Friday, March 30, 2007

Quack of the week

This week's quackery is a bit less expensive, and a little less dangerous and it looks like a small purple dildo. The Tesla purple personal oscillator can not only serve as a sex toy but apparently also as an electro-magnetic shield, and an energy source. According to Life technology (TM), this invention comes from exclusive papers from Tesla himself. He must be oscillating in his grave. According to the company "The Tesla Purple Energy Shield™ emits vast quantities of energy, which directly repairs, strengthens and protects the energetic fields of the human mind body and soul". Wow a new energy source you're thinking, finally we can wean ourselves from fossil fuels.

How does it work? : "The Tesla Purple Energy Shield™ outer shell is made of aluminium, which is first anodised (electrolytic oxidation) and then colored. The spin of the atoms and electrons of the aluminium is thus changed in such a way, that The Tesla Purple Energy Shield™ is said to vibrate in resonance with the fundamental energy (Chi, Prana, Orgon) of the universe. (...) With anodising, the field of the plating is changed and interacts with tachyons. The surface of the plating has a unique crystal-structure."
Wow now this is cool, I didn't remember reading about this in quantum mechanics, but I love to think that the anodization of my beer can will create faster than light particles.

What does it do? : well many things, but my personal favorites is that it repairs DNA and retards aging! Wow somebody needs to send one to Aubrey De Grey. "will support the immune system and physical healing (e.g. headaches, cuts, wounds, fractures etc.)". Notice how all these quacks always refer back to the immune system...

How do we measure the effect? : "the use of The Tesla Purple Energy Shield™ will eventually raise your frequency rate of angstrom units per second." hmm lets see, yeah frequency rate, you mean Hz or something (oscilation/second)? hmmm angstrom per second, you mean speed? Like on the highway my car goes at 2.7e11 angstrom/sec. I'll tell that to the cop next time...

At 179$ I don't see how anyone could pass this up.


Thursday, March 29, 2007

Urine does not contain many pathogens

This is just a response to the fact that there is now a sign in the shared washroom in the lab that basically tells people to keep the washroom as clean as possible. Nothing wrong with that.
However the very first sentence of the sign reads,"Urine contains many pathogens." It doesn't. Unless of course you have a urinary tract infection, however this would be tough to spread to another person through urine on a toilet. I would just find it embarrassing that on a floor full of scientists and support staff there is something that is just scientifically untrue. If a visiting scientist has to relieve him or herself here they will think less of our institutes scientific knowledge, and perhaps of our sanitary practices since apparently they warrant a refresher on using the loo.
Maybe we need the sani-seat toilet.
Speaking of toilets and stuff, I think that we should all be responsible and get a bio-toilet.


Cool lab video


Wednesday, March 28, 2007

Lichty's Polydnavirus infection

At a recent oncolytic virus conference in Arizona I drank a beer (or two) with Dr. Brian Lichy from McMaster University. He was pretty excited about a pretty strange group of viruses known as polydnaviruses. These guys have a pretty interesting life cycle and are required for reproduction in some endoparasitic wasps, essentially becoming part of the wasp.


Don't use eGFP.

PLoS ONE has a great paper on eGFP overexpression inhibition of polyubiquitination both through Lysines 63 & 48.
Overexpression of this super popular fluorescent reporter protein effects polyubiquitination and the subsequent digestion via the proteasome to a degree that it signifantly stabilizes p53 and increases p53 downstream signalling.
Crazy. I wonder how it inhibits ubiquitination.


Determinants of agressivity

Dr Mike Eslea in Lancashire is an expert on aggression. He has shown in the past that direct or indirect exposure to violence on TV can influence how aggressively you'll respond to a stimulus. He's also shown also that children with severe behavioral problems fail to respond to positive or negative reinforcements. And we've all witnessed what kind of adults those make. There is even evidence that psychopathic behavior can be the result of brain lesions. In his latest research he's also shown that short people are not more aggressive than tall people. It seems science has busted this urban myth. In fact when prompted with an aggressive stimulus, the heart rate of tall man climbed faster than that of short man. The "chopstick" game they played consisted of hitting each other's knuckles with sticks! However I suspect that differences could be due to physiology rather than aggressiveness. I wonder also if it would be different if the short man were in presence of tall man at the time.


Tuesday, March 27, 2007

IA updates

Once again some great IA updates. I love the firefox extenstions.


Koreans Clone Again

A good friend of mine is leaving soon to go to South Korea, land of the cloned poodle. Reports today indicate that this group, once associated with controversial Woo Suk Hwang succeeded in cloning a wolf. Wolves have not been spotted in the wild in Korea in 2 decades and the lead researcher argues that cloning could help them and other endangered species survive. The results will be published in an upcoming issue of "Cloning and Stem Cells." Let's just hope they don't get their hands on any velociraptor DNA.

In semi-related news, researchers in Nevada have created a chimeric sheep that's 15% human in the hope that future advancement of the technology, achieved by injecting human cells into a developing sheep fetus, can be used to grow matched tissue for organ transplantation. This comes just a year after Bush urged a ban on human-animal hybrids in his 2006 State of the Union.


Monday, March 26, 2007

Bacteria Use RNAi-Like Mechanism to Ward off Viruses

I vaguely remember Rob blabbing in the bay about the RNAi system being an ancient and conserved mechanism by which cells defend themselves from viral infection. Maybe I will start paying more attention to this blabbing now, because I just read an article in Science that suggests that this idea may amount to more than the mere rantings of a degenerate graduate student. While the RNAi machinery of eukaryotic cells has been thoroughly described and well-documented to play a role in anti-viral defence, this recent paper provides the first evidence to my knowledge for an RNAi system in prokaryotes, and its role in anti-viral defence. Interestingly, the system appears to involve integration of phage sequence into the bacterial genome into regions known as "clustered regularly interspaced short palindromic repeats", which can then serve as a template for the production of short interfereing RNAs targeting phage mRNAs. Thus the system appears to be a primitive form of cell-autonomous immunological memory which protects against repeated viral infection.

