Friday, May 29, 2009

Cow's milk allergy & recombinant proteins

A quick post about stuff I don't understand:
A friend of mine has an infant that is allergic to cow's milk. This is common and, who cares, since the infant is being breast fed. EXCEPT for the fact that the infant is allergic to the dairy products that the mother is consuming. This is somewhat uncommon but certainly not unheard of. My interpretation of this is that a protein antigen not only passes relatively intact from the GI tract of the mother into her blood, but is then incorporated into her breast milk without being completely broken down to amino acids and/or incorporated into human milk proteins. I always thought that proteins were almost completely broken down into, at most, a few amino acids long before absorption. The previous link suggests that relatively intact dietary protein is present in our blood.
Does this lend credibility to those who fear the biological activity from ingested proteins that are introduced into our food artificially as in the case of bovine growth hormone in cow's milk or Bt toxin in GE crops?
Anybody with some helpful information?


Wednesday, May 20, 2009


A new search engine has recently gone online, though Wolfram|Alpha seems more a competitor to Wikipedia than to Google. The idea is to serve as a data search and computational engine.
Wolfram|Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. We aim to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. Our goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries.
It can solve equations for you, tell you notable events for a given date, or give you the current sky position of Pioneer 11. Try typing in your favourite gene, or even your first name. It's a cool little resource. I had fun playing around with inputs to see what it could do.


Tuesday, May 19, 2009

Extreme Mammals at AMNH

I was in New York City (and environs) this past weekend, and was fortunate enough to get an invite to a blogger preview of a new exhibit at the American Museum of Natural History. Unfortunately, my camera battery crapped out on me in the early going but luckily the press kit included in the blogger gift bag had some photos to share, so you won't have to suffer pics taken on a camera phone.

Extreme size: Indricotherium, the largest land mammal known, greets you at the exhibit's entrance

The exhibit is Extreme Mammals and is put on in collaboration with the California Academy of Sciences, San Francisco; Cleveland Museum of Natural History; and our own Canadian Museum of Nature here in Ottawa.

As you might guess, mammals were the order of the day, from the largest to the smallest and everything in between. And in between was key - the exhibit features fossils and models of some cool transitional forms as well as those of our stranger cousins such as the extinct Macrauchenia or the familiar platypus.

Macrauchenia is straight out of a Star Wars or fantasy movie

Among the fossils, taxidermy samples and models were the stars of the show: a colony of sugar gliders. Though they were napping while we were there (extreme laziness?), the sole live animal display definitely drew a crowd, particularly among the younger attendees. There were also a few simple interactive displays.

Ambulocetus, or "walking whale" is one of the transitional forms on display

The exhibit is unapologetic about evolution, which features heavily in both the displays and the educator guide as they discuss common ancestry, evolutionary trees and adaptation among other things including the requisite 'fun facts' and trivia. Did you know that a new species of striped rabbit was first discovered for sale in an Asian food market? (extreme deliciousness?)

Overall, Extreme Mammals is a cool exhibit, worth checking out if you're in the NYC area where it will be on display at the American Museum of Natural History until January of next year. After that, it will be on tour and if you're patient it's scheduled to arrive in Ottawa June 4 to November 6, 2011.

Local content: Puijila darwini, an early fin-footed mammal, was discovered in 2007 by a researcher from the Canadian Museum of Nature, Ottawa

Thanks to Brian from Laelaps who put me in touch with the museum for the blogger preview.

Images © AMNH


Wednesday, May 13, 2009


Was looking at this article on the booming market for renting virtual office space for small business.

"I wanted to launch my company, but the cost of having a professional location was simply too high," says Mr. Gerochi. "This gave me the push to do it. I pay $300 a month and I can appear big-time to major clients.

"I use their reception staff -- they take all my calls -- office space, mailing service. The building address is advantageous. It's more professional than a home address and filters out unwanted solicitation. I can rent a cubicle for $15 an hour or a window office on the 57th floor at First Canadian Place in Toronto for $25 an hour instead of sitting in the food court with my laptop." He also uses the boardroom ($70/hour) to network with industry leaders."

Great way for entrepreneurs to overcome crippling infrastructure and basic staffing costs. It occurs to me that even higher infrastructure and start-up equipment costs pose a similar huge obstacle to the would-be biotech entrepreneur. Research space is like office space, except way more high-tech and costly. Rental lab space sounds like a great solution. Does your institute have any empty lab bays or equipment sitting unused? Let's see that shit up on Craigslist. Starving PhDs with great ideas are ready to put it to good use. You could even sell off those unused technical support staff people-hours. Like lunch.

