Wednesday, November 29, 2006

Cancer and Evolution

For those of us way behind the curve, too filled with molecular biology to understand Dr. Scott Findlay's presentation a couple of weeks ago that related ecological concepts to cancer therapeutics, there is a recent paper in Nature Cancer Reviews that nicely summarizes the ideas behind thinking about cancer in terms of ecology and evolution. I ganked the picture from the paper, but since I've been trying to download it again my browser keeps crashing. Coincidence?


Don't sit up straight!

While at WIP today, Bayman suggested it was better for your back to slouch when you are at lectures, since the 135ยบ angle produces the least stress. This piece of research certainly agrees with his assertions: "Alterations of Lumbosacral Curvature and Intervertebral Disc Morphology in Normal Subjects in Variable Sitting Positions Using Whole-body Positional MRI". Time to petition for an imax seminar room with fully reclining chairs. I will never miss an afternoon seminar again. Now we need to find something about ipods leading to better research, since it his now officially banned AND enforced. No words yet if the labs are also banned to the hearing impaired.


Improper use of lab equipment

What could a biologist studying hummingbirds do with a bottle of chlorophorm, and 55 gallons of hydrochloric acid? If you guessed kill his boss' husband and get rid of the evidence, than we should probably start locking the acid cabinet...


Monday, November 27, 2006

Cool Sci visuals

If you're patient enough to wait for the video to load, check out this crazy look at the inside of a cell set to classical music-it was made at the Harvard medical school and so is at least conceptually accurate-my personal favorite part is the myosin "walking" along the actin-some of the protein-protein interactions are pretty touching too! On a different note, the national geographic special "animals in the womb", which first airs dec 10 on the national geographic channel (and will likely be up to download soon thereafter!) features some pretty amazing pictures of embryonic development in different vertebrates-its hard to believe how similiar we start off!-maybe the fact that such a huge portion of the genome in mammals (and sea urchins!) is transcribed during early embryonic development suggests that only a small number/arrangement of genes is actually responsible for the diverse phenotypes we see by the time an individual is born-think about that-you might be only a few gene products away from having a trunk!


Saturday, November 25, 2006

Stem Cell Lies and Misinformation

I randomly came across a site called "LifeSite" by a group lobbying the public and the Canadian government to place a moratorium on human stem cell research. I was horrified to read their "scientific" arguments as to why this should be done, all basically just wrong:
  • Embryonic stem cells appear to be subject to random and uncontrollable growth. On the other hand, adult stem cells seem to be more predictable in responding to the growth factors and hormones that function to re-direct their development.
The Facts: ES cell growth is not "random". For example, mouse ES cells when injected into a host blastocyst in a surrogate mother, are able to give rise to embryonic tissue and undergo the tightly regulated developmental process to form a perfectly normal adult animal. One of the main reasons it's so important to do ES cell research is to learn how to manipulate them in the dish to form whatever tissue one might need, and scientists can do this pretty well already.
  • Embryonic stem cells have been known to grow into the wrong type of cells, in some cases such as hair and teeth growing in the brain of treated patients.
The Facts: ES cells haven't even been used in human therapy yet so of course there has never been any evidence of hair and teeth growing because no patients have been treated. Again the point of researching human ES cells in the lab is to learn how to control their differentiation (what type of cell they become) so that this sort of thing would never happen when they are actually used for therapy, just like drugs are tested on animals to minimize the risk of side effects when used in people.
  • Perhaps the greatest clinical problem with implanted embryonic stem cells is that the body flags them as foreign material. Consequently, they are subject to rejection by the patient's immune system.
The Facts: Any cell, embryonic or not, can be rejected by the immune system if its genes do not match the recipient patient. Therefore it is important to use autologous cells (from the same patient) for regenerative therapy, but whether the cells are adult or embryonic is of no consequence as far immune rejection goes. In fact, customized autologous ES cells generated by nuclear transfer or harvested pre-natally are probably the most promising potential source of cells for future therapies. There is a huge need for autologous cells, since they are often difficult to obtain once a patient already has a deadly diseases like leukemia, multiple sclerosis or muscular dystrophy.

The fools running this site push research into the therapeutic potential of adult stem cells, claiming they are just as useful or even more useful than embryonic stem cells. Also untrue. This goes way beyond simple ignorance to deliberately twisting scientific knowledge to misinform people and it's pretty sad. All the more reason for real scientists to get on the ball in educating the public.


Friday, November 24, 2006

Everything You Need to Know About RNA in Four Pie Charts and a Venn Diargram

Looking through Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution, I came across this great little figure that just says it all. Maybe pie charts and Venn diagrams are useless individually, but together...they may just be an unstoppable combination.


