Wednesday, October 31, 2012

Music and the Brain

The link between human language and our appreciation of music has often been explored, as far back as Darwin and his hypothesis of a musical protolanguage. If, as it has been shown, that music and language share processing locations in the brain, then what is the consequence, if any, of being tune deaf on language ability?
We have previously posted and pondered on the condition, amusia, also known as tune deafness here at the Bayblab. Essentially amusia sufferers have difficulty following pitch changes in music. You have probably heard sufferers of this condition at Karaoke night, and you can take this very interesting test to see if you too are tune deaf and have made others suffer on Karaoke night.
A recent study has found that indeed amusia has consequences for language processing. While the importance of tune in music is obvious, tune is also important to communicate an emotional quality to spoken words. Pitch changes in language can indicate sarcasm, irony, irritation and other emotions that are independent of the words that are spoken. As you might guess, according to this study, it is the interpretation of these emotional tonal cues of language that are deficient in sufferers of congenital amusia. Of course, this doesn't mean that sufferers can not interpret body language or other cues, however the deficit is significant enough that some sufferers are aware of their difficulty in this respect. I have been looking for any information on amusia in people who speak tonal languages as I imagine it would be very debilitating. In any case, next time someone you tell someone how fantastically frequent Bayblab updates have been recently, and they agree, don't let them sing at Karaoke night.


Friday, September 28, 2012

Throwing like a girl

The Washington Post has a recent article examining the "throwing gap". This gap refers to the robust difference between males and females in the skill of throwing. The gender difference in throwing skill spans cultures and has at least some biological basis. The article interviews Jerry Thomas who did the research, and who will bet "there's something neurological" at the root of the throwing gap. This reminded me that men throw like girls with their non dominant hand (video).
Of course there are always exceptions, like ambidextrous baseball pitchers and female quarterbacks (video), but perhaps the throwing gap could be examined by looking at males and females practicing throwing with their non dominant hand. If the gap is closed with the non dominant hand, would that not be conclusive that there is a neurological basis? What is definitely conclusive is that men throwing rocks with their non dominant hand set to music is funny.


Friday, July 27, 2012

Athletes will be tested for the presence of nicotine at the Olympics..

Finally there is a good reason to quit smoking. The governing body overseeing regulation of drugs at the Olympics, WADA, has included nicotine on the list of monitored substances. The inclusion on the monitoring list occurred almost a year ago however the 2012 London Olympics will be the first where nicotine levels of athletes will be monitored.

From the WADA website:

"In order to detect potential patterns of abuse, nicotine has been placed on WADA’s 2012 Monitoring Program.
It is NOT WADA’s intention to target smokers, rather to monitor the effects nicotine can have on performance when taken in oral tobacco products such as snus."
Nicotine is an addictive stimulant found in tobacco products and is therefore in a class of WADA banned substances. Classes of banned performance enhancing drugs have been previously outlined on the Bayblab.

 From Sports Illustrated:
The performance-enhancing effects of nicotine included increased "vigilance and cognitive function," and reduced stress and body weight.
The possibility that it is being used as such in sports such as hockey and rugby is indicated by the higher incidence of use by athletes of these sports. Unfortunately this is complicated by the fact that nicotine use could be a part of the culture of some sports.

Ashtrays are scarce on the track.


Sunday, June 17, 2012

Cleverbot Gene Annotation

I came across an interesting article, via Slashdot, summarizing a publication about automated gene annotation. Automated gene annotation has progressed to the point where, by a couple of criteria, it is superior to non-experimental human annotations. Computers as better chess players is interesting but when it comes to assigning function to the building blocks of life the author suggests this is computational biology's uncanny valley.


