Wednesday, December 31, 2008

Early Detection and Cancer Survival

The January issue of Wired magazine features a cover story about early cancer detection and its effect on survival rates. The article focuses on some detection methods, some of the difficulties in identifying real from false positives and one group in particular, The Canary Foundation, a research group whose focus is on developing early detection methods.

The article argues, based on cancer survival statistics, that "scientists should stop trying to cure cancer and start focusing on finding it early." The author notes that in the case of ovarian cancer, for example, discovery at stage I or II the 10-year survival rate is almost 90%, while the survival if diagnosis occurs later - at stage III or IV - drops dramatically to 20%. This makes sense. In early stages, before cancer has metastasized and spread, straightforward surgical intervention can remove most - if not all - of the cancer. Once it has spread, it is more difficult to treat and options are limited to more harsh chemo and radiation treatments.

The article, however, ignores another reality of the numbers it cites: early detection will improve survival rates even without any other intervention. The reason is the way cancer survival is reported. Typically survival is measured as relative 5-year survival, meaning the percentage of people still alive five years after diagnosis, compared with the general population. Early detection shifts the goalposts: the 5-year window now starts at an earlier stage. Even if these people have exactly the same progression as someone with a late-stage diagnosis, the survival rates will look much better.

Of course, we don't want to give up on early detection any more than improving treatment options. We do, on the other hand, want to understand what the numbers mean and how they're derived before we start changing policies or strategies based on them. Ideally with a combination of early detection and improved intervention we can start using intervals longer than 5 years as our standard measure of cancer survival.


Tuesday, December 30, 2008

Cancer Carnival Coming

The 17th edition of the Cancer Research Blog Carnival is coming at the end of the week, but it's not too late to submit your posts. The carnival will appear on Friday at Blind Scientist.


Wednesday, December 24, 2008

Dolphin the Grey

Check this amazing video of dolphins blowing bubble rings. Seriously do it, it's crazy.
The video is not fake. Here is the snopes analysis.
Made me think of Gandalf the Grey and his smoke galleon made from the best weed in the South Shire.


Friday, December 19, 2008

Laboratory Wisdom

Making my usual TAE agarose gel for electrophoresis of some DNA constructs I am attempting to make, I was wondering about some of the 'lab wisdom' that I have received over the years. I think molecular biology is particularly full of superstitions passed from person to person. Probably because it is such usually a 'means to an end' instead of actual science. Specifically I was wondering about the practice on our research floor of cooling the molten agarose to below 70C before addition of Ethidium Bromide (EtBr). The wisdom is that if EtBr is added before the agarose cools you are exposing yourself to vapours containing EtBr. Not good if you know about EtBr.
Quickly, EtBr is a chemical often used to visual DNA in agarose gels. It intercalates between DNA strands and in such an environment is a fluorescent orange/gold colour. Useful, yes. Also it is a mutagen, as determined by the Ames test. According to the Ames test EtBr is somewhere between mothballs and a cigarette in terms of mutagenicity. I guess this is not surprising because of its intimate interaction with DNA.
Lab wisdom is often suspect, as the previous link discusses. Check out some forum discussions on the very topic of EtBr in agarose gels. Scientists apparently like to talk about anecdotal evidence.
My favourite example of bad lab wisdom is about ethanol precipitations of DNA. Most people when performing this common procedure keep the solution of DNA, salt and ethanol on ice or at -20C for a certain time before centrifugation to pellet the precipitated DNA. You can be the biggest annoying know-it-all if, next time you see someone doing this, slap down this reference. This says that this cooling is completely unnecessary and can actually decrease yields. I keep a couple printed out on my bench for just such occasions.
A quick look at the MSDS for EtBr reveals that its vapour pressure is undetermined as is its mutagenic and carcinogenic potential. Sounds like this particular lab wisdom is unfounded but in this case perhaps it is wise.
Any other examples of bad lab wisdom that you happen to know about? Pass it on to the bayblab so that we can correct everyone in a very annoying, know-it-all manner.
[the festive agarose gel was ganked from tim holzer.]


