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...


Friday, November 28, 2008

The Rise and Fall of Phrenology

Recently, my sister sent me a paper she wrote on phrenology to proofread. Being the wonderful older brother that I am, I obliged, after all it's not a subject I'm overly familiar with and it was definitely more up my alley than the women's studies papers I often receive to read the morning they're due.

For those who didn't grow up in Victorian Europe and are otherwise unaware of this particular "science", phrenology is the determination of a person's personality and mental capacity according to the shape of the skull. Phrenology earned a fair bit of popularity in the early 1800s, but is now (rightly) shunned by the psych and neuroscience communities.

The idea behind phrenology stems from the notion that mental functions are localized to discrete areas of the brain. German physiologist Franz Joseph Gall's interest in the area was piqued at an early age when he noticed that among his classmates, those with prominent eyes also excelled at verbal memory tasks. He deduced that the frontal lobes were the centre for verbal memory and suggested that the size of a brain region is directly connected to its functional strength. From there it followed that stronger (and therefore larger) areas would create bulges in the skull to match the corresponding bulges in the underlying brain tissue. Using a map of brain function and scalp massage to determine cranial topology, an individual's personality could be assessed. And thus was born phrenology (then called craniology).

It was Gall's student, Johann Spurzheim, who really helped the spread of phrenology. He popularized it in the English speaking world and, notably, America, where one of the first Phrenological Societies was established. Spurzheim switched the focus from the anatomical to the social and political applications, appealing to those looking for guidance, and offering people a way to change through mental exercise.

Interest in the technique picked up, largely due to the innate human desire to understand - and predict - oneself. We can still see this today with the inordinate interest in things like fortune cookies, psychic readings, palmistry and astrology. The trend then, as now, was for man to try to rationally explain his own behaviours. Gall's craniology provided a tool understand, predict and maybe even control human behaviour and its popularity began to snowball.

In the US, popularity was booming. Journals such as the American Phrenological Journal granted legitimacy to the practice, earning praise from the likes of Thomas Edison and Alfred Russell Wallage, and the businesses popping up popularized it through talented salesmanship. The Fowler brothers turned phrenology into big business in the tradition of the great snake-oil men, with an entertaining and riveting show advising individuals on all aspects of their lives, from love lives to employment prospects, and ending each show with a practical demonstration. Phrenology had established itself both as a science and in the public mind as a legitimate industry.

Obviously, the shine of phrenology didn't last forever - it certainly isn't an acceptable specialty at any medical school I'm aware of. It was a combination of things that contributed to its downfall. While phrenology was enjoying popularity in North America, it was coming under attack across the pond. One of the primary figures challenging the science was Peter Mark Roget, the English physician famous for his contributions to Encycolopedia Britannica and the eponymous Roget's Thesaurus. Roget, and others, disputed phrenology on both methodological and physiological grounds.

The first objection raised was against the very underpinnings of the phrenological movement. While the field was predicated on skull topology being directly related to brain topology, there was no evidence of a connection between the two. In fact, whether 'high energy' (i.e. more developed) parts of the brain were quantitatively larger was the object of dispute, nor could the hypothetical sub-organs being proposed by phrenologists to explain their science be observed on dissection. On top of physiological arguments, phrenology fell prey to the classic fallacy of equating correlation with causation.

Phrenology was also under assualt from outside the scientific community, with religious leaders taking aim. Central to the phrenological 'science' was materialism, which is in contrast to the church's position of mind-body dualism. That is, the idea that personality and behaviour is strictly a consequence of the physical attributes of the brain is contrary to teachings of a soul. As a result, phrenology was condemned as implicit atheism. This, coupled with growing rejection in the scientific community and waning novelty of the practice led to the disappearance of phrenolgy and its being discarded as a credible science.

Now, there are other pseudosciences that have a similar history to phrenology, yet they endure. Astrology, for example, was widely accepted as reality. It was (and continues to be) opposed by religious leaders and has been rejected as a real science. However, astrology columns can still be found in any newspaper. Likewise, you can still get a tarot card reading, have your palm read or visit a psychic very easily. How is it that they persist but phrenology did not? There are a couple of reasons that might be.

