Canada's impact factor

I ran across some statistics that showed Canada has a pretty decent citations per paper published according to in-cites.com. Apparently after Switzerland, Sweden, Netherlands, England and the United States, Canada has an average of 11.14 citations / publication. That suggests to me that Canadian researchers are producing some quality research publications. The USA publishes WAY more papers than any other country and it's all obviously in English. So perhaps having English as an official language in Canada helps as we publish a lot of papers that may be cited by English speaking US researchers. If you are interested in some better analysis of where Canada sits internationally check out this somewhat old Nature paper (2004, subscription req.) What is disturbing to me is that despite being obviously productive researchers, this is not reflected in the Canadian governments investment in research. We are ranked 14th in health research funding!! Also check out patents granted / capita which is pretty interesting, go Iceland! These stats are of course to be taken with a grain of salt however I still find them interesting.

Cancer Carnival Call for Submissions

The 5th edition of the Cancer Research Blog Carnival is fast approaching, and what better way to ring in the new year. To all those interested in participating and/or reading the upcoming fifth edition, the deadline for submissions is Wednesday, January 2, 2008 (or thereabouts) and the post will be up Friday, Jan 4 here at the Bayblab.

If you have a story regarding cancer research, including (but not limited to) therapeutics, diagnostics, standard care, survivor stories or basic science you can submit a link either in the comments here or the carnival submission form on this site.

I am Legendary Oncolytic Virus

Bad news for those of us who think that oncolytic viruses show great potential as cancer therapeutics is coming out of Hollywood. I haven't seen it but apparently the plot of 'I am Legend' starring The Fresh Prince revolves around an cancer curing virus mutating and killing almost everyone except his Freshness.
From wikipedia (I am Legend):

A genetically reengineered measles virus called Krippen Virus or KV, created as a cancer cure by Dr. Alice Krippen (Emma Thompson), rapidly spreads and wipes out the population of the world by the end of 2009, leaving military virologist Robert Neville (Will Smith) the last human survivor in New York City and possibly the world.

The virus killed 90% of the people on the planet; fewer than one percent are immune. The remaining survivors were infected, initially exhibiting the early symptoms of rabies, but then degenerated into an animal state driven by hunger and blind rage. Neville is watched by these "Infected" people, who react painfully to UV radiation. They therefore avoid sunlight and hide in the dark underground, and in buildings (in groups called "hives" by Neville), swarming out at night. Dogs and rats are also susceptible to the virus. By 2012, Neville has not seen another normal human being since the virus' release three years earlier, and suspects that the Infected have succeeded in killing the remainder of the immune survivors. Neville is outnumbered by the infected and running out of time as he seeks a cure.

Some pretty bad press for a treatment that's just getting out of the gates, and this might be the first time many people hear about the potential of treating cancer with replicating viruses.

Rodeo confusion

Discussion over beers turned to rodeo, specifically bull riding. I thought I had heard that bulls were electrocuted on their testicles just as the gate is opened. This is apparently a mixture of partial truths. The bulls do have a flank strap which some people have thought causes pain to the bull's testicles, however here's the info on the flank strap:
The flank strap is often misunderstood. Its purpose is to entice the bull to kick more. Without it, most bulls would have greater tendency to run or fall. The flank strap serves to regulate their bucking somewhat and cuts down the risk of injury to a bull. If you are familiar with a dog's ticklish spot, then you have an understanding of how a flank strap works. Bulls and horses are notoriously ticklish around the flank area.
There is also an electric shock involved in getting the animals fired up, illegal however in most places. Almost all the information I can find on the internet is about animal rights abuse. Apparently the 'hot shot' delivers 5000volts. It is applied to the rear end of the animal just before the gate is opened. video.
Not quite as bad as getting it straight to the genitals but it sounds uncomfortable. I'm not going to weigh in on the moral issue but I find watching the bull riding entertaining( video -NSFW because of soundtrack = footloose). I think I cheer for the bull though....

