Thursday, April 30, 2009

Investors keen on cancer vaccine

Reuters is reporting that several brokerages have upgraded the stock of a Seattle company, Dendreon, from 'hold' to 'buy'. The reason? Dendreon is the creator of Provenge, a prostate cancer vaccine expected to get FDA approval sometime late this year.

The reason for the excitement is recent data (presented at the American Urological Association annual meeting) showing a modest improvement in prostate cancer survival rates - a 4.1 month increase, with a 3-year survival rate of 42% compared to 23% for the control group. Oddly, the drug extends survival without shrinking tumours. However, Forbes reports that there is some concern over study design:
Much of the skepticism about Provenge until now has related to the perceived limitations of the 500-person study that Kantoff helped run. It was too small, some experts thought, and had an unusual design in which patients who did not receive Provenge and saw their cancer get worse would receive a frozen-then-thawed version of the vaccine.

This is unusual and may be unprecedented, says Donald Berry, head of biostatistics at the M.D. Anderson Cancer Center. It is possible that this frozen-then-thawed vaccine is actually different from Provenge; if it somehow harmed patients (there's no proof it does), it would actually make Provenge appear more effective. He asks how patients did after their cancer had progressed.
What's cool, though, is that if it works and is approved it will be the first cancer vaccine. The treatment itself is manufactured in part from a person's own antigen presenting cells (APCs, in this case dendritic cells). Patient APCs are extracted and co-cultured with a recombinant fusion protein. The now antigen-loaded APCs are then reinfused where they potentially activate a T-cell response against prostate cancer cells. The full course consists of 3 treatments over 4 weeks with only mild side effects compared to standard chemo treatments.

While the survival increase is quite small, it's encouraging and at least highlights the possibility of this kind of therapy. It would be interesting to know the duration of the immune response. Could this method be used as a preventative measure? How effective would it be against other cancers? (using a different antigen, of course)


Wednesday, April 29, 2009

Is Bayman Going to Get the Swine Flu?

64...current number of laboratory confirmed cases of flu strain H1N1 (most nonlethal) reported worldwide in the last week or so. Should I be scared? That's 64/6,706,993,152. Is that a lot? I dunno. What's normal for this time of year? I bet you could find 64/6,706,993,152 people who are postive for anything if you tried hard enough.


Tuesday, April 28, 2009

Thinking About Graduate Studies? Have You Considered A More Humane Form of Suicide?

This story is not really a new one to us graduate students, but I was surprised to find it at the top of the New York Times most emailed list: End the University as We Know It.

Columbia Prof Mark Taylor just comes right out and says it:

"GRADUATE education is the Detroit of higher learning. Most graduate programs in American universities produce a product for which there is no market (candidates for teaching positions that do not exist) and develop skills for which there is diminishing demand (research in subfields within subfields and publication in journals read by no one other than a few like-minded colleagues), all at a rapidly rising cost (sometimes well over $100,000 in student loans)."

Here from my fox hole at final-year PhD student ground zero, I can tell you Mark is not suffering from tenureship delusion. He's right on the money. The demise of graduate school spans disciplines, countries (at least in North America) and affects both core university departments and satellite institutes alike. This painful reality is worth a hard look if you're considering getting into graduate school:

"The dirty secret of higher education is that without underpaid graduate students to help in laboratories and with teaching, universities couldn’t conduct research or even instruct their growing undergraduate populations. That’s one of the main reasons we still encourage people to enroll in doctoral programs. It is simply cheaper to provide graduate students with modest stipends and adjuncts with as little as $5,000 a course — with no benefits — than it is to hire full-time professors.

In other words, young people enroll in graduate programs, work hard for subsistence pay and assume huge debt burdens, all because of the illusory promise of faculty appointments. But their economical presence, coupled with the intransigence of tenure, ensures that there will always be too many candidates for too few openings."

Kudos to Taylor for having the kahones to speak the truth in this rather public forum. I remember several years back an Ottawa journalist, Tom Spears ran a similar story on the plight of the graduate student/biomedical researcher after hanging around our research institute for a couple of days: "Hunting For Miracles at Minum Wage":

"A PhD student will work more than 60 hours a week in the lab, in return for a salary near $19,500, and sometimes payment of tuition. The salary portion is worth about $6.25 an hour -- less than minimum wage, for someone who might hold a key to heart disease, or cancer, or diabetes."

