Wednesday, September 30, 2015

Indian man beaten to death for the principle of non-violence

Welcome to India in the 21st Century: a 50-year old man in the northern Indian state of Uttar Pradesh was beaten death with bricks and stones by a self-righteous Hindu lynch mob a couple of days ago, and his 22-year old son was left with serious brain damage. The man's sin? A rumour that he and his family had been storing and eating beef (yes, a rumour: the family maintains that the meat was mutton, and that the rumour was spread maliciously and unfoundedly by someone in the local Hindu temple).
Mohammad Akhlaq, as his name suggests, was a Muslim, living in the predominantly Hindu state of Uttar Pradesh, not far from the Indian capital of Delhi. But Uttar Pradesh, no doubt emboldened by pronouncements on the subject by the new Hindu Nationalist Indian Prime Minister Narendra Modi, is one of the 11 states in India that upholds a complete ban on the slaughter of all cows, calves, bulls and bullocks (although not actually on the eating of beef). In other states, the killing of cattle is allowed, and millions of Hindus do eat beef.
Many Hindus revere and all but worship the cow, which they see as symbolizing and exemplifying dignity, strength, endurance, maternity and selfless service, and the ancient Vedas exalt the cow as a prime example of the Hindu principle of ahimsa or non-injury. Fair enough, I suppose, random and absolutely nonsensical as it may appear to a non-Hindu. However, how that gives a state or a group of individuals the right to deny beef to a non-Hindu (or, for that matter, to a Hindu who happens to decide that that particular religious injunction is perhaps not so important) is quite beyond me. And how beating someone to death in order to uphold the principle of non-violence can make any sense to anyone is even more absurd.
I am a vegetarian, and have been for 35 years, although not for religious reasons. But I don't feel the need, or profess the right, to deny meat to other people. I am also an atheist, and have been for over 40 years, and I have just seen my decision to forego religion as a 14-year old absolutely vindicated. Again.

Saturday, September 26, 2015

Blue Jays' playoff berth rejuvenates a city

I'm not the biggest baseball fan, but I do follow it some. So, let me chime in with kudos to the Toronto Blue Jays for getting to the playoffs for the first time in 22 years (I still wear a World Series Champs sweatshirt from 1993).
Four games ahead of the Yankees, with nine games to play, New York could still theoretically catch them (although on recent form that seems unlikely). But, after last night's win against Tampa, combined with a bit of luck as both Minnesota and Los Angeles also lost their own respective games, the Jays are now assured of at least a wildcard playoff berth. And what's more, they've done it with some style, with a league-leading offense (217 home runs so far), and a league-leading record since the All Star break (43-19).
But what's really interesting is what it's done to the city. With a bunch of major league sports franchises long used to losing and underachieving (in baseball, hockey, soccer, and to a lesser extent, at least just recently, basketball), the city has been starved of success for decades. The fans are remarkably forgiving, and still turn out in droves to home games, but until this baseball season they turned out with an air of resignation and doggedness rather than enthusiasm.
But with this sniff of a possible return to the good times, the excitement is palpable. The 50,000 seat baseball stadium sells out every home game, and playoff tickets sold out within two hours. People who haven't shown any interest in baseball for years are now professing to be die-hard fans (much to the chagrin of the "real" fans).
There is a kind of electricity in the air throughout the whole city, a discernable animation. Driving back through the city from the theatre last night, there were people everywhere and a kind of hum in the air. Conversations on the radio and in the street are peppered with references to the phenomenon: "How 'bout those Jays, eh?",  or the equivalent. The whole city - no, even the country - seems more upbeat than I have seen it for some years.
It's amazing what a few judicious baseball trades and the consistent sound of bat on ball can do for a city.

