Thursday, December 30, 2010

Eel-powered Christmas Lights

Probably not a viable substitute for fossil fuels...


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Sunday, December 19, 2010

Economist view of academics

An article in The Economist presents a depressing view of doctoral degrees. I also consider myself underemployed, partly by choice. Unfortunately the article doesn't address the view that I have and I think that many other graduate students must have. I really enjoyed my extended time as a student, the work and the lifestyle. Also, the statistics reported in the article about the number of jobs for PhDs actually seems better than I had estimated from my experience as a graduate student.


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Thursday, December 09, 2010

"In the real world, that would be considered a mental disorder!"

CollegeHumor looks at grad school...


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Tuesday, December 07, 2010

Sulphur hexafluoride blooper



Hilarious.


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Monday, December 06, 2010

Arsenic-based life? Not so fast.

Everybody is abuzz with the discovery of a new study that claims to discover a bacteria that can substitute arsenic for phosphorus in its DNA backbone. There's lots of blog coverage of this research, much of it skeptical. If you only read one post about it, I would recommend this one from We Besties. It does a great job of looking at the paper and the experiments from a chemistry standpoint in an easy to understand way. The bottom line seems to be that there are some key experiments needed to be done before we jump the gun on declaring the discovery of alternative biochemistry.


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Friday, December 03, 2010

Cancer Carnival #40

Time again for the Cancer Research Blog Carnival, a monthly collection of cancer research and other cancer-related blogging.

The holidays are upon us, and it's a short carnival this month, so we'll kick things off with a short post. Alexey Bersenev at Stem Cell Assays points us to a new review of aldehyde dehydrogenase in stem cells.
Aldehyde dehydrogenase (ALDH) is a potent and “popular” marker for both normal adult and cancer stem cells in rodents (mice) and human. I was happy to find very recent and comprehensive review about role of ALDH in human stem cells.
ALDH1, it seems, is not just a convenient marker of normal and cancer stem cells, but may play an important role in stem cell physiology.

Speaking of stem cells, I have a post up at the Stem Cell Network blog describing a new method for interconversion between cell types without first producing an induced pluripotent stem (iPS).
Because these cells never enter a pluripotent state, they were shown to not give rise to teratomas, and the resulting engraftments lacked leukemia stem cell properties, this suggests a decreased cancer risk compared to other alternatives that retain tumour potential.
At Respectful Insolence, Orac describes the tolls of second-hand smoke.
One aspect of the results of this study that were particularly disturbing is that deaths due to secondhand smoke were skewed toward poor and middle-income countries, where children tended to die of lower respiratory infections associated with secondhand smoke. In Europe's high-income countries, only 71 child deaths were recorded for this study, while 35,388 deaths were in adults. In contrast, in Africa, there were an estimated 43,375 deaths potentially attributable to secondhand smoking in children compared with 9,514 in adults.
Orac also discusses flaws in the described study, but overall evidence points to the dangers of second-hand smoke inhalation. Meanwhile at HighlightHEALTH, with over 1 billion smokers in the world producing second-hand smoke, Walter Jessen points out that tobacco prevention funding is at a 10-year low.
According to the latest data from the Federal Trade Commission, tobacco companies spend $12.8 billion a year on marketing; that equates to $25 tobacco companies spend to market tobacco products for every $1 the states spend to fight tobacco use. Perhaps not surprisingly, a recent CDC study reports that the number of adult smokers dropped between 2000 and 2005, but the adult smoking rate has stalled at 20-21% since 2005.
Given that tobacco is the number one cause of preventable death in the US, and the toll of second-hand smoke on non-users described above, this isn't great news.

Finally, ERV talks about a paper discussing Merkel Cell Polyomavirus and it's role in Merkel cell carcinoma.
This paper isnt perfect. I have a lot of issues with it too-- BUT! I think it is a fantastic step in the right direction of establishing the role of a virus in a cancer and establishing the biochemistry of that interaction. This not only helps with the logic (there are some logical issues I have with XMRV-->prostate cancer) so people believe you, but if you elucidate the biochemistry/genetics/physiology, taking the issue beyond "WE CAN FIND THE VIRUS IN 80% CANKERS!", you can figure out potential avenues of treatment.
Read the post for the full story.

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.


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Wednesday, December 01, 2010

Gay Prostates

There is a long history of research on digit ratio, that is, the ratio of the length of index to ring fingers. Interestingly a correlation of a larger index to ring finger length (2D:4D) to homosexual orientation in males has been found although it is controversial. Many other quite varied traits also seem to correlate with digit ratio including skiing ability, financial trading success, and musical ability (check out the wikipedia entry for a comprehensive list and references). It has also been shown that those with a lower 2D:4D have a higher risk of developing prostate cancer. The data seems quite convincing and I don't think that the correlation of high 2D:4D with homosexuality is as strong, however, is there less prostate cancer in gay men?
As an aside, can we get any pics of great (creepy) Movember mustaches now that its all over?Link


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Monday, November 29, 2010

Call for Posts

The Cancer Research Blog Carnival is coming up this Friday, December 3 and we want your blog posts. Submit your cancer science blogging here or email us at the address in the sidebar, then stay tuned this Friday for the latest edition.


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Wednesday, November 17, 2010

The Costs of Cancer Treatment

Something to think about from a Slate book review, via Thus Spake Zuska:
Provenge has shown some success against advanced prostate cancer. But it also costs about $93,000. Gleevec can cost $4,500 per month. Revlimid, another cutting-edge treatment for multiple myeloma, can cost $10,000 per month. It's hard to see how these prices might come down when the market consists of patients increasingly fragmented not only by type of cancer but even by types of mutation.
Or course this isn't a call for 'silver bullet' treatments; cancer isn't just one disease. But the economics can be tricky. Simple supply and demand suggests that market fragmentation and personalized medicine will only drive prices up and split research dollars. It isn't quite so simple, though. Most personalized medicines will be built on common technologies which could even have the opposite effect - higher demand for core technology, modified on a case-by-case basis. Still, looking at the above costs of cancer treatment, I'm glad to live in a country with universal health care.


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Friday, November 12, 2010

Oh, Lately it's so Quiet

It's been pretty quiet in these parts lately, but that doesn't mean we aren't busy cooking up science elsewhere. Over at the Stem Cell Network blog I have a few new posts up, mostly about iPS cells, and there are plenty more interesting posts from other bloggers as well.

Elsewhere, there's some interesting food blogging at Casaubon's Book asking "Is the local food movement elitist", as well as at Tomorrow's Table where the author discusses GE crops and sustainability.

Finally, Scicurious and PZ Myers both highlight some science porn: MRIs of women having orgasms.

Hopefully those links will tide people over while I work on some new Bayblab content. It may be quiet around here, but we haven't gone anywhere.


