Friday, February 29, 2008

Happy Leap Day!

Today is February 29th. Bad Astronomy has a great post explaining the leap day in great detail. And if that's not enough for you, check out this (even greater) earlier post about how we define years and days in the first place.


The Carnival is Coming

The 7th edition of the Cancer Research Blog Carnival is visiting Highlight Health next week.

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 on the carnival submission form on this site.

The Carnival will be up Friday, March 7.


Scientist Bloggers Blogging About Science

The recent surge in the number of scientist-bloggers contributing to discussion here at the bayblab has led me to discover a lot of wicked-ass science blogs. Although, as PZ pointed out is his comment here, many of us find it difficult to find the time to write informative science posts on a regular basis, these guys are proving it can be done. Do yourself a favor and check them out:

Mystery Rays Wow. Has to be the best blogging on real science I've ever seen. Enough reference to literature to satisfy the hard-core virologist, interesting and clear enough to appeal to the non-scientist.

Michael Palm HIV Basic Science Blog Totally hard-core HIV science.

Genomicron Fantastic genomics blog and distinctly Canadian perspective on science.

Laelaps, Tetrapodzoology, Deep Sea News These guys are zoologists and/or paleontologists. Which mean they're not only biologists, but they're also scientists. Which means as a biochemist, this is where I go for a reminder of the beauty of evolutionary theory and life in general. These guys make it all fun, interesting and easy to understand (lots of pictures too!!). They do a good bit of blogging on peer-reviewed research as well.

Cognitive Daily As advertised, "A new cognitive psychology article nearly every day". I don't know how they do it, but they do it.

Drug Monkey Lots of real science being thrown around here. More importantly, Drug Monkey has a sense of humor and this blog is damn fun to read.

Life of a Lab Rat Well-written tidbits of insight into laboratory culture.

Henry Some good stuff on human evolution.

CSHL Protocols General science and the latest in molecular biology methodology.

Sorry to the great blogs out there that I missed. Feel free to add your favorite science blogs to the list below.


Thursday, February 28, 2008

iPOD Culture in the Lab

Black Knight over at Life of Lab Rat has a couple of humorous remarks on iPOD etiquette in the lab:
"I suspect that if someone is working at a bench in the wet lab then you have to look at how many earbuds are being worn. One means "Yup, I'm listening". Two probably means "Do not disturb: I've already made a mistake setting up this PCR and if you talk I shall ignore you. If you persist, I shall stab you with my Gilson". Whether the hands are gloved or not might have some bearing on the situation."

Works the same way here. I don't have an iPOD but I appreciate not having to guess when someone's trying to drone me out.

Funny how iPOD lab customs have evolved in parallel in our lab on the opposite side of the world. Maybe it's a colonial thing .

PS - Watch out. Black Knight is apparently not his real name.

Have a look add your iPOD etiquette lessons to the mix...


Mendels Garden

Mendel's Garden is coming to the bayblab in March. For those who don't know the carnival, it covers: "new research in all areas of genetics, not restricted to any specific organism. Everything from transcription to evolution to genetic counseling and social implications of genetics research are welcome.". Please submit any material over at blog carnival.


Wednesday, February 27, 2008

The state of blogging: part2

We have a confession. You have all been part of an experiment in social engineering and blogging. This has been in the planning for a while now. But let me step back and explain the purpose of our blogging experiment before we analyze the results.

You'll notice that the comments on our site appear right on the main page, that's because we believe that the conversation about science is more interesting than the posts. We believe that through reason and introspection blogging can become a kind of meta-conversation, a way to further knowledge and foster discussion. Recently we've been discussing science blogging a lot in the bay and came to the conclusion that the landscape is in transformation. We also realized that we had many diverging assumptions as to what constituted science blogging, and what role in can play in society. This is led us to wonder about who blogs and who reads blogs. And it turns out to be mostly the same people. This overturns one particular assumption that blogging is a sort of soapbox, a type of lecture with a speaker and many listeners. No, I postulate that blogging is mostly a conversation.

This in turn made us think about who controls the conversation, and I think that increasingly, in the small world of science blogging, ScienceBlog is a dominant figure. What happens when the conversation is dominated by a group of vocal individuals under a collective banner? What happens when the group is a commercial entity? Is independence preserved?

This led us to devise a simple (and unscientific) blogging experiment. We wanted to see how scienceblog can polarise a discussion on the science blogosphere. This of course meant that we would have to capture their/your interest. We decided to ask what science blogging is, and word the post in a controversial way so that it would elicit a response from top bloggers, and more specifically ScienceBlog bloggers.

We then made predictions. Does being part of a group stunt the ability of members to be introspective and question the motives of their own organisation? would any form of criticism stir things up and spread rapidly across Scienceblogs with a uniformed voice. We were also wondering if reasonable scientists would turn into raging commenters spewing ad-hominem attacks. Finally we were wondering if top bloggers would post this story or ignore it, letting the smaller bloggers fight their fight.

Well we learned a lot from this small 24h study about what motivates people to blog, and how bloggers view the role of science blogging.

First of all, out of 33 comments (excluding ours), only 12% resorted to ad-hominem attacks, which shows a good degree of maturity and intellectual integrity.

Two thirds offered criticism of the ideas being expressed, sometimes constructive, sometimes not.

18% showed some kind of introspection, questioning their motives or challenging their assumptions.

Now lets see what happened on other blogs.

10 blogs linked to the story, and interestingly, of those blogs singled out in the post, only Sandwalk put up the post. [edit: so did pharyngula].

4 of the 9 linking blogs were hosted by ScienceBlogs. Of those, 3 were willing to critically examine ScienceBlogs.

1 Blog was created for the sole purpose of testing the idea that focused science blogging about peer-reviewed research in a particular discipline can attract readers.

2 blogs examined in dept what science blogging should be about. And they did an excellent job. Hopefully they won't mind me quoting them:

BPR3 says: "

But if that's the case, then why should there be any attempt to control the content of blogs? Isn't that what does? I'd submit that there's a critical difference: Bloggers are under no obligation to write posts that meet our guidelines. They are free to submit posts that they believe do meet the guidelines, but they aren't required to. You can sign up for an account at and never write a post that meets our standards. As long as you don't attempt to get your post aggregated, you can maintain your account indefinitely.

ScienceBloggers are actually required to produce a certain number of posts per week, and ScienceBlogs has the (rarely invoked) right to shut down blogs that don't meet that requirement. But ScienceBlogs has no restrictions on the type of posts its members write, which makes the first requirement less onerous

I think both commercial sites like ScienceBlogs and independent blogs are critical to the online dissemination of science. Independent bloggers are free from the restrictions of a commercial site, but they might not attract as large an audience. A large audience for science blogging is important not only because of the potential for bloggers to make money, but also because of the public service the science blogging represents. If commercial blogs can expand the readership of science on the internet (even if it also increases the number of political/religious rants), isn't that, on the balance, a good thing?"