A brief history of life

From the uncyclopedia, the encyclopedia written by bears to piss Colbert off:

13,775,000,000 B.C. - After a night of sex known as the Big Bang, God creates the universe.
4,550,000,000 B.C. - The Earth is created
3,850,000,000 B.C. - The God of Evolution creates the First Organism
3,000,000,000 B.C. - Evolution becomes the main religion of earth's earliest residents known as the Prokaryotes
2,100,000,000 B.C. - Some of the Prokaryotes break away from the mainstream and start their own sect of Darwinism known as Eukaryia.
1,200,000,000 B.C. - The Eukaryotes permit some of their members to have more than one cell. The Prokaryote sect still forbids this practise.
670,000,000 B.C. - The Plant and Animal branches of the Eukaryote sect arise.
543,000,000 B.C. - Plants and Animals split into numerous denominations.
495,000,000 B.C. - The Vertebrate denomination, to which most practising evolutionists belong to is formed from the Animalian Eukaryote sect. Up to this point all life lives in the ocean, it is considered blasphemy to step onto land.
425,000,000 B.C. - Plants are granted land permits
410,000,000 B.C. - The God of Evolution gives vertebrates and other animals a land permit after years of protests and civil disobedience.
300,000,000 B.C. - The Reptilan branch of the Verebrates is formed.
251,000,000 B.C. - A group of animals reject the teachings of Darwinism and are promptly send to hell in the Permian Mass Extinction. The small sect of Mammalia branches off from Reptila, they remain a minority until after the Asteroid of Judgement.
245,000,000 B.C. - Dinosaurs are selected by God to become the rulers of the Earth.
200,000,000 B.C. - The real Jurassic Park starts filming. Directed by Steven Stegasaurus.
144,000,000 B.C. - Jurassic Park comes out on video.
65,000,000 B.C. - After a long reign, dinosaurs have become more arrogant, greedy, and cruel. Many reject the teachings of Darwinism. God punishes them by delivering the Asteroid of Judgement. A small group of dinosaurs, the Avians are loyal to the teachings and are spared. After this, God assigns Mammals to become the dominant sect of Life.
60,000,000 B.C. - Primates the sect that includes the degenerate Homo sapiens is formed.
50,000,000 B.C. - The early Equine sect of Mammalia which later forms an alliance with Homo sapiens is formed.
48,000,000 B.C. - Whales lose their limbs because of landmines, forced to live in the ocean.
35,000,000 B.C. - The Monkees, a popular group of Primates start their own sect.
20,000,000 B.C. - A group of Monkees, lose their tails and become known as apes.
8,000,000 B.C. - A group of Apes known as Hominids form their own sect.
5,555,555 B.C. - The last known mating between chimps and humans takes place.
4,444,444 B.C. - The prophet Lucy is born. She leads a sect known as Australpithecuses.
2,500,000 B.C. - An Australpithecus gives birth to the world's first, Homo.
2,499,999 B.C. - All Homos are banned from Australpithecus society, forced to start their own sect.
1,800,000 B.C. - Filming of the Ice Age Movie, Pleistocene begins, Homo gets his first erectus
1,000,000 B.C. - Clothes are invented.
750,000 B.C. - Fire is invented
200,000 B.C. - A group of well educated gay people known as sapiens form their own sect and begin to massacre other sects of Homo
50,000 B.C. - Homo sapiens enter into a pact with Canis lupus
40,000 B.C. - The Neanderthal massacre is perpetrated by Homo sapiens.
10,000 B.C. - Under what they believe is the instruction of God, woolly mammoths are massacred. The movie Pleistocene is finally done filming
9,999 B.C. - The movie Pleistocene is released on video. Agriculture is invented. Production of Holocene a sequel to Pleistocene begins.
7,000 B.C. - The wheel is invented.
4,004 B.C. - The false religion of creationism is started by a radical group of Homo sapiens.
3,000 B.C. - Homo sapiens enter into alliances with both the Felis and Equus sects.
2,000 B.C - Most Homo sapiens forced to adopt creationist beliefs by the prophet Moses. Dissidents are slaughtered summarily.
44 B.C. - Julius Caesar is murdered for his Darwinist beliefs'.
0 A.D. - Jesus Christ, the prophet of Creationism is born.
666 A.D. - Mohammed, another creationist prophet is born.
1,809 A.D. - The great evolutionary prophet Charles Darwin is born.
1,835 A.D. - Darwin has a religious revelation while vacationing on the cruise ship Beagle
1,859 A.D. - The Bible of Evolution, The Origin of Species, is published
1,882 A.D. - The Prophet Charles Darwin passes away at home.
1,925 A.D. - High School Science Teacher John Scopes is sentenced to death for having Darwinist beliefs.
1,987 A.D. - Darwinism is tolerated but the majority of Homo sapiens still support Creationism.
1,999 A.D. - Kingdom of Kansas forbids teaching of Darwinist beliefs
2,005 A.D. - Judge Jones upholds Religious Freedom and allows Darwinism to be taught.