Quack of the week (Pt. 2): Water, water everywhere...

What could be better for you than vortexed water with a long energy wave field? Vortexed ALKALINE water with a long energy wave field.

One of the baybs from the Bay sent us this juicy tidbit: The Kangen Water Maker. Behind this slick website is another 'miracle' water treatment that can solve your problems of indigestion, diabetes, obesity, osteoporosis and constipation (among other things). It's good for non-health applications too: artists and painters can expect more vibrant hues and smoother strokes when their paints are mixed with alkaline water! Apparantly Kangen means 'return to original' in Japanese (according to one seller) which is ironic because pure, unadulterated water should have a pH of 7 not the pH 8-9.5 that these guys suggest you drink.

How does it work? The Kangen water maker is basically an electrolysis machine that uses dissolved minerals to acidify or alkalize water. This alkaline water, they claim, contains water molecules that cluster in groups of 5-7 instead of 10-14 like 'normal' water. The theory is that the smaller molecular grouping allows the water to travel to places regular water can't, making it better for hydration and delivery of nutrients. Additionally, they claim that Kangen water alters body pH, which prevents acid build up, an associated leaching of calcium from bone and increase in fatty acid deposits.

Why doesn't it work? Even if you can maintain alkaline water for more than a transient period of time (this is accomplished by adding minerals to the water, which can alter the taste - just think about drinking 'hard' water which is also alkaline) as soon as it hits the strong acids of the stomach any alkalinity will be neutralized. Not to mention there seems to be no scientific evidence that this clustering effect is real or that it would be anything more than fleetingly transient. Most studies support the idea of a dynamically changing, disordered water structure. Not to mention that there are water quacks out there who pitch acidic water or water with LARGER clusters as the true 'healing' water.

Of course this has all the standard hallmarks of quackery to go with the pseudoscience: untested medical claims and large disclaimers about lack of FDA review. Some sellers are part of multi-level marketing schemes, and one goes so far as to combine his selling of water ionizers with marine phytoplankton for 'the best whole food nutrition available' and our pet favourite StemEnhance.

For a more in-depth analysis of the pseudoscience of alkaline water, this chemist from SFU does a pretty thorough debunking.

Bayblab Podcast Episode 14

The famous bayblab podcast is now full of holiday cheer and back where it belongs: at a pub! This time we discuss what's new in cancer research, talk about the psychology of quacks who sell fake stem cell remedies and reveal shocking lab tales of promiscuity in the dark room which may explain why Bayman is absent.

Quack of the week: Healing Water Online

In our last quack of the week, Kamel exposed companies selling algae found in pond water, and claiming they could harness the power of your stem cells. This week I found an even more impressive treatment: tap water. That's right someone has found a way to sell you tap water with the premise that it will heal you. And it's not even Coca-Cola.

Here is the explanation. First you have to accept the fact that genes do not control life. That's a lie. We just repeated it for so long that that we have come to believe it is true. But apparently it was never tested scientifically. If you don't believe me, watch this video. The quack behind this video is Dr. Bruce Lipton, who apparently was teaching medicine at the University of Wisconsin. He also wrote a book called the "Biology of Belief", which is a deceptive title since it's actually about changing your own biology with your mind. The irony of which seems to be lost on the author. Apparently he's also pretty much discovered epigenetics, which if you were not aware explains how energy from the mind alters protein expression.

