Tuesday, August 26, 2014

Cotton Candy Grapes

Fruit hybrids are nothing new as pluots and tangelos become increasingly visible in grocery store produce aisles. Recently I had the opportunity to sample a fruit that looked no different from your run-of-the-mill seedless grape, but with a unique flavour of cotton candy. The taste is more than reminiscent of the pink spun sugar - it's uncanny. The fruit, a product of The Grapery in California are the result of selective breeding of different grape varieties, increasing sugar content and heightening vanilla flavour to result in the familiar taste. Personally, while I found the taste remarkable, I don't think I could eat a whole bowl of them, but maybe this is a way to get picky eaters to munch on fruit. The company is already working on other varieties that taste like strawberry or pineapple.


Wednesday, July 16, 2014

The UV index and cancer incidence

Originally developed by Canadian scientists, the UV index is now a standard measurement of UV radiation that reaches the earth's surface. It is an open-ended linear scale, meaning that there is no upper limit and that, for example, a 4 on the UV index is twice as much radiation compared to when the UV index is 2. The purpose of the UV index is to enable informed choices about sun protection/avoidance as per the recommendations in the chart. In fact the UV index is weighted more heavily for wavelengths in the UV spectrum that cause more skin damage. It is therefore not a pure measurement of the quantity of radiation but a direct measure of the skin damaging potential of the UV radiation. The UV index is typically forecast for solar noon, the time in the day where the UV radiation is at its peak potential. Impressively, the UV index forecast is based on computer models that account for the effects of sun elevation and distance, stratospheric ozone, cloud conditions, air pollutants, surface albedo, and ground altitude.

Slip on a shirt, slop on sunscreen, slap on a hat and wrap on shades.

Getting lots of UV radiation causes skin damage and ages skin. A higher mean UV index has also been associated with increased incidence of melanoma in non-Hispanic whites. A prospective study of UV exposure and cancer incidence also confirms a higher incidence of melanoma in those receiving higher UV exposure. This same study however found a decreased risk of non-Hodgkin's Lymphoma and colon cancer with increasing UV exposure. The study also found significant protection from thyroid, pancreatic and squamous cell lung cancer at intermediate UV exposure levels. Over nine years this study found that UV exposure was inversely correlated to total cancer incidence. The authors hypothesize that the protective effect is due to vitamin D production that occurs in human skin under exposure to sunlight. Is it surprising that the benefits of sun exposure aren't nearly as well known as the risks? I clearly have not done a thorough literature search however there doesn't seem to be much information on UV exposure and total cancer risk. The benefits of UV exposure are possibly less established and have an unconfirmed mechanism which may contribute to the lack of publicity. Also various authorities on skin cancer encourage acquisition of vitamin D through dietary sources.


Friday, July 04, 2014

Yum! Plastic!

It is being proposed that marine animals are consuming 99% of the plastic that was assumed to be accumulating in the world's oceans. Consumption of this plastic by marine animals, and other possible scenarios, are being proposed because otherwise this missing plastic can not be accounted for. I guess I'll just assume that fish now comes with a serving of small pieces of plastic.


Wednesday, May 21, 2014

TED talks - Human Pheromones

Another great place for a quick fix of science is TED talks. Some of them are terrible unfortunately, and some are very good. Almost all TED talks suffer from trying to have a large 'wow' factor, when they don't necessarily need it. The bayblab has linked to many TED talks previously.
A past bayblab post on the topic of human pheromones suggested that there isn't much good data on the topic. A recent TED talk on the subject is an example of a good TED talk. The speaker Tristram Wyatt talks about the background and history of pheromones and the recent discovery of a potentially genuine human pheromone that acts on babies.


Friday, January 31, 2014

Clinicaltrails.gov has more clinical trial data than Pubmed

A recent PLOS publication examined clinical trial results available at clinicaltrials.gov and clinical trial data published in journals. Their results demonstrated that there is more trial data available at clinicaltrials.gov than what is available in the published literature. Data that was significantly more reported included efficacy, adverse events and serious adverse events. Is anyone using this as a resource for clinical trial data?


Wednesday, January 22, 2014

Conflict of Interest in Systematic Reviews

There is a recent systematic review of systematic reviews in PLOS Medicine examining the effect of industry funding on conclusions. The authors found that industry sponsored systematic reviews are 5 times more likely to support a conclusion of no positive association between sugar-sweetened beverages and obesity or weight gain as compared to studies that did not report industry funding. The authors do not give suggestions for the mechanism by which bias may have entered the systematic reviews other than the heterogeneity of literature selection. Examine systematic reviews carefully!


