A Quote for the Day

Maxwell wasn't thinking of radio, radar, and television when he first scratched out the fundamental equations of electromagnetism; Newton wasn't dreaming of space flight or communications satellites when he first understood the motion of the Moon; Roentgen wasn't contemplating medical diagnosis when he investigated a penetrating radiation so mysterious he called it "X-rays"; Curie wasn't thinking of cancer therapy when she painstakingly extracted minute amounts of radium from tons of pitchblende; Fleming wasn't planning on saving the lives of millions with antibiotics when he noticed a circle free of bacteria around a growth of mold; Watson and Crick weren't imagining the cure of genetic diseases when they puzzled over the X-ray diffractometry of DNA; Rowland and Molina weren't planning to implicate CFCs in ozone depletion when they began studying the role of halogens in stratospheric photochemistry.

These discoveries and a multitude of others that grace and characterize our time, to some of which our very lives are beholden, were made ultimately by scientists given the opportunity to explore what in their opinion were basic questions in nature.

Cutting off fundamental, curiosity-driven science is like eating the seed corn. We may have a little more to eat next winter, but what will we plant so we and our children will have enough to get through the winters to come?

-- Carl Sagan, The Demon-Haunted World: Science as a Candle in the Dark

The Crow and the Pitcher

Thousands of years ago, Aesop wrote a fable about a crow who used stones to raise the water in a pitcher so he could have a drink.

The latest issue of Current Biology documents this behaviour in a member of the crow family, the rook.
The authors next plan to use General Relativity/time dilation to determine who actually crossed the finish line first: the tortoise or the hare.

The crows are a resourceful family of birds. They have been shown to employ teamwork, use tools and solve multi-step problems. (Follow links for video) So much for birdbrains.

Cancer Research Blog Carnival #24

Welcome to the 24th edition of the Cancer Research Blog Carnival - your monthly roundup of writing from the cancer blogosphere. This month, the CRBC turns 2 years old (on August 24th, to be precise), so a special thanks to AC for starting the whole thing, Ben who designed our awesome logo, Walter for setting up new subscription options and general support and of course all the hosts and writers who have got us this far. Of course to keep going for another year, or 2, or 4 we still need your help - the carnival is always looking for new hosts, so drop us an email, or a comment here, to sign up and keep sending us your submissions here.

Now, without further ado, here is the latest Cancer Carnival:

First up, we have a new blog, Blue Genes, that offers their first part of a series on understanding cancer.

What is cancer? Everyone knows that it is a terrifying disease and has some ideas about a mass of cells that grow uncontrollably but I get the feeling that many people don’t quite understand how it actually happens.

They promise to continue the series in the futures with posts on cancer treatment, different cancer types, and other cancer topics. Blue Genes is written by a pair of young scientists and is worth keeping an eye on.

Next up, we have a pair of posts from The Spittoon, the blog of genetic testing company 23andMe. From the SNPwatch files, these posts highlight research identifying new genetic variants associated with cancer. First off is a discussion of CDKN2A and CDKN2B variants associated with certain brain and skin cancers.

Five reports, published online this week in the journal Nature Genetics, show that variants near the CDKN2A and CDKN2B genes increase the risk of certain types of tumors. Previous research has implicated these “tumor suppressor” genes in both skin and brain cancer. Mutations in CDKN2A are found in about 2% of all people with melanoma, and outright deletion of CDKN2A and CDKN2B is seen in approximately half of all brain tumors.

The second new SNP is associated with follicular lymphoma.

In a study by Skibola et al., scientists analyzed the genomes of 4,805 people of European descent from the United States, Germany and Canada to search for genetic associations with four different subtypes of lymphoma. The results, published online this week in the journal Nature Genetics, newly linked one SNP to an elevated risk for developing FL in European populations.

A submission from Healthcare Hacks is next, which discusses triple-negative breast cancer

Negative--that's good, right? Unfortunately, this is one of those times that negative results aren't so positive. This form of breast cancer is named "triple-negative" because the tumor lacks the three receptors for the hormones estrogen, progesterone or Her-2/neu.

The post offers some facts about triple-negative breast cancer before briefly discussing some new therapies in the pipeline that offer hope to patients, as well as support resources for people diagnosed with this cancer.

