Monday, December 28, 2015

Standard Gibbs vs Helmholtz Free Energy Change: An Apparent Paradox

Consider the following equilibrium
$$ \text{A} + \text{B} \rightleftharpoons \text{AB} $$
and the following three experiments performed at the same temperature.

Experiment 1: To an empty, rigid container with volume $V_1$ is added $p_{\text{A},0}$ of molecule $\text{A}$ and $p_{\text{B},0}$ of molecule $\text{B}$.  The system is allowed to go to equilibrium, $p_{\text{AB},1}$ is measured, and $K_1$ is computed as
$$ K_{p,1}=K_1=\frac{p_{\text{AB},1}p^\circ}{p_{\text{A},1}p_{\text{B},1}} $$
where $p_{\text{A},1} = p_{\text{A},0}-p_{\text{AB},1}$

Since the experiment is carried out at constant volume, equilibrium is defined as $dA = 0$ so the standard free energy change computed from $K_1$ should correspond to a standard Helmholtz free energy change, $\Delta A^\circ_1$.

Experiment 2: A balloon is filled with $p_{\text{A},0}$ of molecule $\text{A}$ and $p_{\text{B},0}$ of molecule $\text{B}$. After equilibrium the volume of the balloon is $V_2$ and $p_{\text{AB},2}$ is measured and $K_2$ computed.

Since the experiment is carried out at constant pressure, equilibrium is defined as $dG = 0$ so the standard free energy change computed from $K_2$ should correspond to a standard Gibbs free energy change, $\Delta G^\circ_2$.

Experiment 3: Experiment 1 is repeated using a rigid container with volume $V_2$.

$K$ does not depend on the volume, so $K_3 = K_1$ and $\Delta A^\circ_3=\Delta A^\circ_1$. However, since the temperature and final volume is the same as in Experiment 2, the internal pressure and hence the partial pressures must be the same.  Thus $K_3 = K_2$ and $\Delta A^\circ_3=\Delta G^\circ_2$.  It follows that
$$ \Delta A^\circ_1=\Delta G^\circ_2$$

So there is really only one standard free energy change associated with Eq 1, but is it $\Delta G^\circ$ or $\Delta A^\circ$?

The change in standard Helmholz free energy is not the same as the change in standard chemical potential
The equilibrium constant is related to the change in standard chemical potential
$$ K = e^{-\Delta \mu^\circ RT} $$
The chemical potential is defined as
$$\mu _X = {\left( {\frac{{\partial G}}{{\partial {n_X}}}} \right)_{p,T,n'}} = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}}$$
For a one-component system, $G = nG_m$, and the chemical potential is simply the molar Gibbs energy of the substance because
$$\mu = {\left( {\frac{{\partial G}}{{\partial {n_X}}}} \right)_{p,T,n'}} = {\left( {\frac{{\partial nG_m^{}}}{{\partial {n_X}}}} \right)_{p,T,n'}} = G_m$$
so we can write
$$ K = e^{-\Delta G^\circ RT} $$
$$ \Delta G^\circ = G^\circ_m(\text{AB)} -G^\circ_m(\text{A)} -G^\circ_m(\text{B)}  $$
However, the chemical potential is not equal to the molar Helmholtz free energy
$$A_m = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{p,T,n'}} \ne {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}}$$
Notice that the middle term is for constant $p$ and the last term is for constant $V$.  So I can't write the equilibrium constant using $\Delta A^\circ$ computed partial molar standard Helmholtz free energies
$$K = {e^{ - \Delta {\mu ^{\circ}}/RT}} \ne {e^{ - \Delta {A^{\circ}}/RT}}$$
Here's why.  The Helmholtz free energy can be written in terms of the partition function $Q=q^N/N!$
$$A =  -nRT\ln \left( {\frac{{eq}}{{n{N_A}}}} \right) = -nRT\ln \left( {\frac{{eq_0V}}{{n{N_A}}}} \right) $$
The chemical potential is
$$ \mu _X = {\left( {\frac{{\partial A}}{{\partial {n_X}}}} \right)_{V,T,n'}} =  - RT\ln \left( {\frac{q}{{n{N_A}}}} \right)$$
To get the partial molar Helmholtz free energy we need to keep $p$ constant, so we substitute $V=nRT/p$ before differentiating, which cancels out the $n$ in the parenthesis
$$ A_m = -RT\ln \left( {\frac{{e{q_0}RT}}{{{N_A}p}}} \right) = - RT\ln \left(\frac{eq}{N_A} \right) $$
So from this we can see that
$$ \mu_X = A_m + RT$$
In the case of $G$
$$G =  A + RT =-nRT\ln \left( {\frac{{q}}{{n{N_A}}}} \right)  $$
and we make the substitution $V=nRT/p$ before differentiating to find $\mu$
$$ \mu = - RT\ln \left(\frac{q}{N_A} \right) = G_m = A_m + RT $$
So measuring the equilibrium constant for the reaction in Eq 1 gives us
$$\Delta \mu^\circ = \Delta G^\circ = \Delta A^\circ - RT $$

