PhDs in science finish faster in Canada than the USA.

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According to a story in the December issue of University Affairs, PhD students in Canada complete their degrees more quickly than their counterparts in the USA. (I suspect that no one completes faster than students in the UK, but that’s a rather different topic.)

The article suggests that the existence of a distinct Master of Science (MSc) degree in Canada is at least partly responsible for this difference. That is, having the option of starting in a Master’s degree lets students decide whether they are cut out for the considerably more demanding PhD program. In Canada, the expectations for originality and scope are less for an MSc thesis than for a PhD, but both are based on conducting independent research and have only a moderate course component.

The interesting thing is that with the intense pressure from the top down on faculty to get more PhDs out the door, there is a growing emphasis on doing away with the MSc and having students transfer to a PhD program without completing and defending a Master’s thesis1. The data collected by Susan Pfeiffer, which are described in the story, suggest that this is a bass-ackwards way to go about it.

Moreover, completion times are not the only consideration — students also must be competitive for postdocs, fellowships, and eventually jobs. To me, going a semester over but completing some manuscripts appears more beneficial in the longer term than getting out in no more than nine semesters post-MSc. On the other hand, only 3/4 of PhD students in Dr. Pfeiffer’s survey had completed their degrees even after 10 years in the program, which is way too long by any department’s standards.

Some students are perfectly capable of completing an MSc but may not be interested in, or qualified to attempt, the PhD. It also happens that students who do both degrees typically complete more efficiently overall than those who do just a PhD. Therefore, I feel that the option (indeed, usual requirement) of a distinct Master’s program prior to enrolling in a PhD is a good thing, and I would not want to see it vanish.

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1) Full disclosure here: I did not complete a Master’s thesis and instead transferred to a PhD and completed the whole shebang in almost exactly 5 years of graduate studies.


Foolishness from LiveScience.

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I know I said I was going to ignore LiveScience after a string of ridiculous articles. I really have tried to. But today someone brought to my attention a truly silly story and asked if perhaps it was blog-worthy. Indeed it is, even though it required me to visit the site that I had vowed to avoid.

The story is about frogs and snakes. In particular, Dahl’s aquatic frog and the northern death adder in Australia. The frogs are toxic or may be covered by a sticky glue-like substance, but the snakes manage to consume them nonetheless by killing the frog and then waiting for the objectionable substances to degrade before eating the prey. The frog usually travels some distance before succumbing to the snake’s venom, at which time the predator tracks it down and devours it. Assessing the state of non-lethal doses of toxin in their mouths after the initial bite of the frogs allows the snakes to discriminate between species of toxic prey, such that they wait, say, 30 minutes post mortem before eating one species of frogs, but 40 minutes for a different species whose toxins persist slightly longer before breaking down.

This is all well and good, and is an interesting interaction about which I was not aware. But, in typical fashion, LiveScience manages to butcher some basic evolutionary ideas. Here is where the whole thing goes off the rails:

Evolutionary theory predicts that the adder’s tactic is foolproof: Natural selection stops operating after an individual’s death, so the frogs will probably never evolve longer-lasting toxins in response to the clever snakes.

So, just to review. The snake bites the frog, which is toxic, and gets some of the toxin in its mouth. This toxin ingested by the snake is at a concentration too low to be fatal, but the toxin itself is poisonous enough to kill a snake at higher concentrations unless it waits for the compound to degrade after the frog wonders off and dies sometime later.

Can anyone see how mutations of small effect in some frogs might make the “clever” snakes’ “trick”, not very “fool-proof”?

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Follow up


Remembrance Day.

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In Canada, as in many countries around the world, November 11 is a day of remembrance for the sacrifices made during wartime. In Canada, this refers in particular to World War I (1914-1918) and World War II (1939-1945), but also to smaller engagements in which Canadians were (or are) involved, such as Korea and Afghanistan.

The poppy has become a symbol of remembrance, and can be found pinned to people’s lapels more or less from the beginning of November each year. This tradition, which is also observed in various other nations, is derived from the poem In Flanders Fields by Lt. Col. John McCrae (1872-1918), a Canadian physician and soldier originally from Guelph, Ontario who died of pneumonia while serving in the First World War. The poem was composed shortly after the death of McCrae’s friend Lt. Alexis Helmer in the Second Battle of Ypres, and makes reference to Flanders, Belgium, where poppies grew extensively and where many military dead were buried.

In Flanders fields the poppies blow
Between the crosses, row on row,
That mark our place; and in the sky
The larks, still bravely singing, fly
Scarce heard amid the guns below.