Thursday, September 24, 2015

An all-too-fallible Pope

It is almost inconceivable to me that, in this day and age, the Catholic Church and the Papacy still indulge in the beatification and canonization of saints. There is just something so anachronistic, so positively medieval, about it that it is difficult to reconcile with modern 21st Century life.
It's also difficult to reconcile it with the apparently modern and thoughtful current Pope, Francis. However, while he criss-crosses the world doling out more-or-less sensible papal advice about global warming and the iniquities of capitalism, it must be remembered that Pope Francis is still mired in the benighted and fantastic dogma of the "One True Church", and he maintains the traditional repressive and antediluvian Catholic views on abortion, euthanasia, contraception, homosexuality, the ordination of women, priestly celibacy, etc.
The declaration of saints has become something of a cottage industry in the Catholic church in recent decades. Francis' ante-predecessor, John Paul II, in particular was a canonization junkie (and had the favour returned to him in 2013 by the last Pope, Benedict XVI, despite much criticism of John Paul's cover-ups of sexual abuse within the Church). The sainthood process requires one miracle for beatification, and a second for full canonization as a saint, although there do appear to be ways of "fast-tracking" sainthood and by-passing some of these rules. The miracles are typically in the form of healings from prayers to the candidate saint some years after their death, healings which the Vatican mandates must be "complete", "instantaneous", "durable", and medically and scientifically inexplicable.
It's all couched in such reasonable and quasi-legalistic terms that it almost seems to make sense until you stop and think about what it is that is actually being claimed. Pope John Paul's II's first miracle, for example, was supposed to be the healing of a French nun, Sister Marie Simon-Pierre, from a particularly aggressive form of Parkinson’s disease in 2005, although media reports in 2010 suggest that the sister has since fallen ill again, and at least one physician has questioned the initial diagnosis of Parkinson’s disease, suggesting that it may have been some other nervous disorder which is susceptible to spontaneous remission. But the Vatican approved it anyway, and Pope Francis performed the beatification ceremony, and he is, after all, infallible, isn't he?
However cynical you may be about the process, though, the current Pope's canonization of the 18th Century Spanish missionary, Father Junipero Serra, just the other day, is on very suspect ethical grounds. Serra is credited with introducing Catholicism among the Native American communities of California, although many commentators have objected to this on the basis that he actually imposed the religion in dictatorial fashion, including beatings and even claims of genocide, and in the process wreaked incalculable damage on the whole indigenous culture of the region. The Pope also chose to overlook the fact that Serra has only been credited with one miracle (the curing of a nun's mystery disease in 1960, after she apparently prayed to Serra on her deathbed).
To me, all this smacks of political expediency (i.e. the Church needed an American-based saint for the increasingly Latino population of America). Whatever your view, though, it is difficult to sanction this kind of celebration of cultural imperialism, and a modern, thoughtful Pope should be well aware of this.

Yogi Berra was no Yogi Bear

I know most of the Internet is probably doing the same thing, but I wanted to mark the death yesterday of Yogi Berra with a selection of my favourite Yogi-isms.
As well as being one of the best and most successful baseball catchers in history, Berra had a penchant for short snappy witticisms, at once nonsensical and somehow strangely wise, often following a similar format involving paradoxes or deliberate Spoonerisms. His epigrams appear to be designed to give an initial impression of stupidity or lack of education, while nevertheless containing a nugget of truth and a hidden subtlety. But Berra was far from stupid, and it is worth noting that he took great offence at Hanna-Barbera's naming of the genuinely stupid Yogi Bear cartoon character, and even took them to court over it.
Many of these bon mots are now so much a part of common parlance, and so identified with the man, that it is no longer even certain whether he said them first, whether he used those exact words, or even whether he said them at all. His 1998 book was called "The Yogi Book: I Really Didn't Say Everything I Said!" for good reason.
Anyway, for what it's worth, here are a few pearls he probably never said.
  • “It’s déjà vu all over again.”
  • “If the people don’t want to come out to the ballpark, nobody’s going to stop them.”
  • “Baseball is 90 per cent mental. The other half is physical.”
  • “Pair up in threes.”
  • “He hits from both sides of the plate. He’s amphibious.”
  • “Nobody goes there anymore. It’s too crowded.”
  • “We were overwhelming underdogs.”
  • “It’s tough to make predictions, especially about the future.”
  • “It gets late early out here.”
  • “You can observe a lot by watching.”
  • “The future ain’t what it used to be.”
  • “You should always go to other people’s funerals, otherwise, they won’t come to yours.”
  • “When you come to a fork in the road, take it.”
  • “We made too many wrong mistakes.”
  • “A nickel ain’t worth a dime anymore.”
  • “Why buy good luggage, you only use it when you travel.”
  • “I usually take a two-hour nap from one to four.”
  • “Never answer an anonymous letter.”