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Friday, November 05, 2010

Cancer Carnival #39

This month is Movember, the annual prostate cancer fundraising and awareness campaign involving men showing off their (mutton) chops and growing some fine facial hair. Read more about Movember here, and if you'd like to donate but don't know a participant, why not throw a few bucks at this effort and tell him the Bayblab sent you (full disclosure: he's my brother). In Canada, prostate cancer is the number one most commonly diagnosed cancer in men, with an estimated 24,600 new cases and 4,300 deaths in 2010. November is also Lung Cancer Awareness month, the number one cancer killer among both men and women, accounting for more cancer deaths than the next three cancers (colorectal, breast and prostate) combined. (Statistics according to the Canadian Cancer Society).

With that in mind, it's also time for the latest edition of the Cancer Research Blog Carnival. It's a short one this month - remember that the carnival depends on submissions from readers, so be sure to submit your posts for next month.

First off, last month's host Highlight HEALTH sends us news of a campaign to end breast cancer by 2020, the first initiative of which is to develop a breast cancer vaccine.
Key to this strategy and the challenge for researchers will be the identification of molecular mechanisms shared among the various breast cancer subtypes that cause the disease. A breast cancer vaccine may be closer than you think. A report in Nature Medicine earlier this year reported an experimental vaccine that prevented breast cancer in mouse models.
The National Breast Cancer Coalition has done more than just set an arbitrary deadline - January 1, 2020 - but has outlined a plan to get there. Read more about the efforts at Highlight HEALTH.

Here at the Bayblab, I take a look a paper that explores what it means to be "cancer literate" and what kind of public education is needed for a cancer literate public.
[T]he authors assembled a panel of cancer experts (oncologists, GPs, nurses from oncology wards, social workers, public health experts) who refined the answer over a number of rounds. For their purposes, literacy was "the degree to which individuals have the capacity to obtain, process, and understand basic health information and services needed to make appropriate health decisions."
While there are some obvious answers, there are also some surprises as to what is included and excluded from a definition of cancer literacy.

Elsewhere, Christie at Observations of a Nerd debunks the myth that sharks don't get cancer.
There are a lot of myths out there about the marine world, but by far the one that bothers me the most is the notion that sharks don't get cancer. This simply untrue statement has led to the slaughter of millions of sharks via the industry for shark cartilage pills, which are sold to desperate cancer patients under the false pretense that they can help reduce or cure their illness.
Meanwhile, Orac also takes a look "alternative" cancer therapy as he describes "Yet another cancer cure testimonial that tells us nothing".

Finally, White Coat Underground has a post up about sulforaphane-rich vegetables (eg. broccoli), cancer prevention and how to properly evaluate risk.
The other day, I took issue with a press release published on another website. It was titled, Discovery may help scientists boost broccoli’s cancer-fighting power, which I found to by hyperbolic and deceptive. The actual study being reported regarded the ability of certain compounds found in cruciferous vegetables such as broccoli to be absorbed from the cecums of rats. I dismissed the entire piece as being unsupportive of its ambitious headline.
Read the whole post for a more detailed look at some aspects of the broccoli-cancer connection, and important tips on how to critically read the medical literature.

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.


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Wednesday, November 03, 2010

The Starving Student Cookbook

If you've ever been an undergrad accidentally turning your food budget into your booze budget, or tried to scrape by on a grad student stipend, you've probably had a share of unglamorous meals while making ends meet - possibly surviving on Mr. Noodle for weeks at a time (or, if you believe my dad's undergrad stories, spam). For the past while, Scicurious at Neurotic Physiology has been soliciting recipes from grad students, with an emphasis on affordability for those on a shoestring budget, and put them together in The Grad Student Eating in Style Carnival.

There are plenty of great recipes there, whether a grad student or not, so take a look and you might find some new supper (or breakfast, or lunch) ideas.

And yes, there is a Ramen category.


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Tuesday, November 02, 2010

Update your CPR.

I recently obtained recertification for my level one cardiopulmonary resuscitation (CPR). I had previously had level three certification in 2003. Things have changed. CPR is simpler and therefore more effective in the majority of cases since first responders will be less hesitant to initiate this potentially life saving procedure. The counting has become greatly simplified and the establishment of a clear airway has also been simplified. More recently the American Heart Association is recommending that the standard be simplified further to completely eliminate mouth-to-mouth.


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Saturday, October 30, 2010

Update on Sperm Bank Product Liability Lawsuit

A belated update on a story from a year and a half ago concerning a lawsuit brought against a sperm bank under product liability laws after a child conceived with that sperm developed Fragile X syndrome.

Under the laws being tested, it seemed all that needed to be shown was that injury (in this case, genetic disease) occurred as a result of using the product (in this case, sperm), not that negligence or lack of testing was a factor. At the time, I wondered whether genetic disease even qualified as "injury" since the alternative to injury is not being born at all. It turns out the courts had the same consideration.

A few months after the initial ruling by a judge that the case could go forward, the judge reversed his decision - a reversal that was upheld by a federal appeals court, on the basis that the situation basically amounts to a "wrongful life" case:
"Simply put, a cause of action brought on behalf of an infant seeking recovery for wrongful life demands a calculation of damages dependant upon a comparison between the Hobson's choice of life in an impaired state and nonexistence," Barry wrote. "This comparison the law is not equipped to make."

Barry, who was joined by Judges Theodore A. McKee and Morton I. Greenberg, quoted from Becker v. Schwartz, a 1978 decision of New York's highest court, that said: "Whether it is better never to have been born at all than to have been born with even gross deficiencies is a mystery more properly to be left to the philosophers and the theologians."
In addition to "wrongful life" considerations, the decision also points out other ways that treating genetic disease as injury is problematic.
The difficulties that B.D. now faces and will face are surely tragic, but New York law, which controls here, states that she “like any other [child], does not have a protected right to be born free of genetic defects.” To find the contrary would invite litigation for any number of claimed injuries and, even more problematic, require courts to identify certain traits below some arbitrarily established marker of perfection as “injuries.”
So kids, it looks like you can't sue your parents after all.


1 comments:

The Cancer Carnival is Coming

The Cancer Research Blog Carnival is due to arrive this Friday, November 5. If you haven't already, email us your recent cancer related posts, or submit them using this form.


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Thursday, October 21, 2010

The case for public science

Bravo!

"Today, the union that represents federal government scientists launches a campaign to put the spotlight on science for the public good.

“Federal government scientists work hard to protect Canadians, preserve their environment and ensure our country’s prosperity but they face dwindling resources and confusing policy decisions,” says Gary Corbett, president of the Institute.