First is its short history. Compared to the other pseudoscience mentioned above, phrenology was a flash in the pan. It may not have had time to establish itself in the public consciousness in the same way that astrology was able to. Furthermore, despite the poor methodology and basis in reality, phrenology was a scientific endeavor. Being such, results couldn't be rationalized with occult-based explanations. If predictions were wrong, the theory was invalidated. Phrenology was pushed out in favour of other ideas of self, such as the psychoanalysis of Freud or Jung. More importantly, some aspects of phrenology were absorbed into the body of scientific thought, making it easier to discard the invalid ideas. Modern neuroscience obviously still holds a material view of the mind, but the idea of localized functions and specialty areas - the basis of phrenology - have also survived. Every fMRI lighting up the music centre of the brain, for example, owes itself in part to phrenology - the brain science of its day. (Some have even suggested that functionl imaging is the phrenology of the 21st century) Despite having gone the way of the dodo, the study of phrenology remains an interesting piece of science history whose influence can still be seen.


Thursday, November 27, 2008

Call for Submissions!

It's that time of the month again - dig up your best posts about cancer, or hit the keyboard and write something new for the Cancer Research Blog Carnival. You have a week to get your submissions in here. And if you have a blog and want to host a future edition, be sure to contact us!


Wednesday, November 26, 2008

How to make a sandwich

McDonald's tries to patent the greatest thing since sliced bread. Click picture to enlarge.

(h/t: Greg Laden)


Drunk Red Asians

Recently went drinking with a FOB (friend of the bayblab) and, as usual with him, he turned pretty red in the face. Apparently approximately half of people of Asian decent have this reaction to the consumption of alcohol, which has been nicknamed the "Asian glow".This glow shows up really well in this particular FOB, because he is half Caucasian, providing a pale, pastey canvas for his inebriated glow.
I had heard that the Asian glow was the result of a variant or deficit of the acetaldehyde dehydrogenase (ALDH2) enzyme. This enzyme is responsible for the conversion of acetaldehyde into acetic acid. Acetaldehyde is the first breakdown product of ethanol produced by alcohol dehydrogenase and it is this nasty compound that causes all of the "Asain glow" symptoms which also include: nausea, headaches, light-headedness, an increased pulse, occasional extreme drowsiness, and occasional skin swelling and itchiness. It is also responsible for the scurge of mankind; the hangover.
Worse still for the previously mentioned FOB is that the east asian drunken red face variant of ALDH2 is associated with increased risk of alcoholism related cancer. This is likely because acetaldehyde is carcinogenic and would be in increased concentrations if you posses a less active ALDH2 enzyme.
If you're smart and paying attention you'd remember that the FOB is of both Asian and Caucasian decent. So what about his Caucasian allele? How could an enzyme deficiency be domninant? Well, the origonal paper on the subject explain demonstrates that ALDH2 exists as a homotetramer and that the Asian allele has a markedly reduced half-life and in a cell expressing both versions of the subunit passes on it's reduced stability to the resulting heterotetrameric complex. So presumably the increased acetaldehyde is not due to decreased specific activity of ALDH2 in some Asians but due to lower stability of the active enzyme complex. Therefore this allele is dominant.


Shinerama dumps Cystic Fibrosis

This is one of those rare occasions where Carleton University and Ottawa make the news, but unfortunately it's for all the wrong reasons. If you haven't heard already, the frosh week shoe shining activity "shinerama" where funds are collected for cystic fibrosis research by Carleton U (and Ottawa U) students, has ditched Cystic Fibrosis as the recipient. Now I'm not necessarily opposed to raising money for other diseases but the students' association decision was based on the fact that cystic fibrosis isn't "inclusive" enough, apparently it only affects the "white man". What a twisted idea. Apparently we need our diseases to hit all sexes, ethnicities and socio-economic status equally. Of course that's ludicrous because pretty much every major disease be it diabetes, cancer, heart disease, etc has some bias. And to top it all, the council's decision was full of inaccuracies since CF affects males and females equally, and caucasian does not mean "white" in the strictest sense, not that it really matters. It makes me wonder: Are the rare spontaneous genetic disorder the only disease to hit everyone equally? I mean even pathogens, think of those that cause AIDS or dysentery, do not infect equally across those arbitrary lines.... Does anyone know any "PC" disease?


Friday, November 21, 2008

'Tis the Season

Christmas season is almost upon us - and if you're to believe the mall displays, it has been since mid October. With it comes office parties, rum-laced egg nog (marrow rum?) and gift exchanges. And with family gift exchanges, often come Santa 'wish lists'.

The Christmas list remains something of a puzzle to me. Sure it removes much of the stress of gift giving (What should I buy? Will they like it? etc.) but it seems to fly in the face of the conventional "It's the thought that counts" wisdom, since they're meant to take thought out of the equation.

