Monday, July 30, 2007

Duesberg's new hypothesis

As late as 2003 Peter Duesberg, discoverer of the src oncogene, has disputed that the HIV virus is the causal agent of AIDS, the "Duesberg hypothesis" apparently it is caused by drug use and other non-contagious factors. Propagation of this hypothesis, assuming it is incorrect, arguably costs lives. A good blog that debates this hypothesis is He was in some good company with this hypothesis, which includes Kary Mullis, the surfing inventor of the polymerase chain reaction.
From a forward by Kary Mullis: (I think there is a whole chapter on this in his book "Dancing naked in the mine field.)
"So I turned to the virologist at the next desk, a reliable and competent fellow, and asked him for the reference. He said I didn't need one. I disagreed. While it's true that certain scientific discov eries or techniques are so well established that their sources are no longer referenced in the contemporary literature, that didn't seem to be the case with the HIV/AIDS connection. It was totally remarkable to me that the individual who had discovered the cause of a deadly and as-yet-uncured disease would not be con tinually referenced in the scientific papers until that disease was cured and forgotten. But as I would soon learn, the name of that individual - who would surely be Nobel material - was on the tip of no one's tongue."
Kenny G (not the saxophonist but a knowledgeable lab rat), informed me that Duesberg is now debunking the idea that mutations initiate cancer. Instead he proposes aneuploidy is the cause.
"Conventional genetic theories have failed to explain why cancer (1) is not found in newborns and thus not heritable; (2) develops only years to decades after 'initiation' by carcinogens; (3) is caused by non-mutagenic carcinogens; (4) is chromosomally and phenotypically 'unstable'; (5) carries cancer-specific aneuploidies; (6) evolves polygenic phenotypes; (7) nonselective phenotypes such as multidrug resistance, metastasis or affinity for non-native sites and 'immortality' that is not necessary for tumorigenesis; (8) contains no carcinogenic mutations."
I actually don't know enough to properly analyze the credibility of this hypothesis, but the history of the scientist immediately makes me skeptical. Is he just good at cherry-picking the literature or is he on to something?
It's good to have people criticize the science, and at least this time he's not potentially costing lives. I wonder why or if he's stopped focusing on the HIV/AIDS issue?


Friday, July 27, 2007

Reprogramming Mammalian Cell Motility

Wendell Lim's lab continues to lead the way in engineering synthetic cell-signaling pathways (not to mention lab website design). This time it's a Nature paper showing how modular protein-protein interaction domains can be swapped onto Rho guanine nucleotide exchange proteins to rewire morphological signaling pathways to respond to novel inputs.


X-Linked FoxP3 Gene a Tumor Suppressor in Breast Cancer

Interesting new twist on the biology of the FoxP3 gene, a forkhead-family transcription factor you may know as the master switch that defines the T-reg (suppressor T cell) blood cell lineage. Female mice carrying a single copy of the scurfin mutation in FoxP3 had a propensity to develop mammary tumors, apparently due to effects on the infamous breast cancer oncogene HER-2/ErbB2. A role in tumorigenesis for FoxP3's effects on Treg activity was ruled out. The report appears in Cell.


Thursday, July 26, 2007

Alternative Biochemistry

"Follow the water" is a common mantra when searching for evidence of extraterrestrial life. After all, you can support life without water, right? But is that necessarily true? Obviously we have a bias towards carbon based life forms since that's what we know, but what about silicon-based? Or an ammonia solvent? The wikipedia entry on the subject of alternative biochemistry is quite expansive on the subject explaining, for example, why silicon wouldn't work. Of course, many of the arguments are still based on certain assumptions built upon how we know life on earth operates, but it's still an interesting read.


Wednesday, July 25, 2007

IA updates

I hate to start burying some superb posts, however, there are some updates on As usual it is good stuff. Also if you could take the time to email the webmaster there and just let that person know that you read Informationaddiction (if indeed you do). The webmaster is apparently considering quiting the blog. IA was one of the very first blogs I ever read and, while updated infrequently, still has some of the choicest links around.


Tuesday, July 24, 2007

Henry Ford and the Soybean Car

Biotechnology is the next big thing right? The newest big idea that will empower humanity with the technology to supply all their wants and needs. Not really (at least the new part).

While skyrocketing oil prices and the sudden media-chicness of "carbon awareness" have led to a recent resurgence of interest and investment in the use microorganisms to convert agricultural harvests into energy and materials, this is certainly not our first crack at developing biotechnology to save the world.

It is surprising, however, just how long these ideas have been around, and how little biotechnology has moved forward since then, given how much new biology has been discovered during the same period (ie the structure and decoding of DNA and all that followed). In fact, if not for the Second World War, seems we may well have been operating under an agro-, rather than oil-based economy for the past 80 years. It's staggering to imagine where science and medicine would be today with the development of such a biological based economy.

Anyhow, back to the 1930s - when interestingly a food surplus rather than today's oil shortage was the main crisis driving interest in developing biotechnology. At the time of course, farm-based North American economies were being ravaged by agricultural surpluses and prices so low that harvests couldn't be burned quickly enough to get them back up. US Republican Party research revealed that agriculture could not be sustained "unless farm commodities are developed as raw materials for the manufacturing industry" (ie to increase demand and crop value). Smelling opportunity, Dow Chemicals research director William Hale envisioned the development of a "Chemurgy" industry that would convert farm surpluses to chemical products. In particular, he suggested that alcohol, a substitute for gasoline fuel, could be produced from fermented starches (which he cleverly referred to as 'agricrude'). Nice idea, but at the time, a vast supply of domestic North American oil provided little economic incentive for the development of alternative fuel technologies. We may be getting close - 70 years or so later - now as we finally approach the point at which it seems the cost/benefit of extracting oil might be high enough to motivate the energy sector to seriously invest in alternatives - maybe.