While lots of nutjobs seem to love the book, there are few amusing reviews on amazon such as this one by a Columbia University researcher:

"Furthermore, Dr. Lipton claims that illness can be cured by mere belief. This isn't only nonsense; it is incredibly unprofessional and irresponsible. This is the equivalent of a TV Evangelist banging his palm against the foreheads of cancer patients, pushing them back down in their seats and proclaiming them cured, only to then say later to an investigating reporter who mentions that the patients later died that the Lord's magic stopped working because doubt entered into the hearts of the disbelieving patients. What an incredibly cruel sentiment. "

Which brings me back to water. Dr Lipton's ideas have inspired the creators of "Healing Water Online" because apparently your mind can also alter water and vice-versa. Now I'm sure a cold shower can elicit some spiritual experiences in some people (I highly recommend that link). In fact I often praise the lord when somebody flushes while I'm in the shower. But this is different. Somehow, this has to do with the energy you can produce with your mind, and the unique properties of water. For example did you know that:

"Water's reputation as a powerful solvent derives from its ability to absorb energy vibrations and its particular electromagnetic and chemical qualities, being able to break down substances into their constituent parts. Naturally flowing water creates complex structures: micro clusters of vibrating energy centres, constantly receiving and transmuting energy from every contact the water body makes; and laminar structures which generate energy from the interaction of the planes against each other."

So how can I harness this power you ask? Well it's easy, you just need to buy a $144 jug that has a propeller inside. Why? Well isn't obvious by now:

"The compact motor housed in the lid of the 2-litre jug drives a left-turning silver propeller wich forms a beautiful vortex throughout the depth of the plain tap water for 3½ minutes; this re-enlivens, restructures, reoxygenates and purifies the water by the spiral movement alone.
The energy wave field of normal tap water is 35 cm; Living Water Vortex Jug's is 2,4 metres! A healthy person has an energy wavelength of about 1,9 metres, and as a person consists of 75% water, s/he will be regenerated by the greater energy of restructured water."

Wow what a deal. That's almost a 26% increase of your wavelenght, or only 88 cents per centimeter! And they also suggest you combine your healing water with long distance healing. That's right, for only $44 they will channel energy to you, sorta like what kamel's power to make people dumb at a distance. Actually it's exactly like that.

Songbird speech

Just ran into this paper that knocks down FoxP2 in songbirds. We've mentioned FoxP2 before on the bayblab as it is necessary for proper language development in humans. And indeed these songbirds are unable to properly imitate songs after knockdown of FoxP2 in a particular brain area. This really strongly suggests an evolutionary relationship between bird songs, (at least learned bird songs) and human language. An animal model for language development = Cool.

Favourite cell lines & Cedarlame

I was curious as to what were the most popular cell lines. Personally I'm a big Hela cell fan. They are ubiquitous and you don't have to worry about Hela cell contamination of your Hela cells. Many key experiments were done in Hela cells so it doesn't feel like you are using a random cell line where cell line specific artifacts are unimportant.
Any other nominations for favourite cell lines?
MEFS, HFFs??
I sent an email to ATCC asking for a "Top Ten most popular cell lines" and they replied with a LAME response:

Dear Rob:

I am writing from Cedarlane Laboratories, which is now the exclusive
distributor of ATCC products within Canada. Your query regarding top ten
cell lines from the ATCC has been forwarded to us.

ATCC cannot provide the information that you have requested because it
is proprietary.

Thank you,
Cedarlame

Turning Mouse Tails Into Replacement Blood Cells for Sickle Cell Anemia

Induced pluripotent cells (iPS) have been garnering lots of attention (and papers) lately, since it was first shown that adult fibroblasts (and since then, skin cells) can be reprogrammed to pluripotency by forced expression of a handful of genes. Despite much speculation, it has remained unknown until now whether these cells are actually be good for anything, therapeutically speaking.

While it remains to be seen whether iPS can give rise to autonomous souls, Jaenisch's groups has now shown that iPS can be applied therapeutically. They derived iPS from the tail fibroblasts of sickle cell anemia mice, fixed their genetic deficiency ex vivo, differentiated them into hematopoietic progeintor cells and transplanted them back into the affected mice to restore a functional pool of red blood cells. Pretty damn cool.