But conventional wisdom is often wrong and a more fitting aphorism would be "It's the act that counts". And in fact, the act may be as (or more?) important for the giver as the receiver. Families that cut back on gift giving by doing a "Secret Santa" type exchange may be doing themselves a disservice, the New York Times reports:
But while it’s reasonable to cut back on spending during the holidays, psychologists say that banning the gift exchange with loved ones is not the best solution. People who refuse to accept or exchange gifts during the holidays, these experts say, may be missing out on an important connection with family and friends.
Of course retailers are probably thrilled with that idea. Gift giving is a social interaction and by not participating either by not giving or declining gifts you miss out on social cues and opportunities to strengthen bonds
“[Not participating in gift exchange] doesn’t do a service to the relationship,” said Ellen J. Langer, a Harvard psychology professor. “If I don’t let you give me a gift, then I’m not encouraging you to think about me and think about things I like. I am preventing you from experiencing the joy of engaging in all those activities. You do people a disservice by not giving them the gift of giving.”
Psychology Today explains further. Giving a gift forces the giver to reflect on the relationship (at least subconsciously). It focuses the giver on who their important relationships are, and the nature of those connections (the nature of the gift, the effort willing to be made, etc.) and answering these questions is satisfying. And gift giving reinforces itself through these feelings in a sort of feedback loop:
We usually think that the more we care about someone, the more we want to give to them. This is probably true. But what is even more interesting is that the more we give, the more we come to care about the person to whom we are giving. We feel alive in the activity. And it is the receiver who has provided the opportunity for us to feel this good, so we feel loving in return. Moreover, as social psychologist Daryl Bern, Ph.D., has taught us, we deduce our attitudes from our behavior. "I must really care or else why would I have given such a meaningful gift?"
A recent paper in Science supports the idea that giving is good for the giver. The authors show, through both survey and field study, that spending money on others is predictive of happiness. While one might think that happier people are more prone to giving (which may be true), the authors also showed that people randomly assigned to give to others reported more happiness compared to those told to spend on themselves.

So on that count the old wives may have got it right: It is better to give than to receive.


Dancing your PhD

The AAAS had its annual science dance contest, and the results are in! The idea is to use body movement and art to communicate the findings of your first-author publication, so that you may perform in February at the AAAS meeting. Clearly they are taking cues from the evermore popular IgNobel. This will appeal to the subset of people who like both "So You Think You Can Dance" AND are members of the AAAS (judging by my lab, it may be greater than you'd think). Of course they are not the first to create this overlap, it's been done before, but never in a competitive setting. .

Here is the winner for the graduate Student category: "The role of vitamin D in beta cell function"


Wednesday, November 19, 2008

Nobel Prize: Look to the Stars

If you have your eyes on the Nobel Prize, you may want to think again if you were born in the midsummer months. A study published in the Canadian Medical Association Journal (CMAJ) compared the birthdates of 171 Nobel laureates with 375 scientists who had not won the prize and shows that people born under the star sign Leo are the least likely to win the prestigious prize for Medicine or Physiology, while Geminis have the best odds. This is just common sense for any astrologer
Selective retrieval from the multitudinous traits attributed to particular astrological signs showed that "Gemini produces persons of greater intellect and more powerful invention and genius than any other sign of the zodiac" and that Gemini are "thirsty for knowledge and eager to study."
But don't worry Leos, you still have the "natural creativeness and magnetism" that attracts others to you.


Friday, November 14, 2008

Elementary science experiment

A total FOB (friend of the bayblab), who's all talk no post, recently sent me this email about an interesting science story she heard on CBC.
Pretty impressive for an elementary student.

thought this is a cool story... dad (geologist) studies paleoclimatology
on south american glacier... comes across what may be a birds nest up
there on the ice. Brings back some pictures... his son - in ELEMENTARY
SCHOOL at the time - picks up where dad left off.... they recently
published this paper. they found the only other bird known to date that
lays eggs on ice (besides penguins)!! Crazy!

Hardy, D. and S. Hardy 2008. White-winged Diuca Finch (Diuca speculifera)
nesting on Quelccaya ice cap, Peru. Wilson Journal of Ornithology 120:


Thursday, November 13, 2008

It's the plastic, stupid!

One of the original baybz alerted us of this paper in science which discusses contaminants found in plastic that can inhibit enzymes. We use disposable plastics a lot in the lab, from tips to eppies , without thinking too much about it. There are a few people who religiously believe that you should not change any of your plastic supplies (tips/tubes) when repeating an experiment. Well these people maybe on to something as this Canadian team from Alberta has shown as much as 40% inhibition of hMOA-B from coumpounds such as DiHEMDA and oleamide which leak into water or DMSO from tubes, tip, and TCware. And that's not even all. Apparently microbicides are added by manufacturers to the plastic along with other chemicals to prevent water from "sticking' to the sides:

" Related slip agents such as erucamide and stearamide are endogenous molecules used routinely in plastic manufacturing (3), whereas quaternary ammonium compounds are included as biocides or antistatic agents. Many such biocides bind substantially to proteins and DNA and have recently been linked with fertility problems in mice (6). Our findings that processing agents leach from laboratory plasticware into biological media and solvents, particularly when liquids are stored in plastic vessels, identify a likely source of error in many assay systems."