Needless to say, the Directorship of our institute tried to run him out of town. A flurry of follow-up discussion took place here on the Bayblab. See:

"Mr. T. Pities the Fool Who Does Graduate Studies"
"Are Graduate Students Exploited?", and
"More on the OHRI Salary Scandal"

I guess Spears can have the last laugh now with the knowledge he scooped the NYT.

Anyhow back to the original article. Taylor doesn't stop at just nailing down the problems. He proposes some reasonable ways to fix graduate programs. For example:

"Abolish permanent departments, even for undergraduate education, and create problem-focused programs."

"Transform the traditional dissertation. In the arts and humanities, where looming cutbacks will be most devastating, there is no longer a market for books modeled on the medieval dissertation, with more footnotes than text."

Good ideas but I don't think any of his proposals would address the most serious problem, which is the supply-demand/slavery issue.

At any rate, it's clear that research training is broken. We need to fix it. Any other ideas?


Swine Flu map

We have posted about Healthmap before, however, the current swine flu outbreak is exactly the reason why this site is awesome. It's extremely cool to check out the spread of an epidemic on a map. You can also view the data on google earth. The picture here was the healthmap of the swine flu at the time of posting.
Check Healthmap out. HINT: You can deselect all infections/diseases first and then just select the swine flu to get rid of all that background.


Monday, April 27, 2009

The Cancer Carnival Cometh

Don't forget to get your posts in for the 21st edition of the Cancer Research Blog Carnival, which will be hosted this Friday, May 1st over at HighlightHEALTH. Walter always does a fantastic job hosting, and is asking that any posts you want considered for inclusion be submitted either here or via the feedback form on his site, by Wednesday April 29th.


Wednesday, April 22, 2009

Pocket Protector

I always use a pocket protector on my lab coat. Sharpies can explode!! It's as much a part of laboratory bling as a HUGE capacity USB stick around your neck, or a sweet iTouch for rocking out in the tissue culture room, or a nice green coloured laser pointer, or a personal copy of Sambrook & Maniatis.
Check out the interesting history of the invention of the pocket protector on Boingboing.
Is there any cool laboratory bling that I forgot to mention?


Friday, April 17, 2009

A new kind of methylation

By now we're all aware of epigenetics and the role of cytosine methylation in gene expression, imprinting and retrotransposon silencing. We may however, have been fooling ourselves, since there may exist another type of methylated cytosine: 5-hydroxymethylcytosine. The journal Science will unveil 2 papers next week describing this novel modification. How could we have missed it for so long? :

"The reason that this nucleotide had not been seen before, the researchers say, is because of the methodologies used in most epigenetic experiments. Typically, scientists use a procedure called bisulfite sequencing to identify the sites of DNA methylation. But this test cannot distinguish between 5-hydroxymethylcytosine and 5-methylcytosine, a shortcoming that has kept the newly discovered nucleotide hidden for years, the researchers say. Its discovery may force investigators to revisit earlier work. The Human Epigenome Project, for example, is in the process of mapping all of the sites of methylation using bisulfite sequencing. "If it turns out in the future that (5-hydroxymethylcytosine and 5-methylcytosine) have different stable biological meanings, which we believe very likely, then epigenome mapping experiments will have to be repeated with the help of new tools that would distinguish the two," says Kriaucionis."

This is exciting, can't wait to read up on it. It seems very abundant, stable and well conserved too...


Wednesday, April 15, 2009

Canadian Mathematicians Stand Up for Biomedical Research

G&M reports on an open letter to the Canadian government protesting cuts to science funding in the recent budget, now signed by over 2,000 scientists. Basically the gist is that it's not enough to just fund building construction and PhD scholarships, but that grant money is also needed to RUN actual research programs. So that all those students in all those buildings can actually do something useful. Apparently the effort was initiated by a group of mathematicians led by Nassif Ghoussoub from UBC.

A number of points made in the letter, posted on the website, "Don't Leave Canada Behind". An excerpt:

"Whereas the U.S. administration is proposing to boost the funding of the National Institute of Health (NIH) by 30% ($8.5 billion in addition to its current $29 billion), our “stimulus budget” is cutting CIHR’s by 5%, while essentially ignoring the needs of Genome Canada."