Wednesday, September 23, 2015

Diesel cars are not just a problem in the USA

In a huge wake-up call for the automobile industry, German auto giant Volkswagen has been caught out deliberately falsifying the emissions from their popular diesel cars.
Jettas, Beetles, Golfs, Passats and Audi A3s sold in the US market - still a tiny market compared to Europe - have been found to be fitted with sophisticated computerized "defeat devices" that can sense when the car is being tested, rather than being drive on the open road, and switch to a kind of safety mode in which emissions are much lower than usual. Once out on the road again, the devices switch back to full power (and emissions), resulting in cars in daily use that spew out as much as 40 times the nitrogen oxide pollutants (collectively known as NOX) allowed by US Environmental Protection Agency rules. The problem was initially spotted by an NGO called the International Council on Clean Transportation (ICCT), which was carrying out independent emissions testing, including on-road testing, in association with the Center for Alternative Fuels, Engines and Emissions at the University of West Virginia.
Volkswagen AG has admitted to the fraud, and says that up to 11 million Volkswagen cars worldwide are fitted with the device. The company may face up to $18 billion in fines in the USA alone, to say nothing of possible legal action from consumers and shareholders, and CEO Martin Winterkorn has already announced his resignation. Environment Canada has since announced its own investigation into Volkswagens in Canada, as has Italy, France and South Korea, and a Europe-wide probe is likely.
About half of Volkswagen's sales are diesel cars, and in Europe as a whole diesel cars make up about 50% of all cars (closer to 70% in France and Spain), as compared to a measly 3% in the USA. Proponents point out that diesel fuel is more powerful than standard gasoline and 20-40% more efficient, and as a result diesel cars emit less carbon dioxide that gasoline cars (although not as much less as was once thought, and even this is now being questioned). On the other hand, they tend to produce substantially more nitrogen oxides and particulate pollution.
The BBC has produced a good primer on what you should know about diesel fuel, but suffice it to say that, in addition to pumping out almost as much carbon dioxide as gasoline, the other pollutants that diesel produces are perhaps even more worrying. Nitrogen dioxide (NO2) is particularly nasty, and can cause or exacerbate a number of health conditions, including inflammation of the lungs, asthma and bronchitis, as well as an increased risk of heart attacks and strokes. The particulate matter from diesel exhausts has been shown to cause cancer and, although diesel cars are fitted with extremely effective filters, many people remove these filters to improve fuel economy and performance and, in addition, NO2 forms something called secondary particulate matter when it enters the atmosphere, the effects of which are not yet fully understood.
Since the 1990s, many European nations have actively subsidized diesel (and heavily taxed gasoline) in the honest belief that diesel is better for the environment and can help cut greenhouse gas emissions. More recent scientific evidence suggests that this may not in fact be the case, and there are even moves now to limit diesel cars in some cities. NO2 levels are well above European Union legal limits in many cities, including parts of London, Paris and Munich, and tests by the ICCT have shown that modern diesel cars in normal use emit on average seven times the prescribed European limit for NOX (US limits are even more stringent). Indeed, some sources estimate that hundreds of thousands of premature deaths in Europe may be laid at the door of the recent popularity of diesel cars.
After these revelations, big changes may be afoot in the European car market. Volkswagen, however, may or may not be around to see it.