Thursday, November 23, 2006

bayblab podcast: Episode 3 part-II

Finally part 2 of the bayblab podcast episode3 has arrived. Guest speaker Stephen Hawking and the bayblab crew discuss life on mars, how plants move when you're not watching, why male contraception makes us squirm, why old poeple are breeding grounds to cancer, Trogdor the bruminator, and giving wine to mice to extend their lifes... Enjoy!


The Journal of Visualized Experiments

It's been mentioned before on the bayblab that more cool science pictures, and especially science videos are needed. Wait no longer! You can now find all sorts of videos detailing methods in the Journal of Visualized Experiments. The journal is strictly online, open access and free to publish to. Think of it as YouTube for scientists.


Wednesday, November 22, 2006

Kentucky: More Than Just the Home of Creationism

Intrigued to know more about the state that so loves creationism, I immediately consulted Wikiality to get the facts. Looking up Kentucky, I discovered that this state is also the birthplace of the great Abraham Lincoln, founding father of the Bear Hunters of America. Here's an excerpt:

"Abraham Lincoln was born in a one room log cabin in Kentucky in the year 1809. Which when you really think about it, isn't that much of a surprise ... it WAS 1809 Kentucky! 1809 Kentucky was not the inbred, butt raping, banjo playing kind of place full of Democrats depicted in the film Deliverance. But, was actually a haven for gutless and godless bears. The young Lincoln would spend a good portion of his early childhood wrestling with these beasts, until his family moved to Illinois; little did Lincoln know that his hatred of bears would ultimately lead to his demise."


Jack Bauer's Insomnia

I can just imagine the testimonials for the next generation of stimulant drugs.
"When I'm fighting terrorism for 24hrs, I am always on modafinil." Jack Bower.
The always sensationalizing newscientist has an article suggesting that taking drugs, specifically modafinil, instead of sleeping is going to and is becoming more common. Apparently modafinil is safe and has not that many side effects for those extra long covert operations, according to a Canadian militart report from 1995.
I simply have to get me some of that. from some sketchy online pharmacy.
This interested me because I have heard that you can die from lack of sleep or insomnia. In fact there is a condition called Fatal Familial Insomnia that indeed is fatal. There was a recent Science Friday interview with the author of a book about Fatal Familial Insomnia and the history behind it. It is a really good listen, the science is crappy but the history of the disease is interesting.
Amazingly, apparently mentioned by the bayblabs own Kamel in a journal club presentation, this disease is caused by a prion which doesn't start to cause affects until middle age. So those who carry this mutant protein have symptoms that accelerate rapidly resulting in loss of sleep, dementia and death.
So that means I'm going to have to go off the modafinil periodically, just to make sure I can still sleep.


Creationist museum in Kentucky

Earlier this summer I was visiting Washington state, and admiring the canyons of the Columbia river. To my suprise the brass panels explaining the geology of the canyons at a lookout site had been vandalized to remove the age of the formation. The X-million years had been scratched out, probably with great effort. And I thought that state was progressive! Things weren't better in New-York, where I finally got to visit the museum of natural history and its impressive dinosaur collection. I was shocked to learn that some groups where given a "cleaned up" version of the tour that distorts the fact to make them agree with genesis. At least it wasn't sanctioned by the museum... But now Kentucky gets the Dawkins award, for opening a museum specifically devoted to spreading that bullshit. The $25M museum will display the 6000 year history of the earth complete with humans riding on the backs of dinosaurs. The moto: "prepare to believe"...


Monday, November 20, 2006

Good environmental news

Man, I wish there was more good environmental news, but it just seems as though society is designed to exploit their surroundings to excess. This ultimately has lead to the demise of many societies, as in the main thesis of A Brief History of Progress by Ronald Wright.
When I hear good environmental news it actually gives me pause to think that this modern world with unprecedented population density can actually dig itself out of these problems one at a time through science and technology, and sound policy. The most memorable good environmental news for me includes the saving of Clayquot Sound in BC, and the Montreal Protocol banning CFCs.
So when I heard that "tree stock has increased in 22 of the world’s 50 most densely forested countries" I was pretty impressed. I don't know much about how these things are analyzed, however, if by any method this is true, I'm still impressed. The analysis showing a slightly optimistic view of the state of the forest was published in PNAS.
Don't get too excited, of course, forests are still dwindling on a global scale. Interestingly in the article, Canada is not doing that well compared to countries with similar GDP. But surprisingly has a zero net forest loss, and apparently this statistic accounts for size of trees ect. As a primary resource country that is somewhat impressive.
PS I'm still going to enforce recycling in the bay like a fanatic.