Sunday, January 19, 2014

Curling Science - Sweeping

I often ponder the physics of curling, and have previously posted on the drag effect here on the bayblab. These musings have yet to improve my game but as the winter olympics approach and as my beer league curling team suffers embarrassing defeats from inebriated senior citizens, I thought I would post some information I found on sweeping.

Sweeping is done by one or more players on the team whose rock is being shot. The players sweep the ice, using specific curling brooms, directly in the path of the travelling rock. Sweeping reduces the deceleration and the degree to which the path of the rock curls.
A common belief is that sweeping melts a thin layer of ice ahead of the rock and that the resulting thin layer of water decreases friction between the rock and the ice. An investigation into ice temperatures resulting from sweeping demonstrated that sweeping raised the ice temperature by 1.5C and achieved a maximum ice temperature of -1C. It was also found that raising the temperature of the ice was crucial for the effectiveness of sweeping but the temperature measurements, as determined by infrared camera, suggested that sweeping doesn't melt the ice. I do not understand the exact methodology or much about infrared cameras but I remain skeptical that a sufficiently thin layer of ice temperature can be measured in this way. It is known that the melting point of ice is decreased under pressure, such as the pressure experienced by ice under the weight of the rock. Therefore I don't know how conclusive it is that the effectiveness of sweeping is not due to contributing to the creation of a thin layer of lubricating water. Nonetheless, it is the momentarily increased ice temperature created by sweeping immediately ahead of the moving rock that makes it effective.
Not surprisingly, the mechanism by which sweeping increases the temperature of the ice is friction. The evolution of materials used for curling brooms reflects this fact, with the latest fabric broom heads enabling a dense contact surface area with the ice. The latest innovation in sweeping brooms is the incorporation of a heat reflective material behind the fabric broom head [link to patent (pdf)]. This reflects some of friction heat back towards the ice to increase the efficiency of sweeping.
None of the above information is going to help one's curling performance, however I did find a review that does have some practical applications for curlers. The first thing that I learned from this review is that it is actually against the rules to not sweep across the entire width of the contact point of the rock with the ice. 'Corner sweeping', as it is known, is when the rock is swept only on one side. By reducing the friction asymmetrically as the rock travels, the amount of curling can be influenced. While 'corner sweeping' is illegal, it is perfectly legal to sweep from either side of the rock. The review points out that more sweeping force is produced on the side closer to the sweeper. Therefore changing the side on which the rock is swept, or having the stronger sweeper on a particular side, might be advantageous for some shots.
Another big question is 'hurry or hard' when sweeping. The review finds that sweeping fast for fast moving rocks and hard for slow moving rocks produces the most friction heat beneath the moving rock. Sweeping fast for fast moving rocks makes sense as the speed of the rock may prevent multiple sweeping passes over the surface area under the rock. When the rock is moving slower it is easy to do multiple passes so it is best to push down hard when sweeping to maximize the heat produced by friction.
In reality none of this information is going to make me a better curler. However, at least the old boys I play with can't say that my poor performance is due to ignorance.


Wednesday, December 18, 2013

Curie Temperature

The Curie Temperature is a material specific temperature, where thermal motion of dipoles in a ferromagnetic material overcomes forces aligning the dipoles. Above this temperature dipoles do not align and the material looses its ability to be attracted to a magnet. Interestingly this temperature effect is sharp (I have no idea why) and thus leads to some interesting demonstrations.


Tuesday, December 10, 2013

Not Exactly Rocket Science - Ed Yong

As a continuation of shout-outs to awesome sources of online science snacks, I would like to mention Ed Yong's Not Exactly Rocket Science (NERS) blog. The blog has been active for almost as long as the Bayblab and has changed locations on a couple of occasions. It is currently being hosted at national geographic phenomena, where they also host the complete back catalogue of NERS posts, and which also hosts a few other awesome science blogs. NERS articles are entertaining, accurate and full of links, so it is a good starting place for some science surfing.
In a recent example of an interesting article at NERS, Ed Yong writes about the effects of the gut microbiome on cancer drug efficacy. Ed puts together the work of two groups and simplifies the case for a major role for gut bacteria in modulating anti-cancer treatments in mice. NERS is definitely worth a bookmark if you want to keep up to date on interesting and surprising findings like these.