So while chemurgy seems to have been a non-starter for fuel production in the world of the late 30s, the blossoming auto industry was struggling with increasing metal costs, and Henry Ford looked to chemurgy for new materials. Sponsoring chemurgy research and meetings, Ford then decided to build a prototype plastic-bodied car made from soybean source. The Henry Ford Museum cites 3 reasons for his decision to undertake the project:

1.) He was looking for a project that would combine the fruits of industry with agriculture.
2.) He also claimed that the plastic panels made the car safer than traditional steel cars; and that the car could even roll over without being crushed.
3.) Another reason was due to a shortage of metal at the time. Henry hoped his new plastic material might replace the traditional metals used in cars.

Although it seems to have since disappeared (maybe found its way into some veggie burgers?), the car was amazingly built (the work of E.T. (Bob) Gregorie, Lowell E. Overly, and Robert A. Boyer) and unveiled in 1941. As shown in one of the pictures, Henry Ford liked to publicly demonstrate the strength of the soybean plastic car was by taking an axe to it.

Sadly, the project was a casualty of WWII, when automobiles were replaced by tanks, which understandably demanded a little more robustness than soybeans could offer. Since the war the automotive industry has found other ways to satisfy its materials needs, and hence, still no soybeans on the road to this day.
Note - I discovered this great story (and many, many others) in a book I picked up in a recent trip to Cambridge, The Uses of Life: A History of Biotechnology by Robert Bud. A truly mind-boggling and comprehensive account of international experimentation with biotech- I highly recommend it and its better than anything in Oprah's book club.


"Viruses" Rule the World: Dan Dennett on Memes, Consciousness and Religion

This mind-bending lecture from Tufts University philosopher/cognitive scientist Dan Dennett is a must-listen if you haven't already. Kicking it off with the genetic analogy of parasite-driven ant suicide, Dennett picks up where Dawkins left off with The Selfish Gene, expanding on the meme ("idea-gene") concept to demonstrate how Darwinian principles can help us to understand the spread and impact of culture and ideas. In particular, he uses this approach to ask why many people are willing to sacrifice their own life for certain ideas. This leads to a discussion of the religion virus, and it's interesting that he takes quite a different position on the issue than the extremist one currently favored by Dawkins himself. Also manages to get in some important points on the illusion of human consciousness. It's 20 minutes well worth it, I promise you. See his other TED talks for more detailed treatments of religion and consciousness.

PS - You don't have to take my word for it - look at that classic beard and decide for yourself whether the man isn't a wizard-scholar of the highest order...


Seven Scientist-Guinea Pigs

In 2003, impatient for the approval of clinical trials, virologist Pradeep Seth injected himself with an experimental HIV vaccine. He was not the first, and certainly won't be the last, scientist to use himself as a human guinea pig. Obviously not everybody's research lends itself to such dramatic experimentation, but we all make sacrifices in our own way. Here are 7 scientists whose self-experimentation put their health at risk for better understanding of our own.

John Hunter - In the days before controlled clinical trials, many medical researchers used themselves as guinea pigs. Born in Scotland in 1728, John Hunter was a brilliant surgeon. He wrote two books on teeth, and is credited with naming the cuspids, bicuspids, incisors and molars. Upon damaging his Achilles tendon, he used dogs to show how bones and tendons mend. But his interests weren't limited to teeth and bones, and his wild experimentation wasn't limited to cutting the tendons of dogs to analyze the healing process. In writing his Treatise on Venereal Disease, Hunter inoculated himself with gonorrhea to study the course of the disease and response to treatments with mercury and cauterization. His studies added greatly to the understanding of the role of inflammation in healing. Unfortunately, sterile technique wasn't the practice of the day and the needle used to infect himself was also contaminated with syphilis. When he contracted both diseases, this was taken as proof that there was, in fact, only one venereal disease - an error that wouldn't be corrected for another half-century.

Lazzaro Spallanzani - While John Hunter was torturing his own genitals with STDs, his contemporary Lazzaro Spallanzani was playing with those of animals. His work described mammalian reproduction, and he was the first to perform an artificial insemination, using a dog as his subject. He also performed experiments testing ideas of spontaneous generation. His great self-experiment was a study of the digestive process, Dissertationi de Fisica Animale e Vegetale, published in the 1780s. These experiments were done using his own gastric acids either collected by induced vomiting, or, more dramatically by swallowing linen containers containing material to be digested. He would let them pass and find the bag intact, but the contents gone. To show it was a chemical and not mechanical action, he repeated these experiments with perforated metal or wooden tubes, allowing the food to be exposed to the stomach contents, but unable to be ground by mechanical action. He expanded the knowledge of digestion, making the disctintion between mechanical and chemical digestion and postulated the involvement of acid in the gastric juice.

Barry Marshall - If Spallanzani taught us about digestion, Barry Marshall taught us about indigestion. As a physician interested in gastritis he, along with Robin Warren, cultured Heliobacter pylori and hypothesized a bacterial cause for gastritis and peptic ulcer, going against the commonly held belief that spicy or acidic foods and stress were responsible for those ailments (as well as the belief that no bacteria could survive in stomach acid). In the face of overwhelming opposition to his ideas and lacking an animal model in which to test them, a healthy Marshall drank a pyloric culture and fell ill, eventually presenting with gastritis as predicted. By his own admission, Marshall was surprised by the severity of infection, never expecting to become as ill as he did. This experiment both demonstrated a bacterial cause for gastritis and peptic ulcers and laid the groundwork for a simple and cost effective treatment - antibiotics. Barry Marshall won the Nobel prize for his work in 2005.