Omphaloskepsis says:

"Most science bloggers have other commitment apart from blogging. As one person said, the only way the justify blogging is by calling it outreach. And outreach should go beyond the people who would normally read peer reviewed science. Outreach involves reaching out to the people with a casual interest in science. Outreach involves producing content that would be of interest to people who don't normally read about science.

writing about creationists and kooks is important - when scientists say "intelligent design isn't science", the public needs an explanation. And debunking the latest nonsense is valuable. There was a time when people could wait for books to be published or for to be updated. But blogging has become the medium of choice. This is even more important for a blogger like Orac - the amount of quackery in medical fields is overwhelming. A site like Translating Autism is great in that it bridges a gap from technical journals to the public, it only gets things halfway there. Orac is another step, but we need more to reach the Oprah crowd."

Thank you for your attention, sorry if I angered anyone, and I hope you continue commenting about the role of science blogging, and the motives of the ScienceBlog corporate entity.

Edit: even though the 24h has passed I decided to include PZ Myer's contribution to the debate. He is after all the 800lb Gorillaphant.


Tuesday, February 26, 2008

The state of science blogging

Why do we blog about science? For us at the bayblab, it was just an extension to our conversations about science that tended to take place in the "cool" bay of the lab, the only place with a decent sound system. It wasn't initially intended to be public, it was just an efficient way to share stories among us so that we could have some conversation fodder. In fact, back when we started, blogging in general was mostly about personal journals and pictures of pets, and the science blogs were few and far between.

Now there are thousands of blogs dedicated to science, yet only a few are popular. And strangely the popular ones are only loosely related to science. Just take a look at the top 5 science blogs (according to postgenomic):

1 Pharyngula (mostly about creationism)
2 Cognitive Daily (psychology research)
3 Living the Scientific Life (personal journal)
4 Sandwalk (some evolutionary genetics, and creationism)
5 Aetiology (pop science)

Of those only Cognitive daily is consistantly talking about peer-reviewed research. Why is that? Perhaps there is less appeal in discussing recent papers than bashing creationists. But bashing creationists is almost too easy, and not very constructive. It's been said before, you can't reason somebody out of a position in which they didn't reason themselves into. And it worries me because to the lay audience listening to PZ Myers (the 800lb gorilla), it would seem that science's purpose is to attack religion. In fact I suspect the blog gets most of its traffic from creationists. According to technorati, his top tags are "Creationism, godlessness, humor, kooks, politics, religion, weblog, weirdness", so should it really count as a science blog?

If you examine the elephant in the room, ScienceBlogs, the trend is maintained: politics, religion books, technology, education and music are tagged more often than biology or genetics. This suggests that their primary motives are entertainment rather than discussing science. Why? Because it pays. Seed Magazine and the bloggers themselves profit from the traffic. That's right, Seed actually pays these bloggers for their posts. And the whole ScienceBlogs thing is a little incestuous, they really like linking to each other, but not so much to the little blogs. I'm afraid gone is the amateur blogger, and in is the professional gonzo science journalist. Might as well read Seed magazine.


Monday, February 25, 2008

Nature Editorial Blasts Canadian Government for Scientific Ignorance

The fact that the Canadian Harper government has so little regard for anything that slows the pace of oil extraction should come as no surprise, but now their ignorance has even managed to catch the attention of the world's most prestigious scientific journal:

"Concerns can only be enhanced by the government's manifest disregard for science. Since prime minister Stephen Harper came to power, his government has been sceptical of the science on climate change and has backed away from Canada's Kyoto commitment. In January, it muzzled Environment Canada's scientists, ordering them to route all media enquires through Ottawa to control the agency's media message. Last week, the prime minister and members of the cabinet failed to attend a ceremony to honour the Canadian scientists who contributed to the international climate-change report that won a share of the 2007 Nobel Peace Prize.

Harper sees himself as the leader of a 'global energy powerhouse' and is committing Canada to a fossil-fuel economy. More than 40 companies have a stake in mining and upgrading the bitumen from the oil sands in Alberta and churning out 1.2 million barrels a day. This activity generates three times as much greenhouse gas as conventional oil drilling. Emissions from Canada's oil and gas industry have risen by 42% since 1990."

These guys are bad news. They need their asses booted out of office before they manage to completely sell off the country and send the rest of us back to the stone age. Luckily, we may soon have the chance to do just that. See south of the border for a preview of where a few years of a Conservative majority is likely to take us.


Friday, February 22, 2008

The Gosepl According to Darwin III

In this week's Gospel reading, the great prophet tells how the hands of our magnificent Creator have worked upon functionally duplicitous organs to give rise to new structures with new functions, in all their wonder and perfection. Indeed, this is revealed as the very mechanism that He used to carefully craft the swimbladders of our fish ancestors into the perfect yet peculiar structure of the human lungs, and provides us with an explanation for the mystery of the gill slits of the human embryo. Not only this, but Darwin in his infinite wisdom also foreshadows the discovery that our genes themselves are created by this very same process of duplication and refinement, made over a century later by the Disciples of molecular biology.

"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by successive, slight modifications, my theory would absolutely break down. But I can find out no such case... We should be extremely cautious in concluding that an organ could not have been formed by transitional gradations of some kind...

Again, two distinct organs, or the same organ under two very different forms, may simultaneously perform in the same individual the same function, and this is an extremely important means of transition: to give one instance, -there are fish with gills or branchiae that breathe the air dissolved in the water, at the same time that they breathe free air in their swimbladders, this latter organ being divided by highly vascular partitions and having a ductus pneumaticus for the supply of air...In all such cases one of the two organs might readily be modified and perfected as to perform all the work, being aided during the progress of modification by the other organ; and then this other organ might be modified for some other and quite distinct purpose, or be wholly obliterated.

The illustration of the swimbladder in fishes is a good one, because it shows us clearly the highly important fact that an organ originally constructed for one purpose, namely, flotation, may be converted into one for a widely different purpose, namely, respiration. The swimbladder has, also, been worked in as an accessory to the auditory organs of certain fishes. All physiologists admit that the swimbladder is homologous, or "ideally similar" in position and structure with the lungs of the higher vertebrate animals: hence there is no reason to doubt that the swimbladder has actually been converted into lungs, or an organ used exclusively for respiration.

According to this view it may be inferred that all vertebrate animals with true lungs are descended by ordinary generation from an ancient and unknown prototype, which was furnished with a floating apparatus or swimbladder. We can thus, as I infer from Owen's interesting descriptions of these parts, understand the strange fact that every particle of food and drink which we swallow has to pass over the orifice of the trachea, with some risk of falling into the lungs, notwithstanding the beautiful contrivance by which the glottis is closed. In the higher Vertebrate the branchiae have wholly disappeared-but in the embryo the slits on the sides of the neck and the loop-like course of the arteries still mark their former position. But it is conceivable that the now utterly lost branchiae might have been gradually worked in by natural selection for some distinct purpose: for instance, Landois has shown that the wings of insects are developed from the tracheae; it is therefore highly probable that in this great class organs which once served for respiration have been actually converted into organs for flight.

A Reading from The Book of Darwin

- Charles Darwin,
The Origin of Species By Means of Natural Selection or The Preservation of Favored Races in the Struggle For Life, Chapter VI - Difficulties of the Theory. Modes of Transition


Friday funnies

As somebody studying female reproduction, I can't help but agree... If this is your type of humour check out also this case report of an unusual gynecological tumour that turned out to
be an onion, courtesy of the British journal of venereal disease.