More interesting stuff here re PhD student funding:

"The funding of an additional 500 doctoral scholarships is great news...however, it seems this funding is coming at the expense of the highly qualified personnel (HQP’s) that could have been recruited more efficiently by our senior researchers through their Tri-Council grants. We believe that a more efficient strategy for ensuring a successful HQP policy is to give our leading researchers the flexibility to manage the selection, recruitment, and support of their own graduate students through their peer-reviewed research grants, and via well-established leveraging procedures with the universities and the private sector."


"we also regret that the $17.5-million assigned to SSHRC for graduate scholarships have been earmarked towards students in business and finance."


"President Obama is proposing to double federal funding for education over the next 10 years, and pledging to “restore science to its rightful place” with billions in new investments. To advise his government, he has appointed leading scientists to his cabinet and as his advisors (including a Nobel laureate as energy Secretary). The Obama administration has also involved the directors of NIH and NSF in federal budget discussions about the future of research. We need a similar approach in Canada, where top research scientists and humanists can help shape directions in Ottawa for research funding."

Interesting. Will it have any impact?


Shouldn't We All Own the Internet?

Renewed bickering over net neutrality south of the border.

"Time Warner Cable tells FCC to shut up about net neutrality."

Apparently there's a bunch of stimulus money headed for broadband infrastructure development, and the FCC is saying it should be spent in the interest of maintaining an open an universally accessible internet. Telcos, as usual, are much more interested in net profits than net neutrality, and they're telling the FCC to go screw themselves. As you would expect, telcos want to get their hands on that stimulus money as quickly as possible and with as few attached strings as possible.

So if the US government really wants to invest in a open and accessible internet for all, why don't they just spend the stimulus money on public broadband network infrastructure? Maybe just go straight to 3G wireless for everyone in the country. Highways and most other critical infrastructure are publicly owned, why shouldn't the "information superhighway" be as well? Stimulus investment seems like the perfect opportunity to make this a reality. I wouldn't give the telcos a single penny of stimulus money.


What if everyone was funded?

A reader email pointed us to this story (which was also discussed briefly on Sandwalk). A paper published in Accountability in Research (abstract only, subscription required) takes a look at NSERC statistics and finds that the costs for grant application and peer review exceed the cost to give every applicant a grant of $30000.
Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money.
The first thing that struck me was the $40000 cost for grant application and peer review. That seems ridiculous - almost as ridiculous as the fact that it costs more to review the grants than the money being given out. I also had some of the same concerns regarding quality control - but apparantly these are discussed in the paper itself. Unfortunately, I don't have access so I haven't read the full text, but Coturnix at A Blog Around the Clock has, and has made some detailed comments about the paper and the eliminating the peer review of baseline grants. One of the authors has also joined the discussion there and is offering reprints to those who want to join the conversation.



Just when I had finally got BioRad's last viral PCR song out of my head, they come along with a new one. Sing along, to the tune of the Village People's YMCA.


Tuesday, April 14, 2009

What the !!@#$%^&*()_ing ~!@#$%^&*() Is Personalized Medicine?

Other than the catchphrase of the day in biomedical research. The dream of "personalized medicine" is the why for everything. Why sequence every human genome in the universe? Why, this information will herald in a brave new era of personalized medicine, of course. It's GenerationME ME ME!!!!111!!! meets medicine. Download the latest cure from my MY-Pod.

Most of the people talking about personalized medicine don't usually bother to explain what they have in mind, nor do they really seem to care whether that's clear. This leaves me confused about what all the fuss is about. Occaisonally I suffer from fits of sanity and it strikes me that maybe it's bad to be totally confused about the NEXTbigTHING about to hit your field.

So as always, I consult with all-knowing Goog-Oracle. Goog-Oracle spews forth some pretty trippy, but meaningless flow-charts, most wherein people are depicted by male/female icons from the restroom door. People with the gall to put their definitions into words come up with some pretty wishy-washy shit. Andy De of the excintingly entitled blog "Life Sciences and Healthcare Strategy", and self-proclaimed "visionary thought leader" has this to offer:

“Personalized Medicine means knowing what works, knowing why it works, knowing who it works for and applying the knowledge for patients”, is perhaps the most succinct articulation of P/M from the honorable Mr. Michael Leavitt, secretary of Health and Human Services (HHS). This implies delivering treatment to patients that is proactive, predictive, personalized and participatory unlike the status quo today."