Wednesday, November 12, 2008

How do you like them apples?

As I'm typing this I'm snacking on a granny smith apple, one of my favourite varieties. Even though you'll typically find only a half dozen or so different varieties at the grocery store, there are over 7500 different cultivars (though not all are eating apples). The apple is a member of the rose family, and as one might expect they have a long history. They originated in Asia, and Alexander the Great is credited with bring dwarf apples back to Greece in 300 BC. The first apple orchard in North America is said to have been planted in the 1600s in Massecheusetts.

AC wrote before about modern hybrid fruit. It should come as no surprise that having been around for centuries and being an important food crop, the apple has gone through several rounds of its own breeding to produce popular varieties we eat today. It can take 15-20 years to develop a new variety and promising cultivars are selected on the basis of appearance and flavour as well as ease of shipping, longevity in storage, and even length of stem to allow pesticides access to the top of fruit.

The granny smith apple I mentioned above is originally an Australian fruit, but Canada is famous for apple varieties of its own. Every McIntosh apple can trace its lineage to a tree discovered in 1811 in Dundas County, Ontario. One of its offspring, the Spartan (another one of my favourites) was developed in BC in 1936 as part of Agri-food Canada's apple breeding program. It's widely described as a cross between McIntosh and Newton Pippin but recent DNA tests have put the Newton parentage in question.

Over the past few weeks, I've been sampling several different apple types from the common Granny Smith (still my favourite) and McIntosh (which I find too soft) to less 'brandname' varieties such as Honeycrisp (which was almost unnaturally crisp and a bit too sweet) and Braeburn.

Extensive lists of apples, their origins and descriptions can be found here and here.

What's your favourite apple?


Monday, November 10, 2008

Recycling Myths Debunked

Ran across this quick read about the realities of recycling on Bottom line is that recycling makes more sense than ever. Although I have read that the 'economic crisis' has recently caused a drastic reduction in demand for recyclable waste.


Friday, November 07, 2008

Cancer Carnival #15

The 15th edition of the Cancer Research Blog Carnival is now up on the carnival home page. Go check it out here and thanks to everybody for their submissions.


Thursday, November 06, 2008

'Coons Get the 'Fluenza...Who Knew?

The globe and mail reports on the TOTALLY GROUNDBREAKING discovery that wild raccoons get infected with influenza. Thanks guys. Now I know not to eat my garbage after the coons have been into it. As if the fear of rabies wasn't already enough.

It's always interesting to see which science stories newspapers choose to report on. There's a lots of fascinating questions in virology. This is not one of them. Is it really surprising to learn that raccoons, who will pretty much stick their noses into anything, get infected by a virus that will stick its genome into pretty much any available cell? As the author of the study says, "More diseases have been found in raccoons than pretty much any other wild animals,...You name it, raccoons get it. But they're tough as nails." Ok, this is getting a bit more interesting. Apparently infected coons can shed and transmit the flu, but they don't get sick.

Maybe someone needs to establish a coon model for immunology. What's so gosh-darn special about the raccoon immune system? That would be interesting. Warm fuzzy mammals for press releases AND some novelty...


Patents and Graduate Students

I'm about to sign over the rights to a patent application to the institution where I am doing my graduate studies. Does anyone have experience with this? Advice?
I'm pretty sure Bayman has experience with this. (?)
I fully understand that the institution will be the full and exclusive rights holder and financial beneficiary, however, I would still like my name on the patent as the inventor so that I may refer to it in the future in job applications. Is that the default? The paper work I have in front of me seems pretty vague about such details.


Junk DNA and Transposon Driven Evolution

A press release out of the Genome Institute of Singapore is claiming a function for junk DNA. The researchers show that a number of transcription factors bind repeats found in transposable elements.
More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution. [...] The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.
Now I could be wrong, but I thought we already knew that portions of these transposable elements acted as transcription factor binding sites (for example see here) so I don't think Larry over at Sandwalk is going to have to revise his estimates of junk DNA percentage yet. But what about the "deflated ego problem"? Is this an answer to Larry's excuse #5: that humans are more complex than other organisms in spite of similar gene numbers because of more complex regulatory mechanisms? Unfortunately I don't have access to the paper, but the press release and abstract seem to think so.
Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.
The argument here isn't for more complex gene regulation in humans, but rather different regulation depending on where these elements landed in early evolutionary history.