Saturday, September 19, 2015

Misplaced philanthropy and the SWEDOW phenomenon

A timely article by the excellent Leah Maclaren reminds us all of what five minutes thought might easily tell us: sending used baby carriers, slings, pacifiers and sippy cups to the war-torn and displaced is not an efficient use of our commendable and well-meaning charitable impulses.
Apparently, there are any number of charitable organizations out there with names like Ring Slings and Baby Things for Syrian Refugees. But, as any aid worker on the ground will tell you, they really don't need the processing and logistical hassles of transporting and distributing these used goods, especially when the real need is for essentials like food, water, shelter, medical care and emotional support. There is even a Twitter hashtag #SWEDOW ("Stuff WE DOn't Want") for this; it is not a new phenomenon.
So, instead of sending baby accoutrements, hand-knitted blankets and tents, just donate money to a reputable NGO with a presence on the ground, and they will use it to fund trained people to assess the needs and fill them as efficiently as possible. If you really have excess baby gear, then sell it locally and donate the money, or give it to needy individuals in your own area.
But, please, don't send your Baby Bjorns and Bugaboos to Syrian refugees in Hungary and Croatia. They really don't need them, and you are creating more problems than you are solving, however well-meaning your impulses may be.

Only in Texas - negative electricity prices

Slate Magazine reported an interesting, if somewhat bewildering, turn of events in the American state of Texas the other day, when circumstances conspired to make the local price of electricity in Texas negative.
We are perhaps used to thinking of Texas as an exclusively oil-and-gas state, home to rednecks, tycoons and Tea Party-voting ranchers. But Texas is also home to over 10,000 wind turbines, and it produces 9% of its electricity from wind power, over twice the US average. So, on a windy night, when there is little electricity demand requiring baseload generation, wind can actually become the dominant source of electricity there.
OK, but negative prices?
This unusual occurrence is the result of four factors specific to Texas' electricity system. One, it is an electricity island, not connected to neighbouring states, so that it can neither directly import power from other states, nor, by the same token, can it export surplus electricity production elsewhere. Secondly, the aforementioned relatively large wind generation capacity in the state. Thirdly, the Texas electricity grid has a unique system of purchasing its power through online real-time auctions from providers, whereby, every five minutes, it buys the cheapest electricity being offered in order to fill the demand from its consumers. And finally, wind operators receive a $23/megawatt-hour federal tax credit, whatever the price of electricity sold, so it is always in their interests to produce and sell as much power as they can.
Given these factors, on the particular night in question, the spot price of Texas' electricity fell from $17.40/megawatt-hour earlier in the evening down to zero by 1:45am, and then into negative prices for the rest of the night until about 8:15am, as it was cost effective for wind turbine operators to pay the state's electricity system to take power off their hands. At 5:45am, it reached its lowest cost at -$8.52/megawatt-hour. Oh, for a cheap and reliable battery storage system!
As the Slate article remarks: "Only in Texas, folks".