We are the Dead. Short days ago
We lived, felt dawn, saw sunset glow,
Loved, and were loved, and now we lie
In Flanders fields.

Take up our quarrel with the foe:
To you from failing hands we throw
The torch; be yours to hold it high.
If ye break faith with us who die
We shall not sleep, though poppies grow
In Flanders fields.

— John McCrae

The poem has particular relevance in Canada, having appeared on both a stamp (1968) and currency — a portion of it is found on the current $10 bill, which honours Canadian efforts in international peacekeeping (the Nobel Peace Prize-winning idea of Lester B. Pearson, who also went on to become Prime Minister of Canada). A poppy also appeared on a quarter recently, which some may recall created a buzz as it was mistaken for spy technology by our friends south of the border.


There are several parts of Europe that I am eager to visit on the basis of pride and gratitude for what my fellow Canadians did during the two world wars. Those that I have not been to yet include Vimy Ridge and Juno Beach (Normandy), but I did manage to check one off the list two years ago during a visit to the Netherlands: Groesbeek Canadian War Cemetery.

I was in Leiden to participate in a symposium entitled “Extending the synthesis” that featured a handful of speakers including Rich Lenski, Dave Jablonski, Sergei Gavrilets, Paul Brakefield, John Thompson, Niles Eldredge, and me. On one of the days there were no formal plans, so some of the speakers took a bicycle tour of the beautiful region around Leiden, others headed off the The Hague, and I crossed much of the country by train, by bus, and on foot to visit Groesbeek. It was one of the most meaningful experiences I have ever had.

There is a scene in the movie Saving Private Ryan that never fails to break me up. Actually, there are several such scenes, but the one I have in mind at the moment involves the arrival of a military vehicle at the Ryans’ home in which their mother, realizing what this visit must mean when she sees a clergyman exit the car, collapses in grief on her front porch. This grips me with particular force as it happened to my great-grandmother — twice.

My paternal grandmother grew up in the small town of St. Marys, Ontario, which, like most towns across the country, experienced its share of sacrifice during the Second World War as approximately 10% of the country served (1.1 million out of a population of roughly 11 million). With the labour force severely diminished, my young grandmother worked in a converted hand grenade factory. Two of her older brothers, Bill and Roy, served and died in combat.

Click for larger image.

My great-uncle Bill landed in Normandy on D-Day, survived a major assault in which half his battalion was killed or wounded, received a minor wound while fighting in Belgium, and eventually was killed along with many of his friends when his battalion was shelled by German artillery. He is buried at Groesbeek Cemetery.

To reach the cemetery, one must travel by bus from the nearby town and ask the driver to stop at the road leading to the memorial.


From there, it is a fairly long walk down a forested roadway to another main road, and then another short walk up to the cemetery.




The tombstones are arranged, row on row, in order of burial. My great-uncle Bill’s is part of a long line of young men who were lost on the same day. Many of them were probably friends. All were mourned by someone.


My father had previously been the only member of our family to make the trip to see Bill’s grave, which he did many years ago. I am sure his experience was as emotional as mine was to be surrounded by so much sacrifice, and to reflect on what this must have meant for my grandmother and her family, and indeed the families of all of the individuals buried here.


Next to the large memorial at the far end of the cemetery there is a tall maple tree. A leaf from this tree hangs in a frame on the wall of my home office. It has often served as an object of reflection for me as a young man who is fortunate that his life has not been affected directly by war.


There is a guest book at the cemetery that invites visitors to leave a message. I spent quite some time leafing through it, and was deeply moved by the messages I read. “Thank you for our freedom” was among the most common. Some 60 years later, the people of the region, and the many who make a pilgrimage like mine to this site, have not forgotten the sacrifices that were made.

None of us should ever forget.


Better design through evolution.

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Sometimes science news feeds are great. They can let one know about papers well outside one’s discipline that are of interest but that would not have be encountered under a normal literature search.

Case in point. There is a story on EurekAlert! about researchers from the University of Illinois using a computer simulation based on evolution to design a more productive photosynthetic leaf. It’s a good illustration of how real-life organisms represent the products of evolutionary trade-offs rather than of optimal design, and of how evolutionary algorithms can result in solutions to complex problems of practical importance. In short, evolution can produce good adaptations, but these are not optimal.

The news release is here:

Researchers successfully simulate photosynthesis and design a better leaf

And the the original paper, which is open access, can be read here:

Zhu, X.-G., de Sturler, E., and Long, S.P. 2007. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm. Plant Physiology 145: 513-526.


The great Canadian book rip-off.