Max Joeseph von Pettenkofer - Consumption of a pathogenic bacteria is a common theme among self-experimenters and 100 years before Barry Marshall gave himself an ulcer, Max Joeseph von Pettenkofer was performing similar experiments. Sometimes considered the father of epidemiology, von Pettenkofer was a strong proponent for hygeine for good health. In an attempt to prove that the bacteria alone would not cause cholera, but rather dependent on 7 factors (including diet and hygeine), he drank a cholera sample isolated from the excrement of a dying patient. Though he had mild symptoms, "light diarrhea with an enormous proliferation of the bacilli in the stools", he did not have a severe reaction and considered himself vindicated.

Jesse Lazear - Not every self-inoculation has such mild consequences. Jesse Lazear was a physician working in Cuba with the US Army Yellow Fever Commission. Faced with evidence of an intermediate host in the spread of yellow fever and familiar with mosquitoes and the transmission of malaria, Lazear wanted to get to the real vector. He began infecting mosquitoes in August 1900, and allowed himself to be bitten, eventually contracting the disease and dying. While he lost his life in this experiment, "his work contributed towards one of the greatest discoveries of the century, the results of which will be of invaluable benefit to mankind." (Dr. L.O. Howard) Currently Yellow Fever is mostly restricted to sub-Saharan Africa and developing countries in South America, and a vaccine against this infection exists.

William Harrington - Some researchers go to even greater lengths to make themselves ill than drinking a culture or being infected by mosquito. This was the case for William Harrington, a haemotologist in St. Louis. Trying to find a basis for idiopathic thromgocytopenic purpura (ITP), a disease resulting in a low platelet count which causes bruising, and bleeding issues, Harrington infused himself with plasma from a patient with ITP and rapidly developed transient thrombocytopenia, with a severe risk of hemmorhaging. His experiment demonstrated that there was a plasma factor responsible for the condition. Harrington's discovery of an autoimmune component has lead to a number of therapies for the disease.

Werner Forssmann - If blood transfusions and toxic cocktails aren't risky enough, then what about self-surgery? Werner Forssmann showed that the way to a man's heart is through the antecubital vein. At the time, the belief was that any entry into the heart would be fatal, but Forssmann inserted a catheter into his arm and threaded it 65 cm into his heart. He then walked to the radiology department, to have it x-rayed to prove his success. Over his lifetime, he would do this several more times, even using the method to inject solutions into the heart. (Forssmann's goal was to use this technique to directly administer drugs) Though he was fired from the hospital for his initial experiments, Forssman was recognized for his work, sharing the 1956 Nobel Prize for Medicine or Physiology.

Obviously there are many others who have risked life and limb through self-experimentation in pursuit of a breakthrough. Right or wrong, some of them have certainly lead to advancements in medical or other fields. How far would you go for your science?


Monday, July 23, 2007

Rats are no laughing matter

Scientists, who apparently study rat tickling have recorded some ultrasonic laughter coming from the critters. Now I'm not debating that the rats enjoy tickling, and may even squeal in delight, but laughter is an entirely different thing in my mind. I was recently listening to an interview with a primatologist who said that the only human emotion that great apes may lack is genuine regret. Your pet may look guilty after it's done something it knows is wrong, but that doesn't mean it regrets it. Similarly a rat may squeal when you tickle it, but that doesn't mean it cracks up when it sees another rat slip. I would argue that real laughter necessitates a sense of humour, which is dependent on abstract thinking, and creating scenarios in your head with things or situations that do not exist, something which seems to be notoriously absent in animals. In fact, it is often the incongruity which triggers the laughter, in a sense, it may be a way for the brain to dismiss what it can't interpret or file away...

Nevertheless the article is a fun read. If you do have rat pets, this is how you tickle them effectively: "Tickling various areas of a rat’s body is remarkably effective in generating maximal levels of this ‘‘laughter’’ response. Just like humans who are more ticklish on certain areas of the body (e.g., ribs), young rats have ‘‘tickle skin’’ concentrated at the nape of the neck where they direct their own play activities. Tickling at the nape of the neck consistently produced more chirping than tickling the posterior dorsal surface of the animal, but full body tickle was most effective of all. "


Friday, July 20, 2007

Stem cells and cancer, forget everything you know

I was pretty happy with the theory of cancer being a trade off for longevity, and now this nature paper comes and changes everything. It used to be simple, we have evolved a system of balances and checkpoints, which prevents stem cells from growing uncontrollably and turning into cancer as a result of induced or spontaneous mutations. This balance creates a condition where the stronger the system is, the more stem cells get purged and longevity is diminished to the benefit of being cancer free. Conversely a balance which tolerates more errors, has the benefit of conferring longer longevity to the detriment of getting cancer. It was so nice and simple. All the experiments so far such as overexpressing p53 agreed with that hypothesis. But now this team in Spain show that if you add an additional copy of p53, within its natural promoter, you get to have your cake and eat it too, longer longevity by 16% while the animal appear more youthfull and have reduced incidence of cancer. It seems the key is to express p53 when it's appropriate... It reminds me how ras expression in some system, depending on whether it's from a strong promoter, or it's endogenous promoter, gives diametrically opposed results, senescence vs transformation...

On a somewhat related topic, a new twist to the old oct4/c-myc/sox2/flf4 induced stem cells is that if you select for nanog, you can get the formation of germ cells. The drawback is that 20% of the offspring develop tumour, most likely because of c-myc. Is the change induced by c-myc permanent? if it was expressed only transiently, could we get around this problem? Somehow I suspect not, but I've recently been obsessed with generation-skipping epigenetic effects carried in the germline (hopefully more on this subject later...).


friday afternoon read

Just a quick link to one of my favorite Isaac Asimov short stories. If you're having a lazy afternoon, it's a brilliant read. It's called "the last question" and it talks about AI, and thermodynamics, and well I wont spoil it, because the end is brilliant...