The Professional Institute of the Public Service of Canada is a national union. Among its 59,000 federal and provincial members are 23,000 professionals who deliver, among other knowledge products, scientific research, testing and advice for sound policy-making.

The recent decision to end the mandatory long form census is the latest step in a worrying trend away from evidence-based policy making. Restrictive rules are curtailing media and public access to scientists, while cutbacks to research and monitoring limit Canada’s ability to deal with serious threats and potential opportunities.

A new online information and action centre launched today – PUBLICSCIENCE.ca – (http://publicscience.ca) features interviews with the professionals who do science for the public good, experts who understand the critical importance of this work, and Canadians whose lives have been touched by public science.

PUBLICSCIENCE.ca is part of a broader campaign to underline the importance of science for the public good and to mobilize scientists and the public to press politicians to make a clear commitment to policies that support public science.

“Our members are proud of the work that they do as independent and non-partisan scientists and we are going to work with them to tell their stories,” says Corbett. “Their work impacts on the daily lives of Canadians. It is science that is not and cannot be done by industry or by universities.”"


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Friday, October 15, 2010

Alternative medicine flowchart


From this great skeptic blog...


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What Should You Know About Cancer?

A recent paper published in Patient Education and Counseling tries to answer the question: What should a layperson know to be considered "cancer literate"? To do so, the authors assembled a panel of cancer experts (oncologists, GPs, nurses from oncology wards, social workers, public health experts) who refined the answer over a number of rounds. For their purposes, literacy was "the degree to which individuals have the capacity to obtain, process, and understand basic health information and services needed to make appropriate health decisions." Below is the table of their decisions (click to enlarge)

There are some key areas that are focused on: Aspects of cancer risk, aspects of information/detection, treatments, and coping with cancer/support. Some exclusions make sense, such as how tumours develop or rules for financing screenings, which are secondary to the average person being able to make appropriate health choices. Others are a bit more confusing. For example, knowing about behaviour or environmental factors that contribute to cancer are included in the concept of cancer literacy, but not knowledge about hereditary factors. Likewise, knowing about screening tests and their benefits is included, but not knowledge about groups for whom screening is advised. Cancer symptoms and warning signs also doesn't make the list, nor did limitations of screening, diagnostic procedures, or treatments

What do you think? Keeping in mind the goal is that a cancer literate person be able to recognize the need to consult an expert, but not to become an expert themselves, what should a person know to be considered "cancer literate"?


1 comments:

Thursday, October 14, 2010

Deepak Chopra: The Video Game

Deepak Chopra is the author of over 50 books on spirituality and alternative medicine, liberally sprinkled with terms from quantum physics in an attempt to lend weight to what the Committee for the Advancement of Scientific Skepticism at the Centre for Inquiry (Canada) has described as "new age psycho-babble" and what quantum physicist and Nobel laureate Murray Gell-Mann calls “quantum flapdoodle".

You may be familiar with Chopra from the recent flap when he was invited to speak at the Royal Ontario Museum, his issues with evolution, or his ongoing nonsense at the Huffington Post and his distaste for skepticism
Most of my stinging darts come from skeptics. Over the years I've found that ill-tempered guardians of scientific truth can't abide speculative thinking. [...] No skeptic, to my knowledge, ever made a major scientific discovery or advanced the welfare of others.
If you're not familiar with him, you'll soon have a chance to learn all about him on your Xbox or Playstation.

Game developer THQ, whose franchises include Saints Row and Red Faction, and licensing agreements with WWE and UFC, has bought the exclusive video game rights to Chopra's "teachings" for all the major gaming consoles.

It's unclear what the games might entail. I suppose dodging the darts of skeptics and scientists could be kinda fun.


1 comments:

Wednesday, October 13, 2010

Water Droplet Bouncing on a Superhydrophobic Carbon Nanotube Array


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Coolest dad ever


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Friday, October 08, 2010

Everybody's Working for the Weekend

It's Thanksgiving Weekend in Canada. Despite the holiday, many people will still make their way into the lab to get some work done, whether it's big experiments or simply maintaining cell cultures. The rest will be travelling to visit family or otherwise enjoying some well earned time off, right? Or maybe they just lack passion. That's what Dr. Scott Kern of the Johns Hopkins Medical Institute thinks.

In a recent editorial in Cancer Biology and Therapy, Dr. Kern takes a swipe at cancer researchers' lack of passion. Their "country-club mentality". Their desire for a life outside the lab.
During the survey period, off-site laypersons offer comments on my observations. “Don’t the people with families have a right to a career in cancer research also?” I choose not to answer. How would I? Do the patients have a duty to provide this “right”, perhaps by entering suspended animation? [...] Should I note that productive scientists with adorable family lives may have “earned” their positions rather than acquiring them as a “right”? Which of the other professions can adopt a country-club mentality, restricting their activities largely to a 35–40 hour week?
Read the whole thing if you don't mind being irritated.

Or just skip that part and read one of the many great responses by the likes of Isis the Scientist, Mike the Mad Biologist (here also), Drugmonkey, Scicurious, and Janet Stemwedel (and here).

Or just skip it all, and just watch this video:


3 comments:

Friday, October 01, 2010

2010 IgNobels Announced!

It's that time of year again, leaves are changing colour, people are making their Nobel prize preditions and the IgNobels, awarded by the Improbable Research are announced. Here at the Bayblab, we have a decent track record of hitting these stories before the announcement. How did we do this year?

PEACE PRIZE: Richard Stephens, John Atkins, and Andrew Kingston of Keele University, UK, for confirming the widely held belief that swearing relieves pain. (Bayblab link: F-ing Pain)

PUBLIC HEALTH PRIZE: Manuel Barbeito, Charles Mathews, and Larry Taylor of the Industrial Health and Safety Office, Fort Detrick, Maryland, USA, for determining by experiment that microbes cling to bearded scientists. (Bayblab link: A History of Beardism and the Science that Backs it)

BIOLOGY PRIZE: Libiao Zhang, Min Tan, Guangjian Zhu, Jianping Ye, Tiyu Hong, Shanyi Zhou, and Shuyi Zhang of China, and Gareth Jones of the University of Bristol, UK, for scientifically documenting fellatio in fruit bats. (Bayblab link: Fruit bat blowjobs)

Other highlights:
MEDICINE PRIZE: Simon Rietveld of the University of Amsterdam, The Netherlands, and Ilja van Beest of Tilburg University, The Netherlands, for discovering that symptoms of asthma can be treated with a roller-coaster ride.

PHYSICS PRIZE: Lianne Parkin, Sheila Williams, and Patricia Priest of the University of Otago, New Zealand, for demonstrating that, on icy footpaths in wintertime, people slip and fall less often if they wear socks on the outside of their shoes.


See the full list of this year's winners.