Wednesday, December 17, 2008

At it again...

He-who-shall-not-be-named (or he'll threaten to sue you) is up to his old tricks again. Boy, does he know how to pick 'em. This time, instead of going after poor graduate students, he's picking on a small not-for-profit in Atlantic Canada.

Last week I received an email from Breast Cancer Action Nova Scotia, an on-line support group and information resource for breast cancer survivors. They had published a letter critical of ol' Bill and his shady cancer treatment outfit and, unsurprisingly, received the same standard letter threatening them with legal action for libel and defamation.

Here at the Bayblab, we've had some experience with Bill's all-bark-no-bite legal incompetence. At least twice he's notified our employers for blogging critical of his outfit, and one of those times he had the wrong person. (Hey Bill, having an actual case is a good first step, but threatening the right person is a close second)

We've already covered what we think of the brand of "medicine" he practices, but somehow I can still be surprised by his behaviour. If you're out there supposedly trying to help cancer patients, why would you threaten and bully an organization with the same goals of helping and supporting cancer patients? Why not do what a normal person would do, and explain your position and politely ask them to reconsider theirs? Why go straight to legal threats? (Hint: They probably don't have the same goals)

Anyhow, that's the latest bit of threats, bullying and harrassment from our favourite local quack. This seems as good a place as any to remind people of Project False Hope, the Canadian government's effort to combat health fraud.


Giant's Shoulders #6

I've mentioned it before, but The Giant's Shoulders is a cool blog carnival about the history of science. The latest edition is up at Rigorous Trivialities. This edition is particularly cool since it features a post from the Bayblab (nestled amongst a bunch of other great stuff!)


Saturday, December 13, 2008


I have come to the realization a while ago that while my vote is important, how I vote with my money has more impact on how the world works. Money makes the world go around. I therefore try to buy products with less environmental impact. This is not always easy. I admit that I just look around for green coloured packaging, then quickly look for some key words, if they are there the product is in my grocery cart.
I have noticed that there are way too many eco-labels, making comparison between different environmentally conscious products difficult. [Unfortunately it doesn't occur that often that there is a selection of different brands making claims of environmental responsibility for the same product. Usually a particular store will stock only one environmental responsibility marketed product for a particular item.] There are so many eco-labels, in fact, that there is a searchable database of eco-labels here, and a list of all the north american eco-labels here. I guess getting into the certification racket is a good business or something. There are some pretty obscure and small time certification labels. Why does something have to just be salmon safe, for example? Shouldn't products just be environmentally responsible in general?
In any case, I have found that one of the most ubiquitious and apparently respected North American eco-label is EcoLogo, which is celebrating it's 20th year in 2008. It was started by the Candian Federal Government in 1988. Look for it.


Thursday, December 11, 2008

Bayblab podcast: Episode22

Here is the latest podcast episode 22 (mp3, or better yet rss). For those of you who have never experienced the bayblab podcast it's one part science, one part dick and fart jokes and one part beer. It's not meant as a replacement for the nature podcast or science podcast but it will cover science news that other podcast do not and it doesn't take itself seriously. It's about making you think and then making you laugh, then making you cry, but hopefully not bleed from your ears. This edition features: Toxic plastic leaching into your experiments, cystic fibrosis is not PC enough, why drunk Asians turn red, the stem cell conspiracy, sexy time for biology students, and movie review: expelled!


Wednesday, December 10, 2008

IA updates

Some good new posts up on They include a post that the Bayblab should have been all over about evolution and control theory.


