Breathing through what?

Following lunch time conversation, which inevitably gravitates towards all things fecally related, I had to check upon the topic of "alternative" breathing strategies. To be able to breathe in water, you need two things: current and large surface area. And it seems some turtles, particularly one living fossil in australia, has just that, in its ass. It has evolved a pair of cloacal bursae lined with villose mucosa and connecting to the cloaca, fully capable of contracting. And it's not even alone in having evolved this particular ability: the dragonfly nymph can use its butt for both breathing and propulsion! For more information on butt-breathers, this article goes into more details...

Publishing at age 91

When physicist and astronomer James Van Allen passed away at age 91, one of the best scientist of our era was gone. I hold much admiration for this man who discovered the radiation belt named after him and who tirelessly strived to educate poeple about the beauty of space and the political elite about its dangers and opportunities. He famously argued against a manned mission to Mars, saying that robots could do more for less. Ultimately Bush's decision was more about politics than science. This nice article outlines this man who despite his age never quit researching and publishing until the very last day because of his love for science.

Bad Parasites

Just ran accross this link.
Check out some of the nastiest parasites on earth.

As a dark matter of fact

I heard a decent Science Friday podcast about String Theroy (audio link) where one of the guests suggests that it's a bunch of mathmatical hooey. I have actually heard the same from physicist graduatuate students. The real problem seems to be that after a very long time fooling around with mathmatical models there still is no experimental evidence for the theory. As I understand it, there are not that many testable predictions that the theory makes.
Blows my mind also that apparently researchers have just finally found proof of dark matter. Wow. The dark matter guys have much better PR or something. I thought dark matter was fact and already proven by observation.

Bacteria Breath

A couple of quick links
I have always been a bit anti-organic food. I do like the idea and small farming as an alternative to commercial farming that emphasises quantitiy and not quality. However, I have worked on an organic farm where I found out that they use copper-sulphate (basically a poison that predates some rule about pesticides so you can use it and still be certified organic). Also you can't feed the world organically which makes it only a solution to rich westerners and therefore seems shortsighted. Also pesticides are constantly getting better and safer and you just can't argue with the fact that (except for maybe rising obesity) we are the healthiest humans that have ever lived on earth. Case in point about improving pesticides... granted it's a press release from UBC but finally they have developed an organic pesticide. I'm sure this is just the begining.
Also somewhat related is this lactobacillus gum for improving dental health. Imagine the lactobacillus flavour explosion!

We be diggin' for treasure!

In an interesting ruling, AOL has been given permission to dig for buried gold and platinum to collect on a court judgement. The company was awarded $12.8M from a convicted spammer and intends to collect by unearthing the buried booty in his parent's yard. Sounds like maybe AOL has been reading too many of those emails from the recently imprisoned Nigerian president. For a mere $1000, part of his fortune could be yours! Also, I have some great penis enlargment products to sell you.

Of Mice and Men bearing tumours

A good article (free access I think) posted on the Nature website focus area on the problems inherent in studing cancer using mouse models. Not a bad read if you've never really thought about some of the more interesting problems. Apparently only 11% of drugs that look good in mice have any effect in humans. The article suggests the only reason we aren't useing the oncomouse is because of patents and that oncomouse would be better than xenografts.

Wikipedia not classy enough for bayblab

We've been booted off wikipedia. Finally.
However, the bayblab's authority can not be denied. Who is the number 10 authority on gleevec cardiac toxicity?

IA updates

Man, I've been jonesing for some IA updates and here they are. Highlights include a link to info on the latest hack, the XBox360. Awesome.

The land of volcanoes

As I blog this I'm on the road to Iceland's highest summit, typing away on a blackberry. The scenery is impressive, volcanoes and glaciers. Vents everywhere spew out hot smoke and boiling water. People here take advantage of this and huge steel pipes bring the free hot water to the capital. It makes the showers stinky. The hot water was welcomed after a 4 day hike from landmanalaugar to thorsmork. (You can follow us at icelandtrip.wikispaces.com and click jp travelog, or check out more photos here)

Predicting Nature papers

A while back I did a journal club about microRNAs predicted to be expressed by viruses. Pretty much all of it was computational prediction. A new Nature paper (link to summary) shows that HSV-1 inhibits neuronal death during a latent infection through a microRNA mechansim inhibiting TGF-B and SMAD3 validating my journal club as worthwhile. These genes are central targets but the paper points to a great unbiased approach to find key genes. Viral microRNAs must have evolved to target some pretty important genes. Interesting to see what will be next.

Exercise Myths

Wicked Quirks and Quarks podcast this week where they talk about a myth I have told so many people who didn't believe me that I was beginning to wonder if I had heard it right. Turns out that it true that streching before exercise is not a good idea.
Sucks to your yoga.

Rideau Canal Rider

The bay is a bit toasty today and I was thinking about how EXTREME Ottawa is. The winters are freezing and the summers are ridiculously hot. And so the heat got me thinking about the rideau canal skateway. And I've been doing a lot of biking this summer so I was thinking about pimping out my bike for the longest skating rink in the world. How cool would a skate chopper be?

A Word to the Wise: Colbert's Advice for Scientists-To-Be

Some of the best advice for aspiring young scientists I've seen in a while from a great Wired article by my new all-time hero, Stephen Colbert (check out the vid from his scathing and hilarious address to Bush at the White House Press dinner now if you haven't already.):

1 - PICK A FIELD THAT CAN'T BE VERIFIED
"Try something like string theory...We can't question the expertise of scientists, because we aren't scientists".

2 - CHOOSE A SUBJECT THAT'S ACTUALLY SECRET
"Anybody who attacks the secret subject is, by definition, part of the cabal."