Thursday, April 26, 2012


Some people sneeze when they look at the sun. This trait, known as the photic sneeze reflex, or ACHOO (Autosomal-dominant Compelling Helio-Ophthalmic Outburst) syndrome, was thought to be an autosomal dominant trait. Approximately one-third of people are estimated to be sufferers of ACHOO. Recent data analyzed from the 23andMe dataset suggests the genetic influence for this trait is not simply an autosomal dominant trait. Unfortunately this may put at risk the excellent acronym for the trait. Interestingly, or merely coincidently, SNPs in proximity to two genes related to syndromes where seizures are a common symptom demonstrate statistically significant association with ACHOO. The association of the trait with seizures has been hypothesized previously.
What I find surprising is how many people are completely unaware of ACHOO considering as many as one-third of us suffer from this debilitating trait. This is perhaps best epitomized by the 23andMe questionnaire for AHCOO.
Participants were asked one question for this trait: “Do you have a tendency to sneeze when exposed to bright sunlight?” Available answers were “Yes” and “No, what are you talking about?” People who did sneeze were treated as cases, those who did not were controls.


Monday, March 26, 2012

The Coolidge Effect

Male rearousal time can be reduced, in many species, by the opportunity to mate with a novel female as opposed to the same female. This has been termed the Coolidge Effect.
This makes perfect sense in an evolutionary context but I think it also makes an amusing statement about the stereotypical gender perspectives of humans. These different gender perspectives are best exemplified by a joke which was the source for coining the term, Coolidge Effect.

… an old joke about Calvin Coolidge when he was President … The President and Mrs. Coolidge were being shown [separately] around an experimental government farm. When [Mrs. Coolidge] came to the chicken yard she noticed that a rooster was mating very frequently. She asked the attendant how often that happened and was told, “Dozens of times each day.” Mrs. Coolidge said, “Tell that to the President when he comes by.” Upon being told, President asked, “Same hen every time?” The reply was, “Oh, no, Mr. President, a different hen every time.” President: “Tell that to Mrs. Coolidge.”


Thursday, March 15, 2012

Amazing diapers

We usually use cloth diapers on our 10 month old, however occasionally we get some disposable diapers. They are amazing. The polymer sodium polyacrylate is responsible for the super absorbent properties of disposable diapers which allow me to be irresponsible and change our baby less frequently. The sodium within the polymer draws in water through osmosis. Sodium polyacrylate can absorb 500 times its weight in water, however the osmotic potential is decreased in the presence of urine since it already contains some salts. Below is a video demonstrating the amazing absorbent properties of this polymer, fortunately without displaying the graphic nature of a disposable diaper in a real world scenario.


Saturday, March 03, 2012

The Best Prescription

I'm not up to date on the latest stats on the best preventative medications, however here is a entertaining video my wife pointed out to me on the best prescription ever. This intervention decreases risk of death from all causes by 23%. The side effects include an improved quality of life. Is there any intervention that comes close to being as an effective preventative prescription?


Friday, February 24, 2012

Addiction Vaccines

A recently patented heroin vaccine has shown efficacy in reducing heroin consumption in mice. Vaccines to treat addiction are not a new idea and there are many in development. The concept is quite simple. The vaccine induces the production of antibodies in the patient that are specific to the addictive substance. These antibodies then bind to and neutralize the activity of the substance. In the case of a heroin vaccine, an immunized addict would no longer get high after heroin injection.
As a non-expert, this approach to addiction treatment this seems promising to me. The addict goes through all of the behaviors associated with the addiction and receives no stimulus to the reward pathway. Over time it would make sense that this would result in no reinforcement of the behavior making it easier to stop.
The vaccine approach reminds me of disulfiram (aka Antabuse), for the treatment of alcoholism. This drug causes the addict to have an intense hangover shortly after alcohol consumption. Instead of no reward, as with the vaccine approach, the addict receives a negative experience associated with the addictive substance. Perhaps disulfiram represents a superior approach because of the associated negative consequences of taking the addictive substance. The major problem with disulfiram is patient compliance, however with compliance and as part of a comprehensive treatment disulfiram improves outcomes. Hopefully addiction vaccines will also have positive outcomes in humans.
Unfortunately, so far there are no addiction vaccines that have proven effective in humans. The only example of a phase III clinical study that I am aware of is NicVax. NicVax is a nicotine vaccine that has shown no improvement over placebo in aiding smoking cessation, despite showing earlier promise in animal models. It is a poor indicator for the vaccine approach since addictive drugs share the same reward pathway in the brain of the addict. Perhaps I am oversimplifying the parallels between different addiction vaccines as clearly the approach is not being abandoned. Hopefully there is another difference between stimulants, like nicotine, and depressants, like heroin, that will make this approach a success for heroin addicts.


