## Friday, December 28, 2012

### Random thoughts on teaching (thermodynamics for chemists)

The course in question
I recently finished co-teaching Nanothermodynamics - a P-Chem course for nanoscience students covering statistical mechanics, thermodynamics, diffusion, and kinetics.  This is the third time I have taught it and the first time I have been really happy with the way my part went.  I have also gotten the best teaching evaluations ever, so I know the students were happy with it as well.  This blogpost is about why I think it went well and some general musings about teaching in general and teaching thermodynamics in particular.

Repeating questions
I use peer instruction so my "lecture" periods consists mostly of me asking questions that the students answer using Socrative.  This year I decided to ask questions about material covered in previous lectures - either the exact same question or a variation of previous questions - and it was a real eye-opener.

Fundamental questions that had received near 100% correct answers one week received at most 50% correct answers one or two weeks later.  Clearly the students had done the reading for a particular lecture period but that does not mean they remember it after a few days.  Sometimes when I used the exact same question they would remember that the answer was, say, "A" but could not really remember why.  So it's not that they are not paying attention.

Less is more
So I decided there was a few key concepts that needed to be reviewed periodically until they "got it" and that was the connection between the equilibrium constant $K$ and the standard free energy change $\Delta G^\circ$ and a molecular understanding of $\Delta H^\circ$ and $\Delta S^\circ$.  So I started each lecture period with  a few questions such as this one.

Sometime I would spend as much as 50% of the "lecture" period on review.  This means something else has to be covered in less detail and this forced me to think much more deeply about what concepts are most important. (It makes it a lot less painful to cut things when you have amble data that 80% won't remember it for more than a few days.) And I think this is why the course was so successful this year: I had, for the first time really, thought very carefully about what to teach and why.

The "textbook" is a problem
Think about the first step in the "design" of a course: pick a textbook.  The textbook typically defines what you teach, in what order you teach it, what problems you assign and, as a result, the exam.  At best, lectures cover the most difficult parts of the chapters or, at worst, is a mad Powerpoint-fueled dash to cover it all.  Often each chapter is given the same number of weeks of coverage regardless of content.  I know because I have done all these things myself at some point.

Most textbooks on a particular topic have very similar content.  This is not, in my opinion, because textbooks authors have, through exhaustive trial-and-error, converged on an optimum solution but due to a variety of other factors.  It is primarily because the audience/customer is not the student but the instructor, because the customer is the one choosing the book, and the customer is a very conservative person for a variety of reasons.

The main reason is that the customer usually has taught the course before and wants, for whatever reason, to change textbooks without making major changes to the course.  Furthermore, many instructors do have a "favorite topic" and will not pick the textbook unless that topic is covered in some detail.  As a result textbooks rarely leave anything out, no matter how irrelevant the author personally thinks it is.

I would argue that courses end up covering way to many topics, many for no other reason than that they appear in the textbook, and that these topics are in textbooks for no particularly good reason.

A vicious Carnot cycle
The Carnot cycle is in most physical textbooks and is generally a very difficult and abstract concept to do with the maximum efficiency of heat engines.  In Molecular Driving Forces, one of the few thermodynamics textbooks that looks quite different from the rest, it is included in Chapter 7 called "The Logic of Thermodynamics" where concepts like heat and work are introduced.  The first page of the chapter has pictures of pistons.  The opening paragraph states that these new additions to the "toolkit" are "crucial for understanding cyclic energy conversion - in engines, motors, refrigerators, pumps (including your heart), rechargeable batteries, hurricanes, ATP-driven biochemical reactions, oxygen transport around your body, and geophysical cycles of carbon and water, for example."  These things are never mentioned again in the rest of the remaining 27 chapters as far as I can tell.

I am not saying these topics are unimportant to chemists, but they are nowhere near as important as say, the relationship between $K$ and $\Delta G^\circ$.  However, if you spend more time on the Carnot cycle students will think that it is, and as a result will not really understand either.  Example: Who's afraid of Big Bad Thermodynamics?

Tl;dr
For the last few years I have been focussing on how I teach by using simulations and peer instruction.  I still think these tools are important; for example, polling the students proved they needed key concepts repeated a few times before they "sink in" and I challenge you to test this yourself with your class - the tool is freely available.  But using these tools to teach overly abstract concepts that you or your colleagues never utilize in your jobs only because they appear in the textbook won't get you much further.  It's time to take a cold hard look at what you teach and why.