Checkers decontstructed

Tic-tac-toe is a simple game, and virtually every 6-year old on the planet has mapped out every permutation of moves possible. Played properly, it's impossible to lose - which includes a game playing DNA computer.

Checkers, with a search space of 5x10^20 is a much more complicated game. After 18 years, researchers at the University of Alberta have finally 'solved' the game, proving that, like tic-tac-toe, when perfectly played always ends in a draw. This makes checkers, 1 million times more complicated than Connect Four (the previous title holder), the most complicated game to have all its maneuvers mapped out.


Thursday, July 19, 2007

The journal of irreproducible results

I want to further plug this journal, since in my mind it may be even funnier than the annals of improbable research. Virologist Alexander Kohn and physicist Harry J. Lipkin founded The Journal of Irreproducible Results in 1955 in Ness Ziona, Israel.

Anyone can submit their irreproducible results, provided they have a sense of humour:
"IR articles should be humorous. Appeal to scientists, doctors, and engineers. Make your points in good humor. Make readers feel good about having read them. Minimize bitter aftertaste. The rule for length is simple: write it for what it's worth. Include everything that ought to be there, and then stop. Don't leave out anything that helps the article, but don't pad, either. Parts of articles that deal with real science should be valid both in technicalities and in sense of proportion. 70% of JIR readers have doctorates - they can spot problems. "

This philosophy has gotten the journal some critical acclaim:
"I recommend a regular dose of the Journal of Irreproducible Results, the funniest magazine I know." - Toronto Globe And Mail
"The Journal of Irreproducible Results is the funniest thing to happen to science since Archimedes ran naked through the streets of Syracuse."- Discover
"The Journal of Irreproducible Results is our favorite magazine."- New Scientist "

And for good reason. Some of my favorite papers (or graph above) include the effect of national geographic on landmass depression in america. The authors estimate that around 7 million copies are printed annually, and the journal has been around for 141 years, with each copy weighing 2lb and not likely to be discarded by the subscriber. Hence some simple maths tells you that :

"Taking the predictions of Kaub (1974) at face value, the height of a column of National Geographic magazines necessary to depress the continental land mass by 100 feet (30.48 m) was calculated. This would be a vertical stack 82.33 m high, equivalent to 11.45 x 103 magazines. This depression of the land mass would produce a rise in sea level due to displaced mantle material. Assuming the effect is confined only to the ocean basins, a net depression of 100 feet (30.48 m) would be due to an actual depression of the land of 29.82 m and a resultant rise in sea level of 66 cm."


Cockapoos threatening kakapos

The bayblab podcast epi #10 featured some discussion on strange animals. It reminded me of the strangest animal I've ever heard of, The Kakapo. It's a nocturnal ground burrowing flightless parrot found in New Zealand. The introduction of feral cats and dogs threaten it's existence as it is critically endangered. Hopefully this podcast on the kakapo works for you but I refuse to have Quicktime 7 on my laptop.


Wednesday, July 18, 2007

A Myriad of Genetic Fascism

We've talked about the potential evils of biotech patents on the Bayblab in the past, but I must confess I've been ignorant about just how far companies will go in their attempts to abuse the patent system. Based on genetic research it conducted on genetically isolated Mormon families in Utah, Myriad Genetics obtained patents for genetic testing of breast cancer susceptibility genes in 2000-2001. The Cancer Cancer Society describes how Myriad is attempting to abuse its patent rights:

"In July 2001 Myriad issued a cease and desist notice in Canada instructing provincial governments to stop using any test other than BRCAnalysis to detect genetic abnormalities on the BRCA1 and 2 genes. Myriad’s patents give the company the exclusive right to perform diagnostic testing for BRCA 1 and 2 abnormalities. The patents have enabled Myriad to demand that all patient samples be sent to the company’s headquarters in Utah for analysis, which increases the cost associated with the test tremendously. The response of provinces to Myriad’s order has varied. The provinces that continue using tests other than BRCAnalysis risk facing legal action by Myriad."

Excuse me? A patent gives you the right to bar others from extracting revenues using the technology or method in question (ie a genetic test). It is obviously not a title deed granting the holder ownership of a piece of every human being's genome in every country where the patent is held. I think it's pretty obvious that individuals should have the right to use any means they choose to learn about their own genome.

Hopefully Canadian governments will follow through with the Canadian Cancer Society's demands and limit this ridiculous attempt by Myriad to commandeer the Canadian Patent System and plunder Canadian genomes. Maybe we also need to add explicit protection of personal genetic information to the Canadian Charter of Rights and Freedoms.


It's not the stretching stupid!

Here is an alternative hypothesis on injury in sports, it's not a lack of streching but a lack of brains. At least that's what this study on "The relationship between neurocognitive function and noncontact anterior cruciate ligament injuries." seems to imply...

I guess the smarter you are, the more likely you can react fast and make good decisions to avoid injury. The group which suffered ACL injuries had significantly slower reaction time, processing speed, visual memory and verbal memory. The sport most likely to result in non-contact (ie, your own fault) ACL injuries was woman's soccer....


Chess on Rollercoasters

Totally ganked from boingboing. Yes it's photos of people playing chess on rollercoasters. Brilliant. Maybe rollercoasters are dangerous but they are a great venue for chess matches.


Gender gap in scientific publications

A surprising study in American sociological review has shown that over a two year period, man produced on average 33% more papers than woman. Over the length of the career that translated into almost double the number of papers. why should that be? An obvious factor is family life. Woman have more commitments when it comes to child rearing. However, in an interesting twist, the number of children a woman has had is a good predictor of her productivity. Perhaps it is a way to learn how to be efficient at multitasking, or perhaps taking care of hungry miserable dirty children is a lot like taking care of graduate students.