Smoking with Friends

Just ran into this amazing factoid on the latest WNYC Radiolab podcast. Apparently "social isolation" is as risky as smoking for increasing your mortality. Unreal. Maybe however it has more to do with the particulars of the social circle you are in, ie no friends is bad, but maybe your particular friends are just as bad for you as no friends. Especially if you are getting some second hand smoke from them.
Just when I thought that social isolation was a cheap and easy alternative to cigarettes.

Supernatural Science at the BMI Department?

The Biochemistry, Microbiology and Immunology (BMI) department of our university publishes a bi-weekly newsletter for the grad student body. The latest edition, Issue 57, includes an article entitled "Specializing in the Natural and Supernatural Sciences: An Interview with Jason Tetro" (the latest issue can usually be found here but has not yet been posted at the time of this writing). The article profiles a student of the department who has a hobby (and side-job) of tarot card reading.

Personally, I don't care what people believe or do with their spare time, but for a publication of the BMI Grad Student Association to spin and legitimize tarot card reading and the supernatural as science is embarrassing for me as a member of the department. The following is our response sent to the editors of the publication:

Dear Editor,

RE: "Specializing in the Natural and Supernatural Sciences"

Science is the investigation of physical and natural phenomena through observation and experimentation. The supernatural, by definition, is unexplainable by natural law and falls squarely oustide the scientific realm.

I understand the desire to profile members of the department and, as an author of the science blog "The Bayblab", I understand that it can be difficult to come up with ideas for stories. However, a profile of the *scientific* acheivements of the student, or even a critical analysis of research articles (the references of which were omitted) mentioned in the interview, would be more appropriate. (Incidentally, we at the Bayblab devote a considerable amount of energy to promoting critical thinking and distinguishing between science and pseudoscience or quackery.)

To include an article in the departmental bulletin about the supernatural and classify it as science is a disservice to your readers and a disservice to the reputation of the department as a scientific body.

Kamel, Rob
http://bayblab.blogspot.com

Marilyn Kozak, professional critic

I think every field needs a solid critic like Marilyn Kozak. We are talking about THE Kozak of the "Kozak consensus sequence fame". She has published a few papers on criticizing the field of internal ribosome entry sites (IRESs). Her lastest is still critical of the existence of viral internal ribosome entry sites which have not only studied for quite some time now but are used as molecular tools for expressing multiple genes from one mRNA. She is persistant. Here is an older response from some scientists in the field to some of her critisisms. Despite being perhaps frustrating to those in the field it is probably good to have such a dedicated (and famous) critic to point out shortcomings in the published data. I wish there was one in my field, at least just for entertainment purposes.

Cancer Research Blog Carnival #4 is UP!

This edition is by far the best one so far. I really feel like it's taking off. Well worth the read if you're interrested in cancer research, with quite a mix of topics such as VEGF immune therapy, nestin in prostate cancer, cancer vaccines, radioimmunotherapy and much more! Ben again did an incredible job of hosting. If you would like to host the next edition, or submit a post, check out this link. Special thanks To Ben for also designing a new logo for this carnival!

Reading through nonsense

We recently heard a solid journal club presentation about genetic nonsense mutations. Nonsense mutations are point mutations in the DNA sequence that introduce a premature stop (or nonsense) codon and can lead to a truncated protein (or, in many cases, no protein at all as nonsense codons are detected by the presence of exon-junction complexes and the mRNA is degraded). The paper discussed described a drug, PTC124, that is entering the final phase of clinical trials that supresses premature termination and allows readthrough of nonsense codons by the translational machinery and production of a full-length protein.

