Wednesday, December 10, 2008

Smarter, faster, stronger

A stunning opinion piece in Nature on Monday encouraging the use of cognitive-enhancing drugs, which has been all over the news and brought me to remember a problem I have with Ritalin. I'll have you know this is completely different from having a Ritalin problem. I'm not saying I don't believe in ADHD, although I do believe it is over-diagnosed, but I'm not getting into that. What I want to get into is Ritalin. And most of what we have in the way of ADHD drugs.

The simple fact of the matter is that these drugs are cognitive enhancers. They're a couple of chemical steps removed from amphetamines (speed), which are well-known for improvement of certain parts of thinking - short-term memory and attention particularly. Now, the ADHD drugs seem to work in a select number of specific areas of the brain whereas the speedball drives an entire neurotransmission system into overdrive (to make a gross oversimplification), but people without ADHD still see an enhancement of performance on tests of cognitive performance when they take Ritalin. That's why people buy it illegally during exam periods.

I'm about to make a brutal analogy here, so cover your ears - this is like letting Special Olympics athletes go to the other Olympics, but doped up on whatever performance-enhancer is big right now. No, really. My problem with Ritalin is that gives improvement on performance of tests that we use to diagnose ADHD in in both controls and ADHD patients. We're not treating ADHD necessarily - just improving performance on diagnostic tests, performance on which corresponds closely to that on academic exams.

Most of us are already users of cognitive enhancers. During my undergrad I smoked 15-20 cigarettes and swilled maybe 2-4 litres of coffee daily (thankfully, I've since cut down on both significantly). Both nicotine and caffeine are clinically proven enhancers of performance on pretty much any cognitive task you could name. We drink Red Bulls and coffee to make us sharper, we take sleeping pills to help us calm down, we take alcohol to enhance our social performances.

Which brings us back to the topic of the editorial that brought me to this piece in the first place. Why shouldn't we use drugs to become more intelligent? In what way is this possibly a bad thing? There are side effects; many not as bad as are present in a large number of other commercially available drugs (especially alcohol and tobacco). Why shouldn't my doctor, my lawyer, my accountant, my Member of Parliament and my future kid's teacher be on these drugs all the time?

Personally, I think that the means here don't require justification by the ends. There's no ethical dilemma about taking vitamins, or antioxidants, or coffee. We already use pharmacology to improve our quality of life in so many ways, and I see this as no different than taking drugs for anxiety, diabetes, or metabolic syndrome. Better living through pharmacology is still better living, and I don't think anybody should have a problem with a better life.

Tuesday, November 25, 2008

Science cuts and general news

From the news:
  • Interesting article on anti-aging drugs from Wired, where scientists think that this new class of drugs might be the key to fighting cancer, diabetes, Alzheimer's, and just about everything else under the sun.
  • A great piece in CBC suggesting that forward-facing strollers are bad for a child's social and verbal development. This makes a lot of sense: kids of stroller age have brains that are designed for learning about faces and language.
From the InterWeb:
  • Wired's 10 favourite biology videos. Just awesome (except the PCR song - man, I hate the PCR song). I'll be commenting on at least one or two over the next while.
* * *

According to this CBC article, Statistics Canada reported Thursday that federal spending in science and technology is about to drop for the first time in 5 years, which is about the same time we elected Paul Martin to a minority government. Now admittedly these cuts seem small - about 3% - but this represents hundreds of millions of dollars lost for funding science and innovation in this country.

I don't think this is a good idea, but I'll declare a conflict of interest being a scientist who would like to be employed in Canada. Even still, it seems natural that investment in alternative energy production will create domestic skilled jobs desperately needed by Canadians. Of course, it would cost money now, and it will be years before we see any real return from this investment. But unlike investing in shady debt trading - asset-backed commercial papers, or subprime mortgages - this economic activity would create real wealth, and by that I mean jobs, clean energy, and Canadian businesses with a head start in a globally important industry.