The authors go as far as saying "there are relatively more men with exceptional scientific ability than women" because men according to him have a wider skillset (i.e. thinkering, programming etc...). However, when it comes to quality of the publications, women get 20% more citations when compared to men with an equal number of publication. Woman also have a harder time getting started, possibly because of discrimination, and they particularly lag at the beginning of their careers.


Tuesday, July 17, 2007

The alien hand syndrome

We've had a lengthy discussion of consciousness recently, where I introduced the concept of the illusion of free will. For example it was shown by brain scans that the motor command to do something like grab an apple, precedes the actual conscious decision to grab it. Your brain then works its magic by either canceling that command in time, or if you do wish to grab the apple, make it seem seamless and purposeful. From the authors:

"a fully voluntary act is initiated unconsciously (non-consciously). That condition was in fact demonstrated experimentally by us (Libet et al. 1983) when we found that cerebral neural activity ("readiness potential") precedes the subject's awareness of his/her intention or wish to act by at least 350 msec. This applied to fully self-initiated acts that occurred without "pre-planning" by the subject of when to move. (Incidentally, those finding have been replicated by others--see Keller and Heckhansen, 1990 with commentary thereon by Libet 1992, and Wong et al. 1988)."

Case in point is the alien hand syndrome. This bizarre condition uncouples the motor planning area from the free will illusion decision making area of your brain and can lead to disturbing behavior from one of your hands, as if it were "processed":

"In one patient it was also seen as conflict with both feet (e.g. when putting on slippers) or as conflict of intentions (e.g. when planning to enter a room). The other form consisted of massive groping and grasping behaviour as the most dominant features, such as a "tug of war between hands" and was seen in five patients. Avoidance behaviour included sitting on the affected arm, holding it under the table, or keeping objects out of reach. "

Interestingly this uncoupling, often results from lesions in the corpus callosum, dominant medial frontal cortex, and posterior cortical/subcortical areas. A team in switzerland recently discovered the cause of this disorder and liken it to delusion in schizophrenia (soon to appear in the annals of neurology) . This disconnect may be similar to the involuntary uncoupling which occurs in other situations such as speaking in tongues or Ouija boards, but on a smaller scale:

"The experience of conscious will is the feeling that we are doing things. This feeling occurs for many things we do, conveying to us again and again the sense that we consciously cause our actions. But the feeling may not be a true reading of what is happening in our minds, brains, and bodies as our actions are produced. The feeling of conscious will can be fooled. This happens in clinical disorders such as alien hand syndrome, dissociative identity disorder, and schizophrenic auditory hallucinations. And in people without disorders, phenomena such as hypnosis, automatic writing, Ouija board spelling, water dowsing, facilitated communication, speaking in tongues, spirit possession, and trance channeling also illustrate anomalies of will--cases when actions occur without will or will occurs without action. This book brings these cases together with research evidence from laboratories in psychology to explore a theory of apparent mental causation. According to this theory, when a thought appears in consciousness just prior to an action, is consistent with the action, and appears exclusive of salient alternative causes of the action, we experience conscious will and ascribe authorship to ourselves for the action. Experiences of conscious will thus arise from processes whereby the mind interprets itself--not from processes whereby mind creates action. Conscious will, in this view, is an indication that we think we have caused an action, not a revelation of the causal sequence by which the action was produced."

So while the axiom "I think therefore I am" may be true, "I act, therefore I think" might not. Just another nail in the coffin of free will.


The Economics of Parking

Next time you're cruising around the block for 15 minutes looking for a free parking spot there are some numbers to think about. Over the course of a year, this type of parking search results in innumerable excess miles driven (one group puts the number at around 950 000 for a 15-block business district) and all the associated pollution and greenhouse gases. In large cities, this is also a major cause of gridlock with up to 45% of drivers claiming they were just looking for a parking spot. The solution? According to Canadian-born William Vickrey, winner of the 1996 Nobel Prize in economics: increase the cost of curbside parking. By increasing the cost of street parking to market value on par with off-street parking lots, policy makers can fix prices such that they ensure an 85/15 ratio -- "85% occupancy means that the curb spaces will be well used and 15% vacancy means that they will be readily available," says Douglas Shoup, professor of urban planning at UCLA. Of course most drivers would balk at the idea of more expensive curbside parking, but in cities where this kind of idea is being considered and implemented the increased revenues are put directly back into the metered communities.


All theories proven in one graph

Found on JIR.


Stretching Myths

In the Ottawa Metro today there is a full page article on summer sports injuries with a large photo of a woman stretching. A Dr. Douglas Stoddard, a sports therapist, has a large quote in the article stating "the biggest reason people get injured is flexibility or loss of it." I have heard lots of conflicting information about stretching before exercise and it's benefits on injury prevention. A quick search on Pubmed however reveals that there is little doubt that stretching before exercise has no impact on the frequency of injury. A sample of articles: 1, 2 and 3. It is no wonder how myths like this are so prevalent considering the article in the metro quoting an authority on sports injuries. This also gives me a great excuse to maintain my inflexible figure, and is probably a great geeky pick-up line next time you see someone stretching.
However, the stretching institute begs to differ.
Of course there are other reasons for maintaining physical flexibility.


Monday, July 16, 2007

8 facts of the Bayblab

It looks like we've been tagged by Lim from Freshbrainz, with this relatively benign meme which has been spreading in the blogosphere. Now I hate chain letters and by now, my house should have burned, I should have lost all my money and friends, and gotten the plague. Thankfully, all I got was the plague. However, I think it is a great opportunity to make fun of my fellow bloggers .

