Biocurious

/ a biophysics blog

Overheard on campus: Bad advisors?

Posted 2 April 2009 by PhilipJ under

I was walking across King’s College Circle and overheard what I assumed to be a couple of graduate students talking about their advisors. As we were walking in opposite directions I only caught a brief snippet of their conversation, but what I did hear I found very confusing:

Grad student 1: “How do I know if I have a bad supervisor?”
Grad student 2: “I really don’t know.”

Everyone’s advisor is different, but so are the needs of individual students. For different students, the same advisor can have completely different interactions and expectations (in fact, necessarily so: a senior graduate student or post-doc should interact differently with their advisor than, say, an undergraduate hanging around over a summer). It all comes down to whether you and your advisor work well together, which I personally think is only related to your own expectations. Some advisors want you in the lab (or the field, or writing code, or whatever…) 100 hours a week, with group meetings on Saturday mornings. Other advisors are in absentia for most of the year and give you very little hands-on supervision. The balance of supervision, freedom, traveling to conferences, etc: it’s all based primarily on a student’s own expectations.

If I run across these two people having the same conversation again, I think I’ll pipe up with the following: If you aren’t sure, I think there are bigger issues than your advisor.

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Get to know Jorge Cham of Piled Higher and Deeper

Posted 27 March 2009 by Andre under &

Jorge Cham started writing Piled Higher and Deeper as a grad student at Stanford and kept it up through his postdoc at Caltech. Finally though, in 2005 he decided to leave academia and pursue his career as a cartoonist and speaker full time. Needless to say, Phil and I are fans of his work and it’s great to see that he’s been so successful. Science has an extensive profile of Cham this week in the News Focus section. It’s also posted on Science Careers so maybe that copy is more likely to be available without a subscription.

Checking the PHD site I was also happy to see that he recently made it to our Alma Mater in the far east: Memorial University! That’s great to see. Newfoundland is a pretty unique place so I hope he got the chance to have a look around. Even better if it makes it into a “tales from the road” comic.

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Drew Endy on group meetings

Posted 5 February 2009 by PhilipJ under

OpenWetWare tweeted an interesting link to Drew Endy’s take on how to give a good group meeting presentation (though it is clear that this is useful advice for any presentation). Here are a few of my favourite slides:

Giving a good group meeting talk should also benefit you. What are the things you can’t understand or explain, and the rest of your group might be able to help with? If you are in a large group it is often the case that people have no idea what you are doing all the time (particularly if you are spread out over multiple rooms/buildings, as my group is). This is the time to use the collective group knowledge to try and solve problems you might have. For me, item number 3 is particularly important.

This is a pretty accurate reflection of the makeup of a group meeting audience. There will be people who know exactly what you are doing, and those who you never talk to (as per above) might not understand a thing. As my group’s meetings are at 10am on Monday mornings, we also have a fair few Dozers (often me.) Endy’s advice is to peg your talk at both the Lost and the Super Nerds.

Finally, and I can’t agree with this enough:

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Lou Dobbs on "Cheap Science"

Posted 11 January 2009 by Andre under

Lou Dobbs discusses the relatively low pay received by postdocs compared to others with similar or less education. He suggests that it is the large number of foreign postdocs allowed to work in the country that is driving down salaries and thus providing a disincentive for Americans to pursue careers in science.

I think the process Dobbs describes is basically correct. If Americans cut off the supply of foreign scientists by making it even harder to get visas, postdoc salaries would increase because of the sudden drop in available labour, but at the same time, labs would no longer be getting the best available people and the quality and quantity of science would decrease. Wouldn’t this drop in productivity in American labs make it harder to justify research spending to the government and general population?

So the question isn’t whether cutting off foreign labour would increase salaries, the question is whether that’s a smart thing to do. Should the US increase or decrease the number of foreign scientists it allows into the country? What is the optimum postdoc salary and why?

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Traditional lectures don't work

Posted 2 January 2009 by PhilipJ under

As will be no surprise to anyone who has ever sat through a lecture, traditional lecturing doesn’t work, or at least, not as we wish. The most recent discussion of how traditional lecturing is failing students is from physicist Eric Mazur, who writes in the most recent edition of Science in Farewell, Lecture? (pdf, closed access):

The traditional approach to teaching reduces education to a transfer of information. Before the industrial revolution, when books were not yet mass commodities, the lecture method was the only way to transfer information from one generation to the next. However, education is so much more than just information transfer, especially in science.* New information needs to be connected to preexisting knowledge in the student’s mind. Students need to develop models to see how science works. Instead, my students were relying on rote memorization. Reflecting on my own education, I believe that I also often relied on rote memorization. Information transmitted in lectures stayed in my brain until I had to draw upon it for an exam. I once heard somebody describe the lecture method as a process whereby the lecture notes of the instructor get transferred to the notebooks of the students without passing through the brains of either. That is essentially what is happening in classrooms around the globe.

The traditional lecture method ignores the fact that lots of people learn in lots of different ways, and when it comes to things like calculation, watching someone else do them does little for one’s own understanding. It might make sense to you for the brief moment while watching, but it is not a substitute for doing it yourself to really master something.

I think the relative lack of utility of the traditional lecture has been masked by the fact that students are (usually) in a university program out of choice, and will pick up the slack and teach themselves as is necessary to succeed in the course. It is also my philosophy that the quicker a student realizes they should (and can!) be teaching themselves the material, the more enjoyable the learning process and the better they do.

