Friday, July 30, 2010

Mosquito Beer Goggles

It's the time of year when people retreat to campsites and cottages to relax and enjoy a beer on the dock or by the campfire. The only real downside to those kinds of getaways is the bugs.

There are over 2500 different species of mosquito around the world, but sometimes it seems like they've all joined forces to suck us dry unless we arm ourselves with DEET or lasers. And that beer by the lake may not be helping.

A paper just published in PLoS ONE reports that beer drinking makes you more attractive to mosquitoes. (Now if only my beer drinking would make me more attractive to other people) Greg Laden has more.
Researchers working in Burkina Faso recently decided to test the hypothesis that beer drinking would have an effect on mosquito prey preference, and they found that it did. Twenty-five human volunteers drank beer and were explosed to 2,500 A. gambiae mosquitoes, and 18 volunteers drank only water and were exposed to 1,800 A. gambiae mosquitoes (100 mosquitoes per volunteer). The behavior of the mosquitoes was observed, and it was determined that they go after the beer-drinkers preferentially.
As mentioned in the quote, the particular mosquito species being studied was A. gambiae, one of about 40 species that transmit malaria, which is another reason to trade in the beer, perhaps for a gin and tonic.

There was also some speculation as to why beer drinking attracts the bugs. One suggestion is that it might be adaptive: because of impaired reflexes and co-ordination, a mosquito biting a drunk is more likely to survive the encounter.

Personally, I think they're attracted to the increased self-esteem.


Wednesday, July 28, 2010

The Grades Your Grades Could Be Like

Look at this video, now back to me...

If you haven't seen the original, you can watch it here.

[h/t: The Thoughtful Animal]


Thinking About Grad School?

Recently, the BANDIT blog had some kind words to say about us. BANDIT (Biological ANthropology Developing Investigators Troop) has lots of good career advice - how to run a meeting, how to review a manuscript, using new media in the classroom, etc. One post, in particular, (and the accompanying guide) is a must-read for people considering graduate school. While the focus is on studying biological anthropology, most of it can be generalized to other fields. It's good advice, and the kind of advice that many people don't get when considering graduate school.

What are you still doing here? Go check it out.


Sunday, July 25, 2010

Five Years

Bayblab is 5 years old today! Party!

Thanks to our readers, all 4 of you. If you're new, go enjoy our first ever post. There's a lot of catching up to do.


Thursday, July 22, 2010

Direct-to-Consumer Genetic Testing Takes a Blow

That entire genomes can be sequenced, and the prices of those services continue to drop, is pretty exciting stuff. It also presents some unique opportunities for science education, explaining what results mean and how they should be interpreted. Of course, like with any new technology, there are opportunities for abuse and potential need for regulation, for example genetic discrimination by insurance companies, fears of which resulted in the Genetic Information Non-discrimination Act (GINA).

US Congress has been having hearings on direct-to-consumer genetic testing, and part of the fallout was this video:

The recordings were part of a government investigation and some of that is pretty damning. Or at least a very strong case for properly trained customer service representatives. It also underlines a need for proper pre- and post-test counseling.

Daniel MacArthur at Genomes Unzipped has a more in depth look at the full hearing proceedings, but puts things into perspective:
But overall, the document is obscenely one-sided. It conflates responsible companies offering scientifically valid products with small-time con artists. It ignores the remarkable effort that has been expended on creating intuitive interfaces that allow consumers to grasp complex risk predictions far more easily than anything you’ve seen in a GP’s practice. It ignores the remarkable technical accuracy of the companies’ products, which measure hundreds of thousands of genetic markers with an accuracy over 99.99%. It ignores the fact that the vast majority of personal genomics customers are satisfied with the experience, to the point that reporters seeking to present negative experiences need to exaggerate to do so.


Friday, July 16, 2010

Awesome Bird Videos

Enjoy a couple of videos of some impressive birds. First, the Superb Lyrebird. This may have been posted before, but I couldn't find it and it's worth seeing again. Narrated by the incomparable David Attenborough.

Next, a shapeshifting owl, responding to potential threats:

There's some discussion as to what the purpose of the second, "dracula" form is here. Either way, I'll probably have nightmares.


Thursday, July 15, 2010

Merck Frosst shutting down Canadian research

Merck Frosst's research facility located near Montreal and a significant influence for some of us here at the Bayblab is being shut down. Good luck to all those now looking for other opportunities.


Grad Student Documentary

A pretty well produced full length documentary on producing scientists in a life science lab, called Naturally Obsessed is available here. I haven't watched it all yet.


