Monday, December 15, 2014

Richard Dawkins debates homeopathy with Dr. Peter Fisher (2007)

Richard Dawkins made a television documentary called "The enemies of reason" in 2007. A large portion of the first part of the documentary is on homeopathy. You can watch it here. While I think it was a pretty good documentary that consisted of legitimate criticism, it was edited for television and was focused on "gotcha" moments. I think it also missed out on an educational opportunity to explain the rigorous methods of a well conducted randomized controlled trial. I recently ran across Dr. Peter Fisher's defence of NHS funding for homeopathy in the 'uncut' interview with Dawkins from the documentary.

This was probably the best defence of homeopathy I have ever seen. Despite this, with his usual style, Dawkins had Dr. Fisher on the ropes the entire time without even citing the evidence for a lack of homeopathic efficacy. Admittedly Dr. Fisher is an easy target, however I would hate to have to debate Dawkins on any subject. He finds common ground, concedes valid points, asks great questions, and lets his opponent talk him/herself into tight corners. From my biased perspective, in this interview Dawkins essentially had Dr. Fisher admit that homeopathy is a form of placebo. However, is there any context in which homeopathy could provide a safe, cost-effective treatment that is completely placebo? Probably not, however water is pretty cheap and safe.


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Wednesday, December 03, 2014

Nature enables sharing of articles

The journal Nature now enables subscribers to share articles for free though hyperlinks to a proprietary document format. The hyperlink to the article can then be subsequently shared by anyone. A year subscription to Nature costs $200 and an article costs around $30. While this is a somewhat awkward model in my opinion, I appreciate that such a prestigious journal can demonstrate some flexibility and adapt to the changing publishing business.
Here is a link to a paper on the identification of the remains of Richard III in the proprietary ReadCube format.


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Monday, November 17, 2014

Accidental discoveries

Below is a video on accidental chemical discoveries. The last two were particularly interesting to me, the discovery of Teflon, and Gore-Tex. The real challenge it would seem to me would be seeing the potential and figuring out uses for newly synthesized chemicals.


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Monday, November 10, 2014

Mogul Migration

Anticipation for the upcoming ski season is building and it is currently snowing outside. In order to keep my excitement under control I thought I would write a post on the worst aspect of resort skiing, moguls. Moguls are spontaneously forming speed killers and are ubiquitous on certain slopes that don't get machine groomed. They are admittedly impressive as self-organizing structures and their checkerboard regularity can be attractive from a distance. However, how is it possible that the seemingly random actions of skiers going down the slope create and maintain this "mountain acne"? Not only does their formation defy intuition but moguls also migrate uphill! Watch the video.
 

Three scientists, presumably also skiers, published a paper in 2009 on the subject of mogul formation and migration. These guys estimated that it takes as little as 100 ski passes to create moguls. If the snow is hard pack a bump as small as 10cm can start a mogul. Importantly the authors also calculate that a skier requires the equivalent of 'half a light beer' of calories to move a mogul one meter uphill. Unfortunately the authors offer no solutions to moguls, although I don't know if they tried enough beer. The reality is that the only solution is a huge dump of fresh powder!

image of Untitled


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Friday, November 07, 2014

Human Altitude Evolution

An interesting comment on quirks and quarks this week inspired me to do a little research on the adaptations to high altitude in different human populations. The evolution of human traits in response to high altitude environments differs between different populations. There are the legendary Tibetan highlanders of the Himalayas but there are also physiological adaptations of human populations in the Andes and in the Amhara of Ethiopia. Interestingly we also know the genetic basis for these adaptations through comparative genomics.
High altitude environments present many challenges for human physiology. These challenges are due to the thin air at higher elevations. The partial pressure of oxygen decreases with air pressure and air pressure decreases exponentially with altitude. Air pressure is half of sea-level air pressure at 5000m. This decreased availability of oxygen at higher altitudes, or hypoxia, causes altitude sickness and potentially fatal high altitude pulmonary edema and high altitude cerebral edema. The frequency of these conditions and others increase with increasing altitude.
Mere mortal lowlanders are able to partially adapt to these physiological challenges. Initially, low oxygen partial pressure is detected by the carotid body triggering increased breathing rate. Additionally at high altitudes the heart beats faster with a lower stroke volume. Longer term exposure, over days or weeks, results in further acclimatization to altitude. The most well known acclimatization feature is an increase in hemoglobin and red blood cell (RBC) mass in order to increase the amount of oxygen that can be carried by the blood. Increased RBC mass leads to increased demand on the heart, and other complications such as hypertension, chronic mountain sickness, and high fetal mortality.
The Tibetan highlanders often live at elevations of over 3500m above sea level. One of the hallmark evolutionary adaptation of these populations is a lack of increased hemoglobin at high elevations correlating with a variant of the HIF2A gene encoding HIF2alpha. The HIF2alpha transcription factor protein is active under low oxygen conditions and helps control RBC production. The HIF2A gene variant found in Tibetan highlanders traces its ancestry to a recently discovered extinct human relative - the Densisovans. So this particular adaptation is due to interbreeding between the Denisovans and the ancestors of modern Tibetans. EGLN1 and PPARA are also positively correlated with Tibetans low hemoglobin adaptation to hypoxia. Other unique traits of Tibetans contribute to their altitude aptitude including an increased basal breathing rate that does not go away when exposed to lower elevation, a larger lung capacity, and a higher blood nitric oxide (NO) concentration which can help blood vessel dilation and circulation. Tibetans also have experienced selection for genes involved in metabolism, DNA damage response, DNA repair, and genes for high infant birth weight.
Genetic adaptation to high altitude among Andean populations are distinct from the Tibetan adaptations. While HIF2A and EGLN1 both exhibit evidence of selection pressure in these populations the particular variants are not associated with decreased hemoglobin. In fact these populations demonstrate the same temporary increase in hemoglobin with increasing altitude that lowlanders experience. They do have an increased oxygen level in their hemoglobin and thus a more efficient oxygen blood carrying capacity. The Andeans do not have an increased breathing rate, however one Andean subpopulation also has increased NO blood concentrations. The Andeas are the least well adapted to high altitude as evidenced by the frequency of chronic mountain sickness. An examination of Andeans with chronic mountain sickness found that many individuals have maladapted gene variants of SENP1 and ANP32D.
The Amhara of Ethiopia are also unique in their adaptations to a low oxygen, high altitude environment. This population are immune to the dangers of high elevations over 2500m, and have been inhabiting these environments for much longer, yet they do not have either the decreased hemoglobin or high oxygen saturation of the Tibetans or Andeans respectively. However one study had identified several candidate genes for involvement in high-altitude adaptation in Ethiopia. Two of these play a role in the HIF1alpha pathway, suggesting some degree of convergent evolution.
An O2 mask is a pretty good altitude adaptation


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Tuesday, October 14, 2014

Can't replicate your previous experimental work? Publish it.

A morale booster for those cynical about the state of scientific publishing was published this week in PLoS ONE. Psychology researchers from Northwestern University were unable to replicate previous experimental results, and instead of hiding from scrutiny and switching gears, published their inability to replicate in PLoS ONE. While obviously the best thing to do for the field, it may have also been a good idea based upon the positive response. Would such a paper be accepted in a closed-access scientific journal? I wonder if it was submitted to the original journal. In any case this is a breath of fresh air at a time when scientific misconduct seems to be given more attention than the successes of peer-review and scientific integrity.


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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.


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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.


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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.


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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.


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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?


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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!


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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.


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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.


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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.


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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.


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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.


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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.


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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.



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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?


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