Thursday, December 29, 2011


Sunflower.  Source.


I have learned that a typical week for me involves at least one instance of surprise interest in a topic I had previously found mundane.  A week or so ago, this proved to be the sunflower.  I have not heavily researched this topic, but I stumbled across a few tidbits of information I hope we shall all find interesting.

One surprise to me was that the native sunflower of North America is a perennial species [comes up year after year], unlike the farmed varieties which may behave more like an annual [dies outright every winter].  As a result, considerable interest has been generated recently in producing a hybrid of the high-yield annuals with the perennial behaviour of the native varieties.  Since sunflower oil may be used as both a food product and a source for biodiesel, it would be wonderful to have a perennial oil crop.  Eliminating the fuel/energy requirements for planting such crops every year makes for a more sustainable future, and makes the farming process more efficient overall.  While I would prefer to see switchgrass used for fuel, I can certainly appreciate having a perennial food crop.

Graphical representation of sunflower floret placement.  Source.
While I have little to no understanding of the mathematical significance of such a thing, the way in which the florets/seeds of the sunflower arrange themselves is a form of the Fibonacci spiral and the periodic angle of placement is related to the golden ratio.  I have no idea why, but Wikipedia states that it is 55/144 of a circular angle, where 55 and 144 are Fibonacci numbers.  Huzzah, I suppose.  Regardless what it means, it certainly looks to be a very efficient spatial arrangement (no doubt perfected with a genetic algorithm), and is rather hypnotic.  I suppose that is just a fancy way of saying "Ain't it purdy?", but I stand by the statement nonetheless.

In what I thought was a startling application, sunflowers also have a documented propensity for scrubbing heavy metals from the soil.  Lead, arsenic, uranium and radioactive species caesium-137 and strontium-90 will collect in the seeds of the sunflower plant.  Scrubbing would likely be particularly easy with the planting of perennial sunflowers.  One would simply need to cut the seeds from the stem to isolate heavy metals from the soil.  In fact,  sunflower planting initiatives have been put in place in both Chernobyl and Fukushima to scrub the radioactive isotopes from the soil in the wake of nuclear material release.

So there you have a few quick, interesting facts about sunflowers.  My understanding (and thus, this post), is not at all well developed, but I invite you to read more on the topic yourself.  Surprisingly interesting for what seems to be a generic flower.


Saturday, December 3, 2011

Cancer, and related progress.

Cisplatin, a drug used to treat cancer.

Whilst my education concerns the physical sciences and not those of life, over the past few years I have been trying to follow developments in cancer research.  I am certain that most of my readers have seen the devastating effects of the disease.  It is as if the entire life of a friend or loved one drains from them before your eyes.  My reading on the subject is not exactly academic, and my understanding may be rather simplistic, but I would like to write what I know.  There is good news and bad news, so we will go over the bad news first.  As always, I invite feedback if I have made a mistake or had some oversight.

The bad news is that cancer is not a simple disease to fight, from a medical perspective.  As it turns out, "cancer" is sort of a blanket term referring to a mutation which causes uncontrolled replication of cells.  The problem is that cancer will attack various parts of the body at entirely different rates.  The other issue is the rate at which cancer spreads to different parts of the body, particularly the lymph nodes.  While my understanding of this is woefully limited, it would seem that the lymphoid system is a network that traverses the human body.  The nodes of the system are an excellent target from a cancer's point of view, as it allows for easy transport of cancerous cells to the rest of the body.  As a result, once a cancer reaches the lymphoid system, it is exceedingly hard to fight, and even harder to defeat.

To distill this information, to fight cancer medically is to fight many different diseases.  Many researchers do not believe there will ever be a definitive cure for cancer because it is such a varied disease.  Now, to understand the difficulty in curing the disease, I will recall an anecdote from my second year biochemistry course. Dr. Mezl told us that killing a virus/disease is simple.  If presented with a beaker full of harmful cells, one can douse it with corrosive chemicals and the problem will be solved.  The challenge of medicine is to selectively kill the offending cells while leaving the host unscathed.  The development of one silver bullet for such a varied disease is certainly a daunting task.

Recently, there have been some glimmers of hope.  Three patients with leukemia were given an experimental treatment in which their white blood cells were treated to make them aggressive hunters of cancerous cells.  Two patients were cured outright with the third having a 70% reduction in symptoms. The best part of the treatment is that the aggressive white cells remain in the body in case the cancer returns.  You, my non-spambot reader, may wonder how the white cells became hunter killers.  The researchers needed to insert genes which would make the white cells as aggressive as possible, and what do we know of which is notorious for such characteristics?  In what appears to me as a bizarre twist, the answer is HIV.  A virus known for ravaging the immune system can be utilized to hunt and kill a form of cancer.  Unfortunately for now, the treatment remains prohibitively expensive since the patient's own white cells must be treated, but it is a glimmer of hope.

In a separate, equally fascinating development, hot peppers may offer a general treatment for cancer.  My monocled, regular readers will recall capsaicin is the active ingredient in spicy food, so we know that the human body is capable of tolerating the chemical.  Now, the tests performed seem to be mainly in laboratory conditions, so we must be cautious of the results.  However, capsaicin appears to selectively attack the mitochondria of cancerous cells over healthy cells.  Therefore, at least in theory, it appears to fit the ideal characteristics of a cancer treatment.  Since the treatment does not appear to have been performed in actual humans, it may not work in the real world.  However, I am certain that lessons can be learned from this observation which could potentially lead to an outright cure.  It has also been noted that cancer rates are lower in countries where the diet is spicier (Southeast Asia, Central America), though I wonder if the life expectancy of said areas would affect the absolute rates.

So, the news is bleak at times, but there is also hope.  Finding a cure for cancer will not be an easy task for the researchers and doctors of the world, but things worth doing are rarely easy.  I am certain that humanity won't back down from the challenge, and that a cure will be found.  It will take time, dedication and co-ordinated effort, but it will be found.

1) A paper dealing with capsaicin and cancerous cell death can be found here, though searching academic databases for "capsaicin" and "cancer" certainly return a lot of results.
2) If anyone with a background in life sciences notices mistakes, please let me know so that I may change this post for the better.

Wednesday, November 16, 2011

Movember, and Facial Hair.

Karl Marx.  Political ideologies notwithstanding, the man had a remarkable beard.  Source.

It is halfway through the month of "Movember", where men raise awareness (and funds via sponsorship), for prostate cancer by starting November 1st clean shaven, and then growing a moustache for the rest of the month.  My understanding is that this practise started in Australia, and became somewhat of a viral phenomenon.  I must say that it is an interesting way of raising awareness of a male-specific problem in a way that only men can.  However, I have realised that I have very strong (and somewhat irrational) feelings regarding the practise.  I wish to write as much to elicit responses as explore my own feelings on the matter.


While I fully support raising funds and awareness for cancer research, I will say that my problem with this practise is that most men growing moustaches do so for the novelty of a moustache.  Very few men shave off a moustache or beard in order to participate, most are usually clean-shaven all the time.  In this way, the idea of facial hair is trivialised.  It is only to be paraded out when there is a need for it, whereas otherwise it is kept hidden and is considered a bother.

In the interest of full disclosure, I myself am a bearded-Canadian, and probably biased.  I decided after shaving my mutton chops three summers ago that:
1) I look silly and awkward without facial hair,
2) Not having facial hair when winter strikes is terrible, and
3) I would try my best to never be bald-faced again.
I will also note that my father has had a beard for the duration of my life and that my paternal grandfather would never be caught without a moustache.