What??? That doesn't sound very high-tech to me. It kind of sounds more like what I thought I was supposed to be getting from my family doctor all these years...apparently not:

"By way of the “trial and error” medicine (also sometimes referred to as “intuitive medicine”) practiced across the world today, the doctor makes a “most likely” diagnosis consistent with symptoms and them prescribes what he/she considers appropriate treatment comprising drugs, devices or surgery. If the treatment does not work and presents significant side effects or adverse events, the doctor most likely would alter dosage or prescribe an alternative medicine. This iterative cycle is repeated, until the diagnosis and treatment that actually presents the desired clinical outcome in the patient is reached. The paradigm has reached a point of diminishing returns as evidenced by the fact that most drugs prescribed in the U.S. today are effective in fewer than 60% of treated patients(2)!"

Wow. Holy shit! My doctor is a useless piece of garbage. We need to get these inept humans out of medicine and start replacing them with IBM(tm)adding machines computers as soon as possible! If personalized medicine = computerized/roboticized medicine, then give me some personalized medicine, double-time.


Watson's quote of the week

For some reason a quote from Watson about genetic engineering of humans is making the rounds on the interwebs (reddit, digg). Which is funny because the quote in question comes from a conference held at UCLA in 1998 about germline engineering:

"No one may have the guts to say this, but if we could make better human beings by knowing how to add genes, why shouldn’t we?"

The irony of course is that the quote is taken out of context in a speech where Watson says he'll probably be misquoted...

"We've got to be careful not to admit at the outset that we're three-quarters evil and a quarter good. I just don't see the evil nature of what we're trying to do.
Genetics in many people's eyes, has a bad connotation of the State or others determining people's lives. Which is why, again, the State should stay out of it. My feelings is, the State shouldn't tell a person either to have it or to not have it. If the procedures work, people will use them, and if they don't work or if it's dangerous, it will stop.
The real enemy is a preexisting genetic inequality which makes some people unable to function well in the world. Terrible diseases - that's the enemy. Whereas some people are convinced the enemy is the people who study the genes, that we are the evil people. I don't think we're more evil thatn the people who run the music department. You know? I don't know if we're better or worse. And I suspect we're deep down trying to respond to a long term need, and the music people are making us happy by singing hymns, which cheer us up. We should be proud of what we're doing and not worry about whether we're destroying the genetic patrimony of the world, which is awfully cruelo to many people. And I don't think that's what we're trying to fight. French, I think you know we basically agree, but it's the image. I'm sure I will be misquoted by someone who says I'm gung-ho to go ahead and do it [human germline engeneering]. I would do itif it made someone's life better. We get a lot of pleasure from helping other people. That's what we're trying to do."

The transcript unfortunately is not available on the web (I transcribed this short passage) but you can find the book here.


Thursday, April 09, 2009

Systems Biology Discovery of the Week:

"Approximately 100,000 somatic mutations from cancer genomes have been reported in the quarter of a century since the first somatic mutation was found in HRAS. Over the next few years several hundred million more will be revealed by large-scale, complete sequencing of cancer genomes."

Fair enough. But ultimately the job of science is to simplify seemingly complex natural phenomena into smaller, more manageable problems. Do we really need to catalogue EVERY mutation in EVERY cancer cell from EVERY patient, or do we already have enough information to deduce the important concepts?

I for one would like to know a lot more about the mutations that are happening in normal cells.

Anyhow, the Nature review nicely summarizes the systems biology-inspired approach to tackling the "cancer genome".


Harper Won't Be Taking Any Shit From Laid Off Oil Sands Workers

I find that reassuring in these times of economic uncertainty. Last thing we need is the Kitsilano commies getting across the Rockies and stirring up a revolution.

"In terms of the unemployed, of which we have over a million-and-a-half, don't feel particularly bad for many of these people. They don't feel bad about it themselves, as long as they're receiving generous social assistance and unemployment insurance."

- Stephen Harper, 1997 Speech to the (US) Council for National Policy

You can read the rest of the speech here.

In other news, Canadian unemployment hits a 7-year high. Lazy bastards.