Here are the rules:

1. We have to post these rules before we give you the facts.
2. Players start with eight random facts/habits about themselves.
3. People who are tagged need to write their own blog about their eight things and post these rules.
4. At the end of your blog, you need to choose eight people to get tagged and list their names.
5. Don't forget to leave them a comment telling them they're tagged, and to read your blog.

And here are your facts.

1) The origin of the name bayblab is shrouded in mystery. Historians think it comes from the fact that the ancient scientists used to work in an open concept lab, organized in bays. One of these bays had mystical music, and thus became the gathering spot where science ideas were exchanged, or "blabbed" about. However etymologist point out that the root of the word may be based on "Bayb", referring to the female scientists working in the lab.

2) Kamel is afraid of getting stuck in the revolving doors at the hospital, and avoids them at all cost.

3) Rob is obsessed with unicorns, and has a "my little pony" on his bench that he plans on converting into a unicorn. He hopes one day to ride one, all the way to the north pole.

4) Bayman comes from a family of pirates. Rumours are, he has a treasure buried back in Newfoundland.

5)Kamel is an aspiring artist. He's the sixth village people, and an actor, where he's played such critically acclaimed roles as a new-yorker drinking coffee that looks like john Lennon and Jesus.

6)Rob has a secret identity as CrownRoyal-Hero Rob, the sidekick of Stone-Hero Steve. This intoxicated duo rescues people in danger, while in full redneck fishing gear (including fishing hat, fishing vest, waders and John Deer boxers).

7)Kamel is actually the author of wikipedia. Which comes in handy when doing crossword puzzles or trivia games.

8) Bayman is a mad scientist, and has plans to build a secret lair where he will study, and perfect the ultimate miniature "trojan" horse to take over the world, and the ultimate sandwich, whichever comes first...

Well that's it. I will only tag Dr. B, and Ben, since we're all curious what their special abilities/alternate identities are...


Friday, July 13, 2007

Do fish get 'the bends'?

One of the dangers of SCUBA diving is the bends, or decompression sickness, which results from gases (usually nitrogen, but potentially helium or hydrogen) come out of solution and form bubbles upon rapid shift from high to low pressure. These bubbles can cause excruciating pain in the joints (this is where the name 'the bends' comes from) as well as itchiness, shortness of breath and neurological problems.

But what about that delicious PEI lobster stolen from the depths and put on a plane to get to your dinner plate? While most tales of exploding seafood are anecdotal, a small number of studies have shown that fish and other marine life can also suffer from the bends. Biological specimens from the deep ocean have to be brought up slowly (like a diver) or kept pressurized or the drastic change could cause internal bleeding or burst swim bladder. Even catch and release fishermen should be warned. In small-mouth bass, removal from a depth as shallow as 5 metres has caused gas bubble formation and signs of tissue damage, and the survivability of these fish after 'the bends' isn't known. (Dr. Tufts of Queens University and author of the study predicts they'll swim back to the right depth and be fine). And if you're not releasing, but eating instead the stress may affect the taste.


Thursday, July 12, 2007

Science classrooms are for science


Wednesday, July 11, 2007

More moles means longer life?

According to the American Academy of Dermatology "the majority of moles show up during the first two decades of a person’s life while about one in every 100 babies are born with moles." This means that in fact as you age you get fewer moles not more as one would have guessed.

Moles are usually associated with UV exposure and cancer risk: "A basic reference chart used for consumers to spot suspicious moles is found in the mnemonic, A-B-C-D. The letters stand for Asymmetry, Border, Color and Diameter. Sometimes, the letter E (for Evolving) is added. According to the American Academy of Dermatology, if a mole starts changing in size, color, shape or, especially, if the border of a mole develops ragged edges or becomes larger than a pencil eraser, it would be an appropriate time to consult with a physician. Other warning signs include a mole -- even if smaller than a pencil eraser -- that is different than the others and begins to crust over, bleed, itch, or becomes inflamed. "

However a new study involving twins in AACR's
Cancer Epidemiology Biomarkers and Prevention journal, shows that more moles later in life means longer life expectancy: "In the study, researchers found those with more than 100 moles had longer telomeres than those with fewer than 25.The difference between the two mole groups was equivalent to six to seven years of ageing. " . After checking out some pictures of Aubrey De Grey I don't see any moles on his face!


Are your bugs sexy?

Do parasites alter sexual behaviour?

While some parasites clearly manipulate the behaviour of their host to enhance their ability to spread to new hosts (think of alteration of limbic function by rabies leading to biting behaviour or reduced fear from predators in many instances), do they ever alter sexual behaviour?

There is evidence that many organisms discriminate against mates that are parasitized. It has even been proposed that positive selection for bright colours, large appendages, elaborate feathers/fur/etc is a surrogate for selecting mates who can support such useless extravagances... and are therefore free of parasites.

Rats have been shown to be able to identify parasitized individuals by smelling their urine, and avoid mating with them as a result. Female rats appear to prefer the scent of males that are free of lice over lice-infested males.

So do parasites ever lead to increased mating success? Snails (Biomphalaria glabrata) exposed to to Schistosoma mansoni respond by increasing their reproductive output. This is an adaptive response that enhances reproduction before the parasite causes host castration. Makes you wonder how they know?!

Milk-weed leaf beetles (Labidomera clivicollis) also increase their reproductive effort in response to parasitism by a sexually transmitted mite Chrysomelobia labidomera. This is where things get interesting. When a parasite is sexually transmitted, making it's host more promiscuous and/or more sexually attractive would be a great strategy.

Just imagine how rabies might effect its host if it were sexually transmitted...