Wednesday, September 16, 2015

What I don't know about genetics and gene therapy

Once, several years ago, I did an online university course on genetics, just for the hell of it. At the time, it all seemed to make sense, and I did fine on the quizzes and tests. Recently, though, the more I think about it, the more I realize that there are some pretty fundamental parts of the workings of genes that I just don't understand. On the basis that a little knowledge is probably a dangerous thing, I'm here to appeal to the Internet community to set me straight.
Here's what I think I understand:
  • The nuclei of pretty much every cell in our bodies each contain 46 chromosomes, which are made up of long strands of DNA, cunningly twisted, coiled and folded into a very small space. Without going into too much detail, this DNA is in turn composed of billions of nucleotides, which are linked pairs of the four chemical bases (A, G, C and T) supported by structural sugar and phosphate molecules.
  • Shorter sections of these long strands of DNA, from a few hundred to a couple of million base pairs each, arranged in a specific order, make up individual genes, of which we have around 20,000 to 25,000. We have two sets of genes, one inherited from each parent, and it is our genes that provide the instructions for building the 10,000 or so different complex molecules called proteins that make up and regulate the structure and function of the body's tissues and organs. Over 99% of these genes are identical in everyone, and these are what make us human (rather than chimps or beluga whales). Less than 1% of our genes are different between individuals, the variations in genes being called alleles, which is what makes one individual different from another.
  • Each individual cell, though, only "turns on" (or expresses) a fraction of the genes in its DNA, the rest remaining "turned off" (or repressed), and this gene regulation is what causes a particular cell to function as a brain cell or a muscle cell or a heart cell. Just to confuse things, the expression of genes can also be affected by environmental influences like diet, pollution, etc, by a process known as epigenetics, and genes can also mutate over time if they copy incorrectly, or if an mutated gene is inherited at birth, but let's not go there for now.
So far so good. Where I started questioning my knowledge of genetics, though, was when I started reading about gene therapy, initially with reference to my wife's Parkinson's disease, and I could not understand how a knowledge of genetics could be used to make a concrete effect on an individual's body. This is all part of the wider question that I have about how all the millions of dollars being spent on the genetics of various diseases is actually going to result in practical steps in treating those diseases.
So what do I know about gene therapy? As the name suggests, it refers to techniques, still largely experimental, that use genes to treat or prevent disease. This may be by replacing a mutated gene that causes disease with a healthy copy of the gene, getting rid of or making inactive a mutated gene that is not functioning properly, or even introducing a completely new gene into the body in order to fight a particular disease. Apparently, inserting a new gene directly into a cell usually does not work, and so a carrier called a vector, such as a modified virus, can be used to deliver the gene (yes, just like on Helix!).
Right. But, doesn't this mean that the new gene would need to be inserted into every cell in the body (there doesn't seem much point in just one or two cells having an altered copy of a particular gene)? Is it even allowed for different cells to have a different set of genes (I always thought that every cell had exactly the same set of genes/DNA, just that some cells expressed some genes and some others)? Or is it, for example, sufficient for all the lung cells to host the altered genes in order to have a beneficial effect on a lung disease (not that that would be particularly easy in itself)?
In fact, all of this begs an even more fundamental question: how does a particular cell know which genes to turn on, and which not, in the first place? How does one hair follicle on a black and white cat know to switch on the white hair gene and the one next door to it to switch on the black hair gene? And, for that matter, could a cell in your elbow have a gene for blue eyes switched on, and, if it did, what difference would this make? The more I think about it, the more questions I could come up with.
Now, I know that not many people ever read this blog, and most of those are probably not well-versed in genomics. But, nothing ventured, nothing gained: maybe some kind soul will put me out of my misery.

My daughter actually came through for me on this one (she's doing a Biology major, and is currently interning in a genetics lab). Perhaps predictably, I got a lot more information than I either need or understand, but the quick summary is that, as I suspected, gene therapy is still pretty much pie in the sky, a cool idea whose time has not yet come.
Viruses can indeed be used to introduce new genes into cells, but the science is as yet very inexact. For example, a gene might end up integrating into a part of the DNA where it can't be expressed, or where it is inappropriately expressed all the time, or even into the middle of another gene, thus screwing up both genes. There are other methods of injecting DNA into cells, but they just introduce the new material into the cytoplasm of the cell, not the nucleus, and so it will gradually degrade over time. Yet another line of approach might be to introduce new genes into pluripotent stem cells, and then engineer these into the right kind of cell for the required purpose (all of which can indeed be done), but then the problem of delivery still remains.
And, yes, the new genes do have to be introduced to the right part of the body (whether that be bone marrow, muscles, lungs, etc) to have the desired effect, otherwise they will not be able to be properly expressed and will not be able to carry out the required function, and at present there seems to be no clever way of doing that. As for how to deliver new genes into the central nervous system or across the blood/brain barrier (for neurodegenerative diseases, for example), that is a whole new set of problems. And, even once introduced, it is still not clear whether the new altered cells will persist and proliferate, or just degrade and fade.
Finally, on my more general questions at the end:
The way in which different genes are expressed in different parts of the body is, well, complicated, involving tissue-specific transcriptional regulators, factors and enhancers, etc. I don't think I even want to go there. Because of these regulators, though, it is apparently very unlikely that a gene for blue eyes would find itself turned on in an elbow, to use my random example. And even if it did, and a blue pigment was created in an elbow cell (whether this be in bone, blood, cartilage or whatever), it would have no way of physically expressing itself, and so would just degrade and be removed.
The colour of cat hair is apparently a whole subject unto itself, and incredibly complicated and convoluted. Those interested would be better served by going to the detailed Wikipedia article on the subject, than having me try to explain it.
So, it seems that sometimes a little knowledge may actually be safer than getting totally tied up in a whole bunch of things I really don't understand, and don't have several years to devote to figuring out. Sad, but true.