Having said this, I have heard many a reason not to have a beard.  Men complain that a beard is itchy.  This is indeed true, but only for a period of roughly a week while growing a beard.  I personally call this the "itchy phase" (not academically verified, but universally supported when consulting with bearded men), and it is the reason that many men do not have a beard.  Women will also complain that a beard hurts their skin when kissing a partner.  Again this is true for shorter beard lengths, and is like any bodily hair in that short hairs are prickly/rigid, but longer hair is not.

Of course, my dearest monocled, non-spambot reader, you may wonder why women so frequently encounter stubble.  Psychology may have an answer, as outlined in Scientific American Mind on Sept. 23, 2011.  You see,  women are subconsciously drawn to men who can grow a beard.  The problem is that women also judge bearded men as aggressive, which is not a desirable quality in a child's caregiver.  Therefore, men with stubble are consistently rated as more desirable/attractive than their bearded and clean shaven brethren.  It would then logically follow that stubbly gentlemen are more likely to prickle women, and thus women are more averse to facial hair than is fair.

I will also state that in cold Canadian winters, a beard is of great utilitarian value.  Once the temperatures drop and the winds pick up, many people will wrap their face in a scarf.  Beards and other forms of facial hair accomplish the same thing without the need for external support.  My significant other noticed this phenomenon after touching my face when I had come inside after a very cold walk home.  Skin temperature is dramatically warmer under a beard than unprotected.

Paul Mara sporting a playoff beard with the New York Rangers.  Source.

Beards are also grown as "playoff beards" for fans of the sporting world.  A fan will grow a beard for the duration of a team's playoff run, and shave when the team either wins a title, or is eliminated from competition.  While reading an article on the practise (I cannot recall the name of the author), I read an interesting thesis.  The author claimed that the beard was the last bastion of masculinity in today's world, in that it was the only thing that a man could do that a woman could not.  While some women do indeed grow some facial hair, the growing of an entire beard by a woman is usually only accomplished after some sort of hormonal therapy after which the gender of the person in question is no longer technically female.

It is often speculated that the men of western civilisations are becoming neutered.  This is in fact the central premise of the television show "Man Up!", and is also the thesis of an increasing number of songs in popular culture.  I am not sure that it is a problem that men spend an increasing amount of money on cosmetics, or that they pay more attention to their appearance.  However, I feel that the discouragement of growing facial hair is roughly equivalent to demanding women bind their breasts so as to minimise the appearance of femininity.  It is a physical reality of the gender, and I do not think that significant effort should be expended in controlling either phenomena.

These things in mind, I keep a beard.  It is useful, and it is not something that all people, let alone all men can do.  To end this caffeine-fuelled case of mad typing, I will leave you with the attitude of my grandfather towards his moustache.  In the winter he kept a beard, but you would never see him without a moustache.  During the last hospitalisation of his life, my grandfather was kept in a coma.  In order to fit an oxygen mask properly on him, the nurses told him that they would be shaving his face.  When he heard this statement, he opened his eyes, and slowly and deliberately uttered the last words he would ever speak:

"Not the moustache."



Edit: -ed to include notes on psychology and stubble after the caffeine wore off.  I will also leave the following YouTube video for my bearded brothers:

Friday, November 4, 2011


A cup of coffee, served "black."  Source.

I have long thought that I should write a post on my most beloved of beverages (but please don't tell Beer, Gin or Vodka, that's an awkward conversation I'm not ready to have), and, in typical fashion I have been bogged down thinking about how to properly explore it as a topic.  Whilst I may edit or otherwise reconstruct this post in the future, I shall dive in and attempt to share my interests.  I hope that you, my dearest, non-spambot reader will enjoy it all the same.

A brief aside: As always, my claims will be formally unsubstantiated, but I trust that a consultation with Google will either support or refute me.  If you do notice an error, please comment such that I will be able to remedy the situation as transparently as possible.

My historical knowledge of coffee is somewhat lacking, but I do recall a couple notes of interest.  It is said that coffee's rise was due in no small part to that of Islam.  While the consumption of alcohol was forbidden by the faith, coffee was seen as an acceptable substitute (must like cocaine-laden beverages were in the USA during prohibition).  In stark contrast, some European coffee-houses were banned in the 1600-1700s (universally in some countries), due to suspicions that they were used to conspire against the local monarchies.  For various reasons, a non-trivial contribution being the deliciousness of the beverage, I am certain, coffee persisted and became the beverage I know and love today.

The coffee plant persists only between the tropics of Cancer and Capricorn, an area which may be known as the "Coffee Belt".  The plant naturally grows largely in the shade of larger plants and on slopes, likely for drainage.  When you see coffee labelled as "organically shade-grown", this is to what they refer.  It is my understanding that this is the Arabica coffee which we drink.  The other variety, Robusta, was largely developed for the purposes of serving humanity's likely unhealthy dependence on the stuff.  Robusta coffee will grow in (on?) traditional cropland in full sun, but ultimately results in a poorer quality product.  At this point, I shall digress and recall a commercial for Nabob coffee.  The gentleman featured in the commercial detailed how much coffee was shade grown, how much was sustainable/fair trade/what-have-you, and said that of that shade grown/fair trade/what-have-you, Nabob beans accounted for only 10%.  He then smiled and asked that we make it 100%.  Terrible, I declare.  He should simply wish that sustainable/fair trade/what-have-you beans will become a larger share of total bean production, and potentially wish that Nabob will represent a larger portion of the aforementioned beans.  I cannot imagine why he would wish a monopoly on S/FT/WHY [interesting that "what have you" becomes WHY, I digress further] if he truly cared about sustainability.  But anyway...

The fruit of a coffee plant.  Source.
After the coffee has been grown, it must be roasted.  I am given to understand by an excellent comic by The Oatmeal on the subject that the green bean at the centre of the fruit will pop twice upon roasting.  The second popping of the bean indicates that it has finished roasting.  I assume it is at this point which "light" roast coffee beans are removed.  It is my understanding that the duration of roasting determines light v. dark classifications, as well as those in between.  It also determines the concentration of caffeine in the coffee beans.  Caffeine will undergo thermal degradation at roasting temperatures, so light roasts contain more caffeine than the dark counterparts.  Therefore, if one desires caffeine most from their coffee, one would chooses a light roast.  Alternatively, if flavour is paramount for a drinker, one would choose a dark roast (a wonderful example being the Continental from Second Cup).

Once the bean has been chosen, one must choose the grind and brewing method.  These go hand in hand, as the grind is determined by the time water will be in contact with the grinds.  In North America, we tend to use a grind labelled "coarse" and use a drip brewing method.  Here, water is heated to near its boiling point and dripped over coffee grounds housed in a basket.  The resultant extract of the coffee beans drips out the bottom of the basket and into a carafe.  The machine is relatively simple, requires little thought and, perhaps most importantly, is difficult to screw up.  This last feature is incredibly important when one considers that many of us are largely useless before the coffee has been brewed [in the interest of full disclosure, I am always vigilant in finding new and exciting ways to screw up the morning coffee].

The Bodum has enjoyed recent popularity, and is a method of coffee preparation utilizing a French press.  Freshly boiled water is poured over very coarsely ground coffee and kept there for several minutes within the cylindrical vessel.  Afterwards, a [metal grate] plunger is lowered which holds the grounds at the bottom, and allows the brewed coffee to be poured from the top.  I am told the finished product is rather nice, but I have never enjoyed coffee prepared with a French press.

An espresso maker with crema shown.  Source.