Suture for a Living talks about a topic we've discussed a bit in the past: overdiagnosis of breast cancer, in this case putting some actual numbers to the problem.

Are breast cancers over-diagnosed? If so, how often? Those are the questions looked at by the systematic review of incidence reported data/articles done by Karsten Juhl Jørgensen & colleagues. Their results are published online in the June 9th issue of the British Medical Journal. Their review shows an estimated 52% over-diagnosis of breast cancer.

Click through for more stats and analysis.

Elsewhere in the blogosphere, Alexey at Hematopoiesis provides a nice review of ways the immune system can be harnessed to kill cancer stem cells, as well as progress made to date. Orac at Respectful Insolence has a really interesting piece on the problems recruiting patients to clinical trials and what it means for cancer research. And Science and Reason discusses a new targeted therapy for leukemia stem cells.

That's it for the 24th 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.

Late breaking abstract!

The anthropological implications of proper habiliment usage on micturition

The evolution of the erect posture in the genus Homo has created physical constraints on urination, particularly in males. It has also been observed by multiple groups that the act of wearing garment can impede the urinatory process by increasing the latency between the initiation of the behavior and the opening of the urethral sphyncter. In the general population of males there exist variation in the exit strategy employed for the exposure of the phallus through the underclothes. To model the population variation of these behaviours, a questionnaire was designed and given to 41 subject over the course of 7 days. Results indicate that most subjects (70%) choose to expose their penes by going over the elastic band while a minority (29%) use the undergarment flap. These results raise questions about the validity and usefullness of the undergarnment flap given the low propencity of usage. Futhermore it was serendipitously discovered that analogous female garment lack such vestigial features. A correlation was observed between individuals of french background and users of the undergarment flap (16% were French). While correlation does not imply causation, we wish to bring forward the hypothesis that urination behaviour may be ethno-culturally determined. Further studies will be needed to determine how urination behaviour varies geographically.

Funding HQPeeps: "Fellowships" vs. The Grant

Some wacko/Nobelist (Roald Hoffman) is suggesting that American labs should be banned from funding graduate students through the PI's operating grant. Apparently, this is how the vast majority of students are funded in the States and I'm pretty sure the same is true in Canada (ie their salaries are paid through the lab's grants as opposed to an independent fellowship awarded directly to the student.) This idea has some appeal:

"The real power of an individual fellowship is that it empowers a young scientist to act in a more independent manner, on something creative and for which they have a passion," says Thomas Cech... "And that's what science is really about." Under the current system, he says, "a graduate student is told, ‘Do experiment 2a because it's in our grant.’ That turns the student into a pair of hands. So I think a shift to fellowships would be an excellent idea."

I like what Cech is saying here. The same thought occurred to me, except I was looking at POST-DOC, rather than graduate student funding. At least here in Canada, even post-docs, who are supposed to be even further along in developing their independence, are unable to get truly independent funding at all, even through external fellowships. So even if all HQPs, grad students and post-docs alike were funded through external fellowships, Cech's vision still wouldn't be assured.

The problem is that although the would-be post-doc can apply for "independent" funding directly to agencies he/she cannot do so without a PI co-applicant. So before applying for funding, would-be post-doc must meet with PI and discolses his/her interests and ideas, gain a conditional position in PI's lab, identify a putative project that fits into PI's interests and grant funding, write up a proposed project in collaboration with PI and likely write a grant proposal or two for PI pertaining to said project. So much for independence.

On the other hand, true independent funding would consist of the following: Would-be post-doc or graduate student concieves of an interesting problem and possible approaches. Writes up proposal and submits along with CV etc to funding agency. Funding agency awards fellowships to promising candidates. Awardees contacts existant labs..."I have funding to carry out the following research project. Are you interesting in hosting?"

This scheme is ultimately the most liberating for the trainee. The only real potential flaw I can see is that in theory, trainees could be granted salaries to conduct a proposed project for which the proper infrastructure does not already exist. However this could be easily overcome by properly evaluating the feasabilities of proposals.