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Tuesday, December 15, 2015

My Vision for ACS Omega

Update: ACS Omega is too expensive

A few weeks ago I was invited to submit my application (a vision statement and a CV) for a co-editor-in-chief position at ACS Omega.  Here's my vision statement.  I have made one change: at the time I didn't know the final name of the journal and used a working title instead.  The application is still pending.

My Vision for ACS Omega
Jan H. Jensen
University of Copenhagen
Twitter: @janhjensen

Open Access and Open Science: Leading by Example
Since 2012 I have published the bulk of my papers in PLoS ONE and PeerJ - one of the few chemists to do so. My switch to OA was catalyzed mainly by the Research Work Act  - legislation that sought to “prohibit open-access mandates for federally funded research and effectively revert the US NIH Public Access Policy, which requires taxpayer-funded research to be freely accessible online” (1). The RWA was clearly a result of lobbying efforts by commercial publishers and, in my opinion, designed to maximize profits at the expense of servicing science. This got me to try and, ultimately, embrace OA (2) and open science.

I have found the lack of “perceived importance” and “scope” as editorial criteria at PLoS ONE and PeerJ incredibly liberating: they allow me to be more innovative (i.e. take more chances) in my research and makes the papers easier to write. Equally liberating is the fact that my work can be used by me or anyone else without restrictions under the CC-BY licence, which for me and most other open access activists is synonymous with OA.

I deposit all my manuscripts on arXiv or PeerJ Preprints prior to submission. I sign all my manuscript reviews, I post my reviews on (3), and I publish all the reviews I receive, either on PeerJ (4) or on my blog (5). Furthermore I founded Computational Chemistry Highlights (6) in 2012 that openly reviews important recent papers in computational and theoretical chemistry. I actively campaign for these practices on Twitter and I write extensively about open access and open science on my blog (7). As co-editor-in-chief of ACS Omega I would have the track record needed to be an effective advocate of OA for chemistry.

ACS Omega: The Journal of First Choice
ACS Omega has the potential to become the largest chemistry journal in the world and this will be my goal as co-editor-in-chief. Obviously, a lot of papers that are rejected by other ACS journal because of scope and lack of perceived importance should be funneled to ACS Omega. However, my vision for ACS Omega is as a journal of first choice due to its purely objective review criteria that welcomes innovative ideas and frank discussions of the merits and weaknesses of the results.

In fact I propose that a self-critical discussion of possible limitations of the study is a mandatory part of an ACS Omega paper, with the understanding that it will not hurt the chances of acceptance. This is how science is supposed to work: as a scientist you are supposed to be your own worst critic, but you wouldn’t know it from reading the current literature. I would like ACS Omega to be open to all types of papers in addition to conventional research articles including insights/perspectives, software notes, and replication studies. In my view science advances incrementally and benefits from input at every stage: one should publish early and publish often. I would also like to implement eLife’s Research Advances, “a short article that allows the authors of an eLife paper to publish new results that build on their original research paper” in some way (8).  

ACS Omega: The Most Affordable OA (CC-BY)  Option
If one removes the “perceived importance” and “scope” criteria from the editorial decision process then the only meaningful criteria for where to publish is the price. This is the reason I switched from PLoS ONE to PeerJ. Obviously I cannot be a co-editor-in-chief of a journal where I will not publish myself. ACS Omega must therefore offer an APC of $500 or less (or a PeerJ-style APC model) for CC-BY for me to interested in the position. I currently pay an average of $300/paper to publish CC-BY in PeerJ, so $500 is already a compromise for me.