Tuesday, July 10, 2007

Treating addiction

The pharmaceutical industry is aching for new drugs. They are addicted to the blockbuster drug, a drug selling in the billions, and they need one ever so often because otherwise patent life expires and their buzz is gone. And that's when the generics come in and rough them up. The last success of the traditional small molecule "lifestyle" drug was viagra and there's been a bit of a dry spell since. In 1997, Pfizer realized that its antidepressant wellburtin (zyban) was effective at smoking cessation and got it approved. It proved to be a huge cash cow. Now 10 years have gone by, the patent is about to expire and there is a huge opportunity to grab a gigantic market: addiction. It turns out it doesn't matter what the addiction is, the mechanism is the same, and Pfizer's new drug varenicline, a nicotine partial receptor agonist can do the job:

"Varenicline increased the odds of successful long-term smoking cessation approximately threefold compared with pharmacologically unassisted quit attempts.In trials reported so far, more participants quit successfully with varenicline than with bupropion. The effectiveness of varenicline as an aid to relapse prevention has not been clearly established. The main adverse effect of varenciline is nausea, but this is mostly at mild to moderate levels and tends to reduce with habituation.There is a need for independent trials of varenicline versus placebo, to test the early findings. There is also a need for direct comparisons with nicotine replacement therapy, and for further trials with bupropion, to establish the relative efficacy of the treatments."

Imagine one day it could be sold for internet, gambling, porn, the 17% canadians who use pot, videogame, train-surfing, gummy bear, bayblab addictions.... I can't wait to check the results in PNAS.


Putin Trying to Redraw the Maps

In an effort to grab up huge oil reserves and potential shipping lanes, Russian geologists are claiming that a massive piece of the Russian continental shelf extends under nearly half the Arctic ice sheet, and therefore belongs to mother Russia.

The claim could even be a challenge to Canadian sovereignty, so we need to be getting our facts together. I think Rob should return to his family heritage and start re-charting the Arctic. If we play our cards right, we might even still have time to turn the whole thing around and annex Russia:

"Frankly I think it's a little bit strange," Sergey Priamikov, the international co-operation director of Russia's Arctic and Antarctic Research Institute in St Petersburg, told the Guardian. "Canada could make exactly the same claim. The Canadians could say that the Lomonosov ridge is part of the Canadian shelf, which means Russia should in fact belong to Canada, together with the whole of Eurasia." (Quoted in The Guardian)

Our Empire needs you Rob. All hail the Empire of Canada!


Monday, July 09, 2007

Save water, piss in the garden

The environment is on everyone's mind these days with the LIVE earth concerts. And this groundbreaking study in Greenland showing that in warmer times, a forest once stood where we now have 2km of ice. One of the worries of melting glaciers has to do with the availability of water, and the numbers are ugly:

"According to data collected from NASA and the World Health Organization, 4 billion people will face water shortages by 2050. Already in China, water levels in the Yellow River -- a source that supplies more than 150 million people -- are down 33 percent from the average. In China's cities, wastewater pollution and inadequate treatment facilities have contaminated the water consumed by more than half the population. Of its 669 major cities, 440 face moderate to severe water shortages. "

On the local city buses there are advertisements saying a can of tuna of water per week is enough for your lawn. I'm not sure why they chose a tuna can, but, for your information, that's 2.5cm of precipitation. Even more impressive I found an organization which promotes peeing on your lawn instead of watering it. You save water twice, since you don't need to flush or water your lawn:

"So take a piss in the garden, and while you are doing that, look out at your garden and think about how lucky you are, to be surrounded with all of what nature provides. Surely, there is something we can all do to help water conservation."

So far almost 4000L have been saved. I know I'll do my part...


Sunday, July 08, 2007

Sea anemone genome a big surprise

The sea anemone genome was recently completed and published in science. This is a boon for comparative genomics, since it gives us a new branch at the root of metozoans (multicellular animals):

" Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis. The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene "inventions" along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor."

The big surprise was that the cnidarian genome was actually much closer to our own vertebrate genome than other invertebrate groups which include nematodes and drosophila. Our friend over at "the other 95%" is an invertebrate zoologist grad student who explains the implication of this finding...


Bayblab podcast Episode10

Have you ever wondered who doctor B is? Are you interested in using wikis, podcasts and blogs in teaching? Well you're out of luck because we managed to screw up our first interview. But fear not, we have 3 random guys sitting on the next table in crystal clear audio quality thanks to our new mic (thanks invitrogen!). Nevertheless, we talk about some of the most poisonous animals on earth, the list may surprise you, and ponder whether science can help to make jury duty a more reproducible experience...


Thursday, July 05, 2007

Discussion: Religion as Bad Science

I was following an interesting email exchange at Impressions Bioblogiques regarding creationism vs. evolution. The discussion spans several posts that can be read here, here and here (anglophones be warned, the discussion and commentary are exclusively in french). As is usually the case, this turned into a debate-by-proxy about the existance of God. That got me thinking about whether the right questions were being applied (The proper argument for an atheist should be: 'God does not exist', not 'Evolution happened'. Using the latter to argue the former is a straw man argument.)

Of course, Science has a duty to interact with Religion when Religion makes scientific claims, and even more of a duty to take them on when those claims are false (Young earth creationism, for example). But the question of religion, or more specifically the existance of God, is not a scientific question. It is not a testable hypothesis, makes no predictions from that hypothesis, and is not falsifable. I had concocted a post asking whether religion can and should be held up to scientific scrutiny (beyond actual scientific claims it makes, as my example above) when I came across this discussion between Richard Dawkins and physicist Lawrence Krauss in Scientific American which covers much of the ground I was going to attempt to, but far more eloquently. At the very least, it's an interesting read.


The spotted hyena puts you to shame

I Have been accused of writing more about genitals than about science on the bayblab. OK, fine, but I give the people what they want... So I'll unload everything at once so we can concentrate on the science again.