Thermodynamics for the average chemist: some recommendations
* Most chemists think in terms of molecules not equations

* Most chemists would like to understand how to use an equation properly before worrying about where it came from.  Consider deemphasizing derivations.

* Most chemists deal with the molecular interpretation of reactions and binding, not phase transitions.

* Most chemists work in solution where volume changes are usually negligible and are usually trying to shift the equilibrium towards products.  Consider deemphasizing the concepts of work and efficiency.

* Most $\Delta G^\circ$ measurements are done by measuring $K$.  $\Delta S^\circ$ is obtained either by measuring the temperature dependence of $K$ or by measuring $\Delta H^\circ$ calorimetrically and solving for $\Delta S^\circ$ knowing $K$.  Consider deemphasizing $\delta S=\delta q_{rev}/T$.  Consider introducing $K=e^{-\Delta G^\circ/RT}$ as early as possible.

* Most measurements ultimately deal with $\Delta G^\circ$.  Consider deemphasizing concepts related to $\delta G=0$.

* The conformational entropy is important but almost never discussed in textbooks.

* The most often used standard state is 1 M ideal solution and the most often used activity convention is the solute convention.  Consider deemphasizing the rest.

* Enthalpy changes are dominated by $\Delta H^\circ(T=0)$ but this term is generally glanced over in most textbooks.  So students generally have a poor molecular understanding of  $\Delta H^\circ$.

## Thursday, December 27, 2012

### Peer instruction question on entropy

Answer the question first here and see the following slides for an explanation

## Wednesday, December 26, 2012

### New paper: Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry

+Casper Steinmann recently submitted the paper to PLoS ONE and is awaiting announcement on arXiv.org where you can view the manuscript.

This is the first time that a fragment based method has been applied to map out a trajectory of an enzyme - on this case the very popular chorismate mutase.

Abstract
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be 18.3 +/- 3.6$kcal mol-1 using ONIOM with MP2/cc-pVDZ and EFMO/6-31G(d) for the high and low layers, respectively. sidenote and totally off topic: you can now reference peoples Google+ profiles directly in blogger in the same way that you do on Google+. Nicely done. ### The Reflector app: record your iPad screen http://www.reflectorapp.com/ Found this app a while ago, shared it somewhere (probably Twitter) and promised myself I would get back to it. I just spent 30 minutes trying to re-find it and after all this time Twitter is no help. So I am writing this blogpost to remind myself. There is a free trial and it works great. This will be great for demoing iPad apps or integrating online lecturing with other video. 2013.07.29 Update: there is now a native app for this for iPhones called xRec. An iPad version should be available soon. ## Tuesday, December 25, 2012 ### Popular posts in 2012 According to Google Analytics this blog received nearly 16,000 page views this year. Top 5 most accessed posts written in 2012 (according to Blogger) Where am I sending my next paper and why? Finally an arXiv for chemistry! I'm gonna pay$1350 for this? Come on PLoS ONE!
If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper?
Pymol on the iPad (Written by +Luca De Vico )

Top 5 posts accessed posts (according to Analytics)
Where am I sending my next paper and why?
Two Java based Huckel theory programs (Written by +Janus Juul Eriksen )
Computational Chemistry Highlights: a new kind of chemistry journal
Tools for the lazy teacher
That's classic (Written by +Casper Steinmann)

## Sunday, December 23, 2012

### My year in open science

Reinventing Discovery
In 2011 I dipped my toe in the open access waters and in 2012 I dived in head first.  I come from the GAMESS group, which has always made the source code freely accessible (though under a license) and when it came time to releasing the first standalone software package from my own lab (PROPKA) in 2005 this was done under an open source license. (This year we finally moved all group software to Github.)

So when I came across +Michael Nielsen's Reinventing Discovery in late 2011 I could nod along when I read many of the chapters, but far from all of them.  However, the book makes a very compelling case for the idea that secrecy and greed is retarding the progress of science.  Shortly after I read the book Elsevier gave a very blatant demonstration of the latter.

The Elsevier Boycott
Sometime in January I became aware of the Research Works Act, which was an outrageous piece of proposed US legislation designed by publishers to squeeze the last few cents out of scientific publishing by making it illegal for papers describing publicly funded research to be made freely accessible online. This lead to a call for boycotting Elsevier, which I signed early on, but it also got me interested in open access publishing (see next section).

