tom Cruises of the world are allowed to give the North American public medical advice on the Oprah bloody Winfrey show.

We get what we deserve...