While the above two methods are really two ways of making brewed coffee, a slightly different product is espresso.  You will note this is not "expresso", but espresso.  I have often described this method as the end product of an engineer trying to make concentrated coffee.  It is as labour intensive as it is lovely.  One must use a very fine grind of coffee [the water is in contact with it for a very short time] and tamp it into a metal basket [using a tamp, able to press the grinds into the basket evenly].  YouTube videos recommending using roughly 30lbs of weight behind the tamp.  This basket is placed into a holder, which is then locked into the espresso machine.  In my personal machine, steam at ~15 atmospheres of pressure forces water into the basket, allowing the brewed espresso to flow through a pinhole at the bottom of the basket.  The shot is "pulled" for roughly 15-20 seconds before it is stopped.  At this point, the crema [with an accent so the e makes an "ay" sound] should be even, off-white and delightfully foamy. It is worth noting that espresso-ground coffee must either be purchased directly, or ground with a burr grinder.  A regular coffee grinder using a blade will not produce a fine enough particulate size for espresso.  A burr grinder is not unlike a mill stone with sharp burrs attached, and it may also be adjusted to allow for normal "coarse" grind coffee, or the very coarse grind required for French press brewing.  In a fun physics note, when grinding coffee to the finest of grinds, static charges result.  Then, when a very tired operator opens the vessel containing the grinds, they have a tendency of flying everywhere, the static forces easily overcoming gravity for small particles.

Naturally, with human beings consuming coffee the way we do, the health effects of ingesting this brew is continuously studied.  I shall not begin to speculate on all the potential benefits that have been preached, both because I feel I have not read enough into the possible decreased risk of Alzheimer's, prostate and other diseases.  Instead, I will touch on a few interesting notes which I have come across.  Regardless what health benefits one may be chasing [it is touted as having lots of antioxidants, among other things], one must be careful not to consume much more than three cups per day.  Too much caffeine will stress the human body, and ill health will result.  That being said, one may note that a lot of coffee is consumed by those who are thinking during work.  This is due to the fact that caffeine has been found to inhibit the chemical pathways which cause fatigue after mental exertion.  Not only that, but it has positive effects on physical performance as well.  In fact, Cracked has produced an article detailing the super powers bestowed upon mortals when they consume coffee.  Just try to keep it under three cups a day.

The benefits of consuming coffee lead me to wonder whether it is to us what Freud thought cocaine would be.  Freud was a large advocate of cocaine, thinking it a cure-all, and extolling other virtues.  I believe a couple were increasing chattiness and rosiness of the cheeks.  He only stopped when he saw how cocaine destroyed lives.  When working at a rather slow-paced job, I drank an awful lot of coffee. In some ways, I actually fit symptoms of drug dependent behaviour.  My sleep patterns suffered, and I was generally moody and irritable, likely a byproduct of stressing my system too much with caffeine.  Cutting down my consumption was difficult, but unlike with cocaine, my life was not at risk in doing so.  Maybe Freud was right, but he had the wrong substance.

It would seem that what was meant to be a brief discussion of coffee has become drawn out and rambling.  In any case, enjoy your coffee tomorrow.  I know I will.


Wednesday, October 12, 2011

Improbable Research, and the Ig Nobel Prizes.

A pancake.  It will make sense later, trust me.  Source.

The 2011 Ig Nobel Prizes have been awarded.  No, there is no affiliation with the far more prominent Nobel Prizes.  My interest in the Ig variant is the wedding of two things I love: science and humour.

When the Ig Nobel Prizes were established, they were defined as those experiments which "can not, or should not, be repeated."  This included experiments such as the one featured on the popular television show Myth Busters, that concluded a human swims equally well in water as it does in gelatin.  It turns out that the added resistance of gelatin both hinders forward movement is made up for by the resistance to the swimmer's stroke.  Fittingly, the current description of Ig Nobel winning research is that which first makes you laugh, but then makes you think.

To accompany the Ig Nobel prizes is a journal, the Annals of Improbable Research.  It provides an outlet for research gems to which I am occasionally directed.  A recent discovery of mine was this article which shows that, mathematically speaking, the State of Kansas is flatter than a pancake.  Of course, when presented with such knowledge I smile and chuckle to myself.  Then, as intended by the editors of the Annals, I think to myself how remarkable such a discovery is.  I am also reminded of a potentially unsubstantiated claim that, were a billiard ball the size of the Earth, its imperfections would be deeper than the Marianas Trench, and higher than Mount Everest.  I would imagine that this is a testament to the power of gravity, but am certainly not an expert on the subject.

Of course, in the midst of mildly hilarious research material, there is also that which raises more concerning issues.  One winner for literature is Alan Sokal for his paper "Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity".  Sokal submitted the paper to the journal Social Text in an effort to show that it would publish anything that sounded good and supported the preconceptions of the editors.  The paper was written to be nonsensical with heavy usage of quotations from postmodern academics on topics of math and physics (i.e. not entirely accurate).  At the same time Transgressing the Boundaries was published, Sokal revealed to Lingua Franca that the entire article was a hoax, and its submission was meant to discredit Social Text on the basis of the latter publication's lack of intellectual rigor [fact checking].  The publication process is certainly an important part of modern academia, and shortcomings of this nature are important to catch and note.  Sokal just found a hilarious way of doing so, and I enjoyed reading about it.

I would encourage you to google the Ig Nobel prizes and take a look at past winners.  I hope you will smile, and then think.  I enjoy doing so, perhaps you will too.


Saturday, September 17, 2011

Female Aggression.


Recently there has been an increase in the number of news stories and reports of female aggression.  I find some of this information interesting, and some of it troubling.  This post is not nearly as well researched as my norm (the information appears harder to come by), but I would nonetheless like to explore the issue.  I have also consciously foregone including a nice, shiny picture to lead this post, because I feel it would be in poor taste.

To begin, it is worth exploring how female aggression usually differs from that of males.  Men, throughout their life cycle, are far more likely to resort to physical aggression than women.  It has been suggested that this could be due to some evolutionary strategy to impress females, but I digress.  Women are far more likely to "socially assault", if you will, their intended victims.  This usually takes the form of spreading distasteful rumours meant to tarnish the reputation and/or jeopardize the social relationships of the intended target.  This is particularly harmful because, in examples of children, this aggression often goes unnoticed and is not dealt with, it is far easier to break up a physical fight between boys.  One may also argue that it is a far more damaging form of aggression, we humans are geared to be socially accepted by our peers.  The lack of this acceptance can destroy a person's emotional well-being.  Louis C.K. sums it up eloquently, but filthily, by saying that "... women are nonviolent, but they will shit inside your heart."

Of course, this is not to say that no man has ever spread nasty rumours, or that women are never physically violent, but it is a documented trend.  However, this was not the main point of my post.  I have noticed an increase in the reports of domestic abuse with female aggressors.  While I have very little in the way of sources, let me say here that primary researchers in the field seem to be Archer, Straus, Desmarais,  and Ramirez.  These researchers have pointed out some other interesting and potentially problematic trends.  Outside the Western/Developed world, domestic violence is heavily dominated by male aggressors.  However, in developed nations, and in young heterosexual relationships especially, females are becoming the predominant aggressor.  If there is one aggressor in a relationship, it is twice as likely to be the female.  Further, the female is more likely to instigate violence.  As might be expected from Hollywood interpretations, men are more likely to choke or strangle, but women are more likely to use weapons, kick, slap, bite, punch, and commit what is defined by Straus and Ramirez as "severe assault".