Tuesday, December 09, 2008

Pubmed tuesday: inflatable dolls

If you are a biology major, and not an art major, you probably know about gonorrhoea. Gonorrhea is an obligate human pathogen and has no vector, so it can only infect during intercourse. There is however one reported case where transmission wasn't directly by sexual contact. Here is a vintage paper in genitourin. med. 1993:

"The skipper from a trawler, who had been 3 months at sea, sought advice for urethral discharge. His symptoms had lasted for two weeks. A urethral smear showed typical intracellular gram-negative diplococci, and a culture was positive for N gonorrhoeae. There had been no woman onboard the trawler; he denied homosexual contacts; and there was no doubt that the onset of the symptoms was more than two months after leaving the port. With some hesitation, he told the story. A few days before onset of his symptoms, he had roused the engineer in his cabin during the night because of engine trouble. After the engineer had left his cabin, the skipper found an inflatable doll with artificial vagina in his bed, and he was tempted to have "intercourse" with the doll. His complaints started a few days after this episode. The engineer was examined, and was found to have gonorrhoea. He had observed a mild urethral discharge since they left port, but he had not been treated with antibiotics. He admitted to having ejaculated into the "vagina" of the doll just before the skipper called him, without washing the doll afterwards. He also admitted intercourse with a girl in another town some days before going to sea. This girl was traced, but the result of her examination is not known. To the best of our knowledge, no case of gonococcal transmission through an inflatable doll has been reported before."

(HT: "
it's a microworld afterall")


Monday, December 08, 2008

Leaf Camouflage Pictures and Videos

I ran into a collection of awesome leaf mimicry pictures and videos I origonally ran into on boing boing. Definitely worth checking it out. The blog that is hosting these pictures, The Conservation Report, seems to have an ongoing thing with pictures of impressive animal camouflage. While I would love to get some of the leaf mimicing fish for my aquarium, looks like they'd eat my neon tetras!


Salary prospects for biology majors

This may or may not surprise you, but who do you think has the highest median starting salary and mid-career salary between those three: History graduate, philosophy graduate, biology graduate? When it comes to salary you're actually better off with an undergrad in history, philosophy, geography, any engineering, or any science other than biology. If it makes you feel better, it still beats drama and is about equivalent to an English major with $38.8K starting and $64.8K mid-career. Why is that? I'm not sure, but It probably is a consequence of supply and demand. Not much demand for biologists, and way too many graduates.


Thursday, December 04, 2008

Cancer Research Blog Carnival #16

Welcome to the 16th Edition of the Cancer Research Blog Carnival, the monthly carnival of cancer-related blogging. This month's edition has a healthy dose of cancer stem cell news, and we'll kick it off right here at the Bayblab with a post from Rob on that very topic.

Rob describes a recent paper in Nature that casts some doubt on the cancer stem cell hypothesis - or at least the scarcity of these cells - though he doesn't think it's that serious a blow.
Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.
Alexey at Hematopoiesis follows that up with a pair of research blogging posts also about stem cells and cancer. First off, he describes the complexity of the cell cycle and stem cell self-renewal, how disruptions in these processes can lead to hematological malignancies and how the complexity adds a layer of protection
So, on one hand, downregulation of those genes promotes stem cells to exit from a quiescent state and enter into cell cycle, leading to their expansion, exhaustion and cancer development, but on the another hand, the involvement of multiple genes could protect them from it.
This is followed with a post about age related changes in gene expression. Cancer is fairly well recognized as a disease of aging, but Alexey takes a closer look at specifics
Now, let’s get close to cancer. Bmi-1 is known as a tumor promotor, and genes that it repress - Ink4a/Arf are tumor suppressors. Hmga2 is anti-aging, but is a tumor promotor. So, aging of adult stem cell system actually protects us from cancer.
Abel Pharmboy at Terra Sigillata has another piece about the link between aging and cancer. This one focuses on a recent PLoS Biology paper discussing senescence-associated secretory phenotype and how it may complicated therapies taking advantage of the senescence pathways.
Cells induced to undergo senescence with DNA-damaging agents exhibit a secretory phenotype, termed the senescence-associated secretory phenotype (SASP), whereby molecules involved in inflammation and metastasis are released into the local environment. In younger individuals, this
mechanism could prevent the development of cancer but in older individuals could increase the risk of cancer. In cancer, for example, therapies that causes cellular growth arrest and senescence may be of limited utility unless those senescent cells are removed. My takehome message from this paper is that we may have to rethink the benefit of cancer therapies that are cytostatic.
Abel Pharmboy was also able to talk to one of the authors directly about the significance of the paper.

