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.