The spotted hyena has had a bad reputation in the past. They are associated with death, scavenging, uncleanliness, cowardice, gluttony, sexual deviance. Early naturalist thought the hyena was a hermaphrodite, or that it practiced homosexuality. This was an understandable misconception. Female spotted hyena are actually slightly bigger than the male, and they have an enlarged clitoris that forms a pseudo-penis. The females give birth, copulate and urinate through their protruding clitoris. Interestingly, this anatomical feature is not dependent on high male hormones as was once thought, since, if testosterone is removed from the womb, they develop normally. The evolutionary advantage of this apparatus is unclear, as it makes copulation and birth more difficult. However, it does enable the female to have complete control over her mating partner, allowing the matriarchal society to persist.

There is a similar human condition of pseudo-hermatophroditism that results in an enlarged "clitoris". It is the consequence of 5-alpha reductase deficiency (5-ARD). The deficiency prevents the conversion of testosterone into DHT which is necessary for the development of male external genitalia. In fact there is an important cluster of 5-ARD in Papua New Guinea, where locals recognize 3 sexes in the society. Sexuality in New Guinea, has always intrigued explorers. The natives wear a Koteka, or penis-gourd, which can be pointy, curly, painted, massive, small penis-shaped depending on the tribe of origin. While the size of the penis gourd does not reflect status in the tribe, it is often used for communication such as saluting or expressing emotions such as astonishment. The explorer Matthew Stirling notes "They indicate astonishment by clicking their gourd penis covers with their finger nails and needless to say our camp sounded like a Western Union telegraph office most of the day as almost everything we had was a wonder to them."

But Papua New-Guinea natives have nothing on the Australian natives when it comes to penis salutations. The men of the Walibri tribe of central Australia, shake each others penises when they greet, much like we shake hands in the west. You can find numerous accounts of this custom of the Walibri tribe on the web, along with other strange sexual facts also in this book...


Wednesday, July 04, 2007

Penises of the Animal Kingdom

Evolution has graced the Earth with a multitude of different species, and with them an array of genitalia that make the human frank-and-beans look like, well, frank and beans by comparison. Here's a list of some of the most interesting ones I've come across.

6) Barnacle - Despite spending it's entire lifetime bathed in frigid seawater, the barnacle doesn't suffer from shrinkage. On the contrary, the Dirk Diggler of the animal kingdom has a penis up to 50 times it's body length - making it the world's largest penis, relative to size. The reason size DOES matter? They're immobile and need the length to reach their mates.

5) Kangaroo - We've talked about interesting penis shapes before with the corkscrew penis of certain ducks. Pigs also have a corkscrew penis, but why go for a single freakshow when you can double your pleasure instead? Like many marsupials, the kangaroo has a bifurcated (or forked) penis, and the scrotum and testes are in the front. This matches the dual vaginas/uteri of female marsupials. Stranger still, the echidna penis (pictured) has 4 heads!

4) Dolphins - The dolphin, like some other cetaceans, has a retractable penis that is also prehensile, meaning it can grab, hold and wrap around an object (think monkey tail). Imagine the benefits of such an appendage! This guy did. But what's even more disturbing, is this joke faq about how to have sex with a dolphin. At least I hope it's a joke.

3) Argonaut - This specialized octopus can use its penis without having physical contact with a female. Like many cephalopods, the penis is a special tentacle called the hectocotylus. In the case of the argonaut it detaches and swims to its mate, embedding in the female and impregnating her.

2) Bee - Like any man, the male honeybee climaxes with an explosion. Unlike men, the male bee genitals literally explode and snap off inside the queen. Afterwards, the males do what any of us would if our testes exploded and our penis snapped off - they wander off to the corner and die. A similar phenomenon has also been observed in certain spiders. The evolutionary rationale is that the detached genitals act as a plug preventing other males from mating with the queen

1) Bedbug - The bedbug doesn't mess around with foreplay. In fact it doesn't even mess around with female genitals. Instead, the male uses its dagger-like johnson to pierce the body of the female and inseminate her. The bedbug isn't the only species with such a violent mating process. Hermaphroditic flatworms duel with their penises with the loser being pierced and becoming pregnant. I see your Schwartz is as big as mine!


Sex or chocolate?

Every year, new research comes out saying that chocolate and sex are good for your health. But for some reason it always seems like a competition, which one is better? What's the proportion of woman who will take chocolate over sex? I don't know why you have to choose, but what do we have so far....

winner: chocolate, because no use having a big brain if you have Alzheimer's...

Blood pressure:
  • Chocolate improves your aterial blood pressure a new study finds. Especially dark, non-fat non-sweet chocolate. However if you are a fan of the greasy sweet stuff, it's not all bad news either since obese people tend to recover better after a heart attack.
  • Sex on the other hand is a good exercise and as such is good for your vascular health. However if you already have low blood pressure problems and you are a male you probably can't do it anyways.... In fact if you are hypertensive you may experience cephalgia and syncope, so now we know where the headache excuse comes from, it's a consequence rather than a cause....
winner: chocolate, all gain no pain.

Toxicity to pets:
  • Chocolate is toxic to parrots.
  • I'm not so sure about sex with you parrots. But at least between them it is safe.
winner: Sex, I think.

  • Chocolate tastes good, apparently even more so to woman.
  • Sex feels good.
Winner: That's an easy one, because chocolate doesn't fix you a sandwich after.

  • "A 100 gram strip of chocolate will give you about 500 calories of energy, 8 grams of protein, 60 grams of carbohydrate, 30 grams of fat, and small amounts of calcium and iron. But the possible health benefits come from the polyphenols in chocolate, especially the largest group, called flavonoids."
Winner: Sex, if you include the sandwich.

So here you go folks, a scientific proof that a hummer and a sandwich beats a parrot and a chocolate bar any day of the week.