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Cancer Research Blog Carnival #38 - Breast Cancer Awareness Month

The latest edition of the Cancer Research Blog Carnival is up at Highlight HEALTH.
Welcome to the 38th edition of the Cancer Research Blog Carnival, the monthly blog carnival that discusses what’s new in cancer research. In recognition of October being Breast Cancer Awareness Month, this edition’s focus is on breast cancer.
As usual, Walter has done a fantastic job hosting, with a carnival loaded quality posts. Go check it out.


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Wednesday, September 29, 2010

Why squirrels masturbate


Since I mentioned in my last post that the amount of sperm produced by humans is literally astronomical, I've been thinking about which animals masturbate and why. For humans it seems to be a sexual outlet but is that the case for other mammals? How about non-mammals, do birds and bees masturbate? Well the motivating factor for male squirrels has been discovered, and it doesn't seem to be related to blue balls. Firstly, it appears that they are quite acrobatic:

An oral masturbation was recorded when a male sat with head lowered and an erect penis in his mouth, being stimulated with both mouth (fellatio) and forepaws (masturbation), while the lower torso moved forward and backwards in thrusting motions, finally culminating in an apparent ejaculation, after which the male appeared to consume the ejaculate.

Secondly, it seems to be motivated by cleanliness according to this paper:

"These results suggest that masturbation in this species was not a response to sperm competition nor a sexual outlet by subordinates that did not copulate. Instead masturbation could function as a form of genital grooming. Female Cape ground squirrels mate with up to 10 males in a 3-hr oestrus, and by masturbating after copulation males could reduce the chance of infection. Sexually transmitted infections (STIs) can profoundly affect fertility, and their consequences for mating strategies need to be examined more fully."

So who said masturbation was dirty?


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Tuesday, September 28, 2010

Colbert to Congress: More Human-Fruit Hybrids!


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Saturday, September 25, 2010

sperm vs stars

Is there more sperm or more stars in the universe?

*World male population of "reproductive age" = 2.17 billion (Males aged 15-64)

*Average amount of sperm per ejaculate = 300 million

*Total sperm if everyone ejaculated= 6.5e17

*Total amount of stars in Milky Way = 1e11

AND

*total sperm produced in lifetime = 525 billion

*total male population = 3.3 billion

*total sperm for every male currently living during their lifetime = 1.73e21

*total stars in universe= 1e21


sources:
population (CIA)
sperm (wikipedia)
stars (nasa)


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Monday, September 20, 2010

Fact or Fiction: Adam's Rib

And the LORD God caused a deep sleep to fall upon Adam, and he slept: and he took one of his ribs, and closed up the flesh instead thereof; And the rib, which the LORD God had taken from man, made he a woman, and brought her unto the man. Genesis 2:21-22 (King James Version)
I was asked recently whether it was true that women had a different number of ribs than men.

You may have heard this one before: Men have fewer ribs than women, either by a single rib or a pair. This notion follows from the biblical account of creation, whereby Eve was created from one of Adam's ribs and is used to support a literal interpretation of Genesis. But is it true?

The typical adult human skeleton has 206 bones and this number is the same for men and women. Of these, the ribs account for 24 (2 x 12). Seven of these pairs are connected to the sternum by cartilage, 3 are connected to the cartilage of the ribs above and 2 pairs, called floating ribs, are not attached to the sternum at all. These numbers are the same for men and women.

There are abnormalities that can alter the number of ribs. One such abnormality is a cervical rib which can cause thoracic outlet syndrome. A cervical rib is an extra rib arising from the seventh cervical vertebra, above the first rib ("normal" ribs are joined to the thoracic vertebrae). They are present in about 0.5% of the population. One large study of 10,000 radiographs looking at congenital rib abnormalities showed that women more often have cervical ribs, with a rate of about a 2.5 to 1 compared to males. This may be a reason for the propagation of the idea that females have more ribs than males, but in the typical, normal skeleton males and females have the same number of ribs.


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Friday, September 17, 2010

How to make your data significant

Anyone who's been in science long enough to either get a grasp of statistics, or alternatively figure out empirically how to game it, knows that given enough parameters and data points you will inevitably reach statistical significance on something. So what's the difference between a p-value of 0.051 and 0.049? Well this guy sums it up with a good anecdote :

"About two years ago the Wall Street Journal (registration required) investigated the statistical practices of Boston Scientific, who had just introduced a new stent called the Taxsus Liberte.

Boston Scientific did the proper study to show the stent worked, but analyzed their data using an unfamiliar test, which gave them a p-value of 0.049, which is statistically significant.

The WSJ re-examined the data, but used different tests (they used the same model). Their tests gave p-values from 0.051 to about 0.054; which are, by custom, not statistically significant.

Real money is involved, because if “significance” isn’t reached, Boston Scientific can’t sell their stents. But what the WSJ is quibbling, because there is no real-life difference between 0.049 and 0.051. P-values do not answer the only question of interest: does the stent work?
"

[...]

" Significance is vaguely meaningful only if both a model and the test used being are true and optimal. It gives no indication of the truth or falsity of any theory.

Statistical significance is easy to find in nearly any set of data. Remember that we can choose our model. If the first doesn’t give joy, pick another and it might. And we can keep going until one does."


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Wednesday, September 15, 2010

Cancer Carnival #38 - Call for Submissions

The next edition of the Cancer Reseach Blog Carnival is coming up on Oct. 1 and will be hosted by Highlight HEALTH.
Highlight HEALTH will be hosting the next edition of the Cancer Research Blog Carnival, edition #38, on Friday, October 1st. As host, I invite you to send your submissions.

October is National Breast Cancer Awareness Month. Accordingly, the theme for next month’s edition of the Cancer Research Blog Carnival is Breast Cancer.
Submissions can be made through the blog carnival submission form or by email.


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Monday, September 13, 2010

The Simpsons - Comments about PhDs and Grad Students. [HQ]


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Cool video of the week

I'm a huge fan of Feynman, and always admired his curiosity about stuff outside of physics. In his biography (if you haven't read it, you're not a proper nerd) there is a passage about experiments with ants:

"I found out the trail wasn't directional. If I'd pick up an ant on a piece of paper, turn him around and around, and then put him back onto the trail, he wouldn't know that he was going the wrong way until he met another ant. (Later, in Brazil, I noticed some leaf-cutting ants and tried the same experiment on them. They could tell, within a few steps, whether they were going toward the food or away from it—presumably from the trail, which might be a series of smells in a pattern: A, B, space, A, B, space, and so on.)"

"I tried at one point to make the ants go around in a circle, but I didn’t have enough patience to set it up. I could see no reason, other than lack of patience, why it couldn’t be done."

Well Mr Feyman, not only can it be done, but it happens in nature...