Thursday, February 21, 2008

Fact or Fiction: Vitamin C and the Common Cold

Today's issue of the Ottawa Metro features an article extolling the virtues of vitamin C as cold killer. This is a common piece of folk wisdom that we've touched upon briefly before. Is there truth behind the vitamin C advice?

It turns out the subject is quite controversial, with many people preaching the value of vitamin C in cold prevention. The science, however, is less clear. Several studies have been done to examine the effects of vitamin C on the cold prevention and treatment. One meta-analysis of these studies showed that vitamin C has no effect on the incidence of the common cold and slight but variable effects on duration and severity. From the summary:
"It reduced the duration and severity of common cold symptoms slightly, although the magnitude of the effect was so small its clinical usefulness is doubtful."
One of the authors of this review has since argued that therapeutic vitamin C treatment (i.e. treatment after onset of symptoms) may be beneficial in children. Some studies have shown similar modest (but statistically insignificant) effects, while others none at all. Overall the evidence for therapeutic vitamin C use is unconvincing. The NIH has a detailed page describing vitamin C usage, that has the following to say about cold treatment:
"More than 30 clinical trials including more than 10,000 participants have examined the effects of taking daily vitamin C on cold prevention. Overall, no significant reduction in the risk of developing colds has been observed. [...] Numerous studies have examined the effects of starting vitamin C after the onset of cold symptoms. Overall, no significant benefits have been observed. Initial evidence from one study reports possible benefits with high doses of vitamin C taken at the onset of symptoms, but without additional evidence this remains indeterminate. At this time, the scientific evidence does not support this use of vitamin C."
On both cold prevention and cold treatment, the NIH gives vitamin C a grade of D meaning "fair scientific evidence against this use." It is interesting to note, however, that vitamin C does seem to have an effect in people living in extreme circumstaces such as soldiers in sub-arctic exercises or marathon runners. Overall, for the general public, vitamin C is important for health but the evidence does not support its use in cold prevention or treatment.


Wednesday, February 20, 2008

These are the people at your seminar...

Our departmental student seminar day just passed and what a perfect opportunity to play seminar bingo. How many of those caricatures have you identified at a talk? Which one are you?

Unfortunately I came across this *after* the talks. Maybe next year.


Monday, February 18, 2008

Impostor Syndrome

Science isn't always as glamourous as it's made out to be. It can be gruelling or frustrating. I know my share of people who have thought about quitting, or are thinking about other options when their degree is finished. One of the reasons for this is 'Impostor Syndrome'.

Impostor Syndrome is feeling like a fraud. It's the idea that your successes are a fluke, while those of your peers are because of intelligence and ability. It's the feeling that you're in over your head and the fear of being found out. And it can be tough to shake. Because publications and scholarships - evidence against being an fraud - are dismissed as luck, the victims can be difficult to convince of their abilities. The problem is magnified during dry spells - periods when things aren't working and results are hard to come by (which are frustrating enough on their own). Sound familiar? Apparantly it's quite common. Science Careers has an article about the phenomenon:
"Impostor feelings have a way of festering silently for a long time, thanks to the difficulty of accurate self-assessment and the social stigma of asking for help. Connecting with peers anonymously can be a first step toward realising that great scientists are made, not born, and that even some of the best of them faced on-the-job doubts along the way."
Impostor Syndrome is by no means limited to science, and it can lead to other behaviours such as procrastination that can compound the problem. Of course there's no quick fix either, other than a more realistic assessment of one's abilities and the knowledge that some of your peers are probably feeling the same way.

Have you suffered from Impostor Syndrome? Have suggestions how to overcome it? Share your stories.


How Quackery "Works" Part 5: Recall Bias

Most quackery and pseudoscience depends on testimonial evidence rather than scientific evidence. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study.

A common psychological bias that plagues retrospective and self-reporting studies is recall bias. This is when answers aren't based strictly on observation but also on the responder's memory. Because memories can be influenced or otherwise unreliable, relying on recall to draw conclusions can be problematic. This bias is unintentional, and can often be based on expectation. For example, if you have a cavity you may 'remember' eating more sweets than usual, even if it's not the case. There are other examples in the literature: A study of mothers in Brazil found that richer or better educated women were more likely to over-recall breast-feeding durations. A more relevant example is recall bias among parents of autistic children. After publication of a paper suggesting a link between autism and the MMR vaccine, parents were more likely to "recall the onset [of autism] as shortly after MMR more often than parents of similar children who were diagnosed prior to the publicity." Preconceived ideas of what the answer is (or should be) can taint recall.

Testimonials given in support of a product are also subject to recall bias. Given the above example, one can easily imagine a now-healthy person recalling that they started to get better 'around the same time' as starting a supplement even if there are other reasons for an improvement. This inaccuracy of memory, or even differences in what two groups are likely to recall can lead to incorrect conclusions and false positive testimony. Recall bias can be a problem for evidence-based clinical studies as well. Anytime memory and self-reporting is involved, this opens an opportunity for this kind of unconscious bias. A good study needs to take this into account in its design. Ideally, direct empirical measurements are used to eliminate recall and self-reporting altogether, but that isn't always possible. In retrospective studies, good questionnaire design helps minimize recall bias. For example, detailed questions or blinding the subject to the hypothesis help with accurate reporting. While neither evidence-based studies nor anecdote aggregation is immune, a product pitch based on several individual self-reported testimonials is more likely to suffer from recall bias than a well-designed retrospective study.

Read more about recall bias here.


Sunday, February 17, 2008

Depriving the Senses

Occasionally, when reading journalistic reports of various ‘interesting’ experiments, I wonder how the heck some of these proposals got past ethics committees. Take, for instance, the recent BBC ‘Horizons’ report on sensory deprivation.

I confess, I can’t watch it here (if anyone does have a youtube link or the like, please let me know); the BBC have it shared on the net, but you have to be in the UK to view it. However, I’ve read enough of the experiment to make a few conclusions, I think.

The report, apparently, is presented by trauma expert, Prof Ian Robbins, who is well versed in the study of the effects of torture. That’d be my first red flag if I was on the ethics board looking at this.

The study design appears to be simple enough. Take six normal people. Test them for various psychological parameters, including visual awareness, suggestibility, memory, etc. Sensory deprive them for 48 hours. Test them again. Watch the ratings for BBC1 skyrocket.

I’d be asking at this point: “Has this been done before?” Actually, yes. During the 50’s apparently, the US and Canadian military funded a big study by a bloke named Donald Hebb into this whole sensory deprivation thing. They decided it was too controversial, so they dropped it after a year or so. The US military considered this to be too cruel. I’m certain that someone would have raised a red flag at that point too.

So what happens? Apparently, within a relatively short time, the victims… err, sorry… subjects start to become anxious and experience hallucinations. There is evidence that their brains are worse for wear as well… they become more suggestible, and their ability to process information drops significantly. Animal studies have shown that there are significant neurological effects to boot – the brain’s sensory synapses all start falling apart.

Apparently, this is all reversible, but, to be fair, there are some interesting points to make from it. There are plenty of people around the world who are held in prisons under what is effectively sensory deprivation for significantly longer periods than 48 hours. The US are known to use sensory deprivation on people in Guantanamo Bay. Surely if they are suggestible, that makes anything they say after this treatment defunct.
Anyway, everyone made it, and I assume they are none the worse for the experiment. Still, I can’t help but wonder if it was really necessary for a simple TV show.