Monday, November 17, 2008

Garneau vs. Goodyear

The Opposition Liberals have named their new Science critic, and it is former astronaut and generally awesome guy Marc Garneau. This is a good move by the Libs, as Garneau actually has a Doctorate in engineering and therefore knows something about science. Oh yeah, and he was the first Canadian in space, with almost 678 hours over three trips total. That's mad geek cred right there.

Gary Goodyear may not be as well-known as Marc Garneau, but is our newly-appointed Minister of State - Science and Technology (I know, what kind of title is that?). Wikipedia lists him as a physiotherapist and doctor of chiropractic, having graduated from an established college that engages in multidisciplinary research and involves about 4500 hours of coursework. However, I couldn't find him in PubMed so I don't think that he's ever actually performed research.

I'd like to see some more Ph.D.s in our legislature's ranks. People that actually understand the cutting edge of their science and can talk about research in a meaningful way. Harper's treatment of science hasn't been cruel, but it hasn't been kind, either. But I'd like to see someone that can actually sell the importance of research through their experiences to the Prime Minister and the Canadian people. It will be interesting to hear Garneau defend the Canadian Space Agency from further budget cuts.

* * *

Economics rant. Feel free to skip.

Bush was at the G20 summit last week talking about how free markets need to remain free, and that this is how global economic progress will be made.

Let me point out three perfectly obvious things. First of all, the U.S. is not interested in free markets. That's why we have things like NAFTA, to make sure that American economic interests get certain advantages. This is not necessarily a bad thing (for the US, at least), but it is definitely not a free market. Secondly, the government is spending up to $700 billion to bail banks out of bad business practices. The very definition of capitalism and free markets demands that governments not engage in massive market manipulation. Thirdly, the only way to have prevented the current economic meltdown would have been to actually regulate the banks and what they were doing, which is also not a free market approach.

Alan Greenspan, former head of the Federal Reserve (and by extension the US economy) said he made a key error during his tenure - "I made a mistake in presuming that the self-interests of organizations, specifically banks and others... were best capable of protecting their own shareholders and their equity in the firms." In other words, he assumed that the banks would follow base capitalist economic assumptions: turn profits, perform due diligence, cover their asses. But they only got one out of three on that quiz, and a suddenly socialist US government is now paying them truckloads of money - skyscrapers full, actually - for this colossal failure to do their jobs.

This is not a free market approach, which just goes to show that capitalism and free markets don't work, and never have. Not that socialism does, but I'm sick of hearing about the power of free markets when 1) there aren't any, and 2) the closer we go towards a free market, i.e. the less closely government regulates, the worse things get.

Monday, October 27, 2008

Transsexuals, farts, stem cells and memory manipulation. Just another day...

From the news:
  • Australian study finds correlation between transsexuality and the gene coding a male hormone (androgen) receptor. Apparently, the long version of the gene has a less efficient product, and was found significantly more often in 112 male-female transsexuals compared to 258 control subjects. Which makes me wonder what this finding means to transsexuals, if anything at all...

  • Solomon Snyder, an interesting character in the history of neuroscience, stands behind a study linking the stink-inducing chemical in flatulence and blood pressure. Apparently the foul smell, hydrogen sulfide, can lower blood pressure significantly. Reported with a sort of childish glee by both the BBC and the CBC (and others)...

  • While Britain relaxes certain stem-cell laws, it is pointed out that Canada is the about the only country in the world that does not currently allow the use of animal eggs in the production of human embryonic stem cells. I would bet a hefty sum of cash that stem cell technology will cure at least some neurodegenerative disorders within my lifetime. However, it is up to legislators to determine whether it will be 10 years from now or 25...
* * *

A very interesting piece from CBC reports on scientists who seem to succeed at wiping a specific memory from a rat. They do this by using mice who have a very fancy piece of genetic engineering on board. The scientists built a gene construct where they could make a certain protein become more abundant in certain areas of the brain through pharmacological manipulation. Then they tested if a mouse could remember a certain place by shocking him there, and seeing if he shows behavioural signs of fear the next time he gets put there.