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It annoyed me that books remained more expensive in Canada even as our currency moved closer to parity with the American dollar. As I write this, the Canadian dollar is worth roughly $1.07 US. But looking at Amazon.com vs. Amazon.ca, I see that many popular science books are still more expensive in Canada than in the US.
Some examples:

Genome: The Autobiography of a Species in 23 Chapters by Matt Ridley
Amazon.com: $10.17 US
Amazon.ca: $13.83 CDN

A Life Decoded: My Genome: My Life by J. Craig Venter
Amazon.com: $17.13 US
Amazon.ca: $19.53 CDN

The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World by James Shreeve
Amazon.com: $11.16 US
Amazon.ca: $13.86 CDN

Maybe it’s shipping costs, you say? Then how come more technical books are the other way around? I’ll tell you why — because they raised the price for US customers.

A Primer of Genome Science, 2nd Edition by Greg Gibson
Amazon.com: $64.95 US
Amazon.ca: $61.23 CDN

The Evolution of the Genome by T. Ryan Gregory
Amazon.com: $72.95
Amazon.ca: $68.78 CDN

What’s the excuse?


Can (some) crustaceans feel pain?

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As a follow-up to my previous post on speciesism, it is of interest that a soon to be published paper in Animal Behaviour provides tentative evidence of pain in decapod crustaceans (which includes lobsters, crayfishes [crawfishes or crawdads], crabs, shrimps, and prawns). I came across this through a news report in New Scientist that showed up in my RSS feeds and it seemed worthy of mentioning.

Both the New Scientist report and the primary article are behind subscription walls, but here is the abstract of the paper:

Nociception or pain in a decapod crustacean?

Stuart Barr, Peter R. Laming, Jaimie T.A. Dick, and Robert W. Elwood
Animal Behaviour, in press

Nociception is the ability to perceive a noxious stimulus and react in a reflexive manner and occurs across a wide range of taxa. However, the ability to experience the associated aversive sensation and feeling, known as pain, is not widely accepted to occur in nonvertebrates. We examined the responses of a decapod crustacean, the prawn, Palaemon elegans, to different noxious stimuli applied to one antenna to assess reflex responses (nociception) and longer-term, specifically directed behavioural responses that might indicate pain. We also examined the effects of benzocaine, a local anaesthetic, on these responses. Noxious stimuli elicited an immediate reflex tail flick response, followed by two prolonged activities, grooming of the antenna and rubbing of the antenna against the side of the tank, with both activities directed specifically at the treated antenna. These responses were inhibited by benzocaine; however, benzocaine did not alter general swimming activity and thus the decline in grooming and rubbing is not due to general anaesthesia. Mechanical stimulation by pinching also resulted in prolonged rubbing, but this was not inhibited by benzocaine. These results indicate an awareness of the location of the noxious stimuli, and the prolonged complex responses indicate a central involvement in their organization. The inhibition by a local anaesthetic is similar to observations on vertebrates and is consistent with the idea that these crustaceans can experience pain.

Let me say this before the comments begin: I don’t think anyone is claiming that prawns can experience the same kind of pain, including emotional pain and anticipation of pain, that humans can. The point is simply that we cannot automatically dismiss all reactions to noxious stimuli in invertebrates as reflexive nociception. There could be something more to it.

The Great Dying.

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There have been five major mass extinctions in the history of life since the Cambrian. The “Big Five” are the Ordovician-Silurian, Late Devonian, Permian-Triassic, Triassic-Jurassic, and Cretaceous-Tertiary events. The latter is the most famous, having resulted in the extinction of all dinosaurs except birds, and more than half of contemporary biodiversity overall. This was not the most severe pruning of the tree of life, however — rather, this took place at the end of the Permian when roughly 95% of species were extirpated. The causes of the so-called “Great Dying” remain a subject of debate, but some recent work has provided evidence for an asteroid impact (perhaps in combination with various other related or independent factors).

Anyway, the reason I bring this up is that I am trying to find out the source film for the following clip by National Geographic:

If you happen to know the title of the documentary, let me know.

Oh, and if you’re interested in the End Permian event, you can take a look at these fine books:


On speciesism.

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There has been a lot of discussion on the science blogs about “animal rights” recently. Most of the argument has centered around whether animals are necessary for research, but of course the animal rights movement includes issues such as factory farming, using animals for entertainment, the pet industry, and others. I am a scientist, in particular a zoologist, meaning that I study animals, and of course I agree that many medical advances would be impossible without research using animal models, short of using human models.