This fact itself raises a host of interesting questions.  Dutton and Nicholls in 2005 reported that men were far less likely to report domestic abuse, and often did not regard the actions as a crime.  Do traditional gender roles influence this, because men could or should not be meaningfully harmed by a "weaker" sex?  Does it stem from the fact that women are less likely to actually cause physical harm despite the severity of their attacks?  Have we somehow legitimized female aggression with "benevolent sexism"?  This is, for the record, the belief that women are weaker than men, and should be afforded practical (holding doors, paying the cheque at dinner), and legal advantages or protections as a result.  Is this the reason that municipalities such as North Bay now report more female domestic aggression than male?

In fact, a YouTube video here shows a hidden camera segment by ABC News demonstrating the reactions of passersby to a woman publicly abusing a man.  The actions of the actors are largely dismissed as nothing serious.  The female actor was also privately applauded by a few women who saw the abuse taking place.  It is, to say the least, a strange phenomenon.

My main concern with this trend, however, is how it is handled by us as a society at large.  I cannot for the life of me remember where I read this, but it was written by a woman in national Canadian news publication.  The article took the position that there are not legitimate anger management therapies available for women.  When men take anger management classes, they are taught that their anger has the potential to harm others around them.  Their anger is dangerous; their anger needs to be controlled for the benefit of themselves and others.  In contrast, women taking the equivalent classes are taught that their issues are more environmental.  There are people and circumstances in their lives that cause them to lose control.  The emphasis is then placed on how to deal with these people and circumstances, and not so much on controlling the anger that dwells within them.

I would like to pause and say that I am not implying that women are more dangerous than men, and I do not mean to trivialize male aggression or battered women.  I firmly believe that domestic violence, regardless of the gender of the aggressor, is toxic and detrimental to society as a whole.  I also think that how we are dealing with it as a society could potentially lead to harmful situations, if angry outbursts are habitually attributed to environmental stressors.  Should time reveal that this gender-specific method of therapy be effective, you may consider my concerns relieved.  For the time being, I feel more in-depth studies might be of benefit, and potentially find a cause for this female aggression.  This assumes of course that it is a new phenomenon, and historic under-reporting has not skewed the available data.

I ask that you consider what has been presented here.  Perhaps discuss it with a friend or peer.  Awareness and critical public discussion may be key to developing a better understanding of a potentially unhealthy trend.


Wednesday, September 14, 2011

Vaccinations (incl. MMR)


I'm not sure if anyone else has noticed this, but it appears that vaccinations have been brought up in the media lately.  I will lead this post with a disclaimer that I know comparatively little about vaccinations (my education has focused on physical science), but I feel that I know enough to write an informed post on the subject.  Prepare yourself for the starry-eyed wonder of a non-life-science type marveling at the human immune system.

I will start off by explaining the routine influenza vaccination, because I assume most vaccinations work on the same principle.  The vaccination itself consists of virus strains which have somehow been stripped of their ability to harm humans (preventing reproduction or harmful traits).  The strains represent different mutations of the influenza virus, the mutations representing different evolutionary strategies of the global influenza population.  Now, these two facts are important because they represent the rationale for most complaints I hear about the vaccine routinely given during flu season.

The most prominent (and baffling, in my opinion), is that "the flu vaccine gives me the flu."  No.  No it does not.  When the human body detects the presence of the influenza virus, it [sometimes] responds by the same mechanism it would in the event of a full infection.  That is to say, fever, aches, runny nose, et cetera.  The body then forms the necessary antibodies to prevent another infection from that specific strain of influenza (this will be important later).  However, rather than flu-like symptoms on week timescales, you might experience it for a day or two.

Another complaint I hear about the flu vaccine is "I got the flu shot, but I still got the flu!  Also, I hate monocles and top hats!"  Now, while the latter half of this statement is no doubt infuriating, take it as an indicator of the quality of person giving the statements.  This problem can represent that the flu shot only protects against ~90% of the influenza strains in the wild, however, it is often due to misattribution of sickness.  The most likely explanation for this is that people get sick with infections not due to influenza, but attribute it to the broadly misused term "flu" (as in "I have a stomach flu" meaning "I have diarrhea", or "I have a 24 hour flu" meaning "I have a short-lived bacterial infection").

Now, to the point of this post.  The MMR vaccine is a shorthand reference for Measles-Mumps-Rubella vaccination which is commonly administered to small children.  A publication in a medical journal The Lancet in 1998 suggested that the MMR vaccine could cause autism in susceptible children.  A dozen papers to the contrary and twelve years later, The Lancet retracted the incorrect article, but the damage was done.  Misinformed (and potentially over-protective) parents everywhere attempt to refuse the vaccination for their children.  This is due largely to parents reading internet articles without thinking critically (but you can totally trust my blog posts, guys!), and the ready acceptance of anecdotal evidence (e.g. But Shirley has a cousin who's uncle's kids got autism from MMR!)

I have also heard the concept of the "free rider" or "herd immunity" hypothesis used in defense of going without the MMR vaccine.  The theory here goes that if a large enough percentage of a population is vaccinated against MMR, those un-vaccinated children are unlikely to contract the disease.  Naturally, this argument breaks down when one considers globalisation, and that these children are the only vulnerable ones in the larger population, and will probably get sick.

My room mate (with a B.Sc. in Health Science), also raises the argument that in the best interest of publicly funded health care, Canada and/or Public Health would not release a vaccination with any known risks or correlations (or at least not without signing a long and wordy contract identifying all risks of the vaccine).  It's a valid argument, especially considering that the Canadian health care system would then be forced to deal with higher health care costs associated with autistic children.

I admit that children go without getting vaccinated because their parents are trying to protect them.  I do not have children, and have not experienced the profound shift in thinking that parents undergo, but I still do not understand the opposing viewpoints on vaccinations.  All I can do is recommend critical thinking when you read.  It's a profoundly rewarding endeavor.

Note: For the record, the leading graph is the reason that children receive the MMR vaccine.

Sunday, August 28, 2011

Genetic Algorithms.

The hominoids evolved from a common ancestor.  Source.


I have been thinking a lot about genetic algorithms lately.  The idea was introduced to me here, where I lost many an hour watching cars evolve to fit different tracks.  I later saw it being used in the lab where I did my honours thesis, with a peer attempting to design better fuel cells.  Perhaps I shall start with an explanation of what exactly these genetic algorithms (GAs) are.

A GA seeks to mimic the natural evolution that we see in our day-to-day life on Earth.  Take for example how we humans reproduce.  We are produced via sexual reproduction, we get half our chromosomes from our mother and the other half from our father, called "crossover" in terms of genetics and GAs.  After random mutations (which GAs also utilise), we are essentially a genetic experiment.  We have a fairly high success rate currently due to the societies we have built, but in earlier eras survival was not necessarily the virtual guarantee it is now.  Should the organism survive to procreate, it is largely considered a success.  The better the individual, the better the chance of this success.  Therefore, with increasing number of generations, the "good" traits we inherit from chromosomes should come to predominate in the larger population, since ideally those individuals with "bad" traits are less likely to succeed and procreate.

Life, in our case, is the equivalent of a "fitness function" for GAs.  Life determines fitness of individuals by killing off or making the less successful crossovers less likely to breed.  In terms of computers, the fitness will be evaluated based on what the scientist wants to accomplish with the algorithm.  The boxcar example above evaluates the fitness of cars based on how far they get on a given track, and how fast they do it.  A selection process then chooses breeding pairs to create the next generation (with the most successful individuals very likely to reproduce).  Naturally, crossovers of fit individuals does not guarantee fit offspring, but it becomes increasingly likely as the population will "converge" to a solution for a given problem.

Sunlight.  You'll understand if you read the next paragraph.  Source.