While on the topic of unintended consequences, Philip Smith has sent us a story by dsantore at Sociology Eye. The brief piece describes the story of a New York Times editor taking testosterone suppressants as cancer treatment and found them gender blurring.
Among the more notable side effects are Jennings’ shrinking testicles, hot flashes, and potentially enlarged breasts. The gendered implications of these bodily changes are not lost on Jennings
The original story in the NYT is an interesting cap on the month of Movember, and a reminder of some of the lesser thought of aspects of prostate cancer.

With that concludes the 16th edition of the Cancer Research Blog Carnival. The next one will appear Jan 2, but is still in need of a host. If you're sick of seeing it here at the Bayblab all the time, send us an email and we'll set you up as a future host. In the meantime, start writing posts for the next edition and submit them here. You can check out previous editions here.


Going (pro)Rogue

With a recent election overshadowed by Obamamania to our south, the Canadian government decided to draw some attention to itself with a recent parliamentary crisis. In that election, the Conservative Party earned more seats than any other single party, but not enough to command a majority of the 308 seats in the House of Commons. Still, they were asked by the Governer General, to form a minority government with Stephen Harper as Prime Minister. This is what normally happens, and what everybody expected (read: took for granted) based on the distribution of seats after the election. Typically for a minority government to last, they have to play nice with the other parties to reach compromises in order to get a majority of votes in the house. Mr. Harper somehow didn't realize he didn't have a majority and pushed an economic statement that was sure to not sit well with the Liberal, NDP and Bloc Quebecois members that make up the majority of the seats in parliament. They didn't like it, decided "hey, we're in the majority, if we band together we topple this government and try to replace it with a coalition made up of the majority of MPs". This was to happen Monday in a vote of confidence on Harper's ability to lead.

So, less than two months after a federal election, and even less time sitting, Harper saw the writing on the wall and decided instead of letting government, you know, govern (during this worst economic downturn since the Great Depression, yadda, yadda) to take his ball and go home, suspending parliament (called proroguing) to buy time to figure a way out of this mess. The Governer General agreed to his request this morning. So until Jan. 26, this parliamentary showdown has been averted, as well as the ability of parliament to do anything. But it has made for interesting times, one of the most interesting parts being the revelation of how few Canadians understand how their government works. Hopefully this has been an opportunity for learning. Larry Moran at Sandwalk has been following what he calls Conservative Lies more closely, and hopefully we can also clear up some misconceptions here at the Bayblab. First an explanation of our parliamentary system (from a Sandwalk commenter):
Let me refresh your memory as to how a Westminster-style Parliamentary system works. The people of Canada do NOT elect a government; they elect members of the House of Commons. The members of the House choose the government. By tradition, the legal Head of State (the Governor-General, in our case) asks the leader of the party with the most seats in the HoC to form a government; that is, to form a cabinet to try to pass laws.

If the majority of the members of the HoC lose confidence in the ability of the minority, they have the right to express this through non-confidence votes or votes against bills that deal with government's ability to spend money.

In this case, the Prime Minister must ask the GG to dissolve Parliament and call an election (remember, the GG is our head of state, and the only one who can call an election). The GG has the legal option to ask another party or parties to form a government, if he or she feels that this party or parties has the confidence of the majority of the HoC (for instance, if a majority of the legally elected members of parliament got together and forged a formal agreement...).