Friday, February 15, 2008

An Encyclopedia of Life

Biologist E.O. Wilson tells us how the Earth is rapidly losing biodiversity and proposes we catalogue it in an electronic "Encyclopedia of Life" before it's all gone. Great talk below and check out of sampling of the proposed website format. We desperately need this type of resource, and sadly, it will probably be all that's left of many species a few years from now.


Bayblab Bio-Patent Watch

In this feature, I review newly-filed biotech patent applications published by the US Patent and Trademark Office. Comments are welcome. What do you think of the inventions? Are they useful? Commcerically viable? Should the patents be granted? Are they novel? Overly broad and restrictive of future research or individual rights? Will society reap rewards if the patent is granted and the technology is exploited?

This month we have:


Application number: 11/781,818
Filing date: Sep 12, 2007
Inventor: Walter Messier

This invention describes a method for finding gene sequences responsible for the resistance of non-human primates, such as chimps, to diseases that afflict humans, such as HIV/AIDS, cancer and neurodegeneration. The method basically involves comparing genetic sequences from human and non-human primate species to determine which human disease genes have undergone evolution in primates since our lineages diverged. Information about these genes would then be used to design novel therapeutics. As an example, the inventors propose to determine how the gene encoding 17-beta-hydroxysteroid dehydrogenase has evolved in chimps to mediate cancer resistance.

Application number: 11/849,643
Filing date: Sep 4, 2007
Michael JENSEN

This application describes how to engineer cytotoxic (cell-killing) immune cells that target a protein antigen specifically expressed on the surface of neuroblastoma tumor cells. An antibody against the neuroblastoma antigen is fused to the zeta chain of the T-cell receptor. This chimeric receptor can then be introduced into T cells, natural killer cells, neutrophils and macrophages so that they express it on their surface and thereby recognize and kill neuroblastoma cells.


Application number
: 11/851,291
Filing date: Sep 6, 2007
Inventors: Chang-Min Park, Shriram Ramanathan, Patrick Morrow, Kenneth Cadien

This one's pretty self-explanatory. NMR (nuclear magnetic resonance) technology is used in medicine for MRI imaging scans, as well as certain types of chemical analysis. This invention is describes a hand-held device that analyzes clinical DNA samples to perform disease diagnosis.

Application number: 11/854,362
Filing date: Sep 12, 2007
Inventor: Xingping Zhang
Tetraploid watermelons are used to breed the triploid, seedless variety that we all love so much. This invention describes a way to make smaller, tastier tetraploid watermelon with a higher ratio of flesh-skin.

Application number: 11/899,670
Filing date: Sep 7, 2007
Inventor: Kenneth D. Fine

This invention describes methods for diagnosing food allergies by determining whether the patient produces antibodies against commonly ingested foods. The approach is to collect fecal samples ( ie, "poop") and analyze it for the presence of antibodies against food antigens by ELISA. I would not want to be the poor sucker who works in this diagnostic lab:
"One method of concentrating the stool specimen is to spin the stool in a centrifuge to obtain a watery supernatant...Another method of concentrating the stool specimen, which is particularly used when the specimen is watery or diarrheal, is to freeze-dry or lyophilize the specimen to solid material and reconstituting it with water at a dry matter to water ratio equal to that of non-diarrheal stool".


Amateur scientist: the aspartame experiment

We at bayblab have made the case for a distributed web of amateur scientist working together to do real science. Think of it as blogging is to the written press, podcasting to radio, or youtube to television: user-generated science. We also warned in our podcast (episode 15), that it comes with a great risk of animal cruelty, and limited access to proper equipment to get the job done safely. This couldn't have been more prescient when it comes to this story of Victoria Iness-Brown who decided to test aspartame on 108 rats for over 2 years. Any scientist looking at this experiment can clearly see the merit. The study was surprisingly well thought out. The experimenter used mixed strain and missed the point on why we use inbred for experiments such as this but otherwise the design was good. Yet a study like this could have never passed the ethics board in our university. The rats were given aspartame in their water throughout their lifetime, and allowed to carry out their lives. The problem is that there was precious little monitoring, no weighing of the rats, and more importantly, many rats developed tumours, which were left to ulcerate, with the obvious implications on the animal's well-being. The intentions were good, but the experimenter lacked the knowledge on how to reduce pain and discomfort on the animals. The other problem is that there are no results or statistical analysis. There are lots of pictures of rats with tumours, but no dissection, no measurement of tumour burden, no survival curves. How can we avoid rogue experiments like these but foster amateur science?


Thursday, February 14, 2008

Secreted Luciferase

A relatively new paper in Nature Methods describes the use of a new luciferase, GLuc. Apparently it is 2000times more detectable than Renilla luciferase and is secreted from mammalian cells in culture. This property allows one to quantify luciferase in mice that have implanted GLuc expressing cells by a quick assay on whole blood. Of course, as the ultimate test they use an oncolytic virus to show regression of a GLuc expressing mouse tumour in vivo by assaying Gluc activity of whole blood after oncolytic virus treatment. Sounds like an excellent new tool, especially for those who don't have access to an in vivo imaging system..


When Quackery Doesn't Work

As I take a short break from explaining why quackery sometimes seems to work and why so much positive testimony exists (don't worry, there is more of that series to come) I thought I'd point out a site that documents what can happen when quackery doesn't work.

(yes, I realize the irony of using anecdotes to fight quackery)

Found via The Quantum Pontiff


Wednesday, February 13, 2008

Bayblab podcast: episode16

A new edition of the bayblab podcast is already up (don't forget to subscribe to our rss feed)! Our new year resolution is to have more frequent podcasts... This podcast also introduces a new element in our format because we interviewed a guest scientist, which we'll try to do whenever we can get our hands on someone willing to share his/her research with a bunch of degenerate grad students over a beer. And boy did we hit the jackpot, because our guest on this episode is Dr. Ignacio Chapela. Dr Chapela was in Ottawa to give a talk entitled "Reason Exhausted: Science, environment and the end of progress" at the graduate student's interdisciplinary conference. Chapela specifically said he only came to the conference because he was invited by students, and when I asked him to be on the show, he immediately agreed. He gave us a candid and humble account of his story which is well worth hearing even if you're not a fan of the podcast, so do yourself a favor and try this one.

If you're not familiar with Chapela, he is a tenured professor at UC Berkeley, and gained fame in 2001 when he announced in the journal Nature that he had discovered contamination of native maize in mexico by transgenes from GM crops. He then became the "bete noire" of the agro industry which put pressure on the Nature Publishing Group and on his university which happened to be funded by Monsanto to the tune of $50M. Learning from this abuse, he now vehemently opposes the corporatization of universities and more specifically the recent billion dollar deal between British Petroleum and UC Berkley to research biofuels which he argues will benefit no one but the gas giant. To learn more about this you can check this youtube clip of a protest against BP or read his speech. This site also goes over some of the controversies and stories which he shared with us on the podcast...Enjoy!