By now, my dear reader, you must be wondering what on Earth can be accomplished with a GA.  The answer, really, is whatever you want it to.  A video of a TED talk by Bill Gross was my inspiration for this post.  Bill Gross decided that he wanted to design a solar energy solution using mirrors and Stirling Engines, and he used a GA to do it.  He designed the computer to utilise chromosomes based on mirror pieces in three dimensional space (presumably with random placement and orientation), and with enough time, the GA gave what it felt to be the best solution based on the fitness function used (it sought to maximise the hours of sunlight the device would be useful for).  I highly recommend watching the video, at least so that one can view the results, which are truly remarkable.

The strength of GAs is that, so long as they utilise a good fitness function, they can come up with solutions a human engineer might never come up with.  Perhaps we as humans would think of these solutions with enough time, but we are creatures of habit.  Computers, given enough degrees of freedom, can come up with truly remarkable solutions without the bias towards existing solutions that we humans may exhibit.  These solutions often represent the convergence of an entire population within the computer to one design.  It is just as we humans have come to where we are today through genetics and evolution.

Arguably the most fascinating aspect of GAs is that we are not exactly certain why they work.  There exists no theorem or mathematical proof which would explain why a GA would ever be a good solution.  Additionally, the solutions generated by GAs often catch scientists off-guard.  They look strange and new to us, but must be a good solution, as they have already been tested under the constraints of the fitness function.  Bill Gross, too, was surprised to see what his GA had developed, and like other scientists, had no idea how it had come to such a conclusion.  The only reason we have to think GAs will work is the large GA experiment we see around us, commonly known as life.

As a result of all of this, I have found myself wondering where else GAs could improve our lives.  I also think I could utilise a GA to select a fantasy hockey pool team, a thought that titillates me to no end.  I'm not sure I've done the best job of explaining GAs here, but I hope I've piqued your interest enough that you will do some reading of your own.  It's truly wonderful stuff.


Thursday, August 25, 2011

Garbage Incineration.

Municipal waste being incinerated.  Courtesy Wikipedia.

It would seem that there is some kerfuffle in the Greater Toronto Area.  The ground has been broken on a garbage incinerator project, and the locals are certainly worked up about it.  While I will not pretend to be an expert on the subject, I do know some pertinent science that I am sure you, my monocled, Brandy-swirling readers would love to hear about.

I will freely admit that at first, burning garbage seems like a bad idea.  After all, many of us have thrown things onto a fire and seen the evolution of black pillars of foul-smelling smoke.  This, however, is far different from what goes on in a garbage incinerator.  You see, inside an incinerator, it is much easier to get up to high temperatures in an enclosed space than in an open fire pit.  Those of you who have used a chimney to ignite charcoal (or "cookin' biochar", as I am certain no one calls it) may be familiar with this effect.  The objective here is to achieve total combustion, where all carbon [or fuel, the garbage] is fully converted to carbon dioxide ["is fully oxidised"].  This is far better for our air than the results of impure combusion, which include much higher amounts of ash, soot [what I assume to be aerosolised/dispersed ash, really], and harmful products like carbon monoxide.  Fire pits see impure combustion when "smoky".  The combustion above appears to be very pure, by comparison.

The structure and synthesis of polystyrene. Wikipedia.

I will also admit that, in many cases, garbage incineration is often accompanied by the abandonment of recycling plastics.  They are necessary to fuel the blaze, and are included with the garbage.  This, too, sounds like a nightmare to the environmentalist.  I agree that in a perfect world, all plastic would be recycled forever.  Sadly, this is either not the case, or not possible.  Some classes of plastics would be easy to recycle.  Styrofoam, polymerized styrene [or "polystyrene"] is an example.  This is easily dissolved in the solvent acetone.  Acetone also has a very, very low boiling point.  It would be very easy to dissolve all those meat trays and packing chips, then boil off the solvent to have relatively unscathed polystyrene to reuse.  Unfortunately, as with other classes of plastics (water bottles, especially), this is not the case.  The manufacturing process for these types of plastics is inexpensive enough that the recycled product is too expensive for anyone to purchase.

The other challenge facing plastic recycling is the nature of the substance.  As can be seen above, plastics [polymers] are very long chains of some individual molecule [the monomer].  The recycling process must heat plastic so that it can be reformed.  Heating damages the bonds of the polymer, causing the plastic to degrade.  In fact, the reason that one rarely sees 100% recycled plastic products is that the structural integrity of recycled plastic is compromised, and it must be blended with new plastic so that the product may serve its purpose.  For the record, recycled metal does not share this problem, and I think it a fabulous idea, given the environmental costs of smelting metal.  Metal is also easily recovered in the incineration process.

A garbage incinerator in Vienna.  Source.

"Now see here!" You may demand.  "Won't this contribute to global warming?  Spewing out all that carbon dioxide?!"  This is an excellent point, and I am glad that you [might have] raised it.  It is true that greenhouse gas emissions will be added to with garbage incineration, however, it is much better than other emissions associated with dumps.  You may have seen torches burning outside of buried garbage dumps.  I know that I have near Carp, Ontario.  The reason for this is the venting of methane, a common byproduct of garbage disposal.  A methane leak is far, far worse than the leaking of carbon dioxide into the atmosphere.  The reason can be explained with very simple physical chemistry and math (you may skip the next paragraph if you are truly averse to it, though I find it interesting).

The surface of the Earth is heated by the Sun.  As can be seen in math here, the light that an object emits depends on its temperature.  The very hot Sun emits all colours of the rainbow, but the Earth is by comparison only lukewarm.  Objects at that temperature emit infrared (IR) radiation (this is how night and thermal cameras work).  Normally, a substantial amount of heat from the Earth is converted into IR and is lost to space.  Molecules, however, will absorb IR and begin to vibrate, blocking the exit of the heat into space.  This is the cause of the greenhouse effect.  Now, not all molecules are created equally.  The amount of IR that a molecule can absorb depends on how many ways that molecule can vibrate, known as vibrational modes.  The number of vibrational modes of a molecule depend only on the number of atoms.  Carbon dioxide has three atoms, and linear molecules follow the formula 3N-5, meaning it has 4 modes of vibration.  Non-linear molecules have 3N-6 vibrational modes, giving methane, a 5 atom species, 9 modes of vibration (or something like that).  Other math which I do not wish to get into demonstrates that this makes methane 21 times worse to have in the atmosphere than carbon dioxide.

We must also consider the issue of storage.  Many municipalities are running out of space for garbage, and it is much easier to bury the remaining ash of an incinerator than it is for the immense volume it started as.  Also, while most modern dumps are more or less sealed, leaks of contaminants are not impossible.  Many contaminants released by the incineration process can be captured before discharge into the air, meaning that, in my opinion, it is likely safer to incinerate garbage than it is to simply bury it.
Power transmission lines, because I discuss it below, and this certainly is a large block of text.  Source.

I must also discuss the issue of power.  Conventional dumps may use the methane generated by the garbage to spin a turbine and generate power, which seems like a fantastic idea.  Energy from our waste. However, garbage incineration offers a much higher amount of energy to us.  The fire from the incinerator can be used to generate steam from a boiler.  This would spin a turbine in exactly the same way as nuclear, coal and natural gas power plants do, but from a power source we are currently wasting. In a twist on this idea, a company called Plasco has found that heating and exposure to a plasma torch can produce refined syngas (mentioned previously in my biofuels post), which can then be used to make various other products and fuels.  It is also worth noting that steam-generating applications can route waste heat to nearby schools and hospitals to heat hot water, boosting the overall efficiency of the process.