By overexpressing the protein in question when the mouse was put back in the chamber, the researchers could effectively make the memory disappear. Now, as we all know, memory is a strange thing. It consists of four processes that we call "acquisition," "consolidation," "storage," and "retrieval," which we could equally call "getting," "coding," um, "storing," and "remembering." But it's more complicated than that - when a memory is brought back from storage to become part of conscious thought, it has to be re-encoded, and stored. Even worse, it becomes flexible while we remember it - numerous studies show memories are influenced by current emotions and knowledge, become mixed up with the present.

Instead of altering the memory, the overexpression of this protein (αCaMKII for those keeping track) seems to destroy the memory when it's being remembered, perhaps with a sort of excessive brain "noise" level that obliterates the memory signal during the process of recalling it. This paper is a tome, so I haven't been through it very thoroughly, but it's in an amazing journal (Neuron) and looks pretty watertight. Really an amazing study.

That being said, this is a bit of what a former colleague of mine calls a "sledgehammer" approach, because it lacks precision as a tool. Gene expression is affected through an enormous population of cells, so it could be the case that more than the memory being recalled is affected . Other limitations make it extremely tough to try pulling this off using similar methods in humans. Firstly, the behaviour is not very sophisticated, even for a mouse. More importantly, human memories - particularly the bad ones - are probably richer and more complex than those of mice, and will be consequently harder to "knock out."

The best part, however, is this very wise comment by senior author Joe Tsien: "All memories, including the painful emotional memories, have their purposes. We learn great lessons from those memories or experiences so we can avoid making the same kinds of mistakes again, and help us to adapt down the road."

Good advice, and wise words for the future of memory manipulation.

Saturday, October 18, 2008

Glowing rats & adventure!

The other Nobel Prize I felt qualified to comment on was that awarded for chemistry, where researchers were honoured for the discovery of green fluorescent protein (GFP), which is a protein native to jellyfish and, as implied by the name, can glow green. Now green glowing proteins may not seem like a big deal, but this discovery also brought about fundamental changes in the way we do biology (although the use of luciferase, a light-generating protein from fireflies, was also a big step along the same direction).

In my last post I talked about using the HIV virus a "shuttle" for genetic material, able to insert genes into a host's DNA after infection. Now, if you wanted to look at whether your cells were infected or not, a great way to do that would be to make the virus carry GFP. If you want to know whether a gene is being expressed, you can make a construct that has the same regulatory regions as your gene of interest, but make it code GFP. Instead of performing time-consuming experiments to measure expression, you can literally just look. And then there's the "Brainbow" mice, which have genes for several fluorescent proteins in their neurons. Their stunning pictures (amazing gallery here) will drastically change neuroanatomical methods forever.

Discoveries of this magnitude, like the discovery of the HIV virus, are huge not because of any single aspect of the discovery, but also for the development of tools that literally change the way science is done. The same thing was true of Mello and Flame's Nobel last year for the discovery of RNA interference. This was such a paradigm-shifting discovery that the committee gave out the Nobel to what must be two of the youngest researchers to ever be considered for it, and a discovery that was barely a decade old; normally the Nobel is reserved for the final coup-de-gras of a senior scientist's long and storied career (like Kandel, Greengard and Carlsson in 2000). It heartening to see the Nobel going to researchers who are changing the ways we do science, rather than given out as an honorarium, like a degree to PhD students who've been chugging along as best they can for the last decade.

* * *

Most interesting thing I've read this week: in high school, I was taught about a 1953 experiment by a guy named Miller, which remains one of the most fascinating I've ever heard of. He designed a closed system with an atmosphere similar to what was, at the time, believed to comprise the early Earth's atmosphere - methane, ammonia, carbon dioxide and such. He introduced some sparks and water vapour, and voila - found a couple of amino acids were produced, perhaps giving some insight into abiogenesis (how life came from inorganic precursors).

Miller died last year, and the researcher who inherited his labs and equipment found a series of tubes marked "experiments 1952-1953." He took some vials from the very same experiment and subjected it to much more advanced analysis than was available at the time. These researchers found dozens of organic compounds Miller was unable to detect, lending great support to the original experiments.