Carl Sagan and the fourth dimension

Since we're posting funny science videos, I want to share this one with you. I'm not sure what it is, perhaps the diction, perhaps the subtle humour, but Sagan really cracks me up in this one. I wonder if he came up with this monologue under the "influence"...


Watson under fire (again)

James Watson is under fire again for racist comments. No, not new comments but the same ones from last October that lead to his retirement from Cold Spring Harbour Laboratory. Watson is on the board of directors of Seed Media Group as scientific adviser. Seed Media Group is the parent company of, where several bloggers are calling for his head.

What confuses me is the timing. Why the outrage now? Where were the demands that he be dismissed from the Seed board 4 months ago, when the comments were first made? Lost in the shock of what he had said? Maybe there are goings-on behind the scenes that I'm not aware of, but to an outside observer it seems strange. Worse, most of the above bloggers make the point that October's outburst wasn't an isolated incident, but that Watson has a history of racist, sexist and otherwise demeaning or insensitive remarks. Watson was added to the Seed board in 2005, was launched in 2006. Why would these bloggers sign on to work for, as one of them puts it, a "racist corporate overlord"?

Odd timing aside, the real question is: Should Watson get a free pass because of his contributions to biology? Or should he continue to be punished for statements he has made (and apologized for)? What do you think?


Gandalf on Colbert

Our favorite bearded immortal, Aubrey de Grey, made an appearance on Colbert Report a couple of days ago. He actually makes a funny near the end. We have talked at length about the plausibility of the former computer scientists ideas about preventing aging on the blog and on the podcast.


Tuesday, February 12, 2008

The Gospel According to Darwin II

On this, the holiest of days, the birthday of our prophet Charles Darwin, we celebrate with a reading from the divine scriptures. In today's Gospel reading it is revealed how the tool of natural selection was patiently wielded by the almighty Creator to sculpt the perfect structures of life.

"It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrument, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. Further we must suppose that there is a power, represented by natural selection or the survival of the fittest, always intently watching each slight alteration in the transparent layers; and carefully preserving each which, under varied circumstances, in any way or in any degree, tends to produce a distincter image. We must suppose each new state of the instrument to be multiplied by the million; each to be preserved until a better one is produced, and then the old ones to be all destroyed. In living bodies, variation will cause the slight alterations, generation will multiply them almost infinitely, and natural selection will pick out with unerring skill each improvement. Let this process go on for millions of years; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?"

- Charles Darwin,
The Origin of Species. Chapter VI - Difficulties of the Theory. Organs of extreme Perfection and Complication.

Happy Birthday Charles.


IA updates

The always awesome has some updates, including some interesting info on the status of the "Canadian DMCA", and a German nudist airline.
Check it out.


How Quackery "Works" Part 4: Natural healing/additional treatments

Most quackery and pseudoscience depends on testimonial evidence rather than scientific evidence. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study.

Regression fallacies offer an explanation as to how an ineffective treatment can seem to work due to random fluctuations of symptoms. Very similar to this idea is the body's natural healing process. While regression to the mean explains that a person perceives that a treatment is working while overall their condition remains unchanged, with natural healing or additional treatments the body may actually be getting better but not because of the new treatment.

The body is a natural healer. A cold, for example, will go away on its own without any over-the-counter or alternative treatment. More serious ailments do require treatment and it's likely that patients continue with conventional treatments while desperately trying whatever 'alternative medicines' they can find. For example, a cancer patient may be undergoing standard chemotherapy and radiation treatments when they decide to add a new cancer fighting tea blend to the mix. The cancer goes into remission. Which gets credit - the chemo or the tea? It's the most dangerous of quacks who advise against conventional treatment while peddling their own cures. Lifestyle changes can also be included with additional treatments. Someone complaining of fatigue may change their diet and begin exercising more while also taking their favorite algae supplement. The end result may be an improvement, but the reason is unclear.

When it comes to quacks and pseudoscience, all three of these scenarios - natural healing, additional treatment and lifestyle change - can lead to positive testimonial: "I took treatment X, and my condition improved." The reality is that the statement may be true but that doesn't mean that 'treatment X' is the causative agent for improvement. Evidence based medicine relies on appropriate controls (placebo, existing treatment) and large sample sizes to separate treatment effects from other reasons for improvement.


Quack of the week: Rupert Sheldrake

I was recently listening to Rupert Sheldrake on the "how to think about science" series of podcast. While he makes some interesting points about the state of science, and what it means to be on the fringe of science, I couldn't help to think his ideas were too improbable to seriously consider. In fact I won't bother enumerating all of them but you can check them out yourself. In any case he differs from other quacks we've talked about because he's not trying to take advantage of anyone, he just wants his ideas to be tested, and people to respect his science, no matter how improbable it is. One of those ideas is that there are invisible fields (think electro-magnetic) which connect everything in the world, so that when one makes an observation, the knowledge gained travels to every related entity. For example he says that the first time a certain chemical is crystallized, it then decides for every subsequent event how other crystals will form, and the process will also be faster as if crystals were learning. This hypothesis in his opinion is superior to the one chemist already hold, which is that tiny crystals get carried in beards and clothes and hair of traveling chemist which somehow manage to make their way into other people's experiments and gives rise to a "diminishing polymorph". In biological terms this could be compared to a prion: it is a replicating entity which converts a population of related chemical found in various forms, into a single crystalline form. I found this latter idea actually quite interesting and far more likely than ones which needs to conjure up new physics. Is there any evidence for the "crystal beard hypothesis"? Well it turns out that yes there is, and it is fascinating.

The first example is rintonavir, an anti-viral manufactured by Abbott. It turns out that a particular conformation of the drug spontaneously formed in 1998 in their American manufacturing plant. This Form-2 was less effective as a drug, and it was able to catalyze the conversion of the old drug into this new form. The contaminated plant, despite efforts to clean it up was never able to produce form-1 ever again and had to be shut down. Meanwhile the Italian plant picked up the slack, until an American scientist came to visit, and seemingly introduced the rogue drug, probably through his clothing, and wrecked the whole operation there too.

The second example comes from Canada, and lead to some patent litigation. It turns out that paxil, can occur in two variants also. The second variant was useful because it enabled the company which had ownership of the drug to extend patent life. Now comes in Apotex, a Canadian generic manufacturer, which makes the first form of paxil, which is equally effective and now off-patent. Well it turns out that crystals contaminated their plants too and started converting their paxil into the new variant. This of course meant that they were making a drug which was owned by somebody else and prevented them from making the old patent-free version. I'm sure the pharmaceutical industry loved that one.

It makes one wonder about the dangers of self-replicating products of synthetic biology...


Monday, February 11, 2008

How Quackery "Works" Part 3: Regression to the Mean

Most quackery and pseudoscience depends on testimonial evidence rather than scientific evidence. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study.

How a person feels isn't static, it fluctuates. You can feel tired one day but not the next. If you suffer from migraines, one can be more severe than the next. How "well" you feel can vary from day to day, even if overall your condition isn't changing (neither improving nor declining). Regression to the mean is the tendency of extreme measurements to be less extreme (closer to the mean) on subsequent measurements. A example that should be familiar to most sports fans is the concept of the 'sophomore slump'. This is when an athlete has performs more poorly in their second season than they did in the rookie year. The reason for this isn't a slump per se, but rather due to the fact that the first measurement - an outstanding rookie season - lies at an extreme, while the second measurement is closer to the 'mean' performance for that player. That is, it's closer to the average standard of performance for that player. It looks like a slump, but in fact is due to random fluctuations in player performance.