I should mention that I have broken the boycott twice already.  I agreed to do a review without checking the publisher first and I submitted a paper to an Elsevier journal at the request of a coauthor.

Publishing in the open access journal PLoS ONE
So after some soul-searching on my part we took the plunge an submitted a paper to PLoS ONE.  This went alright and 2012 resulted in four PLoS ONE papers and a fifth one submitted.  Though PLoS ONE does not count impact as a review criterion I have found the reviews every bit as thorough as for any other journal I have experience with, but you can judge for yourself as I have started posting my reviews on this blog.

arXiv is for research and journals are for CVs plus my own little boycott
Perhaps the most important "open access thing" I did this year is posting preprints on arXiv when we submit to a journal.   Just like an open access journal it makes the information freely available, but it does so right away (and discoverable on Google Scholar within a week of deposition) rather than many months later after the review process. If every scientist did this it would be a giant leap for open science and, yes, arXiv does accept manuscripts outside of physics.

In fact I think deposition on arXiv is so important that I have started boycotting journals that don't accept manuscripts that have been deposited on arXiv.

Computational Chemistry Highlights
This year I also initiated the overlay journal Computational Chemistry Highlights.  The idea grew from the ensuing on line-discussion of the role publishers and publishing alternatives on Gowers's blog and elsewhere following the Elsevier boycott.  I realized, as have many others, that there are two main reasons people publish in conventional journals: dissemination of results and prestige.  Dissemination is now a comparatively trivial contribution in the age of the internet and prestige is conferred by the scientific community, not by publishers.  CCH is an attempt at generating a platform for conferring prestige on papers that is independent of how its disseminated, using freely available tools like Blogger.com. It will take a while to generate "prestige" for CCH but in the meantime is still provides a useful service to the scientific community by highlighting interesting papers.

Signing reviews
I have started signing my manuscript and proposal reviews. I am not sure what scientific impact this will have but at least it makes science a tiny bit less secretive.  On a more practical note I find that I do think a little bit harder about what I write in the review and I am much more careful about doing the review on time.

Posting funded proposals
I made all my funded proposals available online.  Unfortunately I was not able to add to this collection in 2012.

Open Notebook Science
I don't practice Open Notebook Science in the traditional sense of "making the entire primary record of a research project publicly available online as it is recorded."  But that is because of the sad fact that I don't personally produce any research data (running calculations) anymore.  However, I do try to publicly share my meager contributions the scientific process here and on Molecular Modeling Basics and, increasingly, Google+.

I can't really emphasize the utility of summarizing your thoughts on a topic via a blogpost enough.  If you have clearly thought the issue through it takes no time to write and if not, it helps you to think it through and is well worth the time it takes.  I also find it strangely liberating to write knowing that the comment section is there: if I skip something I think is trivial or well known I know the reader can easily ask for clarification.

### Nature's ten people who mattered this year includes a blogger, again

Last year it was Rosie Redfield and this year it is Timothy Gowers who's excellently titled blogpost Elsevier - my part in its downfall sparked the Elsevier boycott and - more importantly - a lot of new debate about open access.

## Thursday, December 13, 2012

### Poll: citations versus impact factor: which would you rather have

The poll question on the right hand side of this blog came up on the way to lunch.  What would you pick?

## Wednesday, December 5, 2012

### Teaching high school students to fold proteins in less than a day

Program

1. The Computational Chemistry Movie

2. Brief introduction to computational chemistry (slides nr 2-6)

3. The Protein Structure Activity using Molecular Workbench

4. Start on the introductory puzzles for Foldit

5. Lunch

6. Four Peer Instruction questions using Socrative (slides nr 7-13)

7. More puzzles on Foldit

8. Tour of the Department

## Monday, December 3, 2012

### Dear Journal of Computer-Aided Molecular Design: I only review for arXiv friendly journals

From: Jan Halborg Jensen
Sent: Monday, December 03, 2012 12:58 PM
To: Journal of Computer Aided Molecular Design (JCAM)
Subject: Re: Manuscript JCAM-D-12-xxx for review
Dear Dr xxx

Thank you for your invitation to review for JCAM.  I only review for journals that allow pre-print deposition on servers such as arXiv.  According to your instructions to authors this does not appear to be the case, so I must decline.  If JCAM does allow for depositions of preprints please let me know.

Best regards, Jan