While today we acknowledge that the early atmosphere of the planet was not exactly what was envisioned in 1953, this experiment is a fascinating example of a sort of adventurous scientific spirit that I don't think is as prominent today as it was 50 years ago, and I think science is probably the worse for it.

Wednesday, October 15, 2008

Viral Marketing

Well, no surprises for me in the election, which frankly makes me sad, actually. I am predicting that the Libs will have a new leader by November 2009 (if not sooner) and will force another election 18 months or so thereafter. Not really Dion's fault, but he didn't help himself much. It was very telling that the separatist leader Gilles Duceppe is significantly more comfortable in English than the Liberal PM hopeful.

* * *

I wanted to speak briefly about the Nobel Prizes this year, or at least those in medicine and chemistry - I don't know enough about physics to even begin to comment on that work. And of course, the Nobel Prize in economics is really the Swedish Central Bank Prize in memory of Alfred Nobel, because economics isn't so much a science as it is a crapshoot.

The Nobel Prize in Medicine went to a number of people (details here) for work on viruses, two of them for the discovery of the HIV virus. It was a little shameful that a certain other party didn't get some credit, but the Nobel can only be given to 3 people, and he doesn't seem as broken up about it as it might be.

What you probably don't know about the HIV virus is how it blew away the biology community when they discovered how it worked. It is literally capable of taking its own genetic information and downloading it into the hard drive of your genome. Then your own cells start manufacturing the virus and it spreads. It uses a special enzyme for this, known as reverse transcriptase, which itself allowed the development of a process called RT-PCR, one of the most important tools in the field molecular biology.

Now, AIDS and other retrovirally-transmitted diseases are important enough on their own to merit consideration for a Nobel, but an important development in recent years has made the discovery even more important. Since this virus can insert genetic material, scientists wondered if they could use the virus as a tool to put genes into mammalian cells.

I wouldn't be talking about this if it was unsuccessful. The virus has been extensively genetically engineered to be able to carry genetic payloads into cells that it can infect, without replicating new virus and harming the host. Today, I myself use a heavily modified version of the AIDS virus to insert genes into rat brain cells and perform experiments looking at how certain genes affect the expression of other genes.

The importance in this case wasn't just the discovery of the viral agents, or showing that these agents caused much more serious diseases. These things were vital contributions to medicine. This discovery went on to reverberate through the field of biology and changed the way we do experiments and perform the science. There are few nobler things that could have been honoured.

Soon - the chemistry Nobel, another (related) paradigm-shifter.

Thursday, October 9, 2008

Fair is fair - Science Under Harper

So it's been awhile. I've been restraining myself because what I really want to write about is the election next week and the US subprime crisis. But I write about science, mostly (go Habs go), and so have tried to avoid these topics, which then keep me from writing. Which brings me to a summary of Canadian science news during Harper's term as Prime Minister. Election- and science-related, which is a big coup for me.

I could bring up that Harper backed us out of the Kyoto protocol, news about which seems to come up in "Science" sections of the news frequently. Seriously, our response to this relatively slow-moving but incredibly serious threat resembles that of FEMA's to Katrina, i.e. to lay back and hope the problem will blow itself out before anybody has to do anything. Harper's environmental plans are simply awful. I don't know if carbon tax is the right way to go, but Harper's plan will lead to increased emissions. Simple as that. Not that Dion's record on emissions was spectacular as Minister of the Environment, but you have to limit the amount of blame you can put at his feet, as he was only there two years.

I have to mention a positive thing - long deserved tax exemptions for graduate students. Graduate students make very little money - averaging under $20 000 annually - so getting that kickback really makes a difference. Plus, it never made sense to me that our government charged taxes on money they gave my boss in order for me to study. Harper actually increased the number of fellowships available to students - in science, anyways, I don't know about anywhere else - which is pretty good. Harper has given modest increases to funding agencies, but any government will have trouble keeping pace with the Chretien Liberals, who did things like increase the budget of the Canadian Institute for Health Research from $289 million to $666 million over 6 years, which is a stunning feat.