Anyhow there's some interesting argument presented in the Science article on which is better, grant-based or independent fellowship-based funding of students. I'm not sure if either is better, actually both setups can probably work. However it's clear that the current grant-based trainee-funding regime empowers PIs at the expense of grad students and post-docs. It gives them access to a much larger putative work force, allows them to hire whoever they want and as many students/post-docs as their grant funding allows (as opposed to who and how many they can properly train). At the same time it generally tends to screw over the individual trainee by dimishing their intellectual autonomy, decreasing the availability of scientific mentorship, creating a crowded and more cut-throat and overall shittier research environment, and flooding the job market with an excess of jobless PhDs. Conversely, independent funding schemes would tend take power away from PIs and put it back in the hands of trainees to pursue their own ideas in an environment that favors quality of work over quantity. Anyone see this happening anytime soon?

Of course there are exceptions. For example, grad students who get funded through PI grants can possibly focus more directly on their research because they don't have to waste as much time filing fellowship applications or engage in meaningless CV-building arts and crafts. So long s long as they're happy with what PI decides they're working on and what training PI decides to offer, it's a sweet deal.

Overall my opinion would probably be that we don't necessarily need more independent funding for nascent grad students...what the hell do they know anyways? But truly independent fellowships for post-docs would be a great option.

Any other perspectives?

About F-ing Time

Someone in the scientific publishing biz is thinking, there might be a better way to format articles, one that isn't based around the printing press, but the so-called "Information Superhighway". Check out the samples here and here. Imagine the possibilities!!!! Could this be the end to the time-honored tradition of re-formatting scientific data into a useless and archaic format when it comes time to publish?

Monoclonal antibodies

I was recently surprised to find out that there are a TON of approved therapeutic monoclonal antibodies. Monoclonal antibodies are simply clonal antibodies, they all are exactly the same and thus bind the exact same antigen. In the case of therapeutic monoclonal antibodies these are drug targets. And I thought they were just good for western blots and coimmunoprecipitation!
In my defence I was aware of two approved monoclonal antibodies, herceptin and avastin. Both are for cancer treatment, so it makes sense that I would know them. Herceptin targets defective HER2 mitogen receptors that are stuck in the 'on' position, and herceptin is able to stop this activity by binding to these cell surface receptors. Avastin binds to VEGF, thereby preventing VEGF from stimulating new blood vessels to form in growing tumours thus cutting them off from oxygen and nutrients.
This relatively new class of drugs are effective and the market is growing fast, unfortunately they are also extremely expensive. Since they are such big business there are lots of new monoclonal antibody therapies out there. According to wikipedia:
"The current “big 5” therapeutic antibodies on the market: Avastin, Herceptin (both oncology), Humira, Remicade"..." and Rituxan (oncology and AIID) accounted for 80% of revenues in 2006"
But that must mean there are some interesting alternative monoclonals out there, here are a few that are perhaps a bit more unique:
Rituxan is useful for both autoimmune disorders and non-Hodgkin lymphoma because it targets CD20 on Bcells which are producing autoantibodies, in the case of autoimmunity, or are proliferating unchecked in the case of non-Hodgkins.
Palivizumab is a monoclonal that prevensts Respiratory Syncytial Virus infection.
Abciximab blocks platelet activation an thus blood clotting.
Efalizumab binds CD11a and is thus immunosuppressive and used to treat psoriasis, but due to side-effects of this immunosuppression it is being withdrawn from the market.
HCV-Ab^XTL68 is used in HCV positive patients undergoing liver transplant to prevent infection of the new liver.
Most of the monoclonal antibodies are for cancer or for autoimmune disorders.
Check out the diagram from wikipedia for a quick look at the strategies used to treat cancer with monoclonal antibodies.

No Fly Zone

You may have noticed a new poll at the top of our sidebar. Conversation at the pub last night turned towards urination style - whether you used the underwear fly or went 'over the top' - and now we're asking you. So cast your vote, and leave your reasoning in the comments if you like.

You can also check out this brief documentary about the hazards of the underwear fly (video starts at about 10s):

Should copyrights be abolished in academia?