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Wednesday, September 08, 2010

Dance Dance Evolution

Scientists have finally figured out why I fare so poorly at the clubs: my dance moves. A paper published in Biology Letters and reported in the Globe and Mail describes research determining what dance moves are most attractive to women. Close to 40 women watched video clips of 19 different males (none of whom were professional dancers) whose images were motion captured and transformed into genderless, featureless avatars to put emphasis on movement and not on looks, as well as to save them the embarrassment when the dancing videos inevitably hit Youtube (follow these links for video samples from the supplementary materials of good and bad dancing). Males danced to a core drumbeat to eliminate music likeability as a confounder, and women judged the dancing. The researchers determined what movements were correlated with what women rated as "good" dancing. From the Globe and Mail article:
The study found that female perceptions of good dance quality were influenced most greatly by large and varied movements involving the neck and trunk.The speed of the right knee movements were also important in signalling dance quality.

A “good” dancer thus displays larger and more variable movements in relation to bending and twisting movements of their head/neck and torso, and faster bending and twisting movements of their right knee,” the researchers said in a report published in the Royal Society Journal Biology Letters.
So with that information in mind, it's time to design the perfect dance move - we just need to make sure we include some good head, torso and right knee movements. I'm imagining an exaggerated version of GOB's chicken dance:
(or maybe some moves from this pizza commercial)

The authors suggest that these movements signal "traits such as health, fitness, genetic quality and developmental history," likening them to courtship rituals in other animals. Dance being culturally influenced, I'd be curious to see if the elements of an attractive dance hold up across cultures. Likewise I'd be interested to see if their results are reflected by notable great dancers or if dance crazes of bygone eras are centred around these movements. In the meantime, I'll experiment with some of these motions, but I doubt they'll be winning hearts anytime soon.


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Monday, September 06, 2010

2000 years old tetracyclin beer?

When tetracyclin was detected in large quantities in the bones of ancient Sudanese Nubians from 350-550 CE, many wondered if it was accidental. But evidence suggests that it was manufactured on purpose by growing streptomyces in beer. It seems to have been used therapeutically, including in children:

"“The bones of these ancient people were saturated with tetracycline, showing that they had been taking it for a long time,” he says. “I’m convinced that they had the science of fermentation under control and were purposely producing the drug.”

Even the tibia and skull belonging to a 4-year-old were full of tetracycline, suggesting that they were giving high doses to the child to try and cure him of illness, Nelson says."


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Friday, September 03, 2010

Cancer Carnival #37

Friday of a long weekend? The only thing that could be better is a fresh edition of the Cancer Research Blog Carnival. The Carnival relies on posts and hosts, so be sure to submit your posts for next month, where the carnival will be hosted by Highlight HEALTH, who also start the proceedings this month.

In a recent post at HighlightHEALTH, Faith Martin discusses peer-reviewed research into the link between positive psychology and cancer survival.
Enter “Psychoneuroimmunology” – the field of study exploring the direct link between the nervous system and immune system, including the endocrine system, covering hormones. The brain controls these systems. Part of psychoneuroimmunology is the study of degree to which the action of these systems is impacted on by mental health and the way we think and process information around us. This is of particular interest when we exam the relationship between psychological experience, nervous/immune/endocrine systems and health conditions.
Faith goes on to describe how stress and psychology can impact physiology in ways that can affect tumor growth.

At Stem Cell Assays, Dr. Alexey Bersenev highlights high-throughput cancer stem cell-based screening assays to identify therapeutic compounds, in particular for neuroblastoma.

David at Health and Life, offers a brief summary on the history of cancer treatment and what future directions it is taking, with a particular mention of anti-angiogenic therapy. On the subject of anti-angiogenesis, Blane Tarr points us to a TED talk about anti-angiogenesis and dietary sources for certain anti-angiogenic compounds, such as ellagic acid from strawberries. Sticking with a dietary theme, Valentina Rey sends us a post about research into the effectiveness of produce in preventing lung cancer.
According to this new findings, a subject’s risk of developing lung cancer decreased when fruits and veggies were eaten, regardless of the amount—here, variety, not quantity, was important. Each different type of produce eaten reduced the risk of cancer by another 4%, up to a total decrease of 23%. This decrease occurred for all types of lung cancer, including squamous cell carcinoma, a type of cancer developed by smokers.
Here at the Bayblab, I provide an update, describing some sad news surrounding research into Devil Facial Tumor Disease. Other bloggers have also covered this story.

Finally, Orac has a post about the angiogenesis inhibitor Avastin, and the politics of drug approval.
Another lesson of the ongoing Avastin saga is about the very nature of science-based medicine itself. We have stated that we believe that medical care should be science-based. However, although medicine should be based on science, medicine itself can never be a pure science because so many non-science-based considerations impact on it. On the patient level, there is patient choice and how the doctor and patient weigh the patient's personal situation and personal considerations in choosing from among science-based therapies. At the national level, considerations of cost, politics, and values cannot be separated from medical policy considerations. Science can tell us that Avastin does not prolong overall survival in breast cancer patients and that it only very modestly prolongs progression-free survival. It can tell us that even that modest increase in PFS comes at a cost of complications that prevent improved PFS from translating to improved OS. What science can't tell us is whether that modest benefit is worth the cost. That's a value judgment that must be made both at the level of society as a whole and at the level of each patient and physician.
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.


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Next time you talk about a piss-warm beer...

Scicurious has a post up about - quite literally - piss beer. It describes a situation where yeast infections cause the fermentation of bodily fluids:
The second patient had “turbid” urine (that’s cloudy), and they suspected yeast, especially when they opened the bag of urine, and smelled BEER. Apparently this was so odd that the urine sample passed to every doctor in the room and down the hall. I can just picture a group of people in white coats, all gathered around with a cup of suspiciously yellow liquid, sniffing and saying “HEY GUYS! You gotta smell this!!!” Apparently the poor patient was so yeasty that her breath, and literally everything about her smelled like beer, and alcohol could actually be detected as a byproduct of the yeast.
(cue comparisons to your least favourite brew) I guess this is a bit of a different take on the human decanter.


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Thursday, September 02, 2010

Ghosts of Stem Cells Past

Are all induced pluripotent stem (iPS) cells created equal? How similar are they to ES cells? My latest post at the Stem Cell Network looks at two recent papers asking these questions.


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RIP Cedric

You may remember stories here and elsewhere about transmissible cancer among tasmanian devils. Devil facial tumour disease (DFTD), as it's called, isn't spread by a virus but rather by allografts of tumour cells of Schwann cell origin that spread from animal to animal by biting. This had raised some interesting questions about the immunology of these tumours. How do they avoid immune rejection? Is it possible to create a preventative vaccine?