Another big thing that Harper got press for was dropping the position of National Science Advisor. This got him condemned by Nature, one of the most important journals in the world. They readily admit that the post was woefully underpowered and underfunded upon its creation by the Liberals, but relegating it from direct Prime Ministerial interaction to a subdivision of some Ministry, and then phasing it out for the Science, Technology and Innovation Council wasn't a step forward. This represents a typically Canadian approach to politics - create 18 jobs where one would do, and give at least 9 to your friends.

But then there some other things I wasn't a fan of. Him opposing safe injection sites when there's a pile of evidence they work. Health Canada started calling for them as early as 2002, and Harper wants to eliminate those few that exist. This is an example where the Prime Minister is refusing to let science shape policy. Him firing the head of the nuclear commission when she shut down a potentially unsafe Chalk River nuclear plant. His then-Environment Minister Rona Ambrose engaging in a little old-fashioned Big Brother-type censorship.

All in all, I think science and technology would fare better under someone that wasn't Harper, and allows science to have a role informing policy, and doesn't engage in downright lying and bullying to advance their agenda. Science should change your policies - it apports new information. That's what it's for, and why the government funds billions in research and development projects. The least we can ask our politicians to do is to take some return from that investment.

Next week - the Nobel Prizes.

Tuesday, September 9, 2008

Genome or Playstation? Hmmm...

Well, we're still here, so the LHC hasn't destroyed the universe... yet. Good news.

Recently there was some not so good news for people who deposited their genetic information (not that way!) into public databases - there is some concern that this information can be tracked back to individuals. This doesn't seem like such a big deal, and it won't be until one day we apply for life insurance and they tell us, "Well, we found your genome online and it looks like you have a 10-fold elevation in your risk for contracting the hoobajabbies within the next 11.6 years, so we're going to need to increase your premiums." Seems a little science-fiction and Big Brother, until you find out that 23andMe (who I've talked about before) can now "sequence your genome" for the same price as a Playstation 3.

Now, I say sequence in quotation marks because they don't really sequence the whole thing, which so far only Craig Venter can really do, at the cost of tens of millions of US dollars. Before the currency started plummeting. Only two people have a data file containing their whole genomes at this point, and they are Dr. Venter and James Watson, and even what they have is a "best guess" from a computer-guided reassembly of their whole genomes from sequenced fragments.

The As, Cs, Ts, and Gs that make up your DNA are known as nucleotides, and there known places where there are differences in the population. These are known as single nucleotide polymorphisms (SNPs), and we have discovered thousands of them. Some of them are even associated with certain (real) diseases, although these studies represent correlations rather than causes. Still, insurance companies calculate premiums based on actuarial tables - statistical correlations - and I don't want them exploiting a $400 sequencing service to make a couple bucks by nailing people who happen to be born with a couple bad nucleotides.

I am seriously impressed that our legislators have already been thinking about this, but clicking on the government link for information about genetic discrimination legislation gets 404'd, which leads me to be believe that it's not exactly a hot issue these days. Like puffin poop.

Sunday, September 7, 2008

The End of the World?

The Large Hadron Collider comes online Monday and starts doing weird things that the universe hasn't seen happen to its particles since around the Big Bang, apparently. For an easy-to-follow lay explanation, see this link, which beats the hell out of the biology songs cropping up on YouTube. Some are arguing that this thing could end our world by creating black holes on the planetary surface, but I feel that if black holes were that easy to make, we'd have them in our backyards. Or maybe that's where lost dryer socks really go.

In a similar vein, it's also the end of the longest minority government ever in Canadian history, as Stephen Harper asked Michaelle Jean to dissolve the Parliament this morning. We'll head to the polls for another election on the 14th of October - the 3rd time in 11 years - and we'll end up with another Conservative minority. Harper's strategy must have something to do with massive turkey consumption influencing voter choices, as last time we had elections just after Christmas.