HT: Sandwalk, Canadian Cynic


What a Real Science and Technology Policy Advisor Looks Like

John Holdren is Assistant to the President for Science and Technology and Director of the White House Office of Science and Technology Policy under the Obama administration. He did an undergraduate degree at MIT, a PhD in plasma physics at Stanford, and taught at UC Berkeley for many years before serving at Harvard University as director of the Science, Technology, and Public Policy Program at the John F. Kennedy school of government.

He was recently interviewed by a reporter from the world's leading scientific journal, Nature. Believe it or not, he managed to answer all the question without deferring to his religious convictions.

Here a few bytes from the interview, good examples of the types of things you might expect to hear from a competent science and tech policy advisor:

"Clearly initiatives related to science and technology as they affect economic recovery, job creation, growth and competiveness have to have high priority, given the circumstances."

"The second big issue, and it's related to the first one, is the energy and climate interaction. How do we need to be thinking about the scientific and technological dimensions of the energy challenge and of climate change? And particularly, again, how can we link those things positively to the economy?"

"Steve Chu and I are the two scientists in that group. Steve and I are the ones who bring science and technology to the table."

"We have a strong set of international interactions and will continue to have them. Issues of energy, climate change, nuclear arms control and non-proliferation are all big deals. These are problems that we have to get right globally, not just nationally, and there are big benefits in cooperating, in terms of sharing costs, in terms of sharing risks, in terms of propagating the best answers."

"The nuclear weapons we already have are more than adequate for the limited purpose for which we should reserve them, which is deterring other people who have nuclear weapons from using theirs. I think the pursuit of a wider range of missions for nuclear weapons is a prescription for continuing proliferation."

"I also think the wider community has a huge role to play in the education of the public and policymakers about the role of science and technology. I can't do that by myself."

Makes Canada look a little silly, no?


Tuesday, April 07, 2009

Associated Press Going To War With The Blogosphere?

According to the New York Times. This excerpt from the article makes them sound particularly draconian:

"One goal of The A.P. and its members, she said, is to make sure that the top search engine results for news are “the original source or the most authoritative source,” not a site that copied or paraphrased the work.

The A.P. will also pursue sites that reproduce large parts of articles, rather than using brief links, and it is developing a system to track articles online and determine whether they were used legally."

Uh-oh. Am I going to get sued for that copy-paste? Well I'm not making any money off it, but since this blog is hosted by Google and indexed on their search engines, I suppose it could be argued that they are. So if the AP gets their way maybe we won't be quoting NYT in the future.

I guess the AP is betting they're the only source of reliable information with access to an internet connection. If they start doing this kind of crazy stuff, my guess is we'll soon find they were wrong. The information will keep on flowing, except the AP will find they've cut themselves out of the picture. I think that's kind of too bad because we need good journalists and organizations to employ them. But the ones we have now seem determined to screw themselves straight out of the age of new media. Is the AP on the stock market? Start selling.


Haidinger's Brush

Wilhelm Von Haidinger discovered a quirky entoptic phenomenon in 1844. Like many other animals (insects, cephalopods) some humans can see the polarization of light. If you stare at the blue sky in the opposite direction from the sun, or at a white space on an LCD and notice some small blue and yellow artifacts, chances are you may have this extra perception. Anyone who's into photography or fishing will know that polarized lenses can help you for example, exclude reflection from the surface of water, allowing you to see what is happening underwater with greater clarity. Those 3D movies that are all the rage these days also use this property by giving you glasses with a different angle of polarization in each eye. It is thought that the underlying reason for this perception may be circular deposition of pigments in the macula. The pigment in question is lutein which is anisotropic and sensitive to the polarization of light. Lutein is also a strong anti-oxidant which gives the yellow colour to egg yolks. It makes we wonder whether this ability is related to a certain gene and if it has been selected for in certain sea-faring populations. Also if anyone has this ability, can you see the movies in 3D without the glasses (I suspect not, unless only one eye is affected)?

Interestingly the visual perception changes in patients afflicted with macular degeneration:
"Haidinger's brushes are an entoptic effect of the human visual system that enables us to detect polarized light. However, individual perceptions of Haidinger's brushes can vary significantly. We find that the birefringence of the cornea influences the rotational motion and the contrast of Haidinger's brushes and may offer an explanation for individual differences. We have devised an experimental setup to simulate various phase shifts of the cornea and found a switching effect in the rotational dynamics of Haidinger's brushes. In addition, age related macular degeneration reduces the polarization effect of the macula and thus also leads to changes in the brush pattern."