Wednesday, November 05, 2008

Research Funding: Low Hanging Fruit

A few weeks ago, Bayman posted a story from the Globe and Mail about unrealistic expectations for a cure for cancer and in the comments AC wrote
I think the expectation comes from the fact that we've basically cured many diseases that were low-hanging fruits [...] And it might or might not be worth the money; perhaps we could cure 100 smaller diseases for that price.
It turns out that focus on low-hanging fruit is also an issue within the cancer research community. The Independent reports that in spite of record levels of funding for cancer research in the UK many "unfashionable" cancers are being neglected:
Some of the deadliest cancers, such as those affecting the lung and pancreas, get the least amount of public money, while five cancers with some of the best survival rates, including breast and leukaemia, receive nearly two-thirds of the money.
This seems counterintuitive. One would think that cancers such as lung cancer - which remains the leading cause of cancer death for both men and women - would receive a higher percentage of funding dollars. But that isn't the case. This is attributed to the fact that current research focuses on areas where major discoveries are more likely or the disease is easier to study, and this is partly due to the fact that future grants can depend on past success so reaching for those higher fruits can be risky career-wise. Is this a problem? Should focus shift from areas with diminishing returns to those where there's still a lot of ground to be covered? Or should we finish off the 'low hanging fruit' before climbing the ladder? And if the former, how do we accomplish it?


Tuesday, November 04, 2008

Coffee and cancer

I recently had an armchair expert tell me that french press style coffee vs a filtered coffee preparation method increases your risk of cancer. [Don't confuse french press coffee for the biological apparatus]. This person was foggy on the details but indeed got rid of their Bodum(tm). Personally I find coffee from a french press tastes superior, but then again, I'd drink it off a dog some mornings. Some googling revealled one source of the idea that unfiltered coffee increases your risk of cancer the source they cite is an article that shows increased homocysteine levels in drinkers of unfiltered coffee vs NO COFFEE. (no coffee?!?!) Homocysteine itself is not directly derived from your diet, however, high levels in the blood are indicators for high risk of heart attack and stroke, and possibly cancer. The thought was that filtering coffee removed what the authors assumed was causing the rise in homocysteine levels. Turns out filtering coffee doesn't change the fact that drinking coffee raises homocysteine levels.
To me this is a good example of something I see often, that is, cancer research NOT serving the public who funds it. If this is the crappy way that the public is informed about cancer research I'm surprised it still is funded. Someone gets rid of their french press because their concerns for their health based on the mainstream medias reporting of an incorrect assumption in the literature. What is also strange is that the damage is done. I think I would have a hard time convincing this person that their french press coffee is no worse for them.
Also I think there is a leap of logic here that I have heard is similar to the leap in logic made for the statin class of drugs. That is that since higher homocysteine levels correlate with higher risk of cancer (let's assume the one article I found linking the two is correct), then homocysteine is a cause of cancer. An indicator is not necessarily the cause but is merely associated with increased risk.
Also it may be that coffee raises cancer causing homocysteine levels by an appriciable amount, however, other factors associated with coffee drinking may result in an overall reduction in cancer incidence. So again even if homocysteine causes cancer, coffee may not.
Of course, perhaps coffee has so taken over control of my thought processes that I am in denial.


Last Call for Cancer Posts!

The 15th edition of the Cancer Research Blog Carnival will be up on Friday at the carnival home page. For all you procrastinators/last second folks it's time to write or dig up something and submit it to the carnival.


Thursday, October 30, 2008


As the more observant would have noticed already, the month formerly known as 'November' is rapidly approaching.

Starting in Australia, and New Zealand, there's now a fairly large international group of people who call this month 'Movember', and refuse to shave the bit of their face below the nose, and above the mouth for the 30 days. The movement has now spread to Canada, the US, the UK, Spain and Ireland, hopefully there'll be moustaches cropping up all over the globe.

There is a reason for all this... down under November was already 'Men's health awareness month'. Without detracting from the importance of breast cancer, women's reproductive health and wellbeing, and all the other various facets of women's health which were all too painfully ignored until recent decades, it's also worth noting that men suffer from some pretty nasty medical conditions themselves, and often need their own brand of gender-specific care. In addition to breast cancer (which is often forgotten about in men), men also get prostate cancer at an alarming rate (every year 4,300 Canadian men die of prostate cancer), testicular cancer, erectile disfunction and depression.

To quote from the movember website:
"However we look at it, men are far less healthy than women. The average life expectancy for men is five years less than women (presently 77 compared to 82).