So what are we going to do with all these professors who still need to teach courses? Mazur’s take is to change the way the classroom is run:

[…] I have begun to turn this traditional information transfer model of education upside down. The responsibility for gathering information now rests squarely on the shoulders of the students. They must read material before coming to class, so that class time can be devoted to discussions, peer interactions, and time to assimilate and think. Instead of teaching by telling, I am teaching by questioning.

I’ve had a couple of profs over the years who have taken this approach, and I have always felt it works so much better than the traditional method. The only problem is that it is most effective in the small class setting such as upper-level undergraduate courses. It can be implemented in a large introductory class through the use of so-called “clickers”, but the implementation is key. Quoating Mazur again:

I often meet people who tell me they have implemented this “clicker method” in their classes, viewing my approach as simply a technological innovation. However, it is not the technology but the pedagogy that matters. Unfortunately, the majority of uses of technology in education consist of nothing more than a new implementation of old approaches, and therefore technology is not the magic bullet it is often presumed to be.

Are any of our readers using clickers and changing their teaching methodology (I think Rosie has used them in her courses)? If so, I’d love to hear your feedback on how they were received by students, and whether it was more or less work to prepare for the course. I fear (but appreciate) that the effort involved will be a deciding factor on whether these new teaching tools (implemented properly!) will be embraced.

* I don’t agree that science is somehow different from other subjects when it comes to traditional lectures and their relevance to learning. No subject is just a collection of facts to be regurgitated on an exam.

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University libraries, budgets, and open access

Posted 27 November 2008 by PhilipJ under &

I’ve been playing with numbers in my head based on the statistics from my home institution – the University of Toronto – relative to publications, the real cost of open access publishing, and the U of T library’s annual budget for journal subscriptions.

It turns out that U of T is listed as an institution on some 6470 publications per year (averaged during 2000-2004, data from Thomson Scientific), and as of 2005-2006, the U of T libraries (spread over a couple of campuses) have a periodicals budget of just over $10 million per year (see section 7, “LIBRARY ACQUISITIONS COMMITMENTS” in the 2005-2006 budget). For the rest of this article, let’s assume the American and Canadian dollars are roughly equal in value (which was the case until a couple of months ago).

At present, that $10 million a year largely goes to closed-access publishing houses (not just the Elseviers and Macmillans of the world, but also the much-loved not-for-profit societies which publish journals as well). This gives the university students, faculty, and staff access to the literature both on campus and off, via the internet. While this in principle works well, journal subscription costs have been skyrocketing, and university library budgets have not been able to keep up (and I surmise things will only get worse with the hit to university endowments recently). The breadth of subscriptions will surely fall in the coming years.

What, then, if the university decided to embrace the open access movement entirely? This is obviously a pie-in-the-sky idea, but bear with me, as the result is interesting.

Subscription costs would obviously be nil for an open access journal: we are all free to access the content of an open access journal via the internet, with no restrictions on who can read the content. In contrast, the author would pay to publish the article. This is perhaps the biggest resistance from scientists (and I’m sure the situation would be similar in the arts, or law, or what have you) to the open access movement, many feeling they don’t have enough funding for students or experimental equipment as is, and couldn’t possibly afford to pay to publish as well. I can appreciate this argument, though some progress is being made as you can specifically request funding to cover open access publication charges from some of the granting agencies.

(Also, let’s be honest, the current situation of paying for page charges and to have colour figures means the author is already paying to publish, and sometimes non-trivial amounts.)

The funding supplied to the library for journal subscriptions could instead go towards paying for the publishing costs in open access journals. Using the PLoS journals as our benchmark, premium quality publications would cost around $2500/article (the current fee to publish in PLoS Biology or PLoS Medicine), while the bread-and-butter publication costs are maybe closer to those of PLoS ONE — $1300/article.

Let us imagine that 10% of the publications coming out of U of T are of the premium variety, while 90% are your more run of the mill papers, and that there are open access journals in which to publish them. Using the current costs from the Public Library of Science, 650 premium papers would run around $1.6 million dollars, while the 5850 “bread-and-butter” papers would cost an additional $7.6 million each year. This is already less than the 2005-2006 periodicals budget of slightly over $10 million!

Let’s further assume that the economies of scale would kick in if universities around the world decided to embrace this philosophy. This should lead to an overall lowering of the publication costs, all the while bringing access to academic literature to everyone with an internet connection. It is also easy to imagine the costs being even lower, as the collaborative nature of academic work means many papers now have authors from multiple institutions, all of whom could share in the cost of publishing. (Determining the rules for who-pays-what would be tricky, but should be doable.)

There are probably some key issues I’m missing here (the most obvious one which I’ve even mentioned is that we need open access journals to publish in!), and my idea is prefaced on the assumption that universities are the significant driving force in the academic literature game, but I think the take-home message is reasonably clear, at least using the University of Toronto numbers: we could already afford going entirely open access.

I certainly wouldn’t feel bad if Elsevier and their ilk went out of business given the exorbitant increase in subscription costs and the non-obvious reasoning why, and I’m sure the societies could come to embrace the open access movement, which would bring the majority of high quality journals into the fold.

So, what’s the hold up?

Update — Peter Suber’s commentary (showing my conservative estimate of how much it would cost is potentially much higher than would be the case) is well worth a read.

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