Monday, April 06, 2009

Gary Goodyear: Reasonable Investigation or Acceptable Bigotry?

A few weeks ago, there was a buzz surrounding Canadian Minister of Science and Tech Gary Goodyear and his religious beliefs. Bloggers, including here at the Bayblab took him to task, suggesting that his lack of understanding of evolution disqualifies him from being in charge of science in Canada. In response to that post, we received an email from a reader arguing that as long as it's not interfering with his job, what Goodyear believes doesn't matter and the stories in the Globe and Mail and attacks on blogs were manifestation of the last acceptable form of bigotry: anti-Christian bigotry. (emails reproduced with permission)
Hey Bayblab,
Sorry to come so late to the Gary Goodyear convo. I tried to post a reply, but it doesn't seem to be working. You guys usually have such level headed positions that it has shocked me that you'd fall into the traditional bigotry expressed by 'progressives.'

The Gary Goodyear situation is a typical 'just asking questions' meme. The way these 'questions' (read character assinations) are phrased and presented it's a damned if you do, damned if you don't condition. Mr. Goodyear rightfully refused to respond to the question, and look at where we are. Imagine if he had responded in faith with his true beliefs;

Goodyear is a conservative, and he's a devout christian. Just because he believes in a literal interpreation of the New Testmant in his private life (which he's FULLY entitled to under the Charter of Rights and Freedoms) doesn't mean he can't take positions that are in the best interests of Canadian scientific community in his public life.

Let's be clear; Goodyear has never once been accused of navigating his cabinet duties according to his devout Christian beliefs. There isn't a shread of evidence to suggest he has. Not one shread. And I was under the impression that you all in the Barb lab were good Scientists.

This is a clear cut example of anti-christian bigotry, which is the only acceptable form of bigotry Canada.

Imagine if the media had asked a gay, lesiban or transgendered minister about their personal beliefs and if they're in conflict. Or a muslim for that matter. People would be calling for heads to roll at the media outlet. But because it's a conservative, and a christian on top of that, it's only 'asking questions.'

For a good debate on this exact topic see;
This was expanded upon in response to my response in which I argued that yes, some beliefs do disqualify you from certain jobs.
Hi Kamel,

Sure, you can post my email if you'd like. I do completely agree that if, for example, he were a biologist then his opinions on Creation vs. Evolution may be important to gauge his authority as a biologist. However he's not a biologist, he's a politician. More to the point and this touches on something you mentioned; there is absolutely no evidence that his private Christian beliefs guide him in Public service. If Mr. Goodyear were to have donated money to, or set aside public funds for, an anti-scientific organization like The Discovery Institute, then I could see this line of questioning as legitimate. However there is no foundation for such lines of questioning in Mr. Goodyears Public performance. So the questions are posed entirely because of his identified faith. The presumption of how someone will act based on their social categorization is the very definition of bigotry. The fact that this presumption is still maintained with an abundance of evidence to the contrary only compounds the bigotry.

Recently there was a quote in the Victoria Sun where Mr. Goodyear qualified himself and said he believes in evolution. However, his subsequent comments made it clear he doesn't understand evolution at all. I don't believe he should have even had to further qualify himself as his Public performance in no way has been guided by his private beliefs. That said, with this qualification are we to disqualify him as Science and Technology Minister because he doesn't understand evolution? It is the founding principle of biology after all. How about complex physics concepts? He is the Science and Technology minister, and science and technology isn't only relegated to biology. I'm sure you can see where this is going. The point is his Public record as the Minister of Science and Technology holds no evidence to suggest that his private beliefs are guiding his public life. So these sorts of questions are direct attempts are character assassinations and overtly bigoted.

My point is that if this weren't a Christian MP there wouldn't have been any questions regarding faith. Could you imagine the Globe asking a devout Muslim Science and Technology Minister "do you honestly believe you are a descendant of Mohammed?" I think we both can agree heads would roll. But because this is a Christian MP, it's all par for the course, and in fact people defend it as 'only asking questions'. And even more than that; The people who point out the bigotry are accused of trying to silence opinion.

I hope you agree that no form of bigotry is acceptable, even if it's targeted towards identified majorities, or convenient targets. The fact that such highly educated people who contribute to your BayBlab blog have not seen the bigotry inherent in the Gary Goodyear story is worrying to say the least.