Once again, a bayblabber is the first to predict a major breakthrough in biology. Now, if you can outline a full mathematical model describing the dynamics of the interaction between viral quasispecies and the host cell RNAi machinery, then I'll be impressed.


University of Ottawa Researcher Blazing a Trail Through the Human Interactome

While the yeast protein interactome has been exhaustively mapped by a number of research groups using several approaches, the larger and more complex human interactome has yet to be conquered. Taking a step forward in this direction, a group led by University of Ottawa Prof and Ottawa Institute of Systems Biology director Daniel Figeys has published the interactomes of 338 proteins in NPG's Molecular Systems Biology. The set of 6486 interactions between 2371 proteins was mapped using a high-throughput immunoprecipitation/mass spectrometry approach. That's 1% of the human interactome down, 99 more to go!


Semi-identical twins

Fraternal twins occur when 2 eggs are fertilized by 2 sperm and carried to term. Identical twins arise when one egg is fertilized by one sperm and the embryo splits at a later stage. Scientists had previously hypothesized and recently discovered a new type of twinning: semi-identical twins. In this case the twins are chimeras, containing populations of cells that are either XX or XY. The proportion of cells of each type varies from tissue to tissue. Researchers believe that this is the result of a single egg being fertilized by two different sperm and each sperm has contributed genes to each child. While one of the twins is a true hermaphrodite, both babies' growth and mental development seem normal.


Sunday, March 25, 2007

Scientists Who Share Are More Successful

Want to increase your citation rate and the impact of your science? This new publication shows that scientists who made their microarray data publicly available increased the citation rate of the associated paper by 69%, compared to those who witheld the information. This effect was shown to be equivalent to publishing in a journal with double the impact factor, an impressive statistic indeed.



A paper in PLoS Biology demonstrates that Deinococcus radiodurans, a radiation resistant bacteria is not resistant to radiation due to better DNA repair. Surprising, to me, since I always thought this was the power of radiation in order to sterilize foods ect. Apparently it is protein oxidation causes the effectiveness of irradiation, and radiodurans uses a Mn redox cycle to effectively protect proteins but not DNA.


Saturday, March 24, 2007

Bayblab Threathened of Legal Actions -updated

Breaking news! Finally somebody understands how much a couple of graduate students working on cancer with a blog are a powerful authority. It was about time something was done to stop this nonsense. Here is the history of what happened when William O'Neil who has accumulated quite a reputation with his alternative therapy to cancer, and his attacks against a blog run by graduate students actually doing work on cancer.

On March 24th, at 10:51:31 AM somebody with the IP ( who uses a dsl line with Bell Canada (sympatico Hi-speed edition!) and lives in Ottawa, Ontario stumbles upon the Bayblab. The person in question uses a windows XP machine, a screen resolution of 1280X1024 and Microsoft internet explorer 7.0. I warmly recommend to use firefox over MSIE 7.0 by the way.

At 10:51:45 AM He does a search on for "Canadian cancer research group"

At 11:00:29 AM He looks on technorati for who lists the bayblab as their favorite, come up with a name of a fan of the bayblab.

at 11:41:50 William O'Neil then sends an email to the yahoo account of the fan saying something like this: "If you don't remove all material concerning me or my company by monday March 26th, I will sue you for defamation". The crazy part is that the website was not even setup by that person so he's threatening the wrong person. I guess he has no other name to go by.

At 12:32:31 He does a search on the bayblab looking for "O'Neil". Too bad that name is never mentioned by us just quoted ad verbatim from quackwatch.

At 12:33:27 He puts an "anonymous" comment on the blog: "hey fuckwad! post a peer reviewed study demonstrating the efficacy of chemotherapy. goodluck...." Ouch somebody called me fuckwad, that's rude, my feelings are hurt. Yet another chemotherapy denier!

Geez thank god the internet is not anonymous...Somebody got his IP blocked!!!

BREAKING NEWS, seems our admirer is not only harassing some of the OHRI senior scientists but is also trying to manipulate some of our employer (which is an offense under canadian law) and trying to get us fired by contacting Dr. Worton, the CEO of the OHRI. Little does he know that the OHRI's legal department does not care about this, and all he is doing, is angering people higher up.

Due to inadequate libel laws and lack of regulation of alternative medecine here in Ontario, quackery can prevail and free speech is muffled. I decided to slightly modify the post as a precaution. Just shows how antiquated the laws are in Canada and in the USA. Mr Oneil is actually operating his clinic within the law (or gray area), for the time being.

March 26th:
It seems Mr. O'Neil has nothing better to do than harass cancer researchers (from his work at He sent another email this time claiming that he owns copyrights to his name and the name of his company. However according to Canadian law "Titles, names and short word combinations are usually not protected by copyright. A "work" or other "subject matter" for copyright purposes must be something more substantial. "
Links, Url and metatags are definitely not protected under copyright law in Canada. I guess this man just can't handle criticism by real scientists... how about you justify your claims Mr' O'Neil.
Has your method been published in any peer-reviewed publication? How do vitamins and amino-acids contribute to treating cancer and what is the efficacy? We'll gladely invite you to the podcast if you want to debate with real scientists.


Cancer Therapy: Read The Evidence and Make Up Your Own Mind

Peer-reviewed evidence is the difference between scientific fact and people trying to cheat dying people out of their every last dollar. For example, certified physicians prescribe chemotherapeutics, instead of say, leech therapy, because they have gone through a rigorous process of clinical trial testing to demonstrate their safety and efficacy, leading to approval by governmental agencies such as Health Canada and the American FDA. Additionally, there is a huge volume of peer-reviewed studies, from many different sources, attesting to efficacy, published in the scientific literature. This evidence is easily accessed through the internet using database search engines such as PubMed. For example, a 5 min search on PubMed yields numerous studies demonstrating the efficacy of chemotherapeutics currently employed in the clinic:

This is just a tiny sampling of the published peer-reviewed work (ie a PubMed search of "cisplatin clinical trial" yields 460 studies). While of course those in the field of oncology have looked at this evidence and come to the overwhelming consensus that chemotherapy is very often efficacious, one need not take their word verbatim. The evidence is out there, each person can read through it, speak with physicians and scientists, ask questions, and ultimately make up their own mind. On the other hand, quackery must be accepted on faith or presumed authority because objective facts, data and statistics are not made available for rigorous analysis.