The same principle holds for medical testimonial. An ineffective treatment may seem to work based on random fluctuation of symptoms, resulting in positive testimonial. In fact, people who are sick are more likely to look to experimental remedies and unconventional treatment when they feel at their worst. Since this first 'measurement' is at an extreme of their condition, subsequent 'measurements' of how they feel will be an improvement for purely statistical reasons as opposed to an effective treatment. Evidence-based medicines rely on multiple measurements and large sample sizes (a testimonial is a sample size of 1) to account for normal disease fluctuation and get statistically meaningful results.


Craig Venter on global warming

This quote was found as part of a series about scientist who've changed their minds:

"Like many or perhaps most I wanted to believe that our oceans and atmosphere were basically unlimited sinks with an endless capacity to absorb the waste products of human existence. I wanted to believe that solving the carbon fuel problem was for future generations and that the big concern was the limited supply of oil not the rate of adding carbon to the atmosphere. The data is irrefutable. We are conducting a dangerous experiment with our planet. One we need to stop. Now."


Sunday, February 10, 2008

How to think about science

As graduate students, we spend a lot of time thinking about science. But we tend to concentrate on the "how-to", the minutiae of daily experiments. Rarely do we concern ourself with the "why". Once in a while experiments work, and we're confronted with something unexpected and we begin to put the pieces of the puzzle together to form a coherent model of reality. This part is what most people would identify as the core of the scientific process. Yet we spend surprisingly little time thinking about epistemology. Do our model reflect reality, or do we impose our biased mental framework onto natural phenomena. What does it mean to do science, is it about the experiments or the theory? Recently I've stumbled upon a series of podcast exploring these types of questions with interviews of prominent figures in ethics, philosophy, history and science which examine science in a social and philosophical perspective. I highly recommend this CBC podcast (Ideas) and particularly this series of interviews "how to think about science". You may not agree with all that is said, but it will make you reconsider many aspects of science which we take for granted.... Here is the roster:

Episode 1 - November 14 - Simon Schaffer
Episode 2 - November 21 - Lorraine Daston

Episode 3 - November 28 - Margaret Lock
Episode 4 - December 5 - Ian Hacking and Andrew Pickering
Episode 5 - December 12 - Ulrich Beck and Bruno Latour
Episode 6 - January 2 - James Lovelock
Episode 7 - January 9 - Arthur Zajonc
Episode 8 - January 16 - Wendell Berry
Episode 9 - January 23 - Rupert Sheldrake
Episode 10 - January 30 - Brian Wynne


Thursday, February 07, 2008

Fact or Fiction: Suicidal Dentists

Which profession has the highest suicide rate? Dentists of course! We've all heard it before, so often it must be true. All that bad breath and gum disease would probably make me suicidal too. On the other hand, the exhorbitant prices of a 5 minute check-up is probably incentive enough to stick with it - you can't spend your tooth fairy money when you're dead. What are the facts though? Are dentists really depressive, or is it a ploy for pity so we don't view them all as Dr. Szell from Marathon Man? The straight dope had the following to say:
"Suicide among white male American dentists is higher than average but not as high as among white male American doctors. (Sorry to limit this to white men, but that's all the data I had to work with.) Don't fret, though. Dentists' death rates from other causes are lower, and on average they live several years longer than the general population. Ditto for doctors."
The literature on the subject indicates that dentists are actually no more prone to suicide than the general population and that gender or dental subspecialty are not good predictors of depression (with the exception of pediatric dentistry and periodontics where females were more depressed than their male counterparts). The most recent data suggests that overall, white male dentists have a lower suicide rate than the rest of the working population but the reverse is true when looking only at older dentists. Despite the persistance of this myth, there is no strong evidence that as a group dentists are more suicidal than other professions, let alone have the highest rate of all of them.


How Quackery "Works" Part 2: Observer Expectancy Effects

Most quackery and pseudoscience depends on testimonial evidence rather than scientific evidence. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study.

Closely tied to the placebo, or subject expectancy, effect is observer expectancy effect. This is when an experimenter gets the results (s)he wants through unconscious manipulation. From wikipedia:
"An example of the observer-expectancy effect is demonstrated in music backmasking, in which hidden verbal messages are said to be audible when a recording is played backwards. Some people expect to hear hidden messages when reversing songs, and therefore hear the messages, but to others it sounds like nothing more than random sounds."
In terms of medical effects, this unconscious bias can manifest in the assessment of symptoms (usually qualitative). A rash looks 'better', hair looks shinier, a person looks less tired. Regarding testimonial evidence, it's hard to separate observer expectancy from placebo effect since the person is both the subject and the observer but both can result in positive testimony even in the absence of a working product. Evidence-based medicines rely on double-blind studies (ie. the researcher doesn't know who has been treated and who has been given placebo) to separate real effects from observer bias.


Wednesday, February 06, 2008

How Quackery "Works" Part 1: The Placebo Effect

A recent comment left on a 'Quack of the Week' post suggested that I should get my ass kicked for disrespecting testimonials. Most quackery and pseudoscience depends on testimonial rather than scientific evidence and the implied (and sometimes explicit) argument is along the lines of "If so many people have tried it and say it works, then it must be true". This is an example of the logical fallacy argumentum ad populum. Of course, the important question to ask is WHY do so many people believe an untested treatment is working? One of the possible answers is that it actually IS working. In the absence of controlled trials, there are many other explanations for why a treatment seems to work, when it actually doesn't. This series of posts aims to address those explanations and to highlight how anecdotal evidence is no replacement for controlled scientific study. The first of these explanations is one that most people have heard of: The placebo effect.

The placebo effect describes a situation when healing effects are observed from taking an inert compound (eg. a sugar pill, saline injection, etc.) The effect is based on the subject's expectation that a treatment will work. In this mind-over-matter scenario, the belief that a product will work leads to an alleviation of symptoms. Studies have shown that up to 30% of people respond positively to placebo, though the effects are temporary and fail to get at the root of the problem requiring treatment in the first place.

There is some debate about how the placebo effect works. Some argue that it's purely psychological, while others say that there is an actual physical effect - particularly in the context of pain relief, where there is data suggesting release of endorphins after placebo administration.

In terms of quackery, this is one reason for positive testimonials. The expectation of results causes the subject to feel better, hence the positive claim. However, with time, symptoms can return and conditions can worsen because the underlying problems aren't being addressed. Evidence-based medicines rely on placebo controls to separate the effects of an active treatment from the act of being treated.

Quirks and Quarks has a show about the placebo effect available here.


Tuesday, February 05, 2008

The Gospel According to Darwin

Lest our minds become preoccupied with the tribulations of the laboratory, and should our consciousness perchance stray from the great path of wisdom that hast been lain out afore us by the prophet Darwin, let us reflect upon this week's reading from the Scriptures of biology:

"To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree. When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science. Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated; but I may remark that, as some of the lowest organisms, in which nerves cannot be detected, are capable of perceiving light, it does not seem impossible that certain sensitive elements in their sarcode should become aggregated and developed into nerves, endowed with this special sensibility."