Of the 15 leading causes of death among Canadians, men lead women in 14 of the causes. Men are 30% more likely to get cancer, than women, and 55% more likely to die from it. Men's suicide rate is four times higher than that of women. "

Specific to younger men is the problem of testicular cancer (the most common cancer among young men), depression (more women report being depressed yet more men kill themselves), and road accidents (accidents are the second biggest killer of young men).

Men also have this nasty habit of not getting medical conditions looked at, prefering instead to just tough it out. It's just not viewed as 'manly' to go and see the doctor about erectile dysfunction and prostate concerns. This'll only change after a considerable amount of public education... and movember is an important part of this. During movember, people can donate money to encourage a moustache, and this money will all go to various men's health organisations.

I, for one, will be sporting a moustache for the month - there's considerable excitement in the lab I'm in to see what style I'll run with (at the moment I'm leaning toward the 'gripper', but might just sport the classic 70's mo). I'd urge some other people to register on the site, and try to raise some money for men's health.


Halloween special: scary medical instruments

The British Columbia Medical museum has an online gallery with some pictures of old medical instruments. They have 2600 items from the past 150 years. Let play a game: try to figure out what is the use of the instrument:






  1. Perforator: Holme's perforator with side grip was used for gynecology. Used as last resort for obstructed labor.
  2. Double-Clawed toothkey: dentistry.
  3. Adenotome: otolaryngology. For the excision of the adenoids.
  4. 'Smith's' type haemorrhoid clamp: proctology.
  5. 'Devilbiss' skull cutter with spring: orthopaedics.


Wednesday, October 29, 2008

Bayblab podcast: Episode21

The latest Bayblab podcast is up (mp3 file here, rss feed here). 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 making you laugh just like the IgNobel which we cover in this show along with: selecting for hotness in chilis, why is melamine toxic, political genes, and rubbing one out in the name of science.


Tuesday, October 28, 2008

Migrating Salmon Video

Ran into this video made of individual Chinook and Steelhead Salmon smolt migration in British Columbia. These individuals are tagged before they are released as stocked salmon in the Snake and Thompson Rivers. Their movements are monitored by an impressive system called the POST array. I don't really know much about the details, however, the punch line is there is an impressive monitoring system in place for these salmon and it makes a great video. Also if you are more interested here is the paper where they have some interesting survival data like survival /100km migrated and on places with and without hydroelectric dams.


Friday, October 24, 2008

Turning Oil Into Neuroscience

This report just in - neuroscientist and Ottawa native Bruce McNaughton was lured back across the border from Arizona to the academic powerhouse that is the University of Lethbridge. The bait? A cool $20 mill from the province of Alberta - the Polaris award. A lot of people are saying "HOLY SHITBALLS!!!!! THAT'S A LOT OF $$$$$$$!!!" And right they are. That's almost as many hits as we get by the minute here at the BayBlab (although we certainly aren't getting paid any coin for it). But let's not get too worked up about the whole thing. After all, the guy had a paper in SCIENCE (tm) just last year. He's a SCIENCE (tm) SuperStar! SuperStars are SuperStars and so we shouldn't be surprised to see that it takes SuperStar cash to reel them in. This deal seems pretty reasonable to me when you line it up with some other Alberta blockbusters:

Bruce McNaughton (Neuroscientist): $20,000,000 over 20 years.
Jarome Iginla (Hockey Player): $21,000,000 over 3 years.
Stephen Harper (Politician): $840,000 over 3 years.
Boone Pickens (Oil Tycoon): $1,000,000,000 + per year.

So be warned world - Alberta oil is waving a big fat wad of cash and they're coming after your scientists! And by the looks of it, some of them might even be crazy enough to go live there...


Cancer Carnival Call for Submissions

The 15th edition of the Cancer Research Blog Carnival is coming up, but we've only had a trickle of submissions. It's not too late! Either start typing or dig up your best cancer blogging from the past month and submit it here. The carnival will appear Friday, Nov. 7.

As always, we're looking for future hosts so drop us a line if you're interested and head to the carnival homepage for submission and hosting guidelines and past editions.


Thursday, October 23, 2008

Urban dictionary for science?

Nature this week has a news feature concerning the erosion of the definitions of certain terms. It is a pet peeve of mine to hear epigenetic (it has to be heritable!) and de-differentiation (hint: if you're talking mammalian cell, you're probably wrong) misused. And I find stem cell is being used so loosely that it has sort of lost its meaning as we've discussed before.

The article tackles (excerpts to follow):

-paradigm shift:
"Unless a Nobel prize is in the offing, it might be wise for scientists to adopt the caution of contemporary historians of science and think twice before using a phrase with a complex meaning and a whiff of self promotion."