One key thought to hold the answer to DFTD that has wreaked havoc on the tasmanian devil community is Cedric, a devil that was thought to be immune to the cancer. But alas, Cedric was recently euthanized after two facial tumours that had been surgically removed had been shown to have spread to the animal's lungs:
In 2007, Menzies researchers injected Cedric and his half brother Clinky with facial cancer cells. Clinky developed the disease, but Cedric showed an immune response and grew no tumors — giving researchers hope that he could help them create a vaccine.

But in late 2008, Cedric developed two small facial tumors after being injected with a different strain of the cancer, which causes grotesque facial growths that eventually grow so large, it becomes impossible for the devils to eat. Current estimates suggest the species could be extinct within 25 years due to the prolific spread of the cancer.

Researchers removed the tumors, and Cedric appeared to be rallying. But X-rays taken two weeks ago showed the cancer had spread to the 5-year-old's lungs, Kreiss said. Tests confirmed the lung tumors were a result of facial tumor disease.
This is a blow to the scientists trying to understand and curtail the spread of DFTD, but hopefully data from Cedric will push forward new strategies to help the devil population.


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Saturday, August 28, 2010

Cool laser trick

Do you have pond water and a green laser pointer? If so you should replicate this guy's awesome setup. All he did was hang a drop, and shine a laser at it, and voila! It reminds me of those planetarium shows I saw as a kid, but with bacteria.


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Wednesday, August 25, 2010

Fraser river sockeye: A failure of science?


Since 2006 commercial fishing for sockeye salmon on the Fraser River in British Columbia has been closed. In 2009 the run collapsed with a return of 1.5 million despite a prediction of 11 million. This instigated an expensive government inquiry to find out what happened. The end of Fraser River wild sockeye salmon seemed quite likely. Federal government regulation managed to completely fail in eastern Canada, with the cod fishery, and in 2009 it seemed as if they had done it once again in western Canada.
As a sport fisherman I am always under the strong impression that fishing is always getting worse, year after year. The old photos and fishing stories of huge and abundant salmon seem to reinforce my impression.
Now the 2010 sockeye salmon run is a record run with an estimated 25 million fish returning. This is the largest return in almost a century! Good news for salmon, fishermen and the environment but it is an indication of really inaccurate science. An estimate in late July suggested there might be 11 million returning sockeye, far from reality. At this point I think that it is clear that the Department of Fisheries and Oceans is incapable of making accurate estimates. I am not suggesting that estimating salmon returns is easy but making policy decisions based upon their predictions seems like a bad idea. Is there a very important variable that is not being accounted for?
How is it possible that the estimates can be so wrong? Taking a brief look at the pre-season estimate report for 2010 shows that estimates are strongly based on retrospective data. Perhaps this data is insufficient for estimating returns and other sources need to be utilized. I hope that this results in some changes in the methods used for making these estimates. Even better, the government could fund some more ecological studies of this important commercial resource in order to better understand how an error of this magnitude could have happened.


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Tuesday, August 17, 2010

Dig Deeper

Christina Pikas has a post up about the danger of using only sources with recent coverage. That is, not digging far enough back in a literature search.
...an editorial from Nature Reviews Microbiology that says youngsters today aren’t getting the proper baseline literature because they’re relying on PubMed and Google Scholar. They cite the subject area of bacteriophage biology – developed well before the Medline era. Some researchers in this area have created their own bibliography of articles prior to PubMed, but they are concerned about losing access to the publications as they are moved out of the library to storage.
One solution is to make students aware of other databases and resources (your university library likely has access to plenty of them) and encourage them to use librarians as a resource. At our grad school, the first departmental seminar of the year is given by the library staff, though I think it tends not to be taken seriously. An even worse problem is an attitude that if it can't be accessed online - if you have to go the the library and find it on the shelves, or deal with interlibrary loans - then it isn't worth the trouble.

Christina points out a very real danger in ignoring older literature: The case of a Johns Hopkins researcher whose 'current only' search missed an association between the intervention and lung toxicity, leading to the death of a volunteer. This is an extreme case, but there is a real danger of missing important findings in your field or duplicating previous work. Think about the time and effort that could be saved by digging a little deeper!


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PLoS Journals Open to Everyone - Except Tobacco Researchers

"At PLoS, we believe that articles in all journals should be assessed on their own merits rather than on the basis of the journal in which they were published."
Assessed on their own merits, that is, unless they were funded by in whole or in part by a tobacco company. A few months ago, PLoS Medicine followed PLoS Biology and PLoS ONE in changing its editorial policy to one of no longer considering research where support comes from a tobacco company.

This change comes mainly on the grounds that tobacco is indisputably bad for health and see tobacco-sponsored research articles as advertising, and they refuse to help enhance the image of the industry. They also have concerns about industry ethics.
we remain concerned about the industry's long-standing attempts to distort the science of and deflect attention away from the harmful effects of smoking. That the tobacco industry has behaved disreputably—denying the harms of its products, campaigning against smoking bans, marketing to young people, and hiring public relations firms, consultants, and front groups to enhance the public credibility of their work—is well documented. There is no reason to believe that these direct assaults on human health will not continue, and we do not wish to provide a forum for companies' attempts to manipulate the science on tobacco's harms.
There is no doubt that smoking is unhealthy and that tobacco companies have acted in dubious ways to support their business interests. Sadly, that's not uncommon in big business - whether it's tobacco, oil, pharmaceutical or junk food. Will PLoS journals be rejecting all papers coming from Merck?

The issue here is that it runs counter to openness and the idea that research should be judged on its merits. Maybe I'm naive in thinking that "Smoking is Cool!", study funded by Philip Morris, will raise red flags for everybody. Isn't that why authors declare competing interests?

Strangely, PLoS justifies the decision arguing that it doesn't happen much anyway.
It is the case that we do not receive many tobacco industry sponsored papers—PLoS Medicine has published none since our inception in 2004 and PLoS ONE only two—and we have made previous editorial judgments on papers that might be favorable to the tobacco industry agenda on a case-by-case basis.
This seems to undercut the argument that Big Tobacco is persistently trying to manipulate science, and by refusing to review the few that are submitted, doesn't that just push them to venues where they might receive a less critical eye?

Worse, this policy could have an effect on tobacco's legitimate contributions to science. How might a ban on tobacco-funded research affect studies exploring plant-based vaccines, agricultural research or even virology (eg. tobacco mosaic virus research or interferon production)?

I love the free and open nature of the PLoS journals and have no love for Big Tobacco, but I'm not a huge fan of this editorial decision.