Wednesday, February 15, 2012

DIY molecular biology

Perhaps the real reason for not publishing lab-bred H5N1 strain data is hiding in his mother's spare bedroom. Check out Cathel Garvey's blog chronicling his work on making molecular biology more accessible to the hobbyist. You have to admire his Steve Jobs-like vision.


Tuesday, January 31, 2012


Canada is the largest producer of potash in the world. Recent investment in the development of potash resources in Saskatchewan is raising the usual issues of economic prosperity vs environmental sustainability. As potash is becoming a larger part of the Canadian economy I thought that I would share what I learned about potash because I knew essentially nothing about it until recently.
Before the late 1800s, potash was produced by leaching salts from the ashes of wood or plants and boiling the solution in a pot, hence the name potash. Historically, Canada was a large producer of potash as the frontier was opened up and deforested. Excess wood was burned and brought to asheries, where the ash was converted to potash.
Modern methods exist to obtain potash from mineral deposits and Canada has the largest reserves of these deposits in the world. The deposits are the result of the complete evaporation of sea water and the deposition of crystallized salts in beds of ore, called sylvinite. This ore consists of a mixture of sodium and potassium chloride (NaCl and KCl). The KCl is then purified using various processes and sold as potash.
Due to historical methods of production potash can refer to various salts of potassium, however mined potash is largely KCl. The element potassium derives its name from potash.
The majority of potash is used in fertilizers. Plant growth is often limited by available potassium. Therefore there is no substitute for potash and in a world of seven billion it is essential for food production. The best we can do is ensure that Canada responsibly extracts this valuable resource.


Real Space Lego

I was very impressed with the Lego-astronaut of Mathew Ho and Asad Muhammad. These two seventeen year olds from Scarborough sent a Lego man 24km above the surface of the earth. Using a weather balloon, some long ropes, a cellphone GPS, Styrofoam, cameras and some patriotic Lego they captured some spectacular footage. The footage has captured widespread media attention. It is amazing that the technology for what is essentially an unmanned space probe is within the budget of two smart seventeen year olds.


Tuesday, January 24, 2012

Asilomar Conference on Recombinant DNA

The recent call for a 60 day moratorium on engineered avian flu virus research reminded me about the Asilomar Conference.
The Asilomar Conference on Recombinant DNA was held in 1975 and its purpose was to establish guidelines for safely working with new recombinant DNA technology. The need for such a conference was instigated in 1974 by the construction of a bacterial plasmid that was deemed potentially hazardous. This plasmid contained elements from the monkey virus, SV40, which had been shown to cause cancer in mice. The idea of transforming this plasmid into a bacterium caused enough concern that a worldwide moratorium on recombinant DNA technology was called for by American scientists. The goal of the Asilomar Conference was to establish the conditions under which research in this area could continue. Many recommendations for experimental protocols were agreed upon. Additionally, three kinds of experiments were to be deferred until a later date. These experiments that were deemed too risky were cloning of genes from highly pathogenic organisms, cloning of toxic genes, and large scale production of gene products harmful to humans, plants or animals. Some of these kinds of experiments are now done routinely, and I do not know if there was ever a consensus of when it was determined these experiments were safe.
By taking initiative, the Asilomar Conference avoided potential governmental or other regulatory involvement that may have severely limited recombinant DNA technology in the long term. Instead, a timely relaxation of the guidelines, as knowledge about the true risks of these experiments accumulated, was a perfect fit for scientific progress.
Interestingly, I have spoken with scientists who were doing recombinant DNA research at the time who said that, in reality, the moratorium was not observed. Research continued in the field as it was an exciting and competitive time. I was also told during this time recombinant plasmids were exchanged between researchers by drying them on paper and mailing them, a practice still done occasionally today.
While there are some definite differences between these two calls for halting research, the current call for a moratorium on avian flu virus research has similar goals as the moratorium on recombinant DNA research. I think it would be a success if it had similar outcomes to the Asilomar Conference.
Certainly the moratorium has different goals than the censorship of two recent H5N1 papers, which is directed at stopping the dissemination of information about specific transmission determinants of H5N1. I have read a couple of articles that seem to get confused about the goals of this censorship and the goals of the recent moratorium. Indeed the current call for a moratorium doesn't mention the word terrorism or suggest censorship as a security measure.