3 - BE SURE TO USE LOTS OF ABBREVIATIONS AND ACRONYMS
"Real experts don’t have time for extra syllables."

4 - SPEAK FROM THE BALLS, NOT FROM THE DIAPHRAGM
"In America, you’ve got to steer clear of nuance and ambivalence – and don’t even contemplate doubt."
(That's right!...and definitely not from the ovaries).

5 - DON'T BE AFRAID TO MAKE THINGS UP
"Experts make things up all the time. They’re qualified to."

6 - DON'T LIMIT YOURSELF TO CURRENT KNOWLEDGE
"If you worry too much about being up-to-date, you miss out on vast territories of obsolete knowledge just waiting to be reclaimed."

7 - GET AN HONORARY PHD
"All I did was give a speech, and now everybody has to call me Dr. Colbert."
(Probably taken more seriously than a real one.)

8 - MAKE A HABIT OF NAME-DROPPING
(So I was talking granulosa cells with Ken the other day...)

9 - BE FAMOUS. IT HELPS.
(The name of the game, and the only way to have half a chance at feeding yourself by doing science.)

Flying Spaghetti Monster hate mail

Resident bayblabbers will be familliar with pastafarian beliefs. Here comes the hate mail section, for endless hours of laughter at some fundamentalists who take this way too seriously. From the site: "you are a stupid little guy with no girlfriend, so you're depressed. writing about your fake, gay loving man whore god. to get attention. all its gonna get you is a foot so far up your a** your gonna have ingrown toenails growin out your ears. you need to stop this stuff. all you're doing is getting yourself closer and closer and closer. to hell. not heaven. not paradise. not getting laid. not having children. not having a penis. nothing. shut the heck up already. no one likes you..except your gay friends who believe all this stupid crap. and whoever they are.. i hope they use protection with eachother, along with you. tonight. oh by the way. i am having spaghetti and meatballs tonight u little prick. i think i will just throw it in the trash cause thats where it belongs. along with your fake whack religion and fake god. so have a nice day, and hope u have fun gettin raped by your spaghetti and meatball, FAKE god."

VSV contradicts evolution?

I personally don't find structure papers very interesting. I bet they are facinating if you are in the field, however, for biology they seem to have little relevance. I ran accross this great article in Science talking about the recent crystal structure of the VSV glycoprotein (AAAS access required) and how it is way too similar to a glycoprotein from HSV. Apparently this raises questions about virus evolution because VSV and HSV are nothing alike, except apparently in the three dimensional structure of one protein that contains is no amino acid sequence similarity. I couldn't believe they didn't even mention the possibility of some sort of convergent evolution. They do say something about 'gene capture', something I've never heard of but assume they are speaking of horizontal gene transfer.
BTW blogger is terrible and not uploading images.

An alternative to FACS

Finally an application of nanotechnology we can really use. Better and more precise cell sorting using magnetic nano-particles and microfluidics on a chip! you can tell these guys aren't biologists though, embarassingly, in the abstract they don't even know what HeLa cells are.

Learning while being distracted

I am definately guilty on that one, I find I can listen without really paying atttention and still remember stuff afterwards. Well it turns out that when you are focused on one task you use declarative memory (memories that can conciously be discussed). But when you multitask, you use a combination of declarative and procedural (i.e. "task oriented") memories and a totally different part of your brain. It has the advantage of being harder to forget (e.g. riding your bike), but less flexible to apply to new conditions... So according to this study in PNAS , ADD may not be all bad...

LAN Partying Prevents Alzheimer's, Parkinson's?

Further proof that there's no need to be taking untested drugs with unknown side effects to combat age-related illness. What the drug companies aren't telling you is that the cure for neurodegenerative disease is video games, and the only side effects are bug-eyes, butt sores, a bit of carpal tunnel syndrome, a caffeine hangover, total loss of coolness and a tendency toward violent behaviour. And yes, it's free. (Ok so the link hasn't been proven yet, but someone's studying it. Maybe someone would even pay people to have LAN parties...)

Gleevec: Tough on Leukemia, Rough On the Heart?

Imatinib mesylate (or Gleevec), a small-molecule inhibitor of the ABL kinase, is, as we all know, the flagship of the molecularly-targeted cancer therapeutics. According to the Novartis literature (and lots of other people I'm sure) it cures a lot of patients with chronic myeloid leukemias (CMLs) expressing the BCR-ABL gene fusion (ie the famous Philadelphia chromosome). That same literature claims that the drug has no important toxicity, so they apparently didn't notice when patients' hearts started conking out, despite their lack of prior cardiac problems. Some clinicians were paying attention, and they now report on congestive heart failure in 10 patients and cardiotoxicity observed upon adminsitration of gleevec to healthy mice in Nature Medicine. This study highlights the important need to study the potential side effects of new drugs, something that a lot of drug companies financing their development would rather we forget. Not that gleevec should be pulled from the market - CML is obviously a serious and hard-to-treat disease and the benefits might be worth risking the cardiotoxiticy. Then again, heart failure is pretty serious too and the risk might not be worth it. Obviously then what's needed is more detailed and quantitative study of the cardiotoxic risk associated with Gleevec so that clinicians and patients can make the most informed decisions. It's interesting to note that the cardiotoxicity now reported can apparently be observed simply by giving the drug to mice and examining their hearts. It's hard to believe Novartis couldn't have done that during more than a decade of preclinical investigation, but probably typical of the way drug research is currently being carried out. As a result patients are less informed and ultimately the companies themselves risk knee-jerk public reaction and their products getting pulled off the market when bad things start happening. Another important point made here is that even the most well-targeted drugs can have side effects - all the more reason to investigate toxicities as thoroughly as possible and be more open to examining not just the more profitable small molecule drugs, but all other possible types of novel therapeutics.