This blog will get hijacked by incredibly amusing (and potentially vindictive and offensive) political tales every once in a while, because election time is my favourite. We'll start by ripping into David Emerson, the shifty representative from Vancouver who crossed the floor 2 weeks after being re-elected as a Liberal in his traditionally left-wing riding. His quotes in the CBC's article are gold - "I was never a Liberal," he says, seemingly forgetting the years 2004-2006 and missing the signs festooned around his riding during both those elections proclaiming him as a Liberal candidate. "I think I had a good shot at winning [this election]," he speculated, although a Conservative hasn't been elected in that riding since 1958, and his own Conservative opponent in 2006 finished 7, 000 votes behind the 2nd-place NPD candidate.

A particularly astute commenter on the CBC site theorizes that, although Emerson says he's leaving politics because of the commute from Vancouver to Ottawa, Harper will appoint Emerson to the Senate and his Cabinet, much like he did with Michael Fortier in 2006. Although I'm not sure that he'll end up as a Minster again, I think Harper will push Senate reform to the back-burner of this election campaign, and there will be another Senate appointment when he wins another minority. After all, it's not like Emerson would even have to show up for that job...


I don't have a lot to say on science today, although it was kind of gratifying to see an entire issue of Nature devoted to "Big Data" and its impact on science, which I touched on months ago. More on this to come later in the week, with incisive political commentary on the mousiness of Stephane Dion.

Another interesting tidbit - a huge ice shelf has broken free of our very own Ellesmere Island (the big one in the Arctic beside Greenland). This is not only just a sign of global warming and the problems we can expect, but also a none-too-subtle reminder that the fabled Northwest Passage will soon be open for business. We don't tend to think that much about borders in this country, but we definitely have them, and there is definitely territory under dispute in the Arctic between ourselves and the USA, Russia, and Denmark. Most of these disputed borders are in areas close to the Northwest Passage, and will become the subject of heated diplomacy between our countries as the prospect of profiting from goods shipped through this nautical shortcut to the Panama Canal becomes a reality.

Tuesday, September 2, 2008

We are nihilists, Lebowski! We care for nothing!

I commented a while ago on something that Dean Ornish calls genetic nihilism, a great turn of phrase that I will deftly procure for myself. This is a sort of view in which we say "well, my DNA has already programmed my health and/or behaviour, whether I will get diabetes or cancer or an aneurysm while doing backstroke in the community pool." Which, in addition to being untrue, is a pretty irresponsible way to live.

I thought of it because of a Swedish study showing that the presence of a certain variant of a gene in males is associated with increased prevalence of "marital crisis" in the last 12 months, reduced proportions in number of men married, and lower scores on a sort of "pair-bonding index." And the headlines were awesome - "Why men cheat" (Science Magazine), or "Commitment phobes can blame genes" (BBC). These are great examples of genetic nihilism. We are expected to take it at face value that men fear commitment and cheat on their wives and girlfriends, and furthermore that these are parts of being male programmed into DNA as much as a penis is, so we should be able to find a gene that makes it so.

No one is ever going to find that gene, because it doesn't exist (along with the "penis gene"). The authors of this study do some fancy calculations and say that about 28% of the variation they saw in the study were inheritable from their parents. Now, I'm going to say that heritability is not just a question of genes being passed down, and if you want to argue about that let me know. The rest is from "environmental factors," which is to say everything other than your parents.

We have roughly 25 000 protein-coding genes in our cells. Let's say 1% are involved in mating behaviour, which is probably a ridiculous underestimate given the importance of mating to continuing the species. That's 250 genes involved in mating behaviours, which are only the genetic part of their heritability measure, which in turn only accounted for about 28% of the variation in the study. While some of these genes might be more important than others, the assertion that a different version of a single gene will double your chances of being unmarried or in a turbulent relationship seems unlikely at best.

This study does have an interesting design, however, involving some 500 same-sex twins both married and unmarried. I hope they run some fishing trips (technical term: gene microarray) looking at polymorphisms on other genes that might be related.