This proposed coalition is absolutely in keeping with Parliamentary law and tradition. It has been forged by people who have been legally elected by the people of Canada. Of course, the GG is completely within her rights to call an election at the request of the Prime Minister. She will have to decide whether it is in Canada's best interest to hold the 4th election in 4 years, and second election in 3 months, or if it is in Canada's best interest to bring in a duly-elected government that has the pledged support of the majority of the HoC, and has proposed specific measures to rectify certain issues currently facing us.
Some of the misconceptions that have been repeated during this debacle:
I voted for Stephen Harper for Prime Minister.
In Canada, a federal election is a series of local elections. Unless you live in a specific riding you never cast your vote for Harper (or Dion, Layton, Duceppe). Yes, many people vote based on party affiliation and pretty much all the time the Prime Minister is the leader of the party with the most seats but the reality is that you vote for a parliament, not a governement.

The Liberal/NDP/Bloc coalition...
The Bloc Quebecois would not be part of a coalition governement (they would have no cabinet positions, for example). They have simply agreed not to bring down a proposed coalition government within 18 months (which some reservations, I would imagine). Furthermore, the accusations of the coalition 'being in bed with separatists' are divisive, offensive appeals to emotion. It suggests that the duly elected officials from Quebec shouldn't have a role in government and that votes from that province shouldn't carry as much weight as from the rest of the country.

A coalition government is undemocratic
Which is more undemocratic: a broad, cross-party agreement between elected MPs who represent the majority of Canadian voters, or shutting down government and locking them out? A coalition government (common in many other democracies where minority governments are the norm) or a PM going (pro)rogue?

Read the coalition agreement here and their economic plan here [pdf]


Science nerds can't score

A recent study in the journal of sexual health (castration or institutional subscription required) looking at the prevalence of chlamydia screening uncovered some interesting facts about university student sexuality:

"Arts students were younger, more likely to be sexually active and to report having little or no knowledge of chlamydia. Males in the study were less likely to have had sex as a group compared to the group of females in the sample. Science students were also less likely to have had sex compared to their counterparts in other faculties."

So why are science boys unable to seal the deal? According to the authors:

"Boys also start having sex later than girls, [...] And who are the people at unis that go to the rave parties and the bar? ... it's not the nerdy boy science students. They're carrying on doing their experiments, going to the library or doing their assignments."

Ouch. Is that true? I thought that was only the engineers!

Also while you're there, you can check out these papers on understanding oral sex or on how impotent males feel vibrators, in the same issue of the journal.


Doubts on the Cancer Stem Cell Hypothesis

The cancer stem cell hypothesis states that a tumour consists of a subpopulation of cells that give rise to all the heterogeneity found in the cancerous tissue. These cells have some common markers and characteristics of normal stem cells. These, the hypothesis suggests, give rise to the tumour and are therefore the best target for cancer therapeutics.
A recent paper in Nature seems to have caused a bit of a stir in the cancer stem cell field. (first born child or expensive subscription required). Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.
A wired artcle on the work really tries to stir the pot:(free)
"The controversial idea that all tumors are created by cancer stem cells received a setback Wednesday."
There are also some great summaries of what the impact of this paper may be in this field of research in Nature. News and Views. Nature News. Again you will have to sell organs or have an institutional subscription.

I can't say that I know much about cancer stem cells, only that I find the hypothesis interesting. As the summaries suggest, I would not find it surprising that some cancers do indeed consist of a subpopulation of cancer stem cells wereas others do not. I also don't know if specifically targetting cancer stem cells is going to cure a patient since these cells, while capable of causing a recurrance don't cause the symptoms of cancer.
I also don't follow the logic that the cancer stem cells are the reason that chemoresistance occurs, and other hypothesis that have come out of the cancer stem cell hypothesis.
That being said I certainly don't find this study to be blow to the cancer stem cell hypothesis.


Monday, December 01, 2008

Happy Movember

For all those who participated, thank you. We've collected just short of our $200 goal for prostate cancer, and hopefully reduced discrimination against mustaches...