With ACS Omega ACS has a unique chance to fulfill its mission to “advance the broader chemistry enterprise and its practitioners for the benefit of Earth and its people” by making the APC for CC-BY $0. Think of ACS Omega as part of the ACS’s other activities such as education, outreach, and awards and not as a means of generating funds for such activities. I strongly urge the ACS to consider this option and will happily do the job for free should the ACS choose to do so.

To keep the APC as low as possible I suggest several cost-saving measures:
  • Typesetting is optional and costs extra for the author. Your CV says “Peer Reviewed Publications”, not “Typeset Publications” and I predict many chemists would gladly do their own formatting (perhaps given suitable template) if they can save $500/paper. Other disciplines are catching onto this (9,10) and ACS Omega might as well be on the forefront in chemistry.
  • A smaller editorial board relative to journal volume. I predict that ACS Omega editors will be able to handle more submissions compared to other ACS journals due to ACS Omega’s more objective editorial criteria and more open review process (see below).
  • Less travel/more on-line communication. Communication within other ACS journals are still based on the premise that most editors reside within the US and would go to ACS meetings anyway. We need to do things differently at ACS Omega for purely practical reasons, but this will also lower costs.
  • I would also like to investigate the possibility of corporate sponsorship of the journal to see if it can be done in an ethical way and without conflict of interest issues.         

ACS Omega: A Truly Open Journal
I strongly believe that openly sharing preprints prior to submission greatly benefits science. As co-editor-in-chief I will publicly encourage authors to deposit preprints prior to submission to ACS Omega. Furthermore, I will work with arXiv on establishing a chemistry section and encourage the ACS to support arXiv. The current running costs of arXiv is $826,000. I think the ACS should contribute 10-15% of the running costs if arXiv establishes a chemistry section. Alternatively, the ACS should start their own preprint server.

I am a strong believer in open peer review. I suggest that ACS Omega follows the PeerJ model where the reviewers choose whether to remain anonymous, while the authors choose whether to publish the reviews. If the authors choose to publish the reviews there should be an option to append it to the manuscript when downloading the pdf. I realize that implementing such a feature increases the cost of the journal, so alternatively the journal should encourage reviewers to post their reviews on  Related to this I suggest that editor’s names be openly associated with individual papers.

I am a strong believer in open post publication peer review and I would like to see a comment section for each ACS Omega paper. I realize that implementing such a feature increases the cost of the journal, so alternatively the journal should encourage reviewers to post their comments on PubPeer. Similarly, I suggest a partnership with to keep track of PubPeer discussions, Tweets and blogposts on individual papers.

I am a strong believer in open data and code. ACS Omega should strongly encourage this practice and make it an explicit part of the editorial decision (11) for several reasons: Often the data turns out to be the most important contribution (e.g. data for benchmarking or modeling), it is crucial for informed pre- and post-publication peer reviews, and it helps ensure reproducibility. I am very happy to see that ACS already has partnered with Figshare.

ACS Omega: Transforming the Field of Chemistry
Chemistry is in my opinion the least open of the natural sciences and that as result the field is not progressing as fast as it could. Most chemistry papers are not accessible to the taxpayers who paid for the work (12). The ideas and data within these papers remain inaccessible for other researchers for months or years until “the data tells a story”, “there’s enough for a JACS paper”, or while the manuscript is makes its way down the “impact ladder”. The criterion that something has to be demonstrably “first” to be published means that ideas and data are jealously guarded and most conference talks are used to rehash published results and ideas rather than to get feedback on or develop new ideas. The ACS shares a large part of the blame for this state of affairs as it tends to “set the tone” within our community. For example, all ACS journals have “importance” as a criteria, and aggressively promote an impact factor-based journal hierarchy. Many ACS journals forbid preprint depositions and the ones that allow it do not state so explicitly, leading to a “better not to, be on the safe side” attitude among most chemists.

However, with ACS Omega, the ACS has the unique opportunity to almost single handedly change all this and, ultimately, increase the pace of discovery and genuine innovation in chemistry. As PLoS ONE has shown for the bio/medical community, this is done by actively and explicitly encouraging openness on all fronts - both in the journal policies and by the people who lead it.  I would be honored to be part of this transformation as co-editor-in-chief and would work tirelessly to make it happen.


