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2012 April 8

Princeton University’s Integrated Science course

Filed under: Uncategorized — gasstationwithoutpumps @ 13:33
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I recently heard about the Integrated Science course at Princeton University, though they’ve apparently been running it since 2004.  The class is rather heavily crosslisted: ISC/CHM/COS/MOL/PHY 231, 232, 233, 234.  The class must be somewhat expensive to run, as it involves a dozen top-notch faculty from chemistry, physics, biology (both molecular and evo-eco), and computer science.

I’m usually a bit dubious of integrated science classes, as they tend to be an excuse for sacrificing depth for breadth.  This course does not seem to have that problem. In fact, it looks more like an honors course, requiring students to come in with strong high school backgrounds in chemistry, physics, and calculus (BC, not just AB).

They use computer modeling (both dynamical models and statistical models) extensively, which makes me wonder why they are using Halliday as the physics text, rather than Matter and Interactions—was it just familiarity with the book, or are there some good pedagogical reasons for preferring Halliday in the course?  It may be because they actually get a little into quantum mechanics at the end of the year, which Matter and Interactions does not cover well.

Somewhat unusually, the course has a heavy component of computational biology (mainly systems biology, it seems, but a little on finding genes and comparing them between yeast and human).  Overall, it looks like a pretty intense course for a first-year college class (it counts in total as 4 courses at Princeton, and is supposed to be the equivalent of first-year chem, first-year physics and the first semester computer science).

There is a second year integrated science course that covers organic chemistry and biochem.  The six courses look to me like excellent preparation for a student going into bioengineering or bioinformatics, though students wanting to do traditional physics or chemistry might be better off with a narrower focus their freshman year.

I don’t think UCSC can currently afford to teach honors courses like this one, as much as I would like us to.  It is a shame, but it seems like honors courses are the first thing that gets cut when department budgets get squeezed. I can understand why, because relatively few students are affected and honors classes, by their very nature have low student/faculty ratios, so are expensive to run.  But the loss of honors classes causes a disproportionate loss of top students to other universities—a problem UCSC administration has worried about for quite some time (our attrition is bimodal, with an unusually high loss of top students as well as the more common loss of students failing out).  Unfortunately, the loss of top students never seems to worry the administrators enough to actually create and maintain honors courses.  Honors courses get taught occasionally, but they never last long—the administration only ever provides startup funds for such classes, never continuing budgetary allocations.

The Princeton course looks like a good model to follow, if we ever had the money to do it.  Princeton, of course, has a huge endowment and high tuition, so they can afford to continue expensive courses if they work (they’re in their 8th year of teaching this course).  I doubt that UCSC could scrape together the funds to offer such a course even once, though the probably could put together a watered-down large-lecture version of it, if there were any point to doing so.

2012 February 25

PLoS Computational Biology: Bioinformatics: Starting Early

The Public Library of Science has a a service where they group together open-access articles from their journals to make  PLoS Collections: Article collections published by the Public Library of Science.

One collection that might be particularly interesting to readers of this blog is PLoS Computational Biology: Bioinformatics: Starting Early, which has articles from PLoS Computational Biology about getting bioinformatics into high-school courses.  So far, there are only 4 articles, all from the 27 October 2011 issue of the journal, but I expect that more will come out in the next year.

2011 November 24

Harry Potter’s World—junk science at NLM

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I was recently pointed to a site at the U.S. National Library of Medicine that uses a popular literary figure to inspire kids to learn real science: Harry Potter’s World Renaissance Science, Magic, and Medicine.  They have both an English-class lesson plan (7th–10th grade) and a science-class lesson plan (7th–11th grade). I was prepared to praise them for this integrated curriculum, which seems to me like an excellent way to try to bridge C.P. Snow’s two cultures in academia.

But I glanced quickly down their list of resources and saw Human Mendelian Traits and Human Mendelian Traits for Teachers. A quick look revealed that both were propagating serious myths about human genetics—myths that have been comprehensively debunked at Myths of Human Genetics.

Unfortunately, the myths form a core part of the lesson, and so there is not a lot salvageable once the myths are removed.  I think that it may be appropriate for the NLM to take this lesson plan off their site until they can rework it into something consistent with what is known about human genetics.  They are not doing anyone a favor by putting their brand name on junk science.

2011 November 19

Starting a local effort to get bioinformatics into AP bio

Filed under: Uncategorized — gasstationwithoutpumps @ 00:32
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As those who have been reading my blog for a while know, I’m on a task force attempting to get bioinformatics into high school biology (particularly AP bio) classes, and I have a series of posts about Advanced Placement Biology courses and the AP Bio exam.  I recently posted about an attempt in Colorado to introduce bioinformatics into AP bio and invited grad students in my department to do something similar.

I had a couple of students respond right away, and I sent out queries to three local high school biology teachers that I had previously had contact with.  One responded enthusiastically, and so I set up a meeting for him, the two students, and myself to meet Friday afternoon (Nov 18).  In the morning, a third student (who had not subscribed to the mailing list I’d announced effort on) indicated an interest also, but she could not come to the meeting.  I expected the other two students to be there.

I was a little surprised to find not two students, but three at the meeting (the two who had sent me early e-mail had recruited yet another student).  We now have four grad students (Olga, Yulia, Dorothy, and Paola) interested on working on getting bioinformatics into bio classes at one (or more) of the local high schools. (Note: more are still welcome—UCSC grad students should probably talk with Olga, who seems to be recruiting others to join.)