We've all been exposed to strange situations where we had to ask for permission to use our own figures or data from a paper into another paper, or a thesis etc... And the fact that one can retain copyrights is in my opinion one of the best benefits of some open-access journals. But Steven Shavell thinks we should go even further in this paper:

"The conventional rationale for copyright of written works, that copyright is needed to foster their creation, is seemingly of limited applicability to the academic domain. For in a world without copyright of academic writing, academics would still benefit from publishing in the major way that they do now, namely, from gaining scholarly esteem. Yet publishers would presumably have to impose fees on authors, because publishers would not be able to profit from reader charges. If these publication fees would be borne by academics, their incentives to publish would be reduced. But if the publication fees would usually be paid by universities or grantors, the motive of academics to publish would be unlikely to decrease (and could actually increase) – suggesting that ending academic copyright would be socially desirable in view of the broad benefits of a copyright-free world. If so, the demise of academic copyright should be achieved by a change in law, for the ‘open access’ movement that effectively seeks this objective without modification of the law faces fundamental difficulties."

Swimming in the Sand

On a toasty summer day, we might head to the beach, stroll across the sand and go for a refreshing dip. For certain lizards in more arid regions they can still take a swim to escape the heat - only they'll be doing it in sand itself.

The latest issue of Science has a paper [subscription required] describing the movement of the sandfish lizard, a desert reptile that can swim through sand, to cool off or escape predators, by wiggling like an eel. Check out the cool vids from the supplementary material:

Video 1: The sandfish burying itself in the sand

Video 2: X-ray cinematography of the sandfish sub-surface locomotion.

Videos should be free to access, but may require Quicktime.

[h/t: Why Evolution is True, who also includes a neat paper about tiger moths who 'jam' the sonar of predatory bats]

Fly me to the moon

This is a pretty cool, if Flash heavy site: We Choose the Moon.

This month is the 40th anniversary of the Apollo 11 moon landing, and the above site recreates the event for "real-time" (that is, real time minus 40 years) tracking of the mission, with video, images and audio (including astronaut chatter) from 1969.

It's a neat way to let those of us who are too young experience that exciting piece of history.

At the same time, you can check out the NASA gallery featuring current photos of the landing site from the Lunar Reconnaissance Orbiter Camera that reached lunar orbit late last month.

[h/t: Bad Astronomy]

F@$!ing Pain

I cut my finger with a knife last week. Nothing major, though on weekend inspection it looks like the knife went straight through. It hurt like hell though, and the first word out of my mouth when it happend was, "Fuck!" This was probably followed by a string of other colourful language.

I don't think that's an uncommon reaction, and it might not be a useless one either: A study to be published next month explores the impact of swearing on pain tolerance. In the experiment, undergraduate students were asked to submerge their hands in icy water (the only type of pain tested) and either swear or use non-profane words. The blog Neurophilosophy has more:

The researchers measured how long the participants kept their hands submerged in cold water, and asked them to rate the amount of pain they felt. Their heart rates were also recorded after they had submerged their hands in room temperature water as well as after the submersion in cold water. Contrary to their hypothesis, they found that swearing actually reduced the amount of pain felt. The participants kept their hands submerged in the cold water longer for longer, and also reported experiencing less pain, when they repeated a swear word than when they repeated a word describing a table. Swearing was also associated with increased heart rate.

It's uncertain whether this would apply to other types of pain, or if the severity of the word increases its effectiveness (bonus points for creative combos?) but next time you stub your toe or get a papercut try it out. It couldn't hurt.

icanhasPhD

Hot tub rash

After the pinkeye outbreak of 2007 the lab now has a hot tub rash outbreak. The Pseudomonas folliculitis happens when the pseudomona bacteria infects hair follicles, and it usually resolves itself within 2 weeks. For some reason it seems to have only affected some individuals and not others. All of them were female. Any idea why?

At least no-one had a prostate infection, unlike this poor sap:
"A previously healthy 38-year-old white male presented to the emergency room with a 10-hour history of fevers, chills, and significant suprapubic pain. He also complained of dysuria and feelings of incomplete emptying after voiding. He denied any history of sexually transmitted diseases, recent urinary tract infections, or genitourinary trauma. He did mention having sexual relations with his wife three times the previous week in a newly purchased hot tub. His wife was asymptomatic."