Sunday, November 19, 2006

Cloned Meat is Just as Good as the Real Thing

George W. Bush may not be interested in stem cell research that advances our knowledge and treatments of to human diseases, but his buddies down in Texas sure know that cloned animals are good for a nice juicy steak. This is cutting edge research from the journal Theriogenology.


Friday, November 17, 2006

Good Times at the OHRI Stem Cell Symposium

Yesterday's field trip of the official press corps to the OHRI stem cell symposium was definitely awesome. The Sprott Stem Cell Centre features a sweet A/V set-up with a big-ass projector screen, an HD-ready LCD TV, and a fully wired sound system. (Would be a great set-up for a movie night or maybe a hockey game)...Anways, it's also great for science talks. High marks also awarded for copious amounts of delicious sweets, coffee, lunch and the wine and cheese. Definitely the highlight of the day for me was the talk from Rudolf Jaenisch of the Whitehead Institute. The first to make a transgenic mouse in the 70s, Jaenisch now works on somatic cell nuclear transfer. He strongly argues that somatic cell nuclear transfer is absolutely necessary if stem cell therapy is ever to become a reality, since it is the only way to get a truly pluripotent, autologous, embryonic stem cell that would be immunologically matched to each patient. Although non-embryonic adult stem cells could also provide a source of autologous cells, he seems quite unconvinced that they have any real regenerative value. On the other hand, he feels that the other application of nuclear transfer, cloning organisms, is pretty useless because it doesn't work. He cites that nuclear transfer never has nor will give rise to a normal, healthy animal as they invariably suffer from severe epigeneitc defects. Therefore his lab is now mostly focused on developing methods to use nuclear transfer to generate blastocysts from which it is possible to derive ES cells for therapeutic use, but that cannot implant in the uterus and therefore could never possibly give rise to an embryo. This would sidestep any concern that the derivation of human ES cells is killing potential embryonic life or fetuses etc. and open the door to nuclear transfer research using human materials to derive ES cells. So far, they have succeeded in using donor nuclei expressing a cdx2 shRNA to yield a recipient blastocyst incapable of implantation.

Overall bayblab rating: 10e45/10. Cutting-edge biology approached from a big-picture/philosophical point of view. Very political with cutting anti-Bush cartoons (+10 bayblab points), criticizing him for protecting the rights of ES cells while caring less about killing thousands of humans in Iraq, and suggesting that ES cell research would advance unimpeded if scientists simply found a way to derive oil or biofuels from them. Good usage of high- complexity Venn diagrams. Penalty of -1 bayblab point for spreading the idea that "male imprints cause cancer".


ES Cells: Conundrums and Cures

Embryonic stem (ES) cells (self-renewing, pluripotent cells derived from embryos) are often hailed for their potential in regenerative medicine and just as often at the centre of controversy. The minefield of ES cell research has become something of a celebrity deathmatch with heavyweights weighing in both praising (e.g. Michael J. Fox, Christopher Reeve) and condemning (e.g. George W. Bush, Pope Benedict XVI) the field. One possible solution is the use of adult stem cells - pluripotent cells from adult tissues. However these cells are more rare, less robust and more difficult to culture than their embryonic counterparts (for a good primer on ES cells, adult stem cells and the differences visit the NIH resource page particularly the section on stem cell basics).

While conscientious researchers and philosophers argue ethics, some researchers are trying to sidestep the debate by developing techniques and creating 'ethical stem cell' lines. One example is the the 'de-differentiation' of fibroblast cells into ES-like cells by expression of defined factors (Cell 126:663-676). These cells could differentiate into multiple cell types and when injected into a blastocyst, contributed to embryo development. This method has the advantages of not involving an embryo at all -- a patient's own somatic cells could be used, which would also skirt problems of rejection when transplanted. However, one of the factors used in de-differentiation is the oncogene, c-myc, which may limit clinical application and the advantages over naturally occuring adult stem cells.

Another approach is the creation of stem cells of embryonic origin that don't involve desctruction of the embryo. In a recent letter to Nature, ES cells were derived from single blastomeres using a technique similar to that used in preimplantation genetic diagnosis (PGD) where single cells are extracted for genetic analysis at an early (8-10 cell) developmental stage. In this case, the cells were cultured to develop new ES cell lines. This paper has been the centre of some controversy since it's publication and is unlikely to offer a complete solution to the ethical dilemmas. In this study, all the embryos used were still destroyed (the authors claim this was so they wouldn't be wasted) and the success rate for establishing lines was low. (More recently, a group has show that using older embryos makes the process more efficient in mice) Additionally, while the technique used for PGD gives rise to healthy babies, subtle long-term effects of removing cells at such an early developmental stage hasn't been determined.