Friday, March 23, 2007

Novel color vision in mice

This week in Science, a group reports inserting a human cone photopigment gene in mice. The mice actually developped the ability to perceive new colours, giving them trichromatic vision like us: "The researchers conducted tens of thousands of tests in which two different wavelengths or intensities of light were displayed on three test panels. Mice received a drop of soymilk as a reward when they correctly identified which panel differed from the other two. The genetically altered mice demonstrated their new visual ability by choosing the correct panel in 80 percent of the trials. By contrast, normal mice only chose correctly one third of the time, the score that one would obtain by guessing randomly among the three panels. "
Apparently mammalian brains adapt quite readily to new sensory inputs and it is possible to add, colours, but also smells and taste. This has obvious implications to evolution. After laser surgery, I'd like IR vision added please...


Drug ranking

The UK is considering classifying recreational drugs in terms of adverse health effects, to better direct the drug fighting policies. I am surprised by the order that is suggested, ecstasy for example seems to be much safer than alcohol or pot. No word yet where chicken McNuggets fit on that scale but my guess is way to the left.


Thursday, March 22, 2007

Best materials and methods

We've put some memorable M&M on the bayblab before. The digital rectal massage protocol, the rat genital licking protocol etc.. Inspired by our friend D.r. Bergeron (chicken soup above) and one of our baybe-fan Laura (protocol below), I dare you to one-up those materials and methods: "Reservoir function: Rectal reservoir function was evaluated by instilling artificial stool into the rectum. The test solution consisted of a slurry of Veegum in water, thickened to the consistency of soft stools and maintained at 37°C. A small catheter was inserted into the rectum, and aliquots of 50 ml were instilled with a large bore syringe, at an approximate rate of 140 ml/min, up to the point of intolerant sensation or leakage. The volumes for initial sensation, urgency, and first leakage were recorded."


Alternative therapy = fraud

Just a warning, I'm going to rant about this, because I feel pretty strongly about this subject. Alternative therapy or complementary medicine are things like acupuncture, homeopathy or reflexology. Those who practice or promote these techniques are at best fooling themselves and at worst defrauding honest people. Science is a method to get answers, our only limitation is our ability to find testable hypotheses, which isn't a problem when it comes to alternative medicine. The truth about alternative therapies is this: They are unproven, untested, pseudo-medical procedures that are based on faulty logic and are scientifically unsubstantiated. Acupuncture is based on the idea that "vital energy" flows in the body via "channels", which when "clogged" cause diseases. Somehow you can stick needles into these channels to restore flow. All the clinical trials so far looking at pain prevention have shown no effect, and in fact sham needles which do not puncture the skin were just as effective. This is purely a placebo and relaxation effect. Homeopathy is based on the idea that diluting something 1,000,000,000,000,000,000,000,000,000,000 times (actual figure), which causes similar symptoms to your disease (it can be anything really), leaves a memory imprint in water which will rebalance your body fluids. A drop of water is then placed on a sugar pill and then sold to you. Some people will forgo therapy to take that, paying good money too. Obviously readers of the bayblab know better, but many people don't. Health is a human right, and false claims and fraud on this scale should be punished. And it makes me really sad and angry when the therapies are offered as a program in universities, that I have to share a science degree with them.

Speaking of quackery, even cancer treatment is not immune to it, and it's too close for comfort. The alternative therapy offered by the Ottawa-based Canadian Cancer Research Group has more then questionable scientific validity. Even though you can find claims of efficacy on the web I cannot find any peer reviewed research that is happening there, and their methods remain unpublished, and for a good reason, it is not scientifically validated. Don't be fooled. If you want to learn more about the Canadian cancer research group, their amino-acid/vitamin "therapy", or Mr William O'neil you can check the very good quackwatch website and its canadian counterpart the canadian quackery watch, and the ratbag. I also strongly encourage you to see the CTV investigation on the show W5 about the claims made by this individual and his organistion. He's been known to bully his critics, including me, and authorities know about him... In fact there is a standing order at the OHRI to alert authorities and block his entry if he comes on campus.


Wednesday, March 21, 2007

A picture is worth 776 words

Wow, I'm both awed and puzzled. Ever wondered about the connections between cell biology and astrophysics? Well wonder no more, here are all the paradigm relationships: "This map was constructed by sorting roughly 800,000 published papers into 776 different scientific paradigms (shown as pale circular nodes) based on how often the papers were cited together by authors of other papers. Links (curved black lines) were made between the paradigms that shared papers, then treated as rubber bands, holding similar paradigms nearer one another when a physical simulation forced every paradigm to repel every other; thus the layout derives directly from the data. Larger paradigms have more papers; node proximity and darker links indicate how many papers are shared between two paradigms. Flowing labels list common words unique to each paradigm, large labels general areas of scientific inquiry."


Tuesday, March 20, 2007

Gene therapy for cancer : China leading the way

Move over cold FX, the new hotness in questionable approved drugs comes from China. Sibiono Genetech 's drug, Gendicine is based on a replication-deficient adenovirus delivering wt P53. So far it has proven to be quite safe in over 3500 patients, with symptoms resembling the common cold. However we all remember what happened to Jesse Gelsinger. The company claims most patients who have a not too bad prognosis to start with, will show some kind of partial or complete response. Not surprisingly, a lot of foreigners are going to china to get the virus. Are we being unfair to the company only because it originates from China, or is this one of those "stem cell therapy" type shenanigans. This nature news piece weighs in on the issue. In any case China is becoming a major player in the area, and we'll have to get used to the idea of seeing drugs originating there.