That said, I have been amazed at the lack of sophistication in the arguments I have seen. In fact, some of the positions expressed I have not actually encountered since the 8th grade, such as mocking vegetarians or invoking tu quoque arguments about those who oppose some or all animal research but eat meat. Moreover, some bloggers seem to believe that the animal rights movement is populated by only two varieties of people: those who blow up science labs, and those who argue that we should rename the Green Bay Packers because this makes reference to the meat industry. It’s “us versus them”, and they are all either criminal or silly such that the issue can be ignored. This “us versus them” mentality also is relevant in another capacity that I will discuss in a moment.

The issue of animal experimentation has been a contentious one since the 1800s, in particular with reference to vivisection. Many of the same arguments are still being used by both sides, with no resolution in sight. The question, from a philosophical point of view, is not whether animal research works. Yes, some opponents try to make a case on this front, and yes, there are problems with non-human models of human disease, but clearly one cannot do certain things — such as be a zoologist — without studying animals. It’s simply not effective to argue on the basis of whether it works, because obviously it does (with limitations) but this in itself provides no ethical justification. Experimenting on infants would presumably work even better, but I sincerely hope that no one would consider this alone as justification for the practice.

To many of the philosophers and scientists who have discussed this issue over the past 150 years, the central issue is the need to provide justification for inflicting suffering on some (non-human) individuals for the benefit of other (human) individuals. Both sides have invoked the standard moral philosophies, including utilitarianism and Kant’s categorical imperative, and again there has been no resolution. I would argue that neither side will convince the other on the basis of traditional moral philosophy either.

What it boils down to is a philosophical decision that human life is more important that non-human life. Many take this as a given, but a philosophy based on rationality demands that this be justified. Obviously the creationists have their explanation handy: Genesis 1:26-28. Non-religious arguments require a little more consideration than this.

And so I ask, on what basis do you draw the sharp moral line between “humans” and “animals”, “human rights” and “animal rights”, “us” versus “them”? What rational argument do you bring in defense of speciesism? Perhaps you argue that only humans are capable of suffering, or that our intellectual capabilities are of a different kind from those of other animals. As Dawkins has noted, neither is compatible with what we understand about evolutionary history.

I think that opening a discussion about the use of non-humans for human gain is useful. However, I think that simply rhyming off ways in which non-human research is beneficial and dismissing anyone who opposes some or all of it is not. It is a complex issue, and should be treated accordingly.

In one of the more balanced discussions I have seen on this topic, Madhusree Mukerjee made the excellent point that

Animal liberators need to accept that animal research is beneficial to humans. And animal researchers need to admit that if animals are close enough to humans that their bodies, brains and even psyches are good models for the human condition, then ethical dilemmas surely arise in using them.

And, of course, I am not the only biologist with an interest in knowledge about animals to note that the issue of speciesism is one that we cannot ignore.



Happy birthday Sandwalk, and hello to the new Greg Laden.

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As I described in a recent post about the evolution of Genomicron (entitled, um, The evolution of Genomicron), one of the things that got me interested in blogs was finding that topics in my area (genome size evolution) were being discussed. Specifically, the intriguing question about whether birds exhibit small genomes relative to most other tetrapods as an adaptation or exaptation for flight. This discussion was sparked by a paper in Nature by Chris Organ and others, about which Carl Zimmer wrote in Science. Obviously, I have an interest in this subject, having published papers on the topic before.

Anyway, two of the blogs that provided posts on this issue, and thus indirectly got me into blogging, were Sandwalk by Larry Moran [Genome size in birds] and Evolution…Not Just a Theory Anymore by Greg Laden [Metabolic efficiency and genome size]. These were two of the first blogs to which I subscribed, and I continue to read their feeds daily. It is therefore of interest to note two important developments relating to these excellent blogs.

First, today is the first anniversary of Sandwalk. I remember when Larry reached the six month mark and was contemplating the blog’s future. I had been blogging for only a few weeks then, and it was refreshing to see someone with an established blog explicitly evaluating the utility of blogging for scientists.

Second, Greg Laden has officially closed his old blog and moved up to the big time on Seed’s all-encompassing ScienceBlogs — see the dandy new Greg Laden’s Blog. I wish him continued success and look forward to many more informative and interesting posts.


Offensive post or feedburner error?

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Either people were offended by me asking whether they are cat genome people or dog genome people (a proxy for whether they think we should sequence many genomes at low redundancy, or a few at high accuracy), or Feedburner is doing something fishy. Either way, I (and, I think, The DNA Network) seem to have lost half my subscribers overnight.

Could be a daylight saving time* issue? Who knows.

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* It’s not “Daylight savings time”, it’s “Daylight saving time”.