"P. aeruginosa can survive in a variety of moist environments due to its minimal nutritional requirements and growth temperature range (4 to 42°C) (1). Although inhibited by chlorine levels in water of 2 to 3 ppm, P. aeruginosa can multiply to densities of 10⁴ to 10⁶ organisms/ml when levels drop to <1>4). These characteristics allow it to multiply in hot tubs, where chlorine levels are rapidly dissipated by the warm temperatures (39 to 40°C) and aeration (4). Hot tub use has been linked to P. aeruginosa folliculitis and more-serious infections, including pneumonia and those involving the urinary tract (cystitis, prostatitis, and urosepsis) (2, 3, 5-7)."

Rapamycin update

Since some of us in the bay are interested in the translational inhibition activity of rapamycin I thought I would point out an excellent piece at not exactly rocket science reflecting on some new data on rapamycin's effects on aging in mice. Very interesting. The original article at Nature. There are also some great links in the article.

Cancer Carnival #23

Welcome to the 23rd edition of the Cancer Research Blog Carnival! Most of our readers are probably either recovering from Canada Day or gearing up for Independence Day, but there's always time for some science in between.

Kicking things off this month, we have PalMD following up on his Cancer 101 posts (some of which were featured previously in the Cancer Carnival) with Cancer 202 - Radiation Therapy. In it he briefly discusses the basics of radiation treatment including its effects on normal tissue and how to target a tumour.

Radiation is a powerful tool in medicine, but like any tool, whether it be a knife or a pill, it must be wielded properly and ethically. The best medicine combines good science, compassion, and ethical behavior to help people. Radiation therapy is one of medicine's most sophisticated techniques, and must be used only by certain experts. It's also really cool.

PalMD does a great job of explaining the basics in an easy to understand way. If you missed any of the other posts in this series, check them out here.

Next up, MolBio Research Highlights sends us some blogging on peer reviewed research. The topic? Cancer Stem Cells. Francisco Barriga is inspired by three recent papers and tries to make sense of it all with a nice review of current thinking and controversy.

[D]uring the last years there has been a lot of controversy regarding the existence, function and clinical implications of cancer stem cells. This confusion stems (no pun intended) from the lack of clarity in the field nowadays, arising mainly from misconceptions regarding the origin and function of these cells. On top of all of this is the confusion derived from media-hype and some not-so knowledgeable scientific journalists.

Francisco clears up some of this confusion with a summary of the cancer stem cell hypothesis and discussion of unresolved issues in the field.

Cancer stem cells are always a hot topic, and Alexey at Hematopoiesis discusses some ways that existing drugs can affect CSC populations.

Recently, anti-cancer activity of some well known drugs was discovered, which was shown to rely on targeting of cancer stem cells (CSC). Explanations for some very effective anti-leukemic drug combination were recently found in the laboratories. I’ll give you some examples of “from-bed-to-the-bench” translation coming from leukemia clinic.

Three drugs, and their possible uses, are examined.

Over at Scienceblogs, there has been some discussion about NIH funding strategies, and whether they're too conservative. Mike the Mad Biologist draws our attention to a New York Times article that laments the lack of progress in cancer cures and wonders if more money should be put into high-risk, high-reward projects. Orac comments on the same article, asking "Are we playing it too safe in cancer research?" and the Mad Biologist continues his analysis of the culture of caution at the NIH.

Finally, there were celebrity deaths in the news last week with one, Farrah Fawcett, losing her battle with cancer at the age of 62. While it was overshadowed by other events, she did get some attention with some raising awareness about anal cancer, some retrospective and discussions with her oncologist.

That's it for this month. Next month is our the Cancer Research Blog Carnival's 2nd anniversary, so start writing those cancer posts, and submit them here. We always need hosts as well, so if you're sick of seeing the carnival here on the Bayblab, email us to sign up for a future carnival. For older editions, visit the Carnival Homepage.

And don't forget, the Cancer Research Blog Carnival now 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.