Monday, March 19, 2007

It's time to address the other deficits

The March 14, 2007 Globe and Mail had an excellent op-ed piece by Eddie Goldenberg, one of the architects of CIHR, CFI and the Canada Research Chairs. He reminds us all about the importance of research and education as a national priority for a knowledge based economy:

"A decade ago, no one would have believed it would be possible to eliminate the federal deficit, balance the budget, reduce taxes by $100-billion, pay down tens of billions of dollars of the national debt, put the Canada Pension Plan on a sustainable footing and invest more than $12-billion in the promotion of research and excellence in Canadian universities, as well as billions more in health care and a new national child benefit. Yet what seemed impossible then is taken almost for granted today. The federal budgets that provided for all of this didn't just happen. First, they took focus and rigorous priority setting. Government, like business, can be successful only when it sets its mind to doing a few big things right rather than expending its energies and resources on trying to accomplish a lot of little things. Second, they took political courage from the very top to drive the agenda and not be diverted. Next week, the Minister of Finance will deliver his budget. With considerably higher revenues than he had anticipated even a few months ago, he has two options. One is to announce a series of politically popular short-term measures -- more tax and debt reduction, increased unconditional grants to the provinces and a number of actions targeted at specific elements of the electorate. His other option is to take the bold steps necessary to address the challenges Canada faces over the next decade. If he does so, what may seem impossible today may be taken for granted 10 years from now. There are three deficits that the government must address today if Canada is to be competitive in the future and continuing to aspire to higher living standards. First, there is the environmental deficit. Canadians are ready and are expecting governments to act on the environment in ways that might very well have been unacceptable to them even a few short years ago. There will be considerable costs to the taxpayer because action on the environment will require significant amounts of public investment. Second is the public infrastructure deficit. There is a crying need for major investment in roads, water and sewage, public transit, etc. Canada needs to do a few big things well -- for its big cities, for its ports and for its border infrastructure, where bottlenecks impede the transport of goods. Our trade and our standard of living depend on it. Even with a much greater use of public-private partnerships, which in many cases are the way to go and which leverage considerable resources from the private sector, eliminating Canada's strategic infrastructure deficit will still require an investment of tens of billions of dollars of public money over the next decade. Third is the knowledge deficit and the need to encourage excellence. Canada will not move ahead in a very competitive global knowledge-based economy without a real commitment by the federal government to continue investing massively in research and excellence in our institutions of higher learning. There is no getting around the fact that addressing these three deficits will require the investment of a lot of public money over the next 10 years. For that reason, the challenge for the federal and provincial governments is to summon the political courage to set priorities so they can invest enough, not just for Canada to stand still, but to be leading edge and world class. The time to do so is now, when the fiscal situation allows for it. Last year, the federal government reduced the GST by one per cent -- $5-billion a year. Few people noticed that tax reduction and changed their spending habits accordingly. Yet, the Prime Minister is promising another 1 per cent reduction in the GST in coming years, which means an additional $5-billion a year out of the federal coffers. Since 1997, the federal government has paid down $80-billion in debt. Now, the federal government is planning additional debt repayment of at least another $30-billion over the next 10 years. On its own, it is good economics. But debt paydown and tax reductions are not the only priorities when the country has other pressing needs. Instead of more personal tax cuts in the order of at least a billion dollars, and $5-billion more a year in GST cuts, and $3-billion more a year in debt repayment that the minister is apparently planning, the government should simply maintain a balanced budget, and decide to invest those $9-billion a year over the next decade -- a total of $90-billion over 10 years -- in the environment, in physical infrastructure, and in making the best Canadian colleges and universities the place to be in the world for the best students and the best researchers. Instead of more unconditional transfers to provinces, where the federal government merely collects taxes and sends blank cheques to the provinces, the government of Canada should sit down with the provinces. Together, they should look to where the country needs to be in 10 years time, and agree together to focus new federal transfers in areas where the provinces -- with political courage, determination and political will -- would invest the transfers in a strategic way. With the same kind of political courage shown 10 years ago to eliminate the fiscal deficit, it may be possible 10 years from now that the elimination of environmental, infrastructure, and knowledge deficits will be taken for granted, even if it seems almost impossible today. Eddie Goldenberg, a former chief of staff to Jean Chrétien, was involved in the preparation of 10 federal budgets. He is the author of The Way It Works: Inside Ottawa."


Friday, March 16, 2007

Supernumerary heads (or, pseudocephaly)

Ha! The joke is on you. This has to be the ultimate. So far we have humans, pigs, turtles, cows and even a fossilized reptile (what are the odds of that!). The kicker: they are all in China!


Genomic diversity and cancer

First we sequenced the human genome, then we started working on SNPs to generate the Hapmap, and finally we started mapping methylation sites to generate the epigenome. Together these polymorphisms generate the bulk of the human phenotypic diversity. Recently it has come to my attention that there exists an additional source of diversity between humans: copy number variation (CNV). This, I am ashamed to admit, was complete news to me. Apparently you and I differ not only in the alleles we carry but also in the number of copies of the allele we carry. Traditionally we think of allelic variation has having 0, 1 or 2 alleles of a particular gene. However it is also possible to have the locus of the gene deleted, or have that locus duplicated or in multiple copies whitout having any sort of disease. Imagine if you had 4 copies of the gene for brown eyes versus someone who was just a regular homozygous brown+/+. Because of gene dosage your eyes would be darker. A recent study estimates that CNVs account for up to 17% of genetic variation in gene expression. And this isn't even a rare event, most people will have copy variants within their genome, and there are already almost 1500 variable regions covering 12% of the genome. They do tend to be outside of coding areas, probably because of negative selection, but are prevalent in regions containing genes important for immunity, environmental stress, etc... in other words regions where faster evolution is more likely to be beneficial. They may also account for complex "spectrum" diseases like autism. Cancer is another obvious disease which has been known to use this evolutionary mechanism for a long time. It is an evolutionary disease that uses all of the variation producing tricks evolution has to offer to mutate it's way to full blown malignancy. It uses normal genetic events like gene conversion, duplication, deletion, methylation, single base mutation but at an accelerated rate. If it manages to stay alive while generating enough diversity to evade the immune system and come-up with solutions to all of the built-in roadblocks we have it will have reached an "escape velocity". At this point it has reached a perfect balance of mutation rate / functionality in the genome, and has deviated so much from a normal cell it is barely recognizable. The corrolary is that the mutation rate is a fine balance, too low and you can't escape the body's counter measures, too high and you risk reaching catastrophy where the cell is no longer able to duplicate sucessfully. This is why radiation therapy is like having too much of a good thing for cancer. Remarkably the same thing is observed in viruses, as I recently learned at a seminar. The mutation rate is a very fine balance between evading the immune system but not compromising virulence. The lesson of the story is, if we can figure out how to increase mutation rates in cancer cells selectively, we might have a way to fight fire with fire...