Tuesday, January 17, 2012

Ski Wax Science

According to a thesis published in 2006, ski wax is snake oil. Leonid Kuzmin is the author of a couple of papers, both included in his thesis from Mid Sweden University (pdf), that demonstrate that many practices designed to decrease friction between nordic skis and snow are counterproductive. It is the authors assertion that waxing practices evolved when skis were made of wood and that a critical re-examination of these practices was lacking when wood was replaced with modern plastics. The data in the thesis suggest that there is no advantages to waxing skis. At best, the data suggests, an improvement in glide is observed for the first 200m. After this point, a waxed ski picks up debris increasing friction with the snow to the point where it becomes slower than an unwaxed ski. The thesis also pokes holes in two other commonly held beliefs, that wax protects skis from water penetration and offers protection from abrasive wear. While this work was done exclusively with nordic skis, it is the authors belief that the findings hold true for alpine skis.
It is not hard to find lots of passionate anecdotes refuting his findings, however I was surprised that there was no real scientific studies demonstrating benefits of waxing skis.

From the thesis:

Skis treated with any established waxing procedure loose their glide ability faster than the reference skis (dry skis).

A typical counterpoint found in internet forums:

I was in a hurry to get to Sun Peaks a while ago. My skis needed waxing but I didn't do it so we could get on the road. On our first day I was having trouble getting a good slide going and I had to continuously pole and skate to get up over a hump to get to a particular face. That night I waxed my skis. The next day with essentially the same snow conditions I flew over that hump so fast I had to brake at the top, and I certainly didn't need to pole or skate. Wax works.

Despite this thesis, now 5 years old, most skiers get their skis waxed or do it themselves. I wonder if this is a case where the mantras and anecdotal evidence are winning in terms of acceptance or if the studies just did not get publicized well. Perhaps the first 200m where a waxed ski glides better is the source of much of the anecdotal arguments for waxing. Personally, I think much of the resistance to accept these findings is due to the fact that waxing skis can be an enjoyable process. Waxing your skis gets you excited to go skiing. I actually miss it.


Wednesday, January 11, 2012

The Drag Effect

The skip of my curling team competed in the Brier a few years ago. I make him look pretty talented. Recently he was talking about the drag effect. The only thing I understood about it during our match is that when two stones are touching they do not behave exactly like billiard balls.
Take a look at this shot.

That is not how billiard balls would have behaved in that situation. Basically, the struck rock and the yellow rock behind it were frozen together on their striking surface. The struck rock then transfered some of its momentum to the yellow rock. A more detailed explanation of the drag effect is available here.


Sunday, January 08, 2012

Flynn Effect

The Flynn Effect is the observed steady, widespread increase in IQ over generations. In some places this has been occurring for at least 100 years. In fact, if you were to give your great grandparents a modern IQ test, they would test below 75 and be considered mentally challenged. The Flynn Effect is not simply an increase in "crystallized" intelligence due to the increasing availability of knowledge. The way in which IQ scores are increasing is described in a recent Wired article:
1) Scores have increased the most on the problem-solving portion of intelligence tests.
2) Verbal intelligence has remained relatively flat, while non-verbal scores continue to rise.
3) Performance gains have occurred across all age groups.
4) The rise in scores exists primarily on those tests with content that does not appear to be easily learned.
The reason why IQ test results are increasing is a mostly unresolved question and presents some paradoxes described by Flynn and summarized here.