Sunday, August 24, 2008

Best addresses and more

So, apart from having the best corporate domain name (, street address (1 DNA Way) and stock symbol (DNA), Genentech is also doing some excellent science. Antibodies are used ubiquitously in pretty much any biology involving proteins - commercially available antibodies are supposedly highly specific for their target proteins, although inconsistencies in the quality of reagents is a huge problem. I use them regularly for identification and/or manipulation of proteins, and a paper this month is using antibody-conjugated toxins to kill cancer cells.

Now, this is pretty awesome, and the antibodies approved for clinical use are far better than almost all of the of the commercially available "research-only" types. By "better," what I mean is that they are more specific for their targets - ideally, they would bind to that target and nothing else, i.e. an infinite signal:noise ratio. In practice, this is almost impossible, as there is always some random "non-specific binding," but the clinical antibodies are as close as it gets.

As with all biological molecules, their structure dictates their function. For an antibody, the structure of a certain part will determine what protein it will bind. What this team has done is to engineer changes into another part, without changing the protein-recognizing structure. These changes will allow biochemists to tack various useful things onto the antibody, like cytotoxins or fluorescent tags. This is good news for biology, as the antibodies used in research are not as good as they could be. More developments in antibodies as tools will, in the long run, mean improvements to their protein recognition abilities as interest revitalizes investment, and would overall be a good thing for biological science as a whole.


Some Canadian news:
  • Health Canada flexed its regulatory muscle to clean two natural health products off the shelves. Life Choice Ephedrine HCL is getting yanked for having way too much ephedrine in it, which is not very good for you and is also contaminated by a nasty strain of bacteria(!). Life Choice Kava is getting pulled for liver toxicity, which is also a pretty good reason. Compounds marketed as homeopathic drugs are not always subject to the same quality-control tests as pharmaceuticals, which in this case ended up being a bit scary. Interestingly, the "Standards and Ethics" section of the website for the Canadian Association for Naturopathic Doctors is "currently being updated."
  • Canada comes up short on OECD standards for medical imaging machines per capita. While we have have increased our tally significantly over the last 4 years, we have roughly 12 CT scanners and 6 MRI machines per million people, well-short of the average 15 and 7. The Brazilian working in my lab was told that he could get on a waiting list to have an MRI on his knee here in Montreal, but if he was going back to Brazil in the next 6 months, he would get it done there quicker. To me, this raises serious questions about accessibility to health care in urban centres, let alone the beleaguered rural areas...

Tuesday, August 19, 2008

Working out in my chair, reading minds.

So there's been a fair amount of talk lately in the news about how the US defense department special forces researchers are trying to read minds. It shouldn't be a surprise that DARPA is funding research like this, people have been trying it for years (to take a Canadian example, read up on the MKULTRA experiments performed for the CIA at McGill). This is pretty science-fiction so far, but there has been some limited success recently in the literature, where a computer can choose which of a small set of nouns the subject is thinking of.

Now, if you look into it closely, mind-reading is still fundamentally impractical and therfore nothing to worry about. In addition to large, unwieldy and highly sensitive machines, you also need a coherent and compliant subject, and a ton of scan data from that subject - just to achieve the aforementioned limited success. So far, anyways. Expect this research to continue, because it doesn't seem to be a question of "if," but of "when." Legislators should be thinking on seemingly SF topics like mind reading and control already, but probably won't until it's in the courts. "What do you mean, you read her mind?!"

  • Interesting news showing that smoking is probably responsible for less "smoking-related illness" than I thought. My favourite part: "Dellinger noted, however, that one would have to smoke about 300 cigarettes a day to be exposed to the same level of environmental free radicals found in moderately polluted air."
  • Canadian researchers figure out how to program stem cells to develop one step (and only one step) into a certain route towards specialization. This is interesting because it will help lead to the transformation of stem cells into useful, transplantable tools and maybe even allow the production of things like skin grafts or whole livers in culture dishes.
  • Finally, a real use for chemistry and materials science - what may become a seminal work on hair care is released by German researchers. If they get public money for that, I'll consider doing some research there on something appropriately scientific involving beer after my doctorate.