Oh, cool. Apprently you can already do something like this. Like here. Not to be confused with here.


Kids! Sue your parents for defective genes!

This story is a bit old, and a bit odd. A 13-year-old girl born with Fragile X syndrome is suing a sperm bank after genetic tests showed the genetic condition was carried on the father's X chromosome. (Weirdness about a girl inheriting an X-linked condition from her father, and a Fragile X male as a sperm donor explained here. The short version is that it's a spectrum, repeat-expansion disease whose severity varies from generation to generation so a mildly affected father could have a more severely affected daughter, though it's rare)

The legal premise is based on product liability law that is usually applied to manufacturer defects such as faulty car brakes
Donovan does not have to show that Idant was negligent, only that the sperm it provided was unsafe and caused injury. "It doesn't matter how much care was taken," says Daniel Thistle, the lawyer representing Donovan, based in Philadelphia, Pennsylvania. Genetic tests have revealed that she inherited the disorder from her biological father.
The idea of sperm as a commodity subject to product liability laws raises some interesting questions. In this age of personal genomes and genetic testing, how much responsibility does a sperm bank have to screen for genetic disorders with every available test? If a child inherits Fragile X the old-fashioned way, could they sue their parents?

Should genetic disease even be considered 'injury' for the purposes of legal liability? This is quite different from suing a car manufacturer after suffering an injury caused by defective brakes. No defective brakes and you make it to your destination without a crash and a broken leg. No 'defective' sperm and you don't exist at all.

Either way, as more and more genetic tests come into existence and screening becomes more available there will be interesting legal issues to navigate. I should have gone to law school!


Tuesday, May 12, 2009

Systems Tumor Immunology: It's Big Blue Beats Kasparov All Over Again

One innovative approach to cancer therapy involves isolating immune cells (tumor-infiltrating lymphocytes or TILs) from a tumor, and then trying to expand and activate them against tumor antigens in the lab. It can work, but in practice, not an efficient practice. TILs are a mixed bag of cells with all sorts of different personalities, some of which may or may or not be interested in attacking tumor cells. Some, recruited by the ever-devious tumor cells, can even work to supress the activity of the good guys. So sometimes you get a bunch of TILs that work, sometimes not.

A new paper describes a systems biology approach to tackling the complexity of TIL populations with the aim of predicting anti-tumor activity. They profiled the reactivity of a ton of TIL populations, and correlated this inforamtion with a battery of surface markers. They fed the info into some sort of machine learning algorithim, which came up with some pretty clear-cut boolean style predictive rules that a mere organic being (aka tumor immunologist) could never have possibly concieved of with a million years of deductive reasoning and experimental testing.

Check it out:
Rule 1) If the CD8+CD28-CD152- subpopulation constitutes less than 43% of the entire TIL population AND the CD94+constitutes less than 0.4% of the entire TIL population, then the TIL population is tumor-reactive.

Also, by manipulating the relative proportions of different TIL subpopulations, they could affect reactivity as predicted by their adding machine.

Wicked. Who knew an abacus could do immunology?

See: Predicting and controlling the reactivity of immune cell populations against cancer


Monday, May 11, 2009

Nature Editors Still Concerned About Swine Flu

To their credit, they lay down some numbers. Most compelling, on the surface, is the following statement:

"There is ample reason for concern: a new flu virus has emerged to which humans have no immunity, and it is spreading from person to person. That has happened only three times in the past century."

That sounds kinda scary. Is it accurate? Would we have recognized the current H1N1 epidemic in its current form 100 years ago? Pinpointing flu strains down to the molecular level in thousands of patients worldwide, and integrated monitoring on the internet in real-time? It doesn't really seem reasonable to conclude there have only been three epidemics of this sort in the past century. Is our picture of the current, largely non-lethal flu epidemic not based entirely on technological revolutions of the past several years? How many swine or bird flu "pandemics" have gone totally unrecognized because of technological limitations? I guess we'll never know. Just like we have no idea when or if the swine flu will turn into some sort of apocalypse as most of the mainstream media would have had you believe a couple weeks ago. Of course there's always a chance. Like getting struck by lighting. Does anyone have the balls to put some numbers on this shit? I certainly don't.