But once those kind of issues are resolved, where do we go from there? Are stem cells the cure-all they're made out to be? In one case, sight was restored in blind mice through retinal cell transplants. Because human ES cells can be coaxed into the same cell type, this offers some promise for future regenerative therapy using autologous transplantation. In another situation, a vaccine made from stem cells protected mice from lung cancer under various conditions. The vaccine exploits similarities between ES and tumour cells, protecting 20 of 25 mice from tumours in a xenograft model and 8 of 9 mice in a simulated smoking chemical carcinogenesis model, both with no obvious side effects. Safety issues aside, this again demonstrates the potential for stem cells if applied to a human disease.

Parkinson disease (PD) is one of the conditions most often held up as the disease most likely to benefit from stem cell therapies. Indeed, if all the promise holds true, most neurodegenerative and many other illnesses stand to gain from stem cell research. It's not all so rosy, though. Recent studies have demonstrated substantial recovery in a rat model of Parkinson disease. In this paper, human ES-cells were differentiated into dopaminergic neurons (using new techniques to enrich this cell population, which is lost in Parkinson disease) which were then transplanted into PD model rats. These rats showed significant recovery of motor function. The downside? Incompletely differentiated cells in the transplant showed persistant proliferation after engraftment. Among other problems described in the paper, these proliferating undifferentiated cells could potentially lead to the unfortunate side-effect of tumour formation.

So where are we on stem cell research? Limitless possibilities? Highway to Hell? As Steve Goldman, senior author on the Parkinson study, puts it, "Neither gene therapy nor stem cells are ready for primetime." But I wouldn't change the channel just yet.


Strange diseases of the woman

I recently came across two bizarre diseases that affect woman. The first one involves woman who believe they are transforming into a man, against their will. The rare disorder of reverse delusional misidentification syndrome may be encountered in schizophrenic patients. "Evaluation revealed complaints that the patient's ovaries were testes that produced sperm and her clitoris was a penis capable of erection and ejaculation. Gynecological examination revealed only atrophic vaginitis.". The other one, might be even stranger if that's possible. Woman who have persistent sexual arousal syndrome, and are constantly hit by orgasm for doing pretty much anything, despite having no sexual desire. In Japan this disorder is called "iku iku byo" or cum cum disease. It has been associated with anything from withdrawal from SSRI medication, to soy intake, menaupose and traumatic event and apprently makes sleeping difficult.


Wednesday, November 15, 2006

Aubrey de Grey

Wise like Gandalf the Grey is Aubrey de Grey. Maybe not. Make up your own mind as you check out his talk at TEDtalks. I haven't checked it out yet, lemme know if he's under the influence of Sauron. Found on


Genomic Imprinting Evolution

Genomic Imprinting is an epigenetic phenomenon that limits expression of a particular gene to either the paternal or materal allele specifically through silencing one allele. (I believe it is through DNA methylation.?)
A new study indicates (according to the synopsis) that not only is genomic imprinting is still evolving in viviparous mammals, it also appears that evolution occurs in a coadaptive evolutionary mechanism. This is somewhat contrary to theories that I had heard before that include that the mechanism allowed males to pass on genetic fitness specifically to male offspring and females to female offspring. I have also heard that the mechanism reflects a competition of interest in males in their offspring and females in their offspring. A male wants large offspring because the male is unconcerned about the maternal investment in raising a more energetically expensive large offspring and the female is opposite.
I am still not sure if I understood the synopsis ( that is written for a general audience) so if anyone has insight.. have at it.
I included the picture because of all the nipples.


Tuesday, November 14, 2006

Polythelia and polymastia

Recently, a fellow bayblabber claimed to have a supernumerary or accessory nipple. While not quite as impressive as polymastia (an accessory breast), he's in good company: Mark Wahlberg and Anne Boleyn, as well as fictional characters Krusty the Clown, Goldmember and Chandler from Friends all had extra nipples. While I don't recommend a google image search for pics (at least with SafeSearch off) there are some pics and histology here.

Most of the literature on polythelia is quite old. Extra nipples are more common in women than men, but even then are only 'diagnosed' in about 2% of the female population. The extra nipples can vary in appearance from a patch of hair to full blown polymastia. Early studies suggest a dominant inheritance pattern, and Alexander Graham Bell was successful in raising sheep with multiple extra nipples through selective breeding.

So is it a third nipple? It seems to be on the milk-line which runs from the armpit, through the real nipple and down to the groin, which supports his case, but I think we may need to check his parents.


Canada & Kyoto

I have to say that I actually am happy with the conservative government on the specific issue of staying in the Kyoto agreement. It sounds like Canada is being a total ass at the talks in Nairobi, however at least we are staying with it and acknowledging we can't make our targets. We suck basically. And I think we should have to pay. It's not like we aren't affluent enough and if it actually hits us in the pockets we might have some motivation to actually achieve something. Because apparently so far we haven't. As soon as the conservative government has to acknowledge that it's books aren't as good as they could have been because of carbon dioxide production perhaps they will invest in this countries future as a technology leader and not just a big oil sand.
Perhaps I'm preaching to the choir on the bayblab but maybe I'll provoke a response from some redneck in Alberta.
Disclaimer: "Redneck" was added for provocation purposes only. Rednecks are great people too (and we need them to do the actual hard work.)