Thursday, March 15, 2007

Ectopic anus

Well since we got started on this, might as well go all the way. Recently while researching a topic for a grant that I need to write for my class, I was looking for genetic diseases that affect brain development. I came across the "cat eye syndrome" which is of particular interest to me since it is a chromatin remodeling defect. This is when I discovered the concept of "ectopic" anus. Of course I held on to that knowledge waiting for the opportune moment during lunch. Another anal phenotype associated with the disease is imperforate anus, which is when the rectum finishes in a dead end, which thankfully can be corrected by surgery. Ectopic or malformed anuses can be a cause of constipation in neonates and this group devised a method to find and calculate the anal position index (API). Surprisingly out of 200 neonates 6 females and 5 males had abnormal scores on the API. There are also extremely rare cases of ectopic bowel segment in a boy with diphallus, or in a girl with rectovestibular fistula associated with occult distal vaginal atresia, or even vaginal anus. It turns out there is a whole spectrum of urino-genital ectopism which can cause all kinds of fertility problems, including ectopic pregnancy in the rectum à la "Twins", or ectopic testicles à la "South Park". Some of these genetic diseases that cause malformations can tell us a lot about the development of the uro-genital tract, and not surprisingly, HOX genes seem to be involved.


Supernumerary penises (or, Pseudopapa)

This is a bit of an old story, but just because of Coward's recent foot-nipple post, and because our good friend Ben didn't think it could be topped, here's one about a Russian man who grew a penis on his arm.
The man was born with a penis so small that he was unable to have sex and had his teeny weenie removed and grafted to his arm where it was enlarged using flesh from his inner arm before being reattached to his groin.


Canada's next prime minister

One of Dr. Bullman's masters student in the OHRI (home of the bayblab), Graeme Cunningham, will be featured on the CBC reality show, "canada's next great prime minister". He will compete and debate with 3 other contestants and against four ex-prime ministers: Brian Mulroney, Joe Clark, Kim Campbell, and Paul Martin. The show airs this coming Sunday, March 18, at 7pm. If you will be in the Ottawa area, you can join in the fun at the Heart and Crown at 6:30 pm to watch the show. If only we could get more prime-ministers that have science or engineering background, instead of only economists and lawyers. It seems to have worked well for India.


Tuesday, March 13, 2007

Supernumerary nipples (or, pseudomamma)

Here at the bayblab we have a history of being the authoritative source of extra-mammary material: from the dermatology online journal "A 22-year-old woman sought medical care for a lesion in the plantar region of her left foot, a well-formed nipple surrounded by areola and hair. Microscopic examination of the dermis showed hair follicles, eccrine glands, and sebaceous glands. Fat tissue was noted at the base of the lesion. Clinical and histopathologic findings were consistent with the diagnosis of supernumerary breast tissue, also known as pseudomamma. To our knowledge, this is the first report of supernumerary breast tissue on the foot."


Polar Barcoding

The Consortium for the Barcode of Life (CBOL) was a cool project in 2005, where a team went to Churchill Manitoba and collected some specimens and then Barcoded them. They managed to get 593 different species. I think that this is all part of the Consortium for the Barcode of Life (CBOL), which is a pretty neat idea. While just cataloging all the animal life is awesome it does lack some descriptive information. But what is really awesome is that it is something even an amateur scientist will be able to do soon as this technology gets cheaper. The gene that was chosen as the gene to identify species was cytochrome c oxidase 1, and from just a single run of around 600bp. I guess it is too bad that plants are not included in this kind of survey because the gene is mitochondrial.
The CBOL blog is decent with the newest goings on in barcoding.


Xenopus infestation in San Francisco

Free model organisms are swimming in a pond in the Golden Gate park. And apparently they are hungry. Start panicking now! I have a suspicion some bay area scientist is conducting a large scale experiment on killer frogs: "No one knows for sure when this frog species got into the pond or who put them there, but now city officials fear the killer frogs will spread throughout the Bay Area."


Monday, March 12, 2007

What if Global Warming is a Hoax?

A comment on a recent bayblab article on global warming got me thinking: What if he's right? What if man-made global warming isn't a real phenomenon? And the answer struck me: who cares? So what if the polar ice-caps aren't melting, the world's oceans aren't rising and the mercury isn't slowly creeping upward? It still seems to me that many of the changes being pushed are good ideas regardless of whether the earth is warming. Reduction of carbon emissions? Sounds good to me! (Who enjoys smog?) A shift towards alternative fuel? Again, a good idea. Why maintain dependence on limited, and polluting, resources? I'm sure deniers have doom and gloom economic prophecies should Kyoto be enforced, but this article points out that even if it is a hoax, there is still money to be made from it. What do others think? If man made climate change were to be proven false, should we abandon environmental commitments and stick with fossil fuels?


