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.

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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.

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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.