A Reading from the Book of Darwin.

- Charles Darwin,
The Origin of Species. Chapter VI - Difficulties of the Theory. Organs of extreme Perfection and Complication.


Blue Flamers- Are you a methanogen?

I was ASTOUNDED to hear on this weeks Quirks and Quarks that only 30-50% of humans in the western world are methanogens ie methane producing. More precisely only 30-50% of humans have methanogens in their gut flora and have farts that contain methane. Gut flora refers to the microbes that exist in your lower digestive tract previously discussed on the bayblab of course. These methanogens aren't bacteria they are archaea.
From an old nature review "Faecal Matters":
Accumulation of H2 in the colon lowers the efficiency of microbial fermentation, while removal of H2 enhances microbial growth. There are three main groups of microorganisms that are responsible for H2 removal in the human gut — sulphate-reducing bacteria, acetogenic bacteria and archaeal methanogens. Around 30–50% of people in the Western world are methanogenic yet the human gut is thought to host just two species of methanogenic Archaea, Methanobrevibacter smithii and Methanosphaera stadtmanae.
Methane is the flamable stuff in farts that some dare devils have lit on fire using a lighter at just the right place and the right time. If you are unaware of the science of farts I highly recommend "Facts on Farts".
So unfortunately since only 30-50% of people of the western world have methanogenic archaea only these people can light their farts. This is really ashame as I'm sure there is no experience quite like it. (Caution: Facts on Farts warns of the dangers of 'lighting wind'). This calls for probiotics.


Monday, February 04, 2008

Retro Science Vid: The Path of A Red Blood Cell

Cgi has only been around for a few years and already I find it amazing that it was possible to make this video back in the day. Who would've thought you could do cool things without computers?


Eradication of Infectious Disease

Normally, the extinction of a species is met with anger and sadness. Understandably, this was not the case when the eradication of smallpox (Variola minor and Variola major) was certified by the World Health Organization (WHO) in 1979 after a global effort to wipe it out. This was a major achievement in public health. Since then, while control or elimination from specific areas has been established for some diseases, no other infectious agent has been wiped off the map. (In fact, smallpox only has 'eradicated' but not 'extinct' status as it still exists in the laboratory)

The Centre for Disease Control website provides the following definitions for infectious disease status:

  • "Control: The reduction of disease incidence, prevalence, morbidity or mortality to a locally acceptable level as a result of deliberate efforts; continued intervention measures are required to maintain the reduction. Example: diarrhoeal diseases.

  • Elimination of disease: Reduction to zero of the incidence of a specified disease in a defined geographical area as a result of deliberate efforts; continued intervention measures are required. Example: neonatal tetanus.

  • Elimination of infections: Reduction to zero of the incidence of infection caused by a specific agent in a defined geographical area as a result of deliberate efforts; continued measures to prevent re-establishment of transmission are required. Example: measles, poliomyelitis.

  • Eradication: Permanent reduction to zero of the worldwide incidence of infection caused by a specific agent as a result of deliberate efforts; intervention measures are no longer needed. Example: smallpox.

  • Extinction: The specific infectious agent no longer exists in nature or in the laboratory. Example: none."

So why has no other infectious disease managed to reach 'eradication' status? It's not for lack of trying. At roughly the same time that smallpox was being stamped out, a global malaria eradication effort was also underway. In the US, malaria was considered eradicated in 1951, and in 1955 the WHO proposed a plan for a worldwide effort that included anti-malarial drugs, and widespread pesticide use. Success varied wildly - the program never even made it to sub-Saharan Africa - and eventually malaria re-emerged in certain areas. The goal soon shifted from one of eradication to one of control.

Leprosy is another disease targeted for elimination. Like smallpox, the only source of infection is other humans and there is an established multi-drug treatment to prevent transmission making it a good candidate for eradication. However, the long latency period and an inability to diagnose and treat subclinical leprosy make elimination of the disease a more reasonable target.

One disease that is seeing a strong push for eradication is polio. Vaccination programs have eliminated infections in most of the world, and in February 2006 polio was endemic in only 4 countries worldwide: Nigeria, India, Pakistan and Afghanistan (Egypt and Niger were removed from the list in 2006 after 12 months without a new case). From the beginning of the eradication program in 1998 to 2004, the number of reported cases worldwide was reduced from 350 000 to 1189. All signs point to polio being the next infectious disease to be eradicated, though vaccinations and vigilence still need to persist as evidenced by imported cases being reported in countries sugh as Nepal, Angola or Ethiopia.

The success of an eradication program depends on a number of factors. From the disease side, there needs to be a reliable treatment to stop transmission. A vaccine, a drug treatment - something that prevents the spread of an infectious agent. It's also important that humans be essential for the life-cycle of the agent. For example, malaria is difficult to eradicate in part because it's carried by mosquitoes which act a reservoir - a pool that is much more difficult to deal with. Emergence of drug resistance is another barrier to effective elimination. The reemergence of malaria during the eradication efforts was caused, among other factors, by development of resistance to drugs by the parasite and resistance to insecticides by mosquitoes.

There are also social and economic factors at play. The eradication of a disease requires a firm commitment from governments and communities, since lapses can lead to reemergence. At the community level, this means awareness of programs and diligence in vaccination. Anti-vaccination movements are a barrier to eradication programs. Polio may be unlikely to reemerge in North America, but future diseases may require vaccination to be stamped out. (This also highlights that the disease needs to be of importance to the public, with broad appeal - an elimination of HIV would gain more support than, say, Rocky Mountain Spotted Fever.) At the government level, it requires broad co-operation with other countries, a tenable strategy and a financial commitment. This last point is key as developing nations may not have the resources required (or have eradication prioritized in the face of other problems) to invest in vaccination programs. And it is an investment: "A total of $32 million was spent by the United States over a 10-year period in the global campaign to eradicate smallpox. The entire $32 million has been recouped every 2 months since 1971 by saving the costs of the smallpox vaccine, administration, medical care, quarantine and other costs." In the case of polio, an estimated more than $230 million will be saved in vaccine production and administration in the US each year once eradication is achieved, which seems like it's just a matter of time. After polio, what's next? Eradication programs are also underway for other infectious or parasitic diseases such as guinea worm disease, Chagas' disease and lymphatic filariasis. Will they be successful?


Saturday, February 02, 2008

Cool new anti-retroviral

KP1461 is a nucleoside analog which vastly increases the mutation rate of HIV by incorporating into its genome. But really it's the video I dig...

"KP-1212 can replace cytidine when the viral enzyme reverse transcriptase is building a new copy of HIV, and pair normally with guanosine. It does not terminate the DNA chain. But KP-1212 was chemically designed to be a flexible molecule, such that it can also look like thymidine and then pair with adenosine. This introduces an error that then is locked into the viral DNA.

These errors happen at random, anywhere in the virus; and when they do not kill the virus outright, they accumulate over generations in the DNA of the viral population. The result is eventually an error catastrophe that can wipe out the entire quasispecies, at least in laboratory tests. If you then take the drug away, the virus does not come back. And the cells on which the virus grew are still alive -- cured of the infection.