Sunday, March 11, 2007

The Ground of Science is Shattering and the Ivory Towers are Collapsing: A Revolution of the Super-Educated Masses for the 21st Century

As would be expected in any growing and prosperous civilization, the number of PhDs produced in the US continues to rise, as you can see below in these stats from the National Science Foundation, with interestingly the most dramatic increases in PhDs awarded to non-citizens. Don't expect to find these graduates in academic positions any time soon, as the number of permanent faculty and tenure-track positions has been taking a nosedive, at least in North America. Rather, PhDs these days are more likely to find non-traditional employment in science, through industry, entrepeneurial enterprises, patent or investment advisory and part-time/contract teaching. This will probably mean goodbye to the reign of tenureship politics and hello to an era dominated by independence, initiative and adaptability in science for the 21st century. Couple this with innovations in online open publishing (publish first, peer-review later), online networking/discussion tools such as Nature Network and open access to data around the world, and what you have is a revolution. I can't wait to see how science is done in 2050.


Friday, March 09, 2007

phucking Phobos

A humiliating defeat at Pubstumpers trivia two nights ago, typified by the fact that I did not know that Mars had any (let alone two) moons, led me to check out the scoop on Phobos (the moon not the quake3arena model).
Phobos is the largest and nearest orbiting moon of mars. It is messed up and lopsided and has an interesting history. Apparently Phobos has an unstable orbit if tidal forces are not accounted for. This lead to some speculation, from the US space developments advisor, as late as 1960 that Phobos could be an artificial Martian satellite or base. "Phobos had to be very light —one calculation yielded a hollow iron sphere 16 km across but less than 6 cm thick" (wikipedia on Phobos).
It is so photogenic that I have posted two pics. One shows how small and irregular it is, the other shows it passing the sun from the perspective of the Mars rover Opportunity (click on it to see animated gif action).
All this was ganked from wikipedia.


Thursday, March 08, 2007

The Cancer Genome: More Genes Involved than We Thought?

A Nature paper just published by the Wellcome Trust's Cancer Genome Project reports on the findings of a study sequencing 518 protein kinase genes across 210 human cancers of various sorts. Not surprisingly, most mutations were random "passenger" mutations unlikely to play any causative role is disease, but interestingly nearly one-quarter of all kinase genes surveyed (120) carried "driver" mutations. This is in contrast to the mere 350 of the 30,000 human genes previously identified as being involved in cancer using more traditional, trial-and-error type approaches. Bottom line is that there may be a hell of a lot more oncogenes and tumor suppressors out there than we think.


Drive a car, pay the tax

It turns out there are are extra costs attached to alternative fuel use. Tax collectors in Illinois are trying to collect gas tax from a retired chemist who has converted his car to run on vegetable oil. Instead of lauding this guy for reducing dependence on fossil fuels, they want 5 years of back gas-tax (even though he hasn't bought any gas in 5 years!) and are threatening felony charges if he doesn't pay up. The logic is that gas taxes are (supposedly) slated for road maintenance and upkeep and since he's still driving a car and a burden on the highway system he should be paying the tax. That's a fair argument, but totally ignores that fact that there are no laws on the books that address this kind of situation. It seems to me that this is another case of a legislative or corporate body failing to adapt to the times (see: RIAA and MPAA and digital media) and resorting to bullying of the 'little guy' instead of coming up with real solutions (such as shifting the road tax from gasoline sales to odometer readings/road use). Instead they choose to intimidate, not legislate. Shouldn't we be *encouraging* these kind of innovations?


The condensation algorithm

Gotta love that picture of the very nerdy-looking authors. This is a tip from a friend of mine who does artificial retina research at polytechnique in montreal. The condensation algorithm makes it possible to identify and track shapes in an image. Their 1998 paper "Conditional Density Propagation for Visual Tracking" was cited 1239 times according to google scholar. Good work computer nerds!


Being healthy can kill you

I don't know if it's an Ottawa thing or if it has spread insidiously over the globe. They are amongst you, and you might not even know it. It could be your co-worker, your neighbour, your best-friend. They get together several times a week and practice their rituals. Often it eats off their life, taking more and more time away from the people they love and the things they used to do. Yes I'm talking about runners, which is very much a cult. It is no longer just a physical activity, it's a way of life. They even have their own magazines and books and conferences, which I'm sure are all in "tongues". And running is not without risk, a simple search on pubmed for running injury will give you over 2200 hits. Yet little is known about the what is going on in the brains of runners. Is it dammaging to spend 3 hours running a marathon with low blood sugar level, chronic hypoxia and repetitive impact tremors shaking the brain. At least one study suggest it may result in decreased monoamine levels. At least make sure you stay well hydrated, preferably with holy water in case you drop dead at the end of your marathon. So I'm warning you, being too healthy can kill you. Even vitamines are dangerous: "The researchers reviewed 68 studies, but sorted out results from the 47 they considered the most credible and found an overall 5 percent increased risk of death. Beta carotene was associated with a 7 percent increased risk; vitamin A, a 16 percent increase, and vitamin E, a 4 percent increase."


The science of elephants

Inspired by a recent post on this exellent french blog I decided to look up recent findings in elephant research. When I attended the SSR meeting two years ago I came upon a poster which studied the homonal fluctuation in an elephant by taking blood samples every 30 mins for 24h. I felt sorry for the graduate student, because I've done that with mice and it's a pain, I can only imagine what it's like with a 4.5 tons elephant. Reproductive science in elephants is somewhat of a dangerous occupation : "just touching a jumbo penis – they measure more than 1.5metres when aroused – can have painful consequences as German scientist Dr Hildebrandt reveals. One guy I know got a black eye from being hit by an elephant’s penis. It’s a messy business as he massages Jackson’s prostate gland to produce 300ml of semen per orgasm – the equivalent of a can of Coke – which has to be airlifted in giant condoms across America to Christy". Science is also coming handy for conservation efforts. As more and more DNA samples are catalogued, it is now possible to test confiscated tusks from smugglers and determine their origins. What Wasser et al discovered is that the majority of the ivory from the 23 000 elephants killed last year came from Zambia, where it is estimated that the population decreased by up to 90%.