The intelligence paradox: The Flynn Effect suggests that we are getting smarter relatively quickly, but it’s not obvious (and some would say flies in the face of certain evidence) that kids today are so much smarter than their parents or grandparents (except perhaps when it comes to home electronics). As Flynn writes:

If huge IQ gains are intelligence gains, why are we not stuck by the extraordinary subtlety of our children’s conversation? Why do we not have to make allowances for the limitations of our parents? A difference of some 18 points in the average IQ over two generations ought to be highly visible.

The mental retardation paradox: If the rate of change in IQ is extrapolated backwards, it suggests that people in 1900 had a mean IQ score somewhere between 50 and 70 judged by today’s standards. An IQ level of 75 is typically considered ‘mentally retarded.’ Flynn puts this one nicely, too: ‘Either today’s children are so bright that they should run circles around us, or their grandparents were so dull that it is surprising that they could keep a modern society ticking over.’

The identical twins paradox: Twins raised apart tend to have very similar IQ scores, typically considered strong evidence for a genetic basis for differences in IQ. The Flynn Effect instead suggests that intelligence, if it is being measured by IQ, is more malleable and subject to environmental effects. [Clearly there is no genetic evolution basis for the Flynn effect, mostly obviously because the effect occurs too fast, over a single generation.]

The most popular theories as to the cause of our collective increasing genius include:

  1. Increased schooling and test familiarity – This seems like an obvious cause, however it has been shown that previous generations with similar levels of education still score lower than subsequent generations.
  2. Generally more stimulating environments – Our world is increasingly complex, potentially increasing exposure to problem solving situations.
  3. Nutrition – Improved nutrition has increased human stature. It is therefore possible that improved nutrition is also responsible for increases in IQ. Recent evidence outlined in the previously linked Wired article suggests that both ends of the bell curve are showing equal increases in IQ. An increase in IQ of those at the right side of the bell curve argues against a solely nutritional cause as those with a high IQ are likely not undernourished to begin with.
  4. Infectious diseases - The decrease in infectious diseases experienced during development of the brain may be responsible for the Flynn Effect. Fighting off a disease and brain development are both metabolically costly and perhaps early childhood infections might come at a cost to brain development. This perhaps has the same problem as the case for a nutritional cause outlined above.
  5. Heterosis - The genetic component of IQ is so great that some argue that environmental causes would have a minimal effect. Essentially the idea is that the increased mixing of human populations has lead to a "hybrid vigour" effect in population IQ.
These are not the only ideas for a cause of the Flynn effect. It is very possible that the Flynn effect has a complex combination of causes.

Another very interesting aspect of the Flynn Effect is that it has stopped in many developed nations. The cause is unknown.


Friday, January 06, 2012

Infectious salmon anemia

The poor 2009 sockeye salmon return in the Fraser River, mentioned previously on the bayblab, prompted the Cohen Commission in order to better understand what happened. The final report of the Commission is due this year but in the meantime there is a large amount of information about the ongoing findings of the Commission available here. Many potential causes are being examined, however much of the media coverage of the commission has focused on the possible role of infectious salmon anemia (ISA). The possibility of the presence of this virus in wild pacific salmon has become very political and has resulted in accusations of attacks on scientific credibility. It would certainly have implications for the controversial salmon farming operations in the area.
As the name implies the virus causes anemia by infecting red blood cells of infected salmon and has an extremely high mortality, as high as 90%. This virus is commonly associated with atlantic salmon farms and has affected farming operations all over the world in recurrent epidemic outbreaks. Spread of the virus between farms can be examined by correlations between seaway and genetic distances between viral isolates.
ISA is an Orthomyxovirus, like influenza, and therefore has a small segmented negative sense single stranded RNA genome. This genome arrangement allows for reassortment when a cell is superinfected, and confers the ability of the virus to rapidly change in a population, much like influenza. Hopefully this virus is unlike influenza and will not successfully cross the species barrier and maintain a high mortality in pacific salmon.
On a positive note, it is possible that a local ISA strain has been in pacific salmon species for years. It would be interesting to know to what degree it is genetically related to the ISA found in atlantic salmon farms. Fortunately it has also been demonstrated that pacific salmon are highly resistant to previously characterized ISA (pdf).