"The NIH is careful to define the epigenetics it is paying for as including both heritable and non-heritable changes in gene activity, something that Ptashne describes as "a complete joke".) Bird says he remains in favour of a relaxed usage. "Epigenetics is a useful word if you don't know what's going on — if you do, you use something else," he says."

"Even within the precise world of binary code and bit strings, there was computational complexity, which describes how much memory and processing is required to carry out a calculation; algorithmic complexity, which is related to how much a digital description of something can be compressed; and any number of combinations and variations. "So my bottom line is, add an adjective to 'complexity'," Crutchfield says."

"Race was long used to imply a shared, distinct ancestry [...] But in other contexts researchers are abandoning the term in favour of other ways to group humans, by 'population,' genetic ancestry' or 'geographic ancestry'"

-tipping point
"The term was originally coined in 1958 by sociologist Morton Grodzins in the context of studies on the racial makeup of US neighbourhoods. He found that when the migration of African-Americans into traditionally white neighbourhoods had reached a certain level, whites began to move out."

""There is no convincing theoretical argument or model that at some point the planet as a whole will snap into a second state of system," says Timothy Lenton, an Earth scientist at the University of East Anglia, UK."

-stem cell
"Alleged 'stem cells' can fail to meet the definition on many counts. Stem cells should persist long term, yet many 'stem cells' exist only in the fetus. Multipotency — the ability to generate multiple cell types — is a criterion for a haematopoietic, or blood-forming, stem cell, but spermatagonial stem cells only produce sperm. Stem cells specific to tissue such as cartilage, the kidney and the cornea have been reported, with varying degrees of acceptance. The quest for a 'stemness signature', a collection of markers common to all stem cells, has been met with frustration."

"Most statisticians resign themselves to abuse of the term's strict definition. But more grievous trespasses abound. "Statistical significance is neither a necessary nor a sufficient condition for proving a scientific result," says Stephen Ziliak, an economist at Roosevelt University in Chicago, Illinois, and co-author of The Cult of Statistical Significance. P-values are often used to emphasize the certainty of data, but they are only a passive read-out of a statistical test and do not take into account how well an experiment was designed."

"Many definitions of consciousness include the ability to sort through the relentless onslaught of incoming data to create and respond to an internal model of the external world. And some believe that simply gathering data about neurons and behaviours will not be enough."


Wednesday, October 22, 2008

Is that a phantom in your pocket, or are you happy to see me?

Phantom limb syndrome is a well documented and apparantly quite common phenomenon among amputees. It's the sensation that a missing limb is still there, and even responding to stimuli. But the upper and lower extremities (i.e. legs and arms) aren't the only body parts surgically removed. What happens, for example, when a man has his penis removed as part of a sex-change operation? Wonder no more:
[R]eports on the phantom penis and its treatment are very rare. We experienced a patient who underwent sex reassignment surgery in whom the sensation of a phantom erectile penis persisted.
The case study, publised in Acta Medica Okayama this past year, is freely available here (and complete with pictures) and describes the case of a 52-year old man who had male-to-female transgender surgery. Phantom erections are quite common after penis amputation either from sex reassignment or trauma (such as being assaulted by Lorena Bobbitt) but usually stop after a couple of weeks. This man's persisted for over 6 months before he returned to the operating room to have it fixed. The surgeons removed some of the underlying erectile tissue shortly after which the invisible hard-on disappeared. Neurotopia has a more detailed discussion of this case, and the underlying neurology of phantom limbs in general.


10 Reasons to Grow a Beard

I've written about beards before, and I have an obvious bias, but this made me laugh. Put down your razor and check out The Bureau for Bigger, Better Beards.


Tuesday, October 21, 2008

Recall: Melamine Nipple Spread

On our upcoming podcast we discuss the melamine tainted milk scandal and some of the affected products. The average Bayblab reader probably hasn't been affected, until now: The recalls continue, and just this past weekend The Guardian reported that thousands of novelty chocolate products were being pulled from shelves of sex shops because they contained up to 100 times the allowable limit.
"The Food Standards Agency issued an alert over chocolate willy spread, a related nipple spread and a novelty pen set, which contains a chocolate-flavoured body pen, all of which were imported from a Chinese manufacturer called Le Bang.

Food safety experts detected levels of melamine were up to 100 times greater than limits set by the European commission."
I guess I'll be sticking with butterscotch.