Wednesday, March 07, 2007

Preston Manning Says Science is Important

As someone who believes in the value of the scientific outlook, it's easy to be discouraged by the way information is often disseminated through the media. So this same week the National Post struggled with Journalism 101 in getting their scientific quotes straight on global warming, it was refreshing to read a recent Globe and Mail article (click on the first google hit or read below) by none other than former right-wing Reform party leader Preston Manning. In it he makes a convincing argument for the place of science in Canadian society and in particular the critical role it can play in developing a sustainable economy for the future:

Mr. Prime Minister, you've got mail

From Monday's Globe and Mail

Suppose Stephen Harper were to ask the heads of the federal government's various scientific research agencies how they might contribute to an objective of improving and conserving Canada's physical environment. Here's a sample of the responses he might receive. From the Natural Sciences and Engineering Research Council (the largest funding source in Canada for university research and training in environmental science, technology, and innovation):

Mr. Prime Minister, we can offer improved measurement of CO2 emissions and the development of CO2 sequestering techniques for industry; the CarbonSaver approach to sustainable energy production; improved techniques for monitoring ocean health and water treatment; improvements to hazardous waste disposal systems; the development of sustainable management technologies for peat bogs, forestry, and agriculture, and the list goes on... From the National Research Council (the government's senior research and development institution comprising more than 20 institutes and national programs):

We can provide advances in emissions control and fuel reduction, alternate energy sources (such as gas hydrates, fuel cells, ocean energy, and biomass conversion), bio processes and products such as “greener” plastics and better batteries – all developed in such a way as to encourage industrial clusters capable of transferring such research and technologies to the marketplace.From the Canada Foundation for Innovation (which has funded 500 environmental projects worth more than $200-million):

We are engaged in work of the polar laboratory on Ellesmere Island and the Amundsen research icebreaker both of which are relevant to Arctic conservation; we are learning from oil sands pilot plants about more efficient and environmentally friendly approaches to energy production; we have “green building” projects and improved approaches to marine life conservation flowing from the NEPTUNE project in the northeast Pacific (soon to be the world's largest cable-linked seafloor observatory); and so on... From the Social Sciences and Humanities Research Council:

We are supporting scholars studying the socio-economic impacts of climate change, the ethics and governance of environmental protection, the valuation of ecosystem services, and interdisciplinary approaches to environmental change and risk management, among other things.

From the Canadian Institutes of Health Research:

We offer findings concerning the links between human health and impure water, poor quality air, environmental toxicants, and contaminated foods – all helpful in determining what environmental protection measures would have the most immediate and beneficial impact on the health of Canadians.

As one can imagine, while public policy-makers have only recently embraced the concept of environmental conservation, those who engage in basic science long ago discovered and defined the principles of conservation at their most fundamental level. The Prime Minister's inbox would also no doubt receive responses from scientists at the Sudbury Neutrino Observatory, the Perimeter Institute, the Canadian Light Source, the National Institute of Nano Technology, the TRI-Universities Meson Facility (TRIUMF), and Canada's advanced bio-medical laboratories.

All this research has flowed from the most basic laws of conservation: the conservation of mass, as defined by Antoine Lavoisier in 1785; the conservation of energy, by Julius Robert von Mayer in 1842; of thermodynamics by Rudolf Clausius in 1856, and of mass/energy by Albert Einstein in 1905.

These laws declare that when one takes any substance from nature and extracts energy from it in a form that can be used by mankind (what physicists call “work”), there will invariably be “waste.” The sum of the original energy/mass is equal to the energy extracted plus the residual energy/mass of the waste. To date, science has not discovered a process capable of producing pure useful energy (work) without producing waste; thus whenever we produce any good or service we must always be prepared to acknowledge, and to deal with, the waste.

While governments make enormous efforts to measure the “Gross National Product” and devise public policies to facilitate its increase, they are only now beginning to acknowledge the necessity of making equivalent efforts to determine the “Gross National Waste,” and to devise the public policies and encourage the industrial processes required to reduce it, treat it, and return it safely to nature.

Scientists who seek to understand conservation at its most fundamental level no doubt welcome the current interest in incorporating more recent discoveries – such as those of climate science – into public policy. But they also urge greater incorporation into public policy of those scientific principles and findings that have long been known, but never thoroughly applied. And they remind us that those principles and findings are most often discovered, not in the pursuit of immediate solutions to immediate problems, but in the pursuit of a more fundamental understanding of the universe in which we live.

Almost 50 years ago, the president of the United States, through “requests for proposals” issued by NASA, initiated a process for harnessing the scientific, technological, and entrepreneurial resources of that nation to the national goal of putting a man on the moon.

In the 21st century, should it not be possible for our leaders to initiate a process for harnessing the scientific, technological, and entrepreneurial resources of this nation to the goal of reconnecting 30-million Canadians to the environment of planet Earth?

Preston Manning, a former leader of the Official Opposition, is a senior fellow of the Fraser Institute and president of the Manning Centre for Building Democracy.

Kind of makes you wish he had ended up leading the post-merger Conservative party as Prime Minister instead of the very scary, intellectually challenged, George W. Bush wannabe, Stephen Harper, who seems to think that funding science has no value other than as a tool to make rich pharmaceutical and biotech investors richer.

Thanks Preston, you've made my day and validated my existence as a man of science. (I never take anything seriously until a politician agrees, even myself). On a serious note though, it really is great to see politicians of all persuasions taking an interest in science these days, even if they do sometimes resort to cheap theatrics involving hydraulic lifts to show how high their graphs really go (ie Al Gore, An Inconvenvient Truth). Hey, you can't argue with an Oscar and an audience of "billions" of viewers.