You can post this as well if you feel it would contribute to your blog. I feel discussions about socially accepted forms of bigotry are probably some of the most important discussions people can have.
So rather than keep this discussion confined to private emails, I'll turn it out to our readers. What do you think? Is it OK to question Goodyear about his personal beliefs without justification (eg. job performance indicators, dumping tax dollars into the Discovery Institute, etc.)? If not, has his performance to date given such justification? Was this a case of anti-Christian bigotry, or a reasonable investigation into the qualifications of our science minister? Leave your thoughts in the comments, and hopefully our letter writer will return to respond.


Friday, April 03, 2009

Cancer Research Blog Carnival #20

Welcome to the 20th edition of the Cancer Research Blog Carnival - a monthly collection of cancer related blog writing. I think we set a new record for number of spam submissions this go round, but of course I'll ignore those and focus on the good stuff.

Kicking things off, our friend Alexey at Hematopoiesis continues his series on cancer progression and metastasis with a post on the premetastatic niche.
Here we discuss a lot about bone marrow niches for hematopoietic stem cells, but what is the so-called premetastatic niche? It is a specific microenvironment that allows malignant cells to migrate from primary tumor and develop metastasis. I’d like to distinguish the premetastatic niche from the cancer stem cell niche, which is characterized by steady-state tumor and doesn’t necessarily require bone marrow cell involvement.
The article is a nice literature review on the events leading to the establishment of a metastatic site and delves into possible therapeutic interventions to prevent tumour metastasis.

Here at the Bayblab, Rob points us to new research that describes mRNA structures that are preferentially transcribed in cancer cells.
Translation initiation is often over-activated in cancer cells, however, this over-activation does not favour mRNAs equally. In fact it seems translation over-activation favours mRNAs that promote tumourgenesis and tumour progression. Santhanam et al. in PLoS ONE recently took a look at what general mRNA structural characteristics determine translational activity in cancer cells with over-activated translation initiation.
Go check it out to find out what cancer cells look for in an mRNA, and join the discussion in the comments about interpreting their results.

Over at HighlightHEALTH, Walter discusses a common health concern: meat consumption. The post describes a detailed piece of research that compares gender, meat consumptions (red vs. white vs. processed) and mortality risk (including cancer risk).
Two years ago, a similar study identified an association between red and processed meat and cancers of the colorectum and lung, but this is the first large-scale study to assess the relationship between red, white and processed meat consumption and the overall risk of death.
The conclusions? Read the post to find out, but you may want to hold off on that second hamburger in the meantime.

From the survivor side of things, Mike Freije sends us the story of Melissa Buhmeyer who shares her experience surviving breast cancer.
As women, especially American women, much of our femininity is centered on our breasts. No matter where you look, there are pictures, billboards, commercials, television shows, and movies with women with these beautiful breasts and ample cleavage. The thought of losing one or both breasts, to breast cancer, can be devastating for many of us.
It's a detailed story about coping with a mastectomy, particularly in the period shortly after surgery. In a similar vein, Nancy Miller shares with us Kat Sanders' list of the Top 30 Inspirational Cancer Survivor Blogs

Finally, GrrlScientist at Living the Life Scientific (Scientist, Interrupted) points us to a game that lets you help research from your computer screen. While not strictly cancer related, Foldit (which I've mentioned briefly before) tasks the player with solving different protein structures.
The results from this game are helping Baker and other scientists learn how to design proteins to do particular jobs, from vaccinating against malaria to fighting cancer.
The game is available cross platform (Win/Mac/Linux) but no word on when you might see it on Xbox Live Arcade.

That concludes the 20th Edition of the Cancer Research Blog Carnival. We always need hosts and posts so email the Bayblab to sign up, and get your posts in here. Visit the Carnival Homepage for previous editions.

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.


Thursday, April 02, 2009

Androdioecy: the secret sex life of nematodes

I recently attempted to grow triops. If you don't know about triops I urge you to check them out. They are small freshwater crustacean related to fairy shrimps. They lay eggs which are very hardy and can survive months dried up in soil until the next rain occurs. Triops are found pretty much everywhere, from subarctic ponds to Australia, and are easy to grow as pets. I got some eggs from ebay for really cheap (~$10), and I had much fun watching how fast they develop. I was motivated in part by the desire to sneak them into the lab to make a movie of their early development, and try to promote them as a new model organism. I was also wondering whether they could replace shrimps at my diner table. But I never got past the first generation, since I killed them when changing the tank water. I didn't realize at the time that their upside-down swimming is a sign of oxygen deprivation. I did however find out that they have a rather peculiar sex life: they are androdioecious.