Wednesday, November 27, 2013

Research ethics

The presence of falsified data in the scientific literature is arguably more important than the absence of negative results. The absence of negative results in the reporting of clinical trials is a serious problem as excellently outlined in a TED talk by Ben Goldacre. Data that has been fabricated is more offensive to me as it genuinely pollutes the literature and decreases public and professional confidence in science. Scientists who do the 'best' job of fabrication without getting caught could go on to achieve greater success and pollute the literature even more. An article at Nature news highlights some researchers attempting to catch these cheaters. The article also goes further to suggest we should be concerned that these whistleblowers or "data-whisperers" are also being honest.


Wednesday, October 16, 2013

An experiment on open access journals

As you may have already heard, an experiment on open access journals was organized by Science magazine. A spoof manuscript describing a novel cancer drug was submitted to 304 open access journals and had a 70% acceptance rate. The manuscript had many intentional errors that should have been picked up easily by the peer review process.
As a fan of the ideals of open access publishing I do believe this was an important finding. Clearly there are problems with the peer review process in these journals. This needs to be addressed.
What I find strange is that the conclusions of this experiment fail basic logic. This experiment had no controls. There were no submissions of the spoof article to closed access journals, therefore it is impossible to conclude that the acceptance of poor scientific manuscripts is specific to open access journals. This stunt was also not a test of the open access ideology or business model, it was only a test of the peer review process of these journals. No doubt, those open access journals that accepted the article clearly failed the most basic requirement of scientific publishing, however Science magazine has also mistakenly accepted flawed papers. I found a more balanced assessment of the meaning of this experiment at National Geographic.


Wednesday, October 02, 2013

Numberphile - The Enigma Machine

Recently posted praise on the Bayblab was directed at SciShow for its easily digestible science stories. Now it appears remiss not to mention other great sources of science snacks. We'll take some time over several posts to cover some of these entertaining sources. Feel free to make some suggestions in the comments.
One source that we have to mention, despite the fact that it is not strictly science, is Numberphile. Numberphile is a Youtube channel that consists of "videos about numbers and stuff." Again, the host is excellent and there are some very interesting videos.
For example, in these days of revelations of the NSA's activities, the history of encryption seems a relevant topic. The Code Book by Simon Singh is a great read covering exactly this topic. Among other encryption stories, The Code Book explains the detailed workings of the Nazi encryption machine known as Enigma. This impressive encryption machine and the cracking of Enigma encryption played a significant role in the course of WWII. While I highly recommend reading The Code Book if you are interested in this topic, two Numberphile videos covering the amazingly complex encryption arising from a seemingly primitive machine do a very good job. The first video explains how the Enigma machine works and reels you in for the second video explaining the flaw that made the Enigma machine possible to crack. In its historical context it is a very compelling story.
I also found it nerdily satisfying that Simon Singh, author of The Code Book, made an appearance on Numberphile to briefly discuss Fermat's last theorem.


Monday, September 23, 2013

Auto-brewery Syndrome - Free Beer

A personal brewery could fit in there.

A recent 'news' story caught my attention as it was about a man with a bizarre affliction. The subject was apparently drunk to varying degrees for five years straight. Of course this isn't that unusual, except that he was not drinking alcohol, the flora in his gut was fermenting dietary carbohydrates into ethanol. After years of being a suspected 'closet drinker' he was treated with antifungal medication and is now free of his involuntary inebriation.

According to the linked news article the condition is very rare, however upon searching for this syndrome on pubmed I am given a different impression. The only article I found that examined frequency of endogenous ethanol production examined patients blood for a glucose tolerance test. Baseline measurements in 2.7% of patients demonstrated the presence of some ethanol after receiving capsules of glucose. Most surprisingly, over 60% of the patients had an increase in ethanol one hour after receiving oral glucose. Those who had a baseline ethanol measurement also had the greatest increase in blood ethanol levels. Sixty percent is not a rare occurrence and it makes one wonder if endogenous ethanol production is clinically relevant in the context of some health conditions. This has been proposed before but I haven't seen anything convincing.

For context, an 80kg male drinking three drinks in two hours will have a blood ethanol concentration of 33mg/dL, while the measured increases in this study averaged under 3mg/dL and the highest measured increase was 7mg/dL. Clearly, none of the patients would notice the effects of ethanol from dietary carbohydrate ingestion. Additionally, it has already been argued that the possibility of having this syndrome is not a credible defence against a drunk driving charge.