The Human Ecosystem

We've written before about the microbiome and fecal transplants. Carl Zimmer has a great piece in the New York Times about the human body as an ecosystem for microbes and the various ways we interact with them: "How Microbes Defend and Define Us". A snippet:
Some microbes can only survive in one part of the body, while others are more cosmopolitan. And the species found in one person’s body may be missing from another’s. Out of the 500 to 1,000 species of microbes identified in people’s mouths, for example, only about 100 to 200 live in any one person’s mouth at any given moment. Only 13 percent of the species on two people’s hands are the same. Only 17 percent of the species living on one person’s left hand also live on the right one.
Read the whole thing.

[h/t: Why Evolution is True]


Wednesday, July 14, 2010


Jason Goldman at The Thoughtful Animal has a post up about a pretty fun paper on the subject of contagious yawning. We're all familiar with the phenomenon: you see me yawn, then you yawn, etc. This paper documents contagious yawning between humans and dogs. That's right, zoonotic yawning!
The yawning condition made the dogs yawn for 21 out of 29 individuals, and none of the dogs yawned in the control condition. Further, no yawns were observed in the interval between the two conditions (there was a five minute break between each of the five-minute-long conditions). During the yawning condition, dogs yawned an average of 1.9 times, and there were no sex or age differences, and there was no effect of the order in which the conditions were presented.
One of the hypotheses for contagious yawning is empathy
it actually turns out that there is a correlation between the susceptibility for contagious yawning and self-reported empathy. Converging evidence for the empathy hypothesis comes from the fact that contagious yawning is absent in individuals with autism spectrum disorder.
Does this mean dogs have empathy towards humans, or is it just a response to mild tension (eg. to seeing teeth baring)? Can humans catch a dog yawn?


Tuesday, July 13, 2010

'Cool' vaccines

We all know the usefulness of certain thermophiles (I'm looking at you, Taq polymerase), but up here in Canada, with our vast arctic tundra, we should be looking for uses for cold-loving organisms - a resource we're more likely to have in abundance.

A group at the University of Victoria has done just that, using genes psychrophilic bacteria to develop temperature-sensitive vaccines.
One at a time, the team swapped out nine so-called essential genes—involved, for instance, in DNA repair or cell division—in F. novicida for their counterparts from Arctic bacteria, such as Colwellia psychrerythraea, a marine microbe that lives in polar waters and ice. Francisella normally dies at 45˚C; introducing the cold-loving genes lowered that threshold by up to 12˚C, depending on the gene and the species it was borrowed from.

When the researchers injected these altered strains into the relatively cool tails of rats, they found that the microbes reproduced locally but didn't spread to the warmer spleen and lungs, where they would normally replicate as well. The key test was whether the strains could act as vaccines. F. novicida is lethal to mice, but when the researchers injected the temperature-sensitive strains, the animals didn't get sick—and they were protected from an otherwise fatal dose of the unaltered F. novicida given 3 weeks later. [Source]
The idea for a temperature-sensitive vaccine is already out there, with a particular flu vaccine capable of replicating in the throat and nose, but not the lungs. The goal is to create safer live vaccines, but could be put to other uses such as study of dangerous pathogens by creating versions that can't replicate in the warm human body, possibly reducing the need for the strict containment measures to keep researchers safe.

The full research article is available free from PNAS.


Friday, July 09, 2010

Science: Brought to you by Pepsi

If you've been watching the blogs this week, you may have noticed an uproar at ScienceBlogs over a new corporate blog, Food Frontiers paid for and featuring bloggers from PepsiCo's R&D department.

In some ways, this was a cool idea. There's a lot of food science that we don't hear about, and it would be fascinating to get a glimpse, even through a filter, of what kind of stuff is being done by the R&D department of a major multinational. After all, they have scientists and do research too. Better Off Ted was a great sitcom, but somehow I don't think weaponizing pumpkins is really typical of what goes on.

In other ways, it was a terrible idea. Or at least badly implemented. Part of the mission of the blog was to discuss advances in nutrition and health policy. There's an obvious conflict of interest here for a purveyor of junk food. This source of potential bias, and the concern that this might simply be a propaganda arm for Pepsi loomed over the project.

Whether the blog would be more the former or the later (or some [un]acceptable mix), we'll never know. Several ScienceBloggers took issue, and made a fuss threatening to leave the network (and in some cases following through). Others took a wait-and-see approach. After all, this all happened before any real content appeared on the offending blog. Sb admin scrambled to fix the mess, first changing the format so it was more obviously paid content but eventually scrapping the whole thing.