I'd be surprised if our ability to predict the time of occurrence of a deadly flu pandemic has changed appreciably since 1909. How about we all agree that vigilant monitoring (as we are clearly already seeing) and balanced communication with the public (as we are often lacking) are important and leave the predictions, doomsday or otherwise, to Nostradamus?

See: Between A Virus and Hard Place


Thursday, May 07, 2009

exhaustion hunt

I've read before about how the human body is supposedly evolved for running and that the earliest form of hunting may have been running after the prey until it collapsed of exhaustion. I always found that hard to believe. Why invest so much energy into a big brain when your survival depends on your ability to sweat and your endurance. But this video is simply amazing. I never imagined humans could be so much physically superior to other large mammals. Bonus points for David Attenborough narration.


Swine Flu Quote of the Week

"In the United States, Illinois had the most confirmed cases on Wednesday, with 122, surpassing New York with 97. Dr. Besser said that might be because Illinois was testing more. He said that Mayor Michael R. Bloomberg, on a visit to the C.D.C. earlier, had been asked by a reporter why New York had been surpassed, and had answered:

“You want 200 more cases? We’ll test 200 more people.”

More swine flu retrospective:
Global Flu Cases Top the 2,000 Mark


Tuesday, May 05, 2009

On "The Australasian Journal of Bone and Joint Medicine" (aka "The Merck Journal of Advertising Propaganda and other Bullshit"

This is really pathetic. TheScientist reports (Merck published fake journal):

"Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles--most of which presented data favorable to Merck products--that appeared to act solely as marketing tools with no disclosure of company sponsorship."

Elsevier has pulled the journal from its roster, but you can bet there are many more so-called peer-reviewed biomedical journals out there that fit this bill. The only reason we're hearing about this one is that Vioxx gave some Australian guy a heart attack and he's suing.


Swine Flu Hits Ottawa

It's here. Via Mexico. That makes 140 cases in Canada. One girl sent to the ICU, recovering. No deaths.


Sunday, May 03, 2009

Canadian Bacon Is Still Good to Go

Here in Canada we keep a close watch on our pigs. After all, Canadian back bacon is a national symbol. Nothing but the latest in molecular diagnostics for them. They minute they get infected, we know. For H1N1, that moment has arisen, sparking global interest in the fate of our little piggies:

"On Saturday, Canadian health officials said that the virus had been found in sick pigs on one farm in Alberta, the first report of the swine flu’s actually being found in swine. Previously, there had been heated debate about whether the virus could infect pigs, even though its genetic makeup clearly points to its having originated in swine at some point."

Ironically the pig in question got the flu from some dirty human:

"A worker at the farm had traveled to Mexico, fallen ill there and unknowingly brought the disease back to Canada last month. The worker has recovered."

Come on people, let's be a little more careful, this is our national treasure we're talking about. As for you consumers on the international market, not to worry; you can't get the flu from meat. So keep buying Canadian and stuffing your faces with our delicious bacon!

No Signs of Sustained Global Spread of Swine Flu


Friday, May 01, 2009

H1N1 Influenza Alert Upgraded to Level 17: "Bayman Has Concerns (But Mostly For Others)"

  • The number of lab-confirmed cases is still rising, with Bayman's personal hazard ratio jumping up to 367/6,706,993,152 today, up about 6-fold or so since a couple days ago.

  • This strain goes human-to human quite readily, something the wolf-crying bird flu never achieved.
  • It's killed quite a few young people in Mexico. However Bayman suspects its lethality is still waaaay lower than our old friend the bird flu.
  • Some flu people seem to think that making a vaccine could be difficult, as swine flu grows poorly in eggs.

The good news for Bayman: flu season in the northern hemisphere is almost over, so in all likelihood Bayman will get to sit this one out and see what happens in South America, before deciding whether or not to get really scared next winter.

Better information here.


National Cancer Research Month

May is National Cancer Research Month, and what better way to kick it off than with a fresh edition of the Cancer Research Blog Carnival. This month's host is Walter, at HighlightHEALTH, who has done a great job as always. head over there and check it out.

And don't forget, the carnival has subscription options; you can follow by email or RSS feed. An aggregated feed of credible, rotating health and medicine blog carnivals is also available.

Check out past editions here, and drop us a line if you're interested in hosting a future edition.