Unfortunately the most 'beneficial' effects of ethanol are achieved, most often, at levels requiring an exogenous source. Fortunately beer is tasty.


Wednesday, September 11, 2013

Sarin Gas

If you haven't checked out SciShow on Youtube yet, please do yourself this favour. Consisting of quick science related videos it is accessible, entertaining and surprisingly informative. The SciShow team have a pretty good time with the material, probably best evidenced by the recent "Is SHARKNADO Possible?"
A recent SciShow describes some basic facts about Sarin gas, the nerve agent that recently killed hundreds of Syrian civilians. The video describes Sarin as an inhibitor of acetylcholinesterase. Sarin's inhibition of this enzyme prevents removal of actylecholine from neuromuscular junctions resulting in continuously contracting muscles and death from asphyxia due to the inability to control the muscles involved in breathing function.
Interestingly there are antidotes for sarin gas exposure and the resulting irreversible inhibition of acetylcholinesterase. Some antidotes simply inhibit acetylcholine receptors preventing the action of the accumulated acetylcholine and are themselves a poison. However pralidoxime (2-pyridine aldoxime methyl chloride,) or 2-PAM actually restores function to the irreversibly inhibited enzyme. It reacts with organophosphorus nerve agents such as sarin and reverses the covalent bond to the serine in the active site of acetylcholinesterase resulting in a reactivated enzyme. I have never heard of such an antidote or reaction. While I guess it is comforting to think there are antidotes to these weapons they are largely impractical due to the time frame in which they must be administered.
Are there any other examples of molecules that can reverse the irreversible inhibition of an enzyme?


Tuesday, April 23, 2013

Bear Spray

Where I'm living black bears are quite commonly seen around town. While I have yet to hear of a really bad bear encounter many bears are destroyed every year for getting too familiar with town. Most people here merely avoid them when they see them. Alternatively, aggressive responses to threatening bear encounters include firearms and pepper spray. While obtaining a firearm requires getting a firearms license and many restrictions, getting bear spray is as simple as purchasing some from Canadian Tire.

So what is bear pepper spray and does it work?

The active ingredient in bear pepper spray is the same compound that makes some peppers spicy. This spicy compound is caspaicin. Bear spray is also known as capsicum deterrent since capsicum is the genus of plants that includes caspaicin containing peppers.

Capsicum plants have evolved production of caspaicin in order to deter mammals from consuming the fruit of the plant. When consumed capsaicin produces a strong burning sensation in the mouth. This burning sensation is experienced by most other mammals, and is real, at least according to your brain. Capsacin binds a cellular receptor that is also activated by temperatures exceeding 43 degrees Celcius. The receptor, transient receptor potential cation channel subfamily V member 1 (TRPV1), is responsible for communicating pain and has a role in temperature regulation. Evolutionary pressure has caused capsicum plants to produce capsaicin to reduce their consumption by mammals. Exposing seeds to the mammalian gut prevents capsicum seeds from germinating. Bird TRPV1 receptors do not respond to capsaicin and therefore capsicum plants and seeds are readily consumed by birds. The avian digestive system doesn't not destroy the ability of the seeds to germinate and therefore birds contribute to capsicum seed dispersal.

So if this is the same compound found in hot peppers and salsa are we not just giving the bear a bit of a spicy snack? The difference between tasty and bear repellent is concentration. Spicyness or capsaicin concentration is usually quantified by an antiquated unit of measurement called the Scoville unit. The Scoville Unit tries to be objective but ultimately relies on 5 tasters determining the dilution factor that produces a solution with no caspasin taste. So for some spicy perspective, while an average jalapeƱo pepper has about 3500 to 8000 Scoville units, bear pepper spray has about 3.3 million Scoville units.

So spraying a bear with 3.3 MScoville Units causes the animal spicy pain, but does it actually work? In other words, in the real world are there statistics to show that being armed with a canister of pressurized capsaicin reduces harm to you and/or the bear? An article from 2008 reports that in 20 years worth of bear encounters reported in Alaska, bear spray was effective in reducing the severity of the encounter 92% of the time, while firearms were only 67% effective. This is the kind of evidence, almost convincing enough, to justify taking my gun rack off my mountain bike.


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.