What does this have to do with cancer? The paper discusses the therapeutic potential of the drug in terms of cystic fibrosis and muscular dystrophy - two diseases with pathology known to be caused (at least in some cases) by nonsense mutations in specific genes; CTFR for cystic fibrosis and dystrophin for muscular dystrophy. An obvious target for cancer therapeutics is p53. The p53 gene is mutated in over 50% of human tumours and of those mutants, almost 8% are nonsense mutations (source:IARC p53 mutation database). Research has shown that reactivation of p53 has therapeutic potential in mouse models of cancer, leading to growth arrest and regression of tumours. One need not limit this idea to p53. Nonsense mutations in many other genes, such as BRCA or Rb, have been associated with cancer and bypass of nonsense-mediated decay represents an interesting area to explore when dealing with cancer, and other, therapeutics.

Noam Chomsky quote of the day

Since we're discussing the freedoms of being graduate students and the responsibilities of "speaking truth" as intellectuals (if you want proof of that check out how Kamel's wit triumphs over ignorance in the 100 or so crazy comments of this post), I thought I would bring up this quote from Chomsky, one of the leading intellectuals of this era:

"Students are at a stage of their lives where these choices are most urgent and compelling, and when they also enjoy unusual, if not unique, freedom and opportunity to explore the choices available, to evaluate them, and to pursue them. [...] Well, there are really some moral truisms. One of them is that opportunity confers responsibility. If you have very limited opportunities, then you have limited responsibility for what you do. If you have substantial opportunity you have greater responsibility for what you do. I mean, that's kind of elementary, I don't know how it can be discussed. And the people who we call 'intellectuals' are just those who happen to have substantial opportunity. They have privilege, they have resources, they have training. In our society, they have a high degree of freedom-not a hundred percent, but quite a lot-and that gives them a range of choices that they can pursue with a fair degree of freedom, and that hence simply confers responsibility for the predictable consequences of the choices they make. "

Welcome to Gene Genie!

Welcome to the 21st edition of gene genie! In this edition we cover everything from selection constraints on the evolution of the vulva in nematodes, to the importance of the insertion site in transgenic and the history of microarrays...

Gene

Greg Laden presents The Nematode Vulva and the Nature of Evolution. Greg explains how the vulva can be used as a model in comparative genetics to determine whether evolution is primarily governed by selection and/or selection-independent constraints, not stochastic processes such as drift in unconstrained phenotypic space. He concludes that evolution is more deterministic than stochastic.

96well presents Where do you express your transgene? posted at reportergene.com. This post does a good job of explaining one of the biggest problems with transgenics, namely how poorly we understand integration. The transgene can integrate in any place in the genome and be subject to tissue-specific chromatin remodeling which may render results uninterpretable. One way around this is to target insertion near the beta-actin gene as the author explains: "Recently, the lab of Bernd Kinzel (Novartis), published a technology report in Genesis (vol.45), in which the locus of beta-actin was identified as a good dock for gene expression. Beta-actin is a cytoskeletal building-block expressed in almost every mammalian cell, and it is necessary for life, so only heterozygous transgenic can be developed."

other

FitBuff presents What Is Healthy? posted at FitBuff.com's Total Mind and Body Fitness Blog. FitBuff is asking the question "What is healthy"? At first, this may seem like an easy question to answer. However, when you actually stop and think about it, it's not easy at all... here is what he thinks: "In my opinion, healthy is following a positive lifestyle; one that is manageable, as stress-free as possible, involves the eating of several small meals throughout the day (including lean protein, complex carbohydrates, and healthy fats), incorporates a workout program that is realistic and consistent, and always ends with a good night's sleep."

Techniques

AJ Cann presents DNA Microarrays posted at MicrobiologyBytes. AJ gives us a good primer on how microarrays work along with some educational videos.

That concludes this edition. Submit your blog article to the next edition of gene genie
using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page.

Graduate research: is it school or work?

Here's an Opinion piece posted on behalf of Joel:

"I had an interesting (mostly one-sided… sorry Laura) conversation yesterday, which has led me to write a little opinion-piece.