With this in mind, I feel that garbage incineration is beneficial, and ultimately an opportunity.  It would lead to safer disposal of our waste, which is inherently invaluable.  Further, it represents an untapped energy source which could ease strain on our grid, and provide baseline electricity generation which most renewable fuels cannot (as the sun does not always shine, nor does the wind always blow).  I think that, if done properly, widespread incineration efforts would lead to a better tomorrow.


Saturday, August 20, 2011


Temperate, mixed forest.  Courtesy Wikipedia.

It was not too long ago that I was sitting in a crowded environmental issues class, listening to my professor (who has a blog here), extol the virtues of trees.  He summed it up well with the statement "Trees are the answer.  What's the question?" They do have a number of benefits to the environment, and subsequently us humans.  Let me first tell you a little about trees.

Essentially, trees will grow wherever they can.  So long as there is enough water (rain, usually), and the soil is not in some way harsh, trees will start popping up.  First, small grasses and weeds will cover available soil.  Next, taller weeds compete and win against the shorter growth.  With the shade from taller weeds, conifers (usually evergreens with needles), begin to take hold.  Then, with the limited lifespan of conifers, deciduous trees may also be added to the mix.  This is how the mixed forest of North America works, anyway.  In fact, switchgrass may be used to speed along this process as a "tall weed" analog in environmental regeneration efforts.  Its roots are also an excellent tool for fixing soil to avoid erosion, but I don't need to tell you, my monocled, well-dressed, non-spambot readers.

The Taiga in Nordic-Europe.  Courtesy Wikipedia.

Trees do much for the environments of which they are a part.  Excluding habitat considerations, their root systems bind the soil to prevent erosion.  The leaves and needles left on the ground to rot enriches the soil's carbon content, making it more hospitable to other plant life.  They also provide shade to the forest floor, which becomes important in places where water is a little more scarce.  The Taiga forest, that which encircles the globe through Russia, the Nordic countries, Canada and Alaska, will actually affect global carbon dioxide concentrations when the seasons change.  Supposedly, it is as if the trees all take a deep breath in preparation for winter, storing potential energy to use when the sun is scarce and conditions are harsh.  In the interest of full disclosure, I may have this backwards for some reason.  However, I just handed in my last paper of my University career, and I relish this recreational writing in which I do not need to meticulously fact check.  I am a terrible academic.

An approximate representation of the Sahel region of Africa.  Courtesy Wikipedia.

Trees have also been part of a stunning revolution in the Sahel.  Most of my information on this topic comes from a truly fascinating article I read in Scientific American, and not necessarily scholarly resources (ANARCHY REIGNS... *ahem*).  The Sahel is a sub-Saharan region of Africa which is prone to drought and subsequent famine, and by all accounts is a terrible place to live if one values food. However, recent years have seen an incredible increase in food production across the region.  This is not in thanks to Western scientific efforts, but rather the scientific, inquisitive spirit that persists in all mankind.  An especially curious man named Yacouba Sawadogo led this revolution.  He is a subsistence farmer who speaks only the local dialect, and no official language of Burkina Faso.  At a time when crops were poor, he followed the local practice of making small conical holes in the soil to direct the scarce rainfall towards the roots of his plants.

Yacouba's innovation started with the addition of manure to these holes.  Despite being called wasteful by his peers, he felt it would work.  I feel it made good sense, the collected rain would filter through manure, bringing nutrients to the plants.  The true revolution, however, was to follow.  In the manure, one could find seeds of all varieties, a notable constituent being the seeds of the local trees.  The use of trees in farming is by no means a new idea, the shade is good for crops in places like the Sahel (just as grass is useful between rows of corn).  However, live trees do not have a good success rate in being transplanted to these regions, and they often die.  Yacouba saw these trees start to grow, and waited to see what would happen.

The trees, which did not have to endure shock of transplantation, thrived.  In a land plagued by famine and drought, crop production increased.  He also had a new source of income, the trees could be pruned and the wood sold for fuel.  It did not take long for the practice to catch on.  All across the Sahel, crop production has increased upwards of 50%.  Families which once kept one grain elevator now require three to four to house all the millet grown.  The 1980s saw very harsh droughts, during which time crop production was kept stable under those farms practicing farmer-managed natural regeneration (FMNR).  Further, it has been suggested that during these droughts, the water table was actually rising due to the widespread adoption of FMNR.  It is an age of unprecedented food security for the modern-day Sahel.

FMNR did not catch on quickly everywhere, however.  In some countries, policies existed which stated that trees growing on a farmer's land did not belong to said farmer, and the trees and/or surrounding land could be seized by the government.  The natural reaction to this is to kill any saplings.  Luckily, the successes of FMNR were so great that the policies have since disappeared, and FMNR is now common practise all across the Sahel.

A Red Mangrove tree.  Courtesy Wikipedia.
This is by no means the only success story of trees.  Though I am sure many others exist, I wish to share another story I find fascinating.  It is via the kind of tree pictured above, the Mangrove.  These trees exist on the border of ocean and land.  In an interesting twist, the extensive root system of the mangrove trees will trap soil which would otherwise be lost to the sea.  With increasing amounts of trapped soil, the mangrove becomes more land than swamp.  It is this way that mankind can reclaim land from the sea via natural mechanisms.  This is practiced in Bangladesh with help from the Dutch (a people quite adept at reclaiming land from water).

You may, as I did, wonder how the tree can survive in such a salty environment.  It is, after all, not easy for plants to do this.  While the roots of the plant keep out well over 90% of salt, not all can be excluded if the plant wishes to get any water.  So, by some biological mechanism (i.e. "black magic", to a chemist), the mangrove tree pumps the salt to old leaves, which then become sacrificial.  The tree drops the leaves, and continues to grow, the mangroves steadily edging farther and farther out into the ocean.

A sacrificial leaf.  Courtesy Wikipedia.

So there you have it.  Trees are truly wonderful.  A natural beauty; a tool of man.  The next time you are out and about, stop and ponder the majesty of a forest, and just what it means to the planet as a whole.  If you want mood music for the experience, I recommend the Pines of Rome by Respighi.  I listened to it while writing this post, and quite enjoyed myself.


Edit: It would appear that trees are also responsible for the evolution of rivers that we know today, according to this Scientific American podcast.  It seems that water used to flow wide and shallow over the land.  It wasn't until the evolution of tree-like species with deep, soil-fixing roots that rivers took their present shape.

Sunday, August 14, 2011


Grapefruit, courtesy Wikipedia.

It is summer in the northern hemisphere.  There is much fun to be had in the sun, vacations and adventure abound.  Unfortunately, with summer comes mosquitoes, and various other biting insects.  The worst part about such pests is that the only 100% solution is to completely cover oneself, which seems impractical and needlessly warm in such a season.

I have long pondered how to deal with such problems.  In earlier years, I investigated how to breed dragonflies.  I had seen them hunt the pests while camping, and was intrigued.  Regrettably, dragonflies breed in standing water, as do mosquitoes.  I have also considered constructing a "bat box", a box in which bats may rest during daylight hours.  In my search through unofficial literature, I found that one can fairly easily house 300 bats in a larger box.  As an interesting aside, in Canada it is necessary for one broad side of the house to face south, and to paint the box black so that the bats will be warm during the day.  I had no idea this would be a concern in weather that I consider stifling.  I also discovered that pests may be deterred by the sound of the bats (imperceptible to us, but a loud alarm to biting insects), which could also provide relief.  For a second digression, I would be curious as to whether or not the presence of a bat house would discourage nesting within human homes.  I know one family who seems plagued by bats in August.  Would a nearby bat box provide an easier home, or draw more bats to the site, and thus the family home?  Details or case studies would be appreciated.