Monday, November 13, 2006


Check out how disease outbreaks are mapped on Google maps. Healthmap. This thing totally rocks and will be great for the next flu pandemic.


Can a biologist fix a radio?

Bayman was recently discussing in the bay systems biology and modelling of seemingly simple pathways. How for example we've really only just started getting accurate mathematical modelling of the Lac operon and how it confirms what we previously knew but in a quantitative manner. It begs the question, are we efficiently investigating the "black box" that is the cell? Is the biological approach the right one, or is it better to have an engineering approach. Yuri lazebnick explains the "David paradox" in an old issue of cancer cell, on how a biologist would solve the problem of a defective radio and how this relates with our approach at investigating mollecules such as p53... "[...]any engineer trained in electronics would unambiguously understand a diagram describing the radio or any other electronic device. As a consequence, engineers can discuss the radio using terms that are understood unambiguously by the parties involved. Moreover, the commonality of the language allows engineers to identify familiar patterns or modules (a trigger, an amplifier, etc.) in a diagram of an unfamiliar device. Because the language is quantitative (a description of the radio includes the key parameters of each component, such as the capacity of a capacitor, and not necessarily its color, shape, or size), it is suitable for a quantitative analysis, including modeling."


Cellphones and Brain Cancer

I watched Thank you for not Smoking last night, and thought it had some pretty funny parts. The humour was refreshingly satirical. SPOILER: Interestingly the main character ends up being the spin doctor for cell phone companies and the association with brain tumours. I wondered if there was a parrallel between smoking / lung cancer and cellphones / brain cancer. Nowadays would science have enough power to publish links of cellphones to brain cancer? I guess the question is then; Is there a link between the two? A pubmed search of "mobile phone cancer" gives 131 hits and not many that I could find suggested a link between the two. However alot of studies received funding from the telecommunications industry and a competing interest statement resides at the end of some papers. I also found a paper that I had heard about that suggested that while your incidence of cancer is not increased with cellphone usage, if you get a brain tumour it is significantly more likely to be on the side of your brain that you use your cellphone. That sounds really sketchy, however, the researchers chalk it up to recall bias. Here is an old article that summerizes some data that I have not found as well as the abstract of a paper that seems the most authoritative on making a link between cancer and cell phone use.


Sunday, November 12, 2006

Yo' Momma's Ancestor was a Sea Urchin!

Having just come out over the weekend, i've lucked out in getting to post about the recent sequencing of the sea urchin genome. The genome of the male California purple sea urchin (Strongylocentrotus purpuratus) has been sequenced and the depth of analysis to be discussed in the next few months (look for 40 articles in the December issue of Developmental Biology) seems incredible. A team of 240 scientists, including groups from Toronto and BC, have collaborated to determine the GENETIC CODE AND TRANSCRIPTOME (using NASA computers to do microarrays-how cool is that?!) of this highly studied model organism. The sea urchin has been used for over a century as a model for many biological processes and is best known for advances made in developmental biology due to their clear embryos which facilate the study of evolutionarily conserved developmental processes common to deuterostomes. The sea urchin genome which codes for 23 300 genes displays a surprising level of sophistication and suggests a global view of the genes necessary for human evolution-further touting the strength of this species as a model organism. Some of the most interesting findings include the identification of genes coding for human analogues involved in vision and chemosensation (sea urchins were not thought to possess organs to sense light and odour), a very complex innate immune system(including a rhobust defensome), and orthologs of many human disease-associated genes.


Bayman's Book Club

There's nothing I like better than a piece of classic science literature. And in the true tradition of wine-snobs and gold-digging socialites, older is invariably better. Inspired by Discover magazine's compilation of their 25 greatest science books of all time (check out the Dec. issue), I thought I'd throw out a few of my faves to at least fuel some discussion at the next podcast. The list is of course incomplete, as is my reading progress through most of these works.

The Origin of Species, Charles Darwin (1859).
The famous evolutionary theory contained within the hundreds of pages of this biological epic can be described in only a paragraph. While the theory was revolutionary to say the least, reading through the pages of CD's own words offers a great look into a truly rigorous and critical scientific mind. Darwin's ability to influence thinkning and open minds to new ideas was likely in large part to the beautiful exploration of the arguments AGAINST his theory which he systematically deconstructs and ultimately uses to strengthen his position.