There is another model organism that is famous for being androdioecious: C elegans. Nematodes use an X0 sex genetic sex determination system where males have only one X chromosome, XX makes a hermaphrodite, and there are no females. Androdioecy, this strange reproductive system with only males and hermaphrodite, is rather rare and it is unclear how it arises during evolution. Yet it has evolved independently multiple times. In triops, It usually reaches an equilibrium with a large majority of hermaphrodites and a few males. As you can imagine, since the male only invests energy into producing sperm, they can fertilize much more eggs and produce more offspring than the hermaphrodite. However, if the population of males becomes too large, then each encounter with a male is a lost opportunity.

This reproductive strategy has the advantage that only 2 organism suffice to have a threesome. It does however come short of this pair of humans with supernumerary sex organs which managed to simultaneously have sex twice over:

"Blanche Dumas was born on the Caribbean island of Martinique in 1860, to a French father and a biracial mother. She had a third leg attached to her sacrum, and her two primary legs were said to be imperfectly developed. The third leg was without a mobile joint but had a bend in it where the knee would have been. Her pelvis was wider than normal and she had double genitalia as well as a duplicate bowel and bladder. Most remarkably, Blanche had two small rudimentary breasts situated at the junction of the parasitic twin with her own body. Each had a nipple, but they were non-functional. Stories of Blanche all mention her pronounced libido. She moved to Paris later in life and became a courtesan, and allegedly, upon hearing about the three-legged man, dos Santos, who was touring at the same time, she expressed a desire to have sex with him. According to Gould and Pyle, "There were two vaginae and two well-developed vulvae, both having equally developed sensations. The sexual appetite was markedly developed, and coitus was practised in both vaginae."


Wednesday, April 01, 2009

mRNA structures translationally prefered by cancer

Translation initiation is often over-activated in cancer cells, however, this over-activation does not favour mRNAs equally. In fact it seems translation over-activation favours mRNAs that promote tumourgenesis and tumour progression. Santhanam et al. in PLoS ONE recently took a look at what general mRNA structural characteristics determine translational activity in cancer cells with over-activated translation initiation. Previously lots of focus has been on the influence of secondary structure and length of the 5'UTR as this has been demonstrated to influence 'translatability'. With new information about microRNAs binding to the 3'UTR to influence translation, an unbiased approach to evaluate their relative influence seems like a very good idea. The methods in this work essentially involved comparing microarray analysis of cell lines with over-activated translation initiation and those without. In each cell line the translational activity of each message was determined by quantification of the percentage of the message that was being actively translated. Then they looked for commonalities in the sequence of the mRNAs that are specifically translationally activated by translational over-activation. (probably using computers) :) Massive data set and unbiased approach = pretty convincing coorelations (we're talking p values of 10E-6)

Here is what cancer cells look for in a potentially translatable mRNA:
1. GC rich 3'UTR
2. secondary structure involving sequences JUST before the start codon and JUST after the stop codon. These results are more striking for the 3'UTR.
3. Short 3'UTRs
4. No microRNA target sites. Indeed the presence of predicted microRNA target sites was negatively coorelated with translational over-activation. (with some exceptions)

The take home message is, somewhat surprising, that the 5'UTR is less correlated with effects on translation over-activation relevant to cancer than the 3'UTR.


World Fart Day

The Bayblab is pleased to announce that tonight at 8PM is the much anticipated fart hour. As you all know methane is a potent greenhouse gas which has 21 times the impact of carbon dioxide. Since 1750, the levels of methane in the atmosphere has risen 150%, and slightly over half of those emissions are anthropogenic. We have previsouly established that about 50% of humans are methanogenic, and fart large quantities of methane which pollute our environment. That is why tonight, between 8PM and 9PM we urge you to keep your farts in, and clench your butt cheeks in solidarity. This way we can ensure our children's future will not be compromised by butt tuba. It's time to do your part for global warming.