We did a lot of brainstorming today to try to figure out the scope and nature of the project.  We agreed on some general principles:

  • The primary goal is to teach students biology, not computer science or bioinformatics.  The bioinformatics should be good support for the underlying biology lesson.
  • Whatever we produce should be made available on the web (but putting any answer keys behind password protection, should we end up producing anything that needs a key).
  • The students will present the lessons to the class (both to expose the high school students to college student role models and to give the grad students practice teaching), but the lessons should be teachable by non-bioinformaticians.  In particular, the high school teacher should be able to teach it himself next year.
  • If things work out well, it might be worth presenting a paper explaining the project (and advertising the materials) at a high school biology teachers conference (perhaps an NABT conference?).

We discussed various tools and possible topics to teach, but did not settle on any particular topic.  Instead each student will think about what tool or technique they would like to teach and what lesson it will support.  One idea that seemed to have some traction was to go through the process of identifying a gene, getting its sequence (with surrounding DNA) from a genome browser, designing primers for PCR, and verifying that the primers uniquely selected the gene again using the genome browser. We also talked about looking at sequence logos of huge alignments (perhaps of HIV proteins) to identify conserved regions, making phylogenetic trees, and other possible lessons. The use of the genome browser to show introns and exons and the greater conservation in most exons was also discussed.

One cool thing one could do with the PCR lesson is to have the students design primers, order the most promising set, and then do a PCR reaction and gel electrophoresis to confirm amplifying the right length DNA. The problem is that we could design the primers, but not then do the PCR, as the high school does not have a thermocycler, and hand cycling with water baths for PCR is rather tedious. (I did once blog about a very low-cost capillary PCR method I read about, but I don’t know if it actually works.) The reagents for PCR cost about $100 for 200 reactions (for example, for the New England Biolabs kit) and need to be stored at -20ºC.  The primers cost about 30¢ a base (in 10 nmole amounts, which I think is enough for about 200 reactions), so add about $20 to the cost of a PCR experiment for the class.  The most expensive thing is the thermocycler, which costs about $300–500 used—I saw one on ecrater.com for about $220, including shipping.  I wonder if any of our faculty with connections in the biotech industry can get surplus thermocyclers cheaper. In any case, it looks like doing the PCR  wet lab experiment would cost about $500 in startup costs and $40/class in consumables.  This may be too much for the high school, unless we can get donations of reagents or loans of equipment.  The PCR reaction itself takes longer than a 90-minute block, so would have to be an after-school or weekend workshop,which may be too big a project for this year.

Obviously, we have not yet settled on what lesson(s) we want to present, and we’ll be doing brainstorming about it in early December, after the fall quarter winds down.  The hope is to have a lesson or two (probably one or two 50-minute classes followed by a hands-on block of 90 minutes) ready for testing with the high school classes by late January (to reinforce what they will have learned about DNA sequences and replication).

I promised the grad students some links to information about the AP bio curriculum, besides my earlier post about resources for teaching bioinformatics in high school.  Perhaps the most important is the AP bio home page for teachers, which has links to College Board’s resources and to the new AP biology curriculum (which affects AP bio tests starting in May 2013). Another is the BME 110 course at UCSC, which is an intro bioinformatics tools course for biologists.  It may be possible to adapt some of the assignments in that class to AP Bio, though the focus on that class is to teach the use of bioinformatics to students who have already had a few college biology courses, rather than to teach the fundamentals of biology, so most assignments will not be directly usable.

UPDATE (2011 Nov 19)

Ted pointed me to a page where PLoS Computational Biology is gathering resources relevant to bioinformatics in high school bio.  They have 4 things there currently (one the article I blogged about, the other three editorials that provide useful advice).

2011 November 7

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

Filed under: Uncategorized — gasstationwithoutpumps @ 00:32
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As those who have been reading my blog fo awhile know, I’m on a task force attempting to get bioinformatics into high school biology (particularly AP bio) classes, and I have a series of posts about Advanced Placement Biology courses and the AP Bio exam. Of course, I’m not the only person interested in achieving this, and others have done far more than I have.

There is a nice paper in PLoS Computational Biology: A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms, that describes one attempt by researchers at University of Colorado, Boulder to get some understanding of BLAST and tree-building algorithms into high-school bio classrooms in a fairly minimal way (3 lessons of 1–2 class periods each).  They provide the curriculum they used and a “post-game” analysis, where they look at what they would do differently next time, based on the successes and failure of this first attempt.

The tools and basic approach they used seem reasonable, though I question the value of teaching what an algorithm is with the “make a peanut butter sandwich” example, classic as that is. Along with the students, I wonder about the relevance to an AP Bio class.  Doing the living computer exercise seems ok, but it might be better to apply it to a curriculum-relevant algorithm, such as creating a Punnett square.

This paper seems like an important resource, and so I have added it to the list I collected at Resources for bioinformatics in AP Bio.  Incidentally, the authors point to this blog, but to the early post Advanced Placement Bio changes announced, rather than to the more relevant Resources for bioinformatics in AP Bio.

Note to UCSC grad students: I have some contacts with local high school bio teachers, if some of you want to try one of these outreach experiments in education, and I would be glad to facilitate meeting and planning.

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