A round-up of ScienceBlogs posts about the Pepsi fiasco, including admin response can be found here (scroll down)

A list of bloggers leaving the network (and new digs) is being maintained here.

The role of industry at a collective like ScienceBlogs, and how to properly include them is a complicated and interesting issue. As made clear by the range of responses to the initial introduction of the Pepsiblog, not an easy one to get people to agree on.


Gender Imbalance in Science

There is a gender imbalance in science. This is most obvious when looking at math, physics or engineering programs. It's easy to look around biomedical labs, see the number of women, and assume this isn't a problem for the biological sciences. And indeed, in the biological sciences, women make up 62% of bachelor's recipients and 56% of graduate students1. Beyond that, the numbers drop off for a number of reasons. Again, in the biological sciences, only 41% of postdoctoral fellows, 33% of tenure-track and 22% of tenured scientists are women. (Nevermind the fact that their salaries also tend to be lower)

Those numbers are pretty shameful. Some might argue that it doesn't matter, as long as the science being done is good (though I'm really not sure who they might be). The problem is, it isn't. Even the research being done is gender biased, as highlighted by a series of recent editorials in Nature. The first points out that there's a gender bias in clinical trials: except for a few key areas (eg. breast, cervical or ovarian cancers) women are underrepresented
Generally, women remain underrepresented in biomedical research. Studies published in 2000 and in 2008 concluded that women were still not included in mixed-sex cardiovascular trials in numbers that reflect the disease prevalence among the general population. A survey of studies published in 2004 in nine influential medical journals found that only 37% of participants were women (24% when restricted to drug trials), and only 13% of studies analysed data by sex.
It's no secret that women and men have different physiologies, and can be differently affected by diseases and their treatments. So why should sex differences not be considered when designing a clinical trial? You can't treat differently if you don't know the differences, and even where gender is known to affect outcomes, there's still no difference in treatment
A 2005 study of 300 new drug applications between 1995 and 2000 found that even those drugs that showed substantial differences in how they were absorbed, metabolized and excreted by men and women had no sex-specific dosage recommendations on their labels. This may be part of the reason why women are 1.5 times more likely to develop an adverse reaction to prescription drugs than men.
And if you're a pregnant woman, it gets even worse. You're forced to either forego treatment or potentially settle for drugs of unknown effectiveness or safety (for you or the fetus), since pregnant women are usually excluded from trials and new drugs are often not approved for them. This despite the obvious fact, that the second article points out, that "pregnant women get sick, and sick women get pregnant." Obviously diving right into clinical trials with pregnant women is a bit risky, in no small part for the fetus (though a controlled clinical trial is probably still safer than rolling the dice with off-label use), but there are ways this can be approached.
There is an obvious alternative: small, well-designed trials for pregnant women, starting with phase I safety trials that would begin at the same time as phase III efficacy trials in the general population. With this staggered approach, pregnant women and fetuses would not be exposed to any compounds that failed in phase I and II trials.
This strategy is simple, and makes sense: it allows pregnant women the same standard of evidence-based care afforded to everybody else (even better, if you consider the lack of sex consideration described above), accounting for their own particular changes while mitigating risk.

Most surprising, to me at least, is the fact that gender bias even extends to animal models. In some ways, it makes sense to keep models simple and avoid potential complications from hormone cycles. Depsite the fact that male mice tend to fight when caged together and single housing takes both space and money, a survey of 2000 studies done in 2009 found a male bias in animals used.
We found a male bias in 8 out of 10 biological disciplines, most pronounced in neuroscience (5.5 males to 1 female), pharmacology (5 males to 1 female) and physiology (3.7 males to 1 female).
Though this might be more convenient or have a practical rationale, it doesn't necessarily result in the best model. So we have biased models feeding into imbalanced clinical trials, with women getting the short end at each step. And the end result:
However justifiable these imbalances may be on a case-by-case basis, their cumulative effect is pernicious: medicine as it is currently applied to women is less evidence-based than that being applied to men.
Which is just sad.

1All numbers based on US statistics from the NSF, 2006.


Sunday, July 04, 2010

Cheeky monkeys showing off their memory.

Check out how much better a chimpanzee's memory is than yours. Aside: Strange how a Japanese researcher is using Japanese written words on the test screen but uses Western/European Arabic numerals for the actual test on the monkeys. Are Japanese numbers too difficult for the monkeys?


Friday, July 02, 2010

Cancer Carnival #35

Once again, it's the first Friday of the month. Right between Canada Day and Independence Day, and in the middle of World Cup month so it's a bit of a light carnival this time around.