As a final digression on the topic of bats, let us consider ammonia.  Bat feces are rich in the stuff, that which humans use for both explosives and fertiliser (especially for hungry crops like corn).  Brazil (I think) was a world power in the production of ammonia due to its large bat population.  This was, of course, before the Haber process was developed.  This allowed humanity as a whole to produce ammonia from nitrogen and hydrogen gases, and also allowed the Germans to produce explosives in the absence of mined ammonia during The Great War, or WWI.  For the record, there are no evil chemicals, only humans who use them poorly or without due respect.

Digressions aside, whilst bat boxes seem like a good idea to reduce the pest population, I am certain that I would still be bitten throughout the course of the summer.  Currently, the best solution is to use various products one burns to repel mosquitoes, or to use DEET to hide oneself from the pests.  This is a bother to me, that DEET is called a "repellant", but does nothing to repel insects, only hide us from them.

"Now, see here!" I assume you are demanding by this point, brows furrowed over monocles, Brandy angrily swirled.  "Why on Earth did you start this article with a picture of a grapefruit?"  An excellent question, my non-spambot friends.  It would seem that there do exist chemicals which will repel ticks, mosquitoes, biting flies, and all your most hated pests.  One is called nootkatone, and it will repel these insects.  The best part?  It is harmless to us, humans are not affected by the molecule.  The downside?  You will smell like grapefruit (if you dislike that sort of thing).  This is, really, the worst effect of a nootkatone repellent.  It is part of the aroma of a grapefruit, and is added to a beverage known as "Squirt", which I have never consumed.  Grapefruit, so you know, does not contain high enough concentrations of nootkatone to deter the pests itself.  Spreading grapefruit juice on yourself will only make you sticky and dissatisfied.

Nootkatone, courtesy Wikipedia.

The effect of nootkatone on a pest is rather dramatic.  The molecule attacks the nervous system and by some mechanism which I do not understand, causes severe over-stimulation.  The insect will shake itself to death.  The bugs are aware of this, and are deterred by the scent of it.  Whereas an arm covered in DEET will be ignored by mosquitoes, the same arm covered in a 2% solution of nootkatone will repel mosquitoes.  Should the insect pursue your flesh anyway, it will die.

For now, nootkatone is considered "prohibitively expensive" to use in commercial repellents.  Actual repellents, what a concept!  At roughly $4000/kg, there are far cheaper alternatives.  Nootkatol, the alcohol equivalent to nootkatone's aldehyde, has been shown to demonstrate similar effects, and may be much cheaper to manufacture.  Hopefully once organic chemists work their magic, we may have a way to manufacture the nootkat- family of molecules cheaply and efficiently.  I shall continue to hope anyway.  I hate being bitten.


Monday, August 8, 2011

Hot Peppers

Capsaicin molecule, courtesy Wikipedia.


The molecule pictured above may look like a simple technical drawing, but this molecule means pain to all who encounter it.  Capsaicin is the active ingredient in hot peppers, and represents somewhat of a fascinating topic to me.

While my understanding of this molecule's chemistry is somewhat limited, I will discuss it briefly here.  You can see various oxygen atoms, along with one nitrogen.  This often means that the molecule may be dissolved in water.  However, as you peer through your monocle at this article, you will also note that they are a minor part of the overall organic molecule.  I will note that I use "organic" in the technical sense, in that the molecule contains carbon bonded to hydrogen (lines here represent carbon-carbon bonds, and it is assumed that hydrogen fills out the rest of the available bonding sites).  This molecule will bind to pain receptors in mammals, activating them despite the absence of a real threat to the organism.  The consequence of the organic structure of this molecule is that milk and yogurt will help those eating spicy foods.  The fats in dairy will dissolve this molecule and carry it to the stomach.

In the natural world, this amazing molecule is found in the Capsicum genus, the plants we know as peppers.  Sweet bell peppers have little to none of this molecule, but most other chilies (the "hot" peppers) will have comfortable levels to monocle-dropping amounts.  This, of course, leads to the question of how to measure the quantity of capsaicin in a pepper.  The Scoville scale, measured in Scoville Heat Units (SHU), remains the only real measure we have to answer this question.  The chemist Scoville designed this test to take one drop of an alcohol-based extraction of the fiery peppers, then systematically adding equal parts of [saturated] sugar water until the spice was no longer detectable by a panel of judges.  The current method of testing removes the human element, and utilises High Performance (or "Pressure", depending on where you learned about it) Liquid Chromatography, HPLC. Simply, HPLC measures the actual concentration of capsaicin in a pepper sample, and normalises it ["makes it fit with"] the classical Scoville scale.  Either way, sweet peppers represent zero on the scale, while purified (a.k.a. "weaponised") capsaicin measures about 16,000,000.  All other peppers are found somewhere in the middle.

The habanero pepper, ~200,000 SHU

As someone who enjoys gardening, I have found great delight in growing a specific cultivar of the habanero, the Caribbean red habanero (~400,000 SHU).  Initially, I was looking to experiment with a useful plant which could be grown indoors.  Since my girlfriend and I enjoyed cooking with store-bought hot peppers, I thought it would be interesting, perhaps fun, to grow some of my own.  The clerk at Thrasher's in Belleville, Ontario was incredibly helpful, pointing me to the [incorrectly labelled] "hottest pepper in the world".  I thought this would be perfect, all I would need was one tiny pepper to a large batch of spaghetti sauce!  I was correct.  In fact, I learned that it needed to be a large batch, especially if the seeds were not removed.  What I did not realise was that I had purchased a pepper that, while not the hottest in the world, was incredibly flavourful.  After some practice, I produced a batch of spaghetti sauce which was heavily complimented by my apartment-mates.  The Caribbean red has a remarkable fruity flavour, it is truly astonishing how pronounced it is as such a minor constituent in spaghetti sauce.  I was surprised, especially after my North American upbringing had only exposed me to jalapeno peppers (~5,000 SHU), the flavour of which I do not care for.

This delicious flavour, as it happens, is part of an evolutionary strategy of the Capsicum genus.  For reasons I do not quite understand, it is considered not desirable from an evolutionary standpoint to have the seeds of a plant scattered near to the parent.  Land-based organisms such as mammals are then ill-suited to carry and eliminate capsicum seeds.  By comparison, birds which eat the seeds and excrete indiscriminately (I like that phrase), are ideal candidates for spreading the seed.  The plants then have evolved with capsaicin which will deter mammals but not birds.  As a result, you may coat your bird seed with said molecule.  Birds will love it, but pests will find the seed extremely uncomfortable.  As an aside, humans are the only mammals known to eat these peppers.  It is theorised that the adrenaline rush we receive releases "feel-good" hormones, and encourages us to continue eating them.  Leave it to humans to engage in such foolishness.  For the record, when I have eaten scotch bonnet (100,000-250,000 SHU range) peppers on their own, I laugh an awful lot and have a wonderful time, save for the pain.

An unripe Bhut Jolokia pepper (~1,000,000 SHU)

As a result of this foolish behaviour, businesses may thrive on people who wish to torture themselves for a somewhat-natural high.  Breeding experiments are rampant to make the hottest of hot peppers.  From extremely hot, naturally occurring peppers such as the Bhut Jolokia of India (pictured above) around one million SHU, the current hottest pepper according to the Guinness Book of World Records is the Trinidad Scorpion Butch T (which appears to be a location, then manly/scary words), which is just south of 1.5 million SHU.  I remain doubtful this will last given the current pace of things.  A quick Google search will turn up many pictures of this pepper, and YouTube has many a video of deliberate eating of, and pranks involving the Bhut Jolokia.