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Saturday, August 14, 2010

3D Blogging

3-D is all the rage now, with many major studio releases coming out in 3D and 3D TVs starting to make their way into homes (even though some people, like film maker Christopher Nolan dislike the technology). Normally the 3D effect is achieved by wearing special eyewear, like the iconic blue/red lenses, to deliver a different image to each eye. Newer devices, like the Nintendo 3DS, are using different, eyewear-free technology for the same effect. This video, grabbed from Joystiq, explains how it works:


You'll notice in the video, mention of another application for the same kind of technology: delivering different images to different viewers on the same screen. This could have some interesting uses - no more conflicts of TV scheduling (though unless directional audio is also part of the package, we'll still have to resort to headphones). And imagine local multiplayer gaming, without the annoying split-screen! Sony has, and has patents on a multiplayer stereoscopic system.


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Thursday, August 12, 2010

Beer Stats!

Extremely unmanly of me is the fact that I don't really find sports statistics interesting. Sports stats are a common default male conversation for which I usually have nothing to contribute. However, I do enjoy watching sports, and by sports I mean hockey, provided I am consuming beer. Next time I'm at the pub enjoying a nice india pale ale and someone starts on about Crosby vs Ovechkin giving me an earful of numbers, I think I'll try to switch the conversation to numbers that really matter: Beer stats. Your pint vs mine.

Alcohol/Volume

To many drinkers, this is the only number that matters, the higher the number the less you need to consume to feel the effects of the ethanol produced from the fermentation process. Alcohol/volume (abv) is a worldwide standard and is usually the only beer stat you can find on the container. It is simply the amount of ethanol expressed as a percentage of volume. Conventionally brewed beer, using a conventional yeast and a single fermentation step is in the 2% to 12% abv range (almost always in the 4-6% range). Higher alcohol content can be achieved using alcohol tolerant yeast strains, adding sugar during fermentation and by fractional freezing that produces so called ice beers. The process of fractional freezing involves cooling the fermenting liquid until ice crystals float to the surface then removed. This process removes water thus increasing the ratio of ethanol to water and therefore increases the abv. If you really want the Sidney Crosby of beer abv you could try a $800 bottle of The End of History by Brew Dog. Maximum Ice (7.5% abv) drinkers will be impressed with The End of History's 55% abv.

Degrees Plato
The coolest sounding statistic, degrees Plato, unfortunately isn't very useful when comparing pints you are drinking as it is mostly a stat useful during the brewing process to determine the final abv. Degrees Plato is the %w/w sugar ie the grams of sugar per 100g of wort. Since sugars are consumed and converted to ethanol during fermentation, and thus not what was origonally put into the wort, the determination of degrees Plato of beer is usually determined using measurements of specific gravity. Specific gravity is the ratio of the density of the wort or beer to the density of water. Specific gravity is used instead of direct density measurements as at a standard temperature and pressure specific gravity is more easily measured using an instrument such as a hydrometer. The difference in specific gravity between the starting wort and the finished beer can be used to calculate the ethanol produced during fermentation since decreased dissolved sugar and increased alcohol decreases the specific gravity.

Standard Reference Method
This is a quantification of beer colour. The standard refernce method (SRM) is 12.7 times the absorbance of filtered beer at 430nm. So the SRM is really only measuring "darkness" and not truly colour and it looses linearity at higher SRMs. There is a highly related system EBC which also uses an absorbance measurement at 430nm, and I'm unsure of which is in more common usage in Canada. There are some other more sophisticate systems to better quantify colour of beer. For example Tristimulus colour is determined by measurements at many different wavelengths and describe beer colour in a three dimensional colour space.
This is an especially cool stat for those that like uber dark beers. Nothing like bragging about your pint of Guiness with an impressive SRM of 40, until some guy with an Imperial Stout reminds you that his pint has an SRM of 70.

International bitterness units
Hops are added to beer as a flavouring and stability agent. Interestingly from kamel:
Incidentally, the hop alpha-acids also have antibacterial and anti-inflammatory properties. Thats why traditional India Pale Ales (not that Keith's crap) have a strong bitter, hop taste. Extra hops were added to help preserve the beer on its journey from Britain to India.
The determination of international bitterness units (IBUs) involves extraction of the bitter tasting hop alpha-acids and quantification using UV absorbance or HPLC. Since this involves sophisticated laboratory equipment there are alternative methods for the small scale or craft brewery. One involves adding hop alpha-acids to a beer of known IBUs, like Bud, until it has the same bitterness as the beer in question. While this method has the benefit of drinking lots of beer for replicate samples, it, and the IBU measurement itself, suffer from a disconnect between IBUs and perceived bitterness. Malty beers with the same IBU as a pale ale will be taste less bitter.

Carbonation/Nitrogenation
While I haven't seen quantification of beer carbonation, in beverages it is reported in grams/litre and can be determined by infrared absorption at 4.27 um. Such a stat would obviously only refer to an untapped keg or unopened bottle/can. Some beers are nitrogenated instead of carbonated, usually stouts and British ales. Again I have not seen a beer report an amount of nitrogenation, however this would be a useful and descriptive statistic.

More Stats
Kamel's great post about beer foam entitled, Good Head has some information on the composition of beer head. The denatured protein LTP1 is the main structural component of the head along with hop alpha-acids. This reeks of a need for quantification. This information along with carbonation/nitrogenation content would inform the drinker on proper pouring to ensure the best possible head.

Inspiration for this post was from discovering this very useful quantification of beer greatness as my current favourite beer, Tree Breweries Hop Head, prominently displays the fact that it measures 45 IBUs. I'm also enjoying Phillips Hop Circle IPA however I don't know it's IBU. This is unfortunate as I think beer stats are a great opportunity for brewers, especially craft brewers to advertise and quantify their uniqueness. Beer geeks want to know! Yes this might lead to more of the ridiculousness exemplified by Maximum Ice, and I would also say that there is a subjective quality to beer that perhaps would get lost in the numbers. But sports statistics are popular and sports geeks know that just like Ovechkin looks better on paper, Crosby's the real winner.


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Blogospherics

Scienceblogs Pepsigate led to an exodus of bloggers. Some of them maintain independent blogs (Carl Zimmer has maintained a list of their destinations). Others formed a new blogging collective: Scientopia.

If you're looking for other places for 'one-stop science blog shopping' labspaces.net hosts a stable of over 20 science bloggers.

There's also the Field of Science network (which Bayblab was once invited to participate in) and its group of around 20 blogs.

And of course Discover blogs and ScienceBlogs are still big players. (I've been particularly enjoying Rhett Allain's Dot Physics)

That's 5(!) solid science-blogging collectives.

And if you want some individual reads between Bayblab posts, check out:

* If Physical Books Are Dead in Five Years, How Do the Poor Find Books? Whither (or Wither?) the Library? by Mike the Mad Biologist

* The Death of Universities at Sandwalk

(hmm... books and universities both dead in 5 years?)