Tuesday, March 06, 2007

National Post series on global warming deniers

Since this is a hot topic on the bayblab, the National Post has a really nicely put together series on global warming deniers. Obviously some scientists with good credentials. Although I find it Ironic that they lumped-in a global warming believer who thinks it will be good for the economy. So obviously this isn't really about science but about policy. Also amusing how they describe the majority of climatologist as convinced that the science is settled. Obviously science is never settled, so it's a moot point... Also interesting is how a lot of the cited scientists have actually issued statements regarding the articles and clarifying their position because they were misquoted...


Monday, March 05, 2007

Solar-Power Your iPOD

I thought you iPOD addicts out there might want to build yourselves a solar iPOD charger so you can still listen tunes if there's a nuclear holocaust. Also good if you are just looking to save a penny or two on your electricity bill/reduce your burden on the power grid by some infitesimal quantity/listen to music in the backcountry. Or hook it up to a Speak-and-Spell to call the mother-ship for a pickup.


Ottawa U prof takes a stand against global warming

Oh boy, he thinks the greenhouse effect is a conspiracy: " Professor Ian Clark, an expert in palaeoclimatology from the University of Ottawa, claims that warmer periods of the Earth's history came around 800 years before rises in carbon dioxide levels. The programme also highlights how, after the Second World War, there was a huge surge in carbon dioxide emissions, yet global temperatures fell for four decades after 1940.
The UN report by the Intergovernmental Panel on Climate Change was published in February. At the time it was promoted as being backed by more than 2,000 of the world's leading scientists.
But Professor Paul Reiter, of the Pasteur Institute in Paris, said it was a "sham" given that this list included the names of scientists who disagreed with its findings."
I remember him being a signature in the National Post letter to Harper to pull out of Kyoto.


Dumping green sludge in a river: environmental disaster or St. Paddy's Day

After some encouragement from coward this article come to you from wikipedia. It turns out that Chicago has made a tradition of dumping FLUORESCEIN into the chicago river on st. paddy's day.


"A modern day miracle occurs each year as part of the St. Patricks Day Parade celebration when the Chicago River turns an incredible shade of Irish green. This spectacular transformation ranks right up there with the parting of the sea by Moses and the Pyramids of Egypt."


p53 restoration

We have discussed these papers in The Bay (where the baybs blab). But here's a nice summary of a few recent papers that describe the efficacy of reactivating p53 in cancer cells. Basically it works. Surprisingly despite ongoing selection for rapid replication cancer cells still contain sufficient protein networks that allow p53 to kill those misbehaving cells. The costs of activating p53 are likely increased senescence in normal cells.


Phantom Limbs

Another inspired lunch conversation turned its way towards phantom limbs and amputation. Phantom limb pain is a well documented phenomenon, occurring in the majority (up to 80%!) of amputees. From wikipedia: "A phantom limb is the sensation that an amputated or missing limb is still attached to the body and is moving appropriately with other body parts." Sensations in the phantom limb are actually quite complex, and can respond to stimuli (for example, spilling a hot liquid on the non-existant limb). The literature, and associated research, considers this a neurological condition - that is, physically involving the brain and nerve responses.

At the other end of the spectrum is apotemnophilia, or Body Integrity Identity Disorder (BIID), a condition in which a patient has an overwhelming desire to amputate healthy limbs. I've read some pretty horrific stories of patients who were forced to self-amputate (or otherwise remove the limb) when doctors have refused to perform the surgery. In contrast to phantom limbs, BIID is treated as a psychiatric disorder, with no known underlying physical cause.


Sunday, March 04, 2007


We all know that a good supply of music is essential in order to survive grad school. Of course it's all too easy to get busy in the lab and lose touch with pop culture. So I've recently tried to revive my stagnating playlist by going on a music acquisition spree. Thought I'd share a few recently released albums worth getting if you have an aging playlist and little time:

The Kooks - "Inside In, Inside Out"
The Shins - "Wincing the Night Away"
Arcade Fire - "Neon Bible"
Modest Mouse - "We Were Dead Even Before the Ship Sank"
Gomez - "How We Operate"

Anyone else got any suggestions?


Friday, March 02, 2007

New Longevity Genes

A study employing a new screen for genes involved in longevity in C.elegans identified 64 genes that extend life when inactivated post-developmentally (via RNAi). These genes were not included in other knockout studies because of their essential role in development. More than 90% of the identified genes are conserved from yeast to humans, and many of them have an effect on longevity that is as robust as the usual suspects. Move over SIR2. Check out if your favorite gene turned up in the screen on the freely available early online release at PLoS genetics.


Plate tectonics is a conspiracy

Plate tectonics is clearly made up, I mean how can you get subduction and movement of the crust if the earth is flat? Well the newest conspiracy is that the earth is round but plates do not move. Then why do the continents seem to fit together you will ask. Well, it's not the continents drifting it is the earth that is growing. I mean that's the logical conclusion right, but the scientists are keeping it a secret, because they do not want to rewrite science books. In fact I urge you to look at this conspiracy video. Don't be brainwashed by Pangeationists, rather doubt the physicists, they are part of this conspiracy, they never told us matter could expand away from the center of gravity of the earth and that mass can be created from nothing. Next time you experience an earthquakes, remember, the scientists are doing it.


Thursday, March 01, 2007

Singing the Blues

That lump in your throat when you get up in front of a drunken bar crowd to belt out a few karaoke tunes may not be nerves after all. Japanese doctors are reporting an increased incidence of vocal cord polyps that they link to excessive karaoke singing. The popularity of songs requiring high-pitched singing is putting undue stress on the vocal cord resulting in these growths dubbed 'karaoke polyp'. The question remains why the Chris Martin and Thom Yorke falsettos singing the original songs don't suffer from the same affliction. One idea is that they are better trained and aren't as far outside their normal range, limiting the damage compared to those of us who are only rockstars when alcohol is involved and not used to singing those notes. So next time you're out at the pub and there's a microphone involved save yourself - and your audience - and pick songs you can actually sing.