As it stands, I am pro-pepper.  I have a Caribbean red (of Capsicum chinese family, a lovely cultivar of the usual habanero) which is currently flowering, and a "Super chilli", which appears to be a random cultivar of the Capsicum annuum family designed to produce ~30,000 SHU peppers in a large supply.  As of yesterday, I also possess a Bhut Jolokia pepper, the seeds of which I intend to keep and grow.  I also hope to make a good batch of spaghetti sauce, I have heard the bhut is very flavourful, though I am slightly frightened of my purchase.  Its skin is bright red and has a bumpy/rough texture, as if Satan himself resides in the pepper.  Hopefully the $2 was worth it.  Should I fail to post again, dear reader, assume I died a spicy, spicy death.


Edit: I lived.  While I did not make spaghetti sauce, the Bhut Jolokia chili con carne was delicious!

Tuesday, July 26, 2011

Sustainable corn.

Image from Iowa State University to Science Daily

An interesting article came up in my RSS feeds recently.  According to work done at Iowa State University, corn production might just become a little more sustainable.  Mind you, I feel that there is a little more to this story than what you might (or might not) read about in the papers.

Poa pretensis alongside corn seedlings.  Source.
This work experimented with the planting of perennial cover crops (something to keep soil in place when the land is not producing cash or food crops) between rows of corn in a study that lasted three years.  The work revealed that Kentucky bluegrass (aka poa pretensis) was the best fit for the job.  This may be the case for several reasons.  I have no doubt that the plant itself fits well.  It has a low profile compared to corn, meaning it will provide little to no competition for sunlight, but farmers are also familiar with the plant and how to manage it.  The grass is found in lawns across North America, and it would seem that in this case familiarity has not bred contempt.

The foremost conclusion of this study, however, was that crop yields would not suffer should it be grown among rows of bluegrass.  This is important to the story, because farmers would refuse to utilise a method which would somehow cripple crop yields.  Luckily, the yields were the same when compared to a control crop (one grown using conventional methods nearby).  However, there are other reasons to be excited for these results.  I ask that you refrain from sipping brandy before the next paragraph, and hang onto your monocles.

Corn is a notoriously hungry and thirsty plant.  As I have previously discussed, corn requires comparatively high fertiliser inputs.  The benefits of a perennial cover crop have a lot to do with the stabilisation of the soil.  There is less exposed ground to bake in the sun, so water requirements become lower.  Further, with less soil exposed to wind and rain, the erosion of soil and the leaching of fertilisers are also retarded.  It is also worth noting that the study included two years which farmers described as "funny".  Flooding was commonplace in 2008, and 2009 saw the coolest July on record.  Both situations would doubtless challenge crops, but the corn managed to survive.

For the record, soil erosion may become more important in time.  Though I cannot lend credence to the claims as I have not researched them, I have heard rumblings that the price of top soil may rise in years to come as we deplete our conventional sources of the stuff.  Soil is created over millions of years by the wearing down of rocks, and humans have yet to develop a synthetic route for its synthesis.

Bearing what I have said in mind, it would seem that the benefits of this sort of agricultural method might become more and more obvious in years to come.  Perhaps in drought years the grass will allow for more efficient water use.  Further, it may also prove that farmers in the future will require less fertiliser and additional topsoil to replace that which was lost in wind and rain.  This would all lower the costs (both thermodynamic and financial) of growing corn, and thus feeding humanity.  I am pleased to see this work, and wonder if it could be extended to other crops as well.


Sunday, July 24, 2011


Courtesy Wikipedia under GNU Licence Agreement


An issue currently facing the scientific community is that of carbon capture and storage, CCS.  It is essentially trying to reverse what has been done over the course of a hundred-or-so years of burning fossil fuels.  Realistically speaking, storage is the easy part of CCS, in that there have been various proposals for very reasonable places to put captured carbon, including abandoned mines and the seafloor.  As an interesting aside, if one were to pump carbon dioxide to the bottom of the ocean, the pressure is so great that water molecules will align to form a "clathrate", a cage which will hold gases there indefinitely.  Carbon capture, however, has proven to be incredibly difficult and a challenge to the greatest minds of today.  Though I do not rank with those greatest minds, the subject of my honour's thesis was a theoretical study of carbon capture mechanisms using metal organic frameworks.  In case you were wondering, I studied copper II benzenetricarboxylate.  For now, these frameworks show great potential.  Unless some improvement is found, though, they will remain a terrible, terrible idea.  The problem here is that carbon dioxide is a very stable molecule, and is not all that easy to trap.

I hope to have at least conveyed that CCS is by no means a trivial problem.  That being said, I feel that a good solution may have been "discovered" recently.  I use parentheses because the technology is by no means new.  In fact many of you, while not adjusting your monocles and top hats, may have handled this technology.  You see, outside of the scientific world, this technology is known as "charcoal".  Biochar simply refers to charcoal when used for CCS and related purposes.  Please do not ask me why they couldn't call it charcoal.  Bioscientists go all goofy when they have the opportunity to name things.

I was recently introduced to this idea by a former environmental issues professor (he has a blog here).  Biochar has the potential to be an elegant solution to the problem of CCS.  Capture, the hardest part of CCS, is accomplished simply by growing woody or cellulosic biomass (trees, grass, what have you).  Storage is then rather easy, biochar may come in chunks, briquettes, full bricks, or even as a powder, but all that need be done is to bury it.  This scheme gives several advantages over other proposed methods.  For one, burying solids is very easy, especially when juxtaposed with methods proposing pumping carbon dioxide into abandoned mineshafts.  Other solids have been proposed, such as calcium carbonate.  The problem here is that while calcium carbonate (you know it as chalk and Tums' active ingredient), is a solid and very easy to deal with, simply burying it would affect soil pH, and widespread leaching could  be devastating.  Another benefit is that one would be burying carbon only, and not sacrificing an oxygen molecule for each carbon atom that must be stored, as would be the case with both carbonate or carbon dioxide storage.

In case you have furrowed your brow, wondering what the ecological effects of burying biochar would be, I believe I have an answer.  While I am by no means an expert, it is my opinion that no environmental harm would be done by burying this material.  My reason for this thinking is terra preta.  This term, which in Portugese means "black earth", refers to the enrichment of soil with biochar.  It would seem that infertile soil may be made fertile with the addition of biochar.  This effect may be noted to a depth of roughly two meters and is stable for timescales on the order of thousands of years.  It is an effect similar to that which switchgrass accomplishes with its extensive root system, but far more quick and direct.

A further benefit is that biochar is not difficult to produce.  It is the same process as charcoal, in fact, though perhaps with lower-grade feedstocks.  Plant matter is heated, causing it to give off water and syngas (carbon monoxide and hydrogen gas), the latter of which could be useful to heat subsequent batches of biochar.  The result is carbon (and potentially mineral) rich biochar.  I must admit, after learning of this, I became a little upset that my parents have been using a propane barbecue for years when charcoal is a far more sustainable technology.

Looking at this problem from a student's perspective, it all seems so simple and obvious a solution.  Biochar could be an excellent CCS solution, one which does not require teams of undergrads toiling away on computers, dreaming up theoretical mechanisms for accomplishing the same thing.  I suppose in an ideal world, switchgrass could be used not only for our heating and biofuel needs, but surplus could be set aside as biochar, which could sustainably reverse anthropogenic climate change.  Could the biochar even be redirected to fertilise our food crops?  The possibilities sure do seem endless.

Until such a time as biochar seems like a terrible idea, I shall continue to hope and dream that it will be widely adopted.