What is Life? Erwin Schrodinger (1944).
Leave it to a physicist to shake the foundations of science with three words and a question mark. I originally wanted to see what this book was all about because James Watson cited it as his inspiration to seek the structure of the gene. Unfortunately I don't totally know what it's all about yet because the first few paragraphs got me thinking about genetics so much that I set off on a tangent of reading basic genetics (see next title) and haven't yet found my way back to poor old Erwin.

Experiments in Plant Hybridization, Gregor Mendel (1865).

Reading this paper one is struck by the stark contrast between the massive significance of this work (ie the founding of modern genetics) and its sheer humility. A monk counting pea plants in his garden. It doesn't get any humbler than that. He also puts forward in these pages a great example of how to write a real scientific paper. Of course, no mention in the discussion predicting how his discoveries would cure the diseases of humankind, extend lifespan or save civilization...(nor are there any trojan horse analogies for that matter)

Signs of Life: How Complexity Pervades Biology, Richrd Sole and Brian Goodwin (2000). Before anyone was talking about "Systems Biology", this book attracted my attention for its elegant use of nonlinear and "chaos" mathematics to describe the weird and fascinating behaviour of biological systems ranging from viral quasispecies to ant civilizations to the human brain. By no means a fully-developed classic, but I though it was pretty cool at the time.

Viruses and the Nature of Life, Wendell Stanley, Evans Valens and others (1961). Fundamental virology by the people who discovered it. Written back in the day when there was no microarray or RNAi and viruses were still the sexiest and coolest thing out there, it's hard to read this little book even today and not come away thinking that viruses are the answer to everything. Even the black-and-white illustrations are great. If I ever taught a introductory course to virology I'd base it on this book. Also full of great general biological prophecy, for example, in cancer: "Huebner discovered that adenoviruses would destory the abnormal cells of cervical cancer in women...However, the virus could not destroy all the cancer cells before antibodies to the virus developed...Work of this general nature is only in its selective cultivation of mutant virus strains, it should be possible to develop viruses which ignore normal cells but will have a special predeliction for the destruction of cancer cells." Hmmm...sounds kind of like an oncolytic virus...


bayblab podcast: Episode 3 part-1

Finally the latest installment has arrived. This week we have Stephen Hawking as a special guest and he gets piss drunk as we discuss milking the one eyed snake, the size of testes in nerds, and compare coke, clamato&beer and fermented horse urine. Due to the size of the podcast it will be released in 2 parts. So tune in next week for part 2.


Friday, November 10, 2006

Nuclear Translation

I really have no opinion on the existence of nuclear translation because I know nothing about it, however it is an interesting debate. Here is a pro-nuclear translation article and an anti-nuclear translation article. I don't really understand why nuclear translation would be necessary to explain nonsense mediated decay but it's nice to know that someone is challenging the dogma.


Improbable research

You know that bit in "there's something about Mary" when the guy gets his tool stuck in the zipper and the firemen (no pun intended) are called in? Well chances are that they are not using the jaws of life, but rather a pair of plyer and following the instruction of this 1990 paper in the journal of emergency medecine: Acute management of the zipper-entrapped penis.
"A zipper-entrapped penis is a painful predicament that can be made worse by overzealous intervention. Described is a simple, basic approach to release, that is the least traumatic to both patient and provider."
In fact I can find close to a hundred articles on this subject in pubmed, some would say it's a growing field...
Check out more improbable research here.


Wednesday, November 08, 2006


A recent paper from PNAS shows that short 22bp dsRNAs can be used to INDUCE gene expression when the sequence is in non-CpG islands in the promoter of the gene. The effect is dependant on Ago2, sensitive to DNA methylation and works like microRNA in that some mismatch is tolerated. They coin the term RNAa or RNA activation and it looks pretty convincing. This just adds another complication to the RNAi mechanism that just leaves me scratching my head. It also suggests even more potential for off target effects when using the nobel prize winning RNAi as a tool.


IA updates

IA updates . Apparently the UK is leading the world to '1984'. They have some loudspeakers hooked up to video surveillance and have started fingerprinting people who drink in pubs. Also some good info on video software. Basically I have to try Adobe Premier Pro. It's time to get the video podcast going on.
Check out the


Tuesday, November 07, 2006

Richard Dawkins vs. Francis Collins: The Crusading Atheist and the God-Faring Scientist Go Head to Head on God

I picked up the current issue of Time magazine to see if I could find any entertaining quotes in a write-up of a Francis Collins (leader of the NIH human genome project/christian) versus Richard Dawkins (Oxford evolutionary biologist/author/hard-core atheist) debate on religion and science. Although there's lots of photo-ops showing the two of them looking like they're thinking really hard about the mysteries of the universe, it's mostly pretty diplomatic but still pretty decent. Although both men showed themselves to be strong debaters, no punches were thrown or blood drawn. Perhaps the most interesting aspect was that Collins represents the religious camp much better than the yahoos that Dawkins kind of bullies around in his doco "The Root of Evil" (which curiously I can no longer find on Google video).
Some selected quotes:

Dawkins: "What Francis was just saying about Genesis was, of course, a little private quarrel between him and his Fundamentalist colleagues...he'd save himself an awful lot of trouble if he just simply ceased to give them the time of day. Why bother with these clowns?"