Preeclampsia and oral sex

So I'm teaching cardiovascular anatomy and physiology right now, which is funny because Rob is teaching the drugs for that system in pharmacology at the same time. I was reading up on preeclampsia, which is a type of hypertension that can develop during pregnancy, looking for hypotheses for causes. I'm doubly interested because I've recently stumbled upon a potential regulatory protein which could be associated with the disease. To make a long story short there is definitely a strong immune involvement, and a problem in the placental interface although the details are surprisingly not well fleshed out (to an outsider anyways). I was also somewhat amused to find out that there is a putative protective role of oral sex and swallowing of seminal fluids for preeclampsia. The idea being that HLA and HLA-derived peptides may tolerize the mother to the foreign antigens of the fetus in the same way that we tolerize other food-related antigens passing through the gut. While this paper certainly isn't definitive, a correlation at best, the treatment has few side effects, so might as well err on the safe side:

"we investigated whether sHLA antigens are present in seminal plasma. Using a specific ELISA we detected sHLA class I molecules in seminal plasma. The level varied between individuals and was related to the level in plasma. Further studies showed that these sHLA class I molecules included classical HLA class I alleles, such as sHLA-A2, -B7, -B51, -B35 and sHLA-A9. Preliminary data show lower levels of sHLA in seminal plasma in the preeclampsia group, although not significantly different from the control group."

Geothermal energy induced earthquakes

A really quick movie about a new geothermal energy project that raises concerns that it may trigger large earthquakes is available at the new york times.
I found a couple of interesting points in the video. I did not realize that there was any large geothermal projects in North America, but the largest group of plants is in California. Also I was extremely skeptical that drilling into the ground could possibly do anything that would cause an earthquake. An existing geothermal project however already does.
I would have liked to have heard more from the company about why the new project will not cause earthquakes.

Which language has the most words?

I heard an interesting factoid at lunch yesterday. There are apparently one million words in the English language which supposedly puts it far ahead of any other language. This came as a surprise to me, while I've grown to enjoy English for its precision, this would mean it contains over ten times the amount of words of the french language (80k). It is no surprise to me however that French is stagnating, simply because the language is regulated by committee, and we all know how efficient those are. And so when we need a new word say to convey the meaning of "email", a group of people in France have to get together and pick one (courriel). Hardly a natural and vibrant process. But does the English language truly have a million words? Wolfram alpha will quickly tell you that the Oxford dictionary has 600k words, putting it ahead of say Spanish with a mere 225k. English is growing very quickly because it incorporates other languages readily, perhaps because most English speakers are not native. In fact China has the largest population of anglophones in the world. The original claim that there are 1 million words comes from the university of Texas which has an algorithm caching and crawling social networking sites all along identifying any expression used over 25 000 times as a word. Of course many people have problems with this, since it is not an accepted definition of a word. It incorporates any deformation or misspelling of common words, commercial trademarks, onomatopoeia which would include for example: "what", "wat", "waht", "wh4t", "whaaaaat", "whassssssssssssup" etc ... Many people have critisized the methodology itself, since the "Global Language Monitor" claimed the millionth word in 2006, 2007, 2008 and 2009.
So does this mean English really has the most words: not likely. Agglutinative languages such as Finnish most certainly have more words and more readily create new words to adapt to changing time by fusing existing words creating an almost infinite number of combination. Yet English remains dominant perhaps not in the number of words, but in the reach and power of the language.

Ununbium - a "new" element

Some may have noticed a little article on the right of the front page of the Ottawa Citizen... "Hey, science fans, there’s a new element in town". In it, Tom Spears implies that the discovery of element number 112, known as Ununbium, is a novel thing.

Here's the problem. As an avid science fan, and chemist, my first reaction was "wasn't 112 there last time I looked at the periodic table?". And, sure enough, all the PTs in the lab (none of which were printed in the last 12 hours) all indicate element 112 there, smiling at me below mercury and just raising the question about what prompted the article... and its front page position.

So, here's the wikipedia scoop. Ununbium was first discovered in 1996, in Darmstadt, Germany. Like most of it's heavy brothers, 112 is synthesised by smashing things together, in this case, its lead and zinc. So what is new? Well, the IUPAC overseers of these things have re-confirmed that the discovery was real, and have credited those German discoverers with the first atom of Ununbium... meaning they can now name it.

So, is this a case of a journalist getting it all wrong in science? Am I being too pedantic by getting annoyed at how it's taken 12 years for this discovery to be reported by the Ottawa Citizen... and even then that they haven't really told the story.

What are some of the worst examples of science reporting that you can think of?