Over at Health and Life, our friend David has a post about melanoma and a new drug to treat it:
Ipilimumab is a monoclonal antibody that targets cytotoxic T lymphocyte associated antigen 4 (CTLA-4). This marker is associated with promoting a regulatory response by the immune system, slowing it down. By knocking it out, ipilimumab may shift the body’s immune response from inaction into action.
Health and Life often features new drug info and is a good place for pharm-minded folks.

At the Stem Cell Network blog, I have a post up about new developments in the world of hematopoiesis and touch upon some of the implications they might have for cancer research.
[A]cute myeloid leukemia (AML) is a cancer of the blood. As the name implies, it is the result of uncontrolled growth of cells from the myeloid lineage caused by dysregulation of the corresponding stem cell. Effective treatment requires the identification and targeting of the appropriate cells.
The Spittoon, the 23andMe blog, highlights 2 new cancer-associated SNPs. First is a genetic variant contributing to melanoma risk and mole count.
When Duffy’s team examined data from about 2,000 adolescents of European ancestry living in Australia, they found that each copy of a T at variant rs12203592 was associated with a significant increase in numbers of “flat” nevi (the most common type of nevus). When they looked at data from the parents of the adolescents, however, they saw no such effect. In fact, the data suggested that the C version of rs12203592 – not the T version – was associated with higher nevus counts in older people. Comparing these results with data from thousands of individuals from the UK confirmed the differing age-dependent effects of rs12203592.
Mole counts is something we've talked about before. The Spittoon post goes on to describe how these same variants affect melanoma risk. The second set of SNPs have to do with testicular cancer, reported in Nature Genetics.
Clare Turnbull and colleagues analyzed the DNA of 979 men with testicular cancer and 4,947 controls, all of European descent. Many of these men were included in the group’s previous study. The four SNPs most strongly associated with testicular cancer were then followed up in an additional sample of 664 cases and 3,456 controls, where evidence of association was also found.
Elsewhere in the blogosphere, Orac discusses cancer overdiagnosis and overtreatment, ERV notes the difficulties in epigenetic approaches to cancer treatment, HighlightHealth points to new information about vitamin D and cancer (which seems contrary to research from a few years ago) and for the epidemiologists, The Pump Handle dissects the recent President's Cancer Panel report.

That's it for this month's Cancer Research Blog Carnival. For older editions, visit the Carnival Homepage. Don't forget, the CRBC 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. For a broader collection of science-related blog carnivals, sign up for the Science, Medicine, Environment and Nature Blog Carnival Twitter Feed.


Thursday, July 01, 2010

Chelation therapy quack sues Quackwatch

You may have heard of chelation therapy: it involves using chelating agents, such as EDTA either IV or orally to scavenge metal ions in the blood and promote their excretion in the urine. It is a standard of care therapy for heavy metal poisoning. However "alternative medicine" proponents have been touting it as a miracle "detoxifying" treatment for all kinds of ailments from coronary heart disease to autism. And it's not without concerns, according to wikipedia:

"side effects include fever, headache, nausea, stomach upset, vomiting, convulsions, bone marrow depression (dropping blood cell counts), a drop in blood pressure, cardiac arrhythmias, respiratory arrest, and hypocalcemia. Other concerns include kidney failure, which can require permanent life-limiting and expensive dialysis, or cause death. "

Chelation therapy has been responsible for over 30 deaths, many of which were autistic children. The reason is quite simple: we need metal ions for our body to work. If you've ever looked at a periodic table you know that elements essential for life such as sodium, calcium, iron, potassium are also metals so it's not just lead and mercury you're removing.

To justify the detoxifying, many of these quacks perform urine analysis after giving a "provoking agent" which artificially increases metal excretion in the urine to scare patients into getting treatment. not only is that deceptive, but there is absolutely no evidence, despite numerous studies, that chelation therapy has any benefits outside of heavy metal poisoning.

Quackwatch, a site which is a beacon of reason and often the lone voice to expose quacks is being sued for $10M by one of these companies. How typical. These companies are flush with cash from taking advantage of credulous patients and when you point out that the treatment has no scientific validity and is potentially harmful they fight reason with the blunt tool of litigation. Libel law is the greatest threat to free speech since lone individuals often cannot afford to legal proceedings against larger corporation. But, if you feel so inclined, quackwatch is taking donations to help cover the cost... At least we can fight back by exposing these quacks. Suing only attracts more attention to you, hopefully knowledge and reason can do the rest.


Inadvertently funny lab stuff

This was written on a mouse cage by the vet...