Collins: "Atheists sometimes come across as a bit arrogant...characterizing faith as something only an idiot would attach themselves to is not likely to help your case"

Collins: "I don't see that Professor Dawkins' basic account of evolution is incompatible with God's having designed it."

Dawkins: "I think that's a tremendous cop-out. If God wanted to create life and create humans, it would be slightly odd that he should choose the extraordinary roundabout way of waiting for 10 billion years before life got started and then waiting for another 4 billion years until you got human beings capable of worshipping and sinning and all the other things religious people are interested in".

Collins: "My God is not improbable to me."


One-Click Referencing As You Surf

From the Nature people, Connotea is web-based reference management. Basically they keep track of your references in a web-accessible, user friendly database for you. Puts a little button on your web browswer and you just hit it whenever you have an abstract or paper loaded in your web browser. The program then automatically puts all the relevent info into your database. You can easily download the library into a reference manager file, and share databases with your science buddies via the web. I've been testing it out, and so far it seems pretty damn cool. Think of it as the cure for "How did I find that abstract on PubMed that one time???


Monday, November 06, 2006

More than one way to (not) age a mouse

Since we've been on the topic of anti-aging recently.... a recent paper in Science (subscription required) and summarized at Nature News shows that lowering the core body temperature of mice can extend lifespan. Is this good news for us Canucks? Caloric restriction (CR), as discussed before, thus far has been one method shown to reliably extend lifespan across species. One side-effect of CR is a reduced body-temperature. The contribution of low body temperature to lifespan extension has been difficult to determine because mice and other mammals maintain body temperature regardless of the surrounding climate. To get around this, the group genetically engineered mice to overexpress UCP2 - a protein that uncouples electron transport from ATP synthesis to generate heat - in mouse hypothalamus cells. Because this region of the brain acts as a thermostat, the mice were tricked into thinking they were warmer and as a result lowered their core body temperature by 0.3 - 0.5 degrees Celsius. The result? An increase in median lifespan of 10-20%, independent of diet. So you see, we don't need to starve ourselves to live longer -- plenty of red wine or perpetual cold should do it. And I'll bet it's SirT1 dependent too.


Friday, November 03, 2006

SirT1 update

Some people actually think that SirT1 is an important protein. Despite the fact that it is non-essential and doesn't affect p53 biological functions.
However hitting the mainstream media is a story that supports these peoples beliefs. Apparently not only does resveratrol (that Sir2 depedant life-extending molecule) extend the life of worms it looks like it works in mice. Even if they are not calorie restricted.
Basically eat what you want and drink red wine.


Thursday, November 02, 2006

Plug for My Journal Club

I'm doing JC tommorrow. The topic will be "Cell Space: The Final Systems Biology Frontier".
Maybe I will get off the bayblab and read some papers before then.




It's that time of year again. I'm thinking of gaining a lot of weight and watching TV and sleeping for the next 6 months or so.
I have been thinking about what animals hibernate and checked it out, the list is pretty short. It's just the ground squirrel types (chipmunks, lemurs ect.), bears, bats, frogs, turtles, skunks, marmots, raccoons, earthworms (!) and snails. I would think that earthworms do not include C.elgans and I couldn't find anything on C.elegans hibernation. There are other forms of hibernation called torpor and estivation, so maybe these are present in more primitive organisms.
Apparently my pet bunny is not supposed to hibernate. If it is showing symptoms of hibernation, I read that I should take it to the vet.
What I ran into that was interesting, however, is that hibernation can be induced in a non-hibernating species using hydrogen sulphide. Apparently it a reversible and harmless process. And it suggests that humans may also possess this latent ability to hibernate. The applications of course are interesting and include getting astronauts to hibernate for those extra long journeys to Mars and for medical purposes.
AUDIO: Quirks and Quarks interviews researchers in the field of hibernation and induced hibernation . (mp3)


Wednesday, November 01, 2006

Rats, cockroaches and a nobel...

We were recently talking about tissue inflammation and cancer. Well it turns out, some people attribute the idea to Johannes Andreas Grib Fibiger. However the man actually thought the cancer in the rats he was studying was a result of parasites-infected cockroaches being eaten by the rodents. He got the nobel in 1926 before anyone could realise it was really a vitamin A deficiency that was the root cause, and that the nematode merely provided the gastric irritation necessary for tumour initiation... The nematode is still called Gongylonema neoplasticum, and was the first proof that an infection could inititate cancer.