AZT and the other approved nucleoside analogs terminate the growth of the DNA chain, killing the copy of virus being built. But that copy is easily replaced by other copies that do not have an abnormal error accumulation, so the population as a whole is not damaged. In contrast, KP-1212 continues to add new errors to the population, in addition to the errors that are already there due to the very high normal mutation rate of HIV."


Friday, February 01, 2008

Bayblab Podcast Episode 15

The new podcast is out. It's a staggering 1h long. Perhaps we should try doing more frequent but shorter podcasts. Any "fans" have suggestions Ben? Subject matter include: cloned meat, natural chemotherapeutics, stem cell transplant and amateur scientists. And don't miss Rob's plan to invade Australia, and why he thinks graduate students shouldn't become PIs.


Cancer research carnival #6

Welcome to the sixth edition of the Cancer Research Carnival! This edition Is packed with information about cancer biology, treatment and survivor stories. For information about upcoming editions and instructions on how to submit articles please visit this link. Enjoy!

Cancer biology

One of the more unfortunate developments in the field of cancer research last month was the death of Dr. Judah Folkman. Dr Folkman was a pioneer in cancer research, and changed our understanding of how cancer tissue growth is dependent on blood vessel growth. He also did much much more in the field of medecine. As such, he will be remembered as a role model for many physicians and scientist including Ben Ferguson who writes on his weblog:
" For instance, in the course of his life’s work, he invented a new technique for repairing patent ducti arteriosi and presented it to the American College of Surgeons while a freshman medical student; made significant contributions to the development of the implantable cardiac pacemaker; happened upon the concept of slow-release drugs; became the first-ever instructor of surgery to be promoted directly to professor of surgery and the youngest-ever professor of surgery in the history of Harvard, having been appointed surgeon-in-chief of Children’s Hospital in Boston at the age of 34"

Dr David, a pediatric oncologist explores the virus/cancer connection in a post about karposi sarcoma. You may be familiar with this rare type of cancer which often manifest itself as skin lesions and oral sores in AIDS patients. What you may be less aware of are the endemic forms which affect men in certain areas of the world and are often fatal. Dr. David discusses the role of the HHV-8 virus in karposi sarcoma but also draws parallels with other viruses which can cause cancer, follow the link to learn how:
"How do viruses cause cancer? Well, EBV and HHV-8 are both thought to cause cancer by controlling the activity of genes already present in cells called proto-oncogenes. A few years ago, a group of scientists in Spain proposed another way viruses might cause cancer."


Highlight in Health brings us a list of the top6 most important advances in cancer treatment in 2007. The list includes MRI screening for breast cancer, The link between HRT and breast (and ovarian!) cancer, The clinical trial of sorenafib for liver cancer, the trials of bevacizumab and interferon for kidney cancer, the link between HPV and head and neck cancer and finally the use of preventative radiation of the brain for cases of advanced lung cancer. To learn more about these discoveries follow the link.

Our very own Kamel does an expose of plant-derived chemotherapeutic agents, showing how natural doesn't necessarily mean fewer side effects and reinforcing the point that once herbal remedies are tested and shown to work they become part of standard, evidence-based medicine. Why settle for anything else? from the post:
"A lot of the push for 'alternative medicine' is based on a fear of traditional medicine - that is, man-made chemical treatment. Personally, I think these fears are largely unfounded and ignore the history of many pharmaceuticals in use. Here are some natural products currently in use in the cancer clinic. Someone preaching natural cures over tested medicine probably doesn't know what they're talking about."

Cancer Survivors

We have two stories this time. The first one comes from Katie who talks about the importance of understanding your diagnosis of mesothelioma and to take charge. She also wants to make sure you spell it correctly. The second one is from Andrew who talks about some of the more uncomfortable side effects of his antibody treatment.


We warned last time that we will not display links to websites promoting dubious alternative treatments for commercial interests. We got a submission from Hueina Su a wellness consultant, motivational speaker, and "certified empowerment coach". She and other members of the multi-level marketing scheme company sell essential oils and Goji berry juice. To learn more about this type of quackery you can revisit one of our previous post on the matter.


The devil's multifocal lenses

I personally find goat eyes disturbing with their horizontal pupils it reminds me of the devil. Crocodiles and cats for example have vertically shaped pupils that also make them look evil. Why? Not why are they evil, but why the non-circular pupils? Despite being evil humans have circular pupils so they must be the best.
It turns out that these pupils evolved to make use of a multifocal lens. Basically the lens of the eye in these animals has different refractive indexes at different distances from the center. This has evolved to enable sharper images focused on the retina. Because different wavelengths of light will be refracted differently the lens has different refractive indexes to focus different colours in the appropriate place on the retina. So to take advantage of this system in bright light the animals still need the outer section of the lens for whatever colour that section focuses. Okay so my explanation and understanding aren't perfect so here is a pretty good article on the subject of multifocal lenses and pupil shape if you want to get a better idea.
But why horizontal and vertical shaped pupils? The only source I was able to find was a forum post that cited some work from 1907, that apparently showed that the ability of humans to distinguish discrete points with and without an artificial slit-form pupil was increased with a slit-form pupil perpendicular to the plane in which the objects were located.
So predators like cats and crocs who hunt on the horizontal plane have acquired vertically shaped pupils. While goats and sheep who navigate some steep mountainous terrain need horizonally shpaed pupils. (I guess?)


Chocolate orchids

There are people who are obcessed about growing orchids, and not all of them are gardeners, some are pediatricians. That's because orchid in greek means testicles (hint: look at the roots). For example crypto-orchidism, is not a closet orchid grower, it's an undescended testis. Pediatricians use an orchidometer, sort of a beads on a string instrument, to track the growth of testes during puberty. Those instruments cost about 50$, and a group of inventive pediatricians have found a practical and much cheaper alternative to do the job: a chocolate egg called Teaser. This appeared in a paper in BMJ :

Five paediatricians (three male, two female) were blindfolded and given, in random order, a Teaser or an 8 ml orchidometer bead in a Teaser wrapper and asked to size the other beads as larger or smaller than the reference. (Real testicles were not used because the image of the medical profession is already bad enough.)


Participants were 100% accurate in sizing the beads against both the Teaser and the reference. The ability to rescue staff weakened by hunger at the end of a long clinic is an important bonus for any item of medical equipment.

The low cost of our alternative orchidometer (6p (10¢)) must endear itself to healthcare systems that are strapped for cash. Finally, we reject any allegation that this paper is another gratuitous attempt by dogs to get themselves on to Medline. 4 5 We do, however, acknowledge that this research was basically a load of balls.

However, perhaps because of the unwanted publicity, the manufacturer tragically changed the shape of their chocolates:

" This is a major setback for paediatric endocrinology, and the manufacturer’s decision to change the sweets’ morphology without consulting the medical profession is a further kick in the Teasers. Despite conveying our concerns to the manufacturer, we have received no clear explanation, nor any reassurance that this issue is being taken seriously. We appreciate that marketing chocolates is a matter of great commercial sensitivity and hope that we have not inadvertently hit a delicate spot by drawing attention to the fact that these sweets looked and felt like testes. Our paper made it absolutely clear that both Teasers and Truffles tasted better than wooden orchidometer beads1 and, we speculate, better than testes"