I obtained my first research experiences working in a basic biology department at a small university. I was lucky enough to find a phenomenal mentor and get some experience in molecular biology in a department with a faculty that focused mostly on ecology, fish biology, teaching, and (for many tenured profs) reading the paper while waiting-out the years until retirement. The graduate students that I worked with were paid primarily by the department; however, they had to earn their living wages (which amounted to about $12,000 a year). They worked as TAs for 2-3 afternoons a week and marked lab reports for at least 10-15 hours every week. They did this to have the opportunity to do research. Similarly, graduate students in basic science programs throughout Canada are paid very little; they also need to TA and to mark reports to earn it. Therefore, they do their research in what amounts to spare time. Although it makes doing their research difficult, it gives them independence. They are not employees of a prof, they are students; they learn in their chosen lab, work on projects that are within the scope of the research interests of their PI, but tailored to their own interests and goals. This should sound familiar: it’s called being a grad student.

In Ottawa, particularly at the OHRI, we are paid comparatively well, and asked only to do our thesis research in return. However, our salaries (unless externally-provided) are paid by our PIs, through their grants. I found the research environment very different when I arrived in Ottawa. People here refer to their PIs as “boss”. They call their research “work”. I have always rejected the term boss for my PI. He is my mentor; I’ll even go as far as to call him my “thesis supervisor”, but never my boss. I don’t go to work. I go to the lab. This matter of semantics has been my private rejection of a system that I have never been able to understand.

To me, a PI has a specific role. They obtain funds to work on projects that they find interesting. They recruit like-minded people to help them work towards their research goals. The PI obtains funds, and thus has responsibilities to both the providers of funding - to ensure that the money is well spent - and to the people that work in their lab, to ensure that they are able to pursue their research in a good environment. This is where the formal authority of the PI ends for me.

Graduate school is a learning experience, not a job. Any PI that tries impose hierarchical ruling on a graduate student (outside of the realm of authority that I described above), is not only exercising unwarranted power, but is also harming the potential of the project and the student. Creativity and invention are what makes good research great research. When creativity is stifled, mediocrity is inevitable. Whenever such unnecessary imposition of force is encountered, it should be rejected and fought. However, it is so pervasive in Ottawa that all incoming graduate students undergo a form of indoctrination that keeps them from questioning the role of their mentor in directing their day-to-day activities.

I will finish with an excerpt from a biography of James Watson (maybe not the greatest role model for potential PIs, but a man who often makes some great points and who obviously achieved great things in his mentoring and administrative careers):

“(Watson’s students and post docs) knew that they were working “primarily to advance their own careers.” Though terrified of Watson, they weren’t working for anyone but themselves. “I never worked for anybody,” Watson recalled on his 60th birthday. “I could never work under others. You only get somewhere with people if they feel they are working for themselves”."

Carnival season

To all those interested in participating and or reading the upcoming fourth edition of the Cancer Research Carnival the deadline for submissions is Wednesday and the post will be up Friday on Ben's blog... Also for those of you looking for the Gene Genie carnival, my bad, it's a day late but it will be up sometime later today.

Want to join the 200 mile high club?

As a joke in my lecture about sperm motility I mentioned some experiments made in space by NASA which have shown that sperm is more motile in microgravity and less motile in hypergravity (high G). There had been numerous rumors that Leica wasn't the only one to have gone doggy style in space. It is now confirmed that both Russians and Americans have joined the 200mile high club. The result: only 4 positions are possible in space, the rest is left to the imagination...

"Twenty positions were tested by computer simulation to obtain the best 10, he says. "Two guinea pigs then tested them in real zero-gravity conditions. The results were videotaped but are considered so sensitive that even Nasa was only given a censored version."

Only four positions were found possible without "mechanical assistance". The other six needed a special elastic belt and inflatable tunnel, like an open-ended sleeping bag.

Mr Kohler says: "One of the principal findings was that the classic so-called missionary position, which is so easy on earth when gravity pushes one downwards, is simply not possible.""

Too bad it's a hoax. When is NASA going to concentrate on some real priorities that people actually care about ;)