We are now seeing the first drugs in what will no doubt one day be a multibillion dollar industry: exercise mimetics. These compounds, which got huge exposure in a Cell paper released last month, work in muscles to improve endurance. The data are really interesting, and some is pretty stunning. First, they use a drug that activated gene expression in a way similar to exercise. However, they didn't see any difference in endurance with just drug treatment. However, by training the mice to run for increasing time at increasing speed over several weeks, they found that the combination of exercise and the drug allowed dramatically increased running times (3.5 hours vs. 2) and distance covered (about 3 km vs. 1.8) compared to mice that only got exercise. Interestingly, the combination of the treatments activated some gene expression that neither exercise or drug alone did, suggesting at the very least some new performance-enhancing drug targets.

They go downstream on the biochemical cascade one step and manage to induce increases in endurance - without exercise this time. However, the running tests were much different - they took completely untrained mice, who could run only about 30 minutes (40 after drug treatment) and cover only about 400 m (around 550 m after the drug). While this is a much more modest effect (and probably wasn't additive with exercise, or they'd have shown data on it), it is very interesting to see the induction of some effects of exercise through only pharmacological means. However, it remains highly unlikely that we will be able to reproduce all the benefits of real exercise with chemistry. I mean, we're still working on bad hair days...

Saturday, August 16, 2008

Robot brains closer than Sundin decision?

Back from vacation a week ago, and now trying to learn an important lesson about writing - I've been trying to work on a piece about personal genomics for a while now, but it just won't materialize. I have been dreading trying to get it done, because it's discouraging to look at something you put effort and thought into and you end up hating. It occurs to me that it doesn't matter, because I can write something else. I'm sure there has been enough interesting stuff published in the last 2 weeks. Although none of it is about Sundin, which is getting pretty irritating. We can try to laugh it off with this gem, forwarded by a friend (thanks, CT). An illustration of why science education is important to everyone (parents: please don't let your kids grow up to be like this woman). What kind of crazy, awful thing must we have done to our Earth to make some substance come out of the ground and make a rainbow in the sprinkler on my front lawn?!!! We all know that didn't happen 20 years ago!

Sadly, I wish I could say that this is probably a unique case, but I don't believe that for a second.

* * *

Bits of news - The FDA has dismissed claims that the trace amounts of bisphenol A (BPA) that leach into our drinks (and into baby bottles) are in any way harmful. BPA is some pretty nasty stuff, but then so are plenty of things we find in trace amounts in our environments. Still, I appreciate the Canadian government's willingness to err on the side of caution and ban its use in products for children.

A shameless plug for a study out of the Institute where I work: Mothers that were pregnant during the huge ice storm of 1998 have kids that are developmentally delayed 5 years later. The babies are slightly smaller, and have a slightly lower IQ than average. On the bright side, other studies have shown that these kids will probably "catch up" to their peers by adolescence. Interestingly, the way that the mother responded to the stress didn't seem to matter - just the presence of the stress itself seemed to impact the development of the child. The primary investigators will continue to follow the children through their lives.

* * *

Frickin' robot brains, man!!! They're getting closer and closer. This is upsetting because I will lose one of my euphemisms for human error/incompetence in the lab ("wetware" problems), but actually really cool to see. This video shows a guy who is using randomly-assembled networks of actual neurons to drive a robot to learn about its environment. I really can't wait for this guy to publish, because this is nowhere near detailed enough for me. He might even be something to consider investing in, once he has a startup. If I were to get back into electrophysiology, this exactly the sort of thing I'd love to do.

In a diametrically-opposed approach, another group has a computer model of something like a brain. This model is "given" a virtual body that interacts with its virtual environment, and the neural network figures out how to move itself using the virtual stimuli and the joints and limbs the programmers give it. What is most interesting here is that structure dictates function, and the "robots" just learn to move what they have rather than needing to have complicated steps programmed into them. This will be a huge step in designing computer games at least, but probably in artificial intelligence and robot tech in general.

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.

* * *

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.

* * *

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...

* * *

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.

* * *

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.

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...