Saturday, September 12, 2015

Canada's refugee policy becomes an election wedge issue

After 10 days in Iceland, far from mainstream politics, and particularly from Canadian politics, I come back and find that the Conservatives' campaign for this October' federal election has been well and truly derailed, and mainly by the unlikely issue of its Syrian refugee policy.
There seems to have been a belated collective outpouring of concern for the plight of the hundreds of thousands of displaced Syrians, and a feeling that the Tories' grudging pledge to take 11,300 of them over three years is insufficient, hard-hearted and downright un-Canadian. There is a sudden hankering for the compassionate and outward-looking Canada of old, the Canada that took in 50,000 Vietnamese boat people in the late 1970s, and the Conservative government of Stephen Harper just does not fit that bill.
Interestingly, the reaction seems to have coalesced around one of those iconic media pictures, that of the body of three year-old Alan Kurdi, dead on a Turkish beach. In a German telephone interview, the boy's father, Abdullah, has put the blame squarely at Canada's door for rejecting the family's claim for asylum, although it actually appears that no such claim was ever made. Evidence is also coming to light that the boy's father may have been the driver of the capsized boat and working with the smugglers, and even that his actions may have been directly instrumental in the tragedy. As usual, the truth is never simple.
The problem has been compounded, or perhaps deliberately confused, by the Conservatives' wilful conflation of refugees and immigrants from other sources in their campaign speeches. When Immigration Minister Chris Alexander said recently, "We also are the most generous country to refugees in the world", he is guilty of this, as is Stephen Harper himself when he said, "Our country has the most generous immigration and refugee system in the world. We admit, per capita, more people than any other." However, terminology aside, this is also just plain wrong: the UNHCR ranks Canada not first, but tied for 41st place, in refugee intake per capita. Even in the case of total net immigration, Canada ranks a mediocre 24th.
But, whatever the impetus, and despite Harper's belated promises to expedite the asylum process and to expand Canada's commitment to 10,000 over the next three years (albeit largely through private organizations like church groups), the political damage has been done, and the Syrian refugee crisis has suddenly become the year's hot button issue.
Even little Iceland is not exempt from it. While we were there, reports surfaced of widespread disgust at the Icelandic government's pledge to take just 500 Syrian asylum-seekers, and a hurried Facebook campaign yielded over 11,000 families who are willing to open up their homes to Syrian refugees (some reports have put this figure at up to 15,000). Bear in mind that the total population of Iceland is about 330,000, about one-hundredth of Canada's population.
The problem is certainly a huge one, as a useful BBC summary of the refugee crisis shows. Some 350,000 refugees have physically entered Europe so far this year, and over 430,000 asylum applications have been received by European countries, by far the largest recipient being Germany, followed by Hungary, Turkey, and Sweden. Some 40,000 refugees are expected to arrive in Germany this weekend alone. The number of claims granted is, of course, much smaller, although Germany and Sweden are the largest asylum granters, with Sweden by far the largest recipient on a per capita basis. Germany is anticipating in the region of 800,000 claims over the entire course of 2015, and says that it may end up taking half a million of these.
The largest single country of origin for European asylum claims was Syria, although many hundreds of thousands are also fleeing their homelands from Afghanistan, Kosovo, Eritrea, Serbia, Pakistan, Iraq, Iran, Nigeria and Russia. Over 2,300 have died making the treacherous crossing into Europe, mainly by sea though Greece, Italy and Spain. Of course, the situation closer to Syria is immeasurably more dire. Turkey has received a total of nearly 2 million asylum applications up to June this year, Lebanon over 1 million, and Jordan well over 600,000.
With all this as background, Canada's acceptance of 1,300 refugees over three years does indeed sound paltry (as does the USA's recent resettlement pledge of 10,000 over the next year). Given all the various sins that can be laid at Stephen Harper's door, it would be ironic if this was the issue that sank the Conservatives' ship in the upcoming election.