* Peeing in Space at Neurotic Physiology

* Are grad students professional scientists? at Genomicron (this is an ongoing discussion spanning several posts)

* Basic science: An "obstacle" to students who want to study medicine? at Respectful Insolence


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Wednesday, August 11, 2010

But Could He Make a Disease so Great Even He Couldn't Cure it?

Here's the abstract from a paper published in Virology Journal:
The Bible describes the case of a woman with high fever cured by our Lord Jesus Christ. Based on the information provided by the gospels of Mark, Matthew and Luke, the diagnosis and the possible etiology of the febrile illness is discussed. Infectious diseases continue to be a threat to humanity, and influenza has been with us since the dawn of human history. If the postulation is indeed correct, the woman with fever in the Bible is among one of the very early description of human influenza disease.

Infectious diseases continue to be a threat to humanity, and influenza has been with us since the dawn of human history. We analysed a case of high fever that happened 2000 years ago in Biblical time and discussed possible etiologies.
At least they formally ruled out demon possession. The rest of the paper isn't much longer and is a pretty bizarre piece of peer-reviewed research. There's too much to write about it, I don't even know where to begin. Luckily Tara Smith at Aetiology already did most of the work.

Who says the quality of peer-reviewed publication is on the decline?

UPDATE: The paper has been retracted.


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Tuesday, August 10, 2010

Blogger is evil

The Pepsigate scandal over at scienceblogs is starting to look pretty harmless in comparison to the recent news that google, which owns blogger.com on which the bayblab is hosted, is an enemy of net neutrality. I encourage everyone to familiarize themselves with the concept of net neutrality if you already are not, but basically the internet as we know it today is founded on this concept of network neutrality. A proposal from Google and Verizon would enable the creation of a tiered internet meaning that large established sites could pay ISPs for better connections. An article in Wired has one of the best summaries of the situation that I have read. Since this Google/Verizon proposal is in conflict with Google's previous stance on net neutrality and, depending on your view, breaks their famous motto, "don't be evil" I am even less inclined to trust the internet giant. Currently this is just a proposal and it is possible the FCC will be able to assert new powers to swart this plan and Obama has stated he is commited to net neutrality. However the fact that these two companies with somewhat competing interests came together on an agreement will make it more difficult and has revealed their true intentions.
Here in Canada the situation is a bit better, however, I'm sure that as usual changes in US policy will directly affect us here.
This, on top of the privacy issues with google, mean that personally I'm no longer considering an android phone and am going to start moving away from a recently created gmail account in a fairly lame attempt at a protest. This protest will be so lame that the bayblab won't be going anywhere.


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PhD Illustrated

Trust me, this will make sense when you visit this blog.


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Friday, August 06, 2010

Cancer Carnival #36

Once again, it's the first Friday of the month, which means it's time for the Cancer Research Blog Carnival. The Carnival relies on posts and hosts, so be sure to submit your posts for next month, and if you're tired of seeing it here on the Bayblab, drop us a line to sign up as a host. On to the posts...

First up, we have a post from Byte Size Bio that arrived just after the last carnival went live. In it, he looks at a paper investigating a role of pseudogene mRNA in regulating tumour biology. By interacting with miRNA, some of these pseudogene mRNAs may act as tumour supressors or oncogenes!
PTEN1 is a pseudogene which shares a very recent common ancestor with PTEN. A mutation in PTEN1 prevents it from being translated into a protein product, but it can still be transcribed to PTEN1 mRNA. Laura Poliseno and her colleagues have shown that PTEN1 mRNA, being very similar in sequence to PTEN mRNA attracts miRNA molecules that target PTEN mRNA. In other words, PTEN1 mRNA lures PTEN-specific miRNA molecules away from PTEN mRNA, lowering the number of inactivated PTEN mRNAs.
This is a pretty cool finding, and the post was an Editor's Selection from Researchblogging.org, so be sure to check it out.

Here at the Bayblab, Rob points to recent research about fructose metabolism in pancreatic cancer. Orac, at Respectful Insolence, also writes about this study.
So how was fructose metabolized in pancreatic cancer cells? For the most part, it was used to generate nucleic acid synthesis. Compared to glucose, fructose induces is preferentially metabolized via the nonoxidative pentose phosphate pathway to synthesize nucleic acids and increase uric acid production. What this means is that fructose provides the raw materials for cancer cells to make more DNA, which cells must do in order to divide and proliferate.
At the Spittoon, 23andMe's blog, their SNPwatch feature highlights mutations associated with liver cancer in Hep-B infected patients.
Rs12136376 is near several genes: KIF1B, UBE4B and PGD. Multiple lines of evidence suggest that one or more of these genes are plausible candidates for HCC susceptibility. Changes in the region of the genome where they are found are commonly seen in many different cancers, including HCC.
Details of the SNP, the analysis and outcomes are all explained in the post.

Keith Robison at Omics! Omics! discusses a project undertaken by Genentech and Affymetrix to scan over 400 tumour genomes for mutations. Keith has a really good explanation of the methodology while MassGenomics has a broader overview of the study findings.

Finally, in another piece of research blogging, Michelle at C6-H12-O6 looks at a paper invesigating the effects of caloric restriction on glioblastoma multiforme, a malignant and invasive brain cancer.
As I said, CR-induced ketosis has been known to reduce non-invasive brain tumors. It appears that cancer cells are highly dependent on glycolysis for energy and for some reason (unknown to me, although I'm sure there's literature out there on it) seem incapable of mitochondrial respiration. As such, they cannot use ketones for energy like healthy cells can. Up until now, this hasn't been tested in more invasive cancers, where the tradeoff in neurological impairment might be worth it to stop or delay the spread of the cancer.
This is a nice write up with a good description of the background metabolism. And I don't just say that because of my own interest in CR.

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.


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Wednesday, August 04, 2010

Awesome Jesus Gecko Video


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Tuesday, August 03, 2010

Fructose induces nucleic acid synthesis in pancreatic cancer cells


A quick read of an article summarized in the mainstream media suggests that at least some cancer cells metabolize glucose and fructose differently. This defies the conventional wisdom that, metabolically speaking, these sugars are interchangeable. While fructose fed cancer cells do not have increased proliferation, the study suggests fructose is used more readily for nucleic acid synthesis. Glucose in the same cells is used primarily for energy resulting in lactate and CO2 production. Additionally another recent article demonstrates that breast cancer cells exhibit a more aggressive phenotype when using fructose as a carbon source. As the Reuters article suggests, this may be of public health significance as consumption of free fructose has increased 10 fold between 1970 and 1990.Link


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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.


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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]


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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.


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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.


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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.


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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.


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