Abiogenesis in a flask

I'm a bit late on this one but the Miller-Urey experiment has produced some more data. This is the classic experiment, conducted in 1953, where possible conditions of the early earth were simulated in a flask. This flask was then subjected to arcs of electricity (to simulate lightening) and allowed to fester. After 1 week (he let it rest on Sunday) 10-15% of the carbon in the system was present in organic molecules, most notably 11 amino acids. Now in 2008, some of the original samples from this and similar experiments have been reanalyzed using modern, more sensitive equipment. Turns out another similar experiment resulted in the production of 22 amino acids. This again validates the strong possibility of the presence of the building blocks of life, as we know it, on many earth-like planets.
Also if your interested check out this fun/funny Miller-Urey Experiment simulator. Note: it's pretty easy to make it blow up.


Fish odour syndrome

I found this story on the interwebs about a woman who smelled like rotten fish, and was finally diagnosed at age 41 with a condition known as Trimethylaminuria. From the article:

"Trimethylaminuria is a genetic mutation that causes the body to produce too much trimethylamine, a compound found in fish. Particular foods, medication and hormones can exacerbate the condition."

This unusual condition is caused by a mutation in the FMO3 gene, and leads to an accumulation of trimethylamine because it cannot be converted to trimethylamine N-oxide. trimethylamine is a pungent compound found abundantly in fish.

However there exist milder variant polymorphisms, and even "normal" woman can be subject to the fish smell during menstruation and have transient trimethylaminuria because of a decrease in FMO3 activity (perhaps an evolutionary deterrent for mating?):

"In comparison, three healthy control subjects that harbored heterozygous polymorphisms for [Glu158Lys; Glu308Gly] FMO3 or homozygous for wild FMO3 showed normal (> 90%) metabolic capacity, however, on days around menstruation the FMO3 metabolic capacity was decreased to ~60-70%. CONCLUSION: Together, these results indicate that abnormal FMO3 capacity is caused by menstruation particularly in the presence, in homozygous form, of mild genetic variants such as [Glu158Lys; Glu308Gly] that cause a reduced FMO3 function"

Like a few other syndromes (such as maple syrup urine), trimethylamineuria can be diagnosed a a simple whiff of body odours, but it may be confused with halitosis. Thankfully this group from Philadelphia produced a better diagnostic protocol to distinguish the two:

"Because of our basic research into the nature of human body odors, our lab has received referrals of people with idiopathic malodor production, from either the oral cavity or body. We developed a protocol to help differentiate individuals with chronic halitosis from those with the genetic, odor-producing metabolic disorder trimethylaminuria (TMAU)."


Saturday, October 18, 2008

A skeptic's song


Thursday, October 16, 2008

Top5 therapeutic uses of coke

Coca Cola was invented in the 19th century as a patented medicine in the drug store of John Pemberton. It was initially known as coca wine, and contained cocaine extracts as one of its active ingredients. It was supposed to cure morphine addiction, dyspepsia, neurasthenia, headache, and impotence. Since 1904 coca-cola has been using dry coca leaves (1oo tons) which are imported from South America under a special permit and processed to extract to cocaine, which is resold for medical purposes while "spent" leaves are used for flavoring. While it is now cocaine-free (other than trace amounts) and primarily enjoyed as a caffeinated soft drink, it still does have some medical uses:

  1. Coca Cola can be used on a wasp sting (but not bee) in an emergency. The phosphoric acid can help inactivate the alkaline wasp venom. The same is true for jelly-fish stings in case you don't have any vinegar handy.
  2. While not strictly medical, coca cola can be used to fade hair dyes and clean stains including blood. However Mythbusters showed that it wasn't a particularly good cleaning agent, and does not dissolve rust or teeth/T-bones for that matter...
  3. Rehydration for infants suffering from diarrhea. While any sweet water will do, it is often the only "clean" liquid available in less fortunate parts of the world...
  4. Dissolving phytobezoar. These are undigested clumps of plants that can accumulate and block the stomach. Think of it as a human "hairball" (pictured above) and check out the awesomely disgusting examples here.
  5. As a contraceptive. However this was disproved by the winners of this year's IgNobel.
Finally, Coke given to rats in an Italian study published in the annals of N-Y academy of science, shows that chronic usage isn't so therapeutic:

"The results indicate: (a) an increase in body weight in all treated animals; (b) a statistically significant increase of the incidence in females, both breeders and offspring, bearing malignant mammary tumors; (c) a statistically significant increase in the incidence of exocrine ademonas of the pancreas in both male and female breeders and offspring; and (d) an increased incidence, albeit not statistically significant, of pancreatic islet cell carcinomas in females, a malignant tumor which occurs very rarely in our historical controls."

However since the control was drinking water I'm not sure what you can conclude from this study other than it's probably not a good idea to substitute all drinking water to a sweet liquid.