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Sunday, November 15, 2015

Why I chose to stay on as a subject editor for the RIO Journal

Two months ago I wrote about my decision to tentatively agree to be a subject editor for the RIO Journal.

The Price (APC)
The APC for a traditionally peer reviewed research article in the RIO Journal is €750 (~\$850).  This is significantly more than what I usually pay at PeerJ (~\$300), but only a little higher than the \$695 per article price they recently announced.  The APC is significantly less expensive than PLoS ONE (whose APC recently increased to \$1450 and the no-questions-asked waiver fee appears to be gone) and less than SpringerPlus (\$1085) and F1000Research (\$1000). RIO Journal is thus the second-cheapest OA journal I know of.  As such I would recommend RIO Journal to people who publish non-bio or review papers. (Well right now I would recommend Royal Society Open Science, since they are waiving their APCs for a while).

Getting "publishing-credit" for my research proposals and other research output
It turns out RIO Journal does not offer traditional peer review for research proposals so posting a proposal there is not very different from posting on a pre-print server with a comment section, such as PeerJPreprints.  The main difference is that it would be typeset at the RIO Journal but at a substantial cost (€190/€650 depending on length).  No thanks, I'll go with PeerJPreprints or ArXiv or FigShare or just posting the pdf on Google Docs.

An interesting alternative
Shortly after I wrote the first post on the RIO Journal, Tim Gowers announced an arXiv overlay journal called Discrete Analysis.  The main difference from a traditional OA journal is that the papers are not typeset (and hosted on arXiv).  The APC is \$10 (which is waived for the foreseeable future).  

I actually think this is the way forward for scientific publishing long term.

If I write a paper that is outside the scope of PeerJ, and if Royal Society Open Science starts charging, then I might submit to RIO Journal based on the current APCs.  This would also be my advice to my colleagues should they ask about OA publishing options.  Thus, I'll stay on for now as subject editor. 

This work is licensed under a Creative Commons Attribution 4.0   

OpenCon2015 shows how to make a conference open

I am currently following OpenCon2015 online and really enjoying the experience.

There are two main components: A YouTube live feed and a Twitter feed (#opencon).  The Twitter feed and the high number of live Tweets is really what makes this work!  You not only watch the talk about you also "hear" the thoughts of the audience (both the "live" and "feed" audience) and you can interact with these people live (and follow up on discussions afterwards).  This makes you really feel like you're there and not sitting on the couch in your living room.

To make this work in practice it appears that you need

1. A camera and someone operating it (zooming/panning)
2. A sound system linked to the camera, a microphone for the speaker and 1-2 rowing mikes for questions.
3. A camera/computer interface for the live feed and reasonably fast internet
4. Some basic html skills to make the live feed page, i.e. embed the YouTube feed and Twitter feed side-by-side. (I found it quite important to be able to view the two simultaneously).
5. Lots of people live Tweeting

I really hope that these talks also will be available for later viewing!

Anyway, if more scientific meetings and conferences would adopt this model it would greatly improve their impact and further science as a whole.  

Also, for smaller meetings the streaming could probably be done with a smartphone and Periscope.

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Saturday, October 17, 2015

Copying multiple files using scp

Perhaps the shortest blog post ever, but it took me while to find the command.  I'll know I'll need it again so here it is:

scp -v -r folder

This command created a folder named "folder" on the local machine and copies the content of "/path/folder" on into it

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Saturday, October 3, 2015

PeerJ vs F1000Research

Update 2015.10.05: Correction based on the comment by +Eva Amsen: F1000Research editors do chase down reviewers to help ensure reviews.  So the main real difference between F1000Research and PeerJ appears to be the price - assuming PeerJ authors post a pre-print.

This post is a comment I left on Michael Eisens post on the Mission Bay Manifesto on Science Publishing

A purely practical comment about point 5 in general and F1000Research price in particular. My main point is that PeerJ offers better service at lower cost (and I am not affiliated with PeerJ in any way).

Let’s take my latest paper which just got accepted in PeerJ and contrast it to how it would have worked at F1000Research

1. I submitted my draft to PeerJ PrePrints who made it available online within a day for free.  It showed up on Google Scholar about a week later.

F1000Research would take about a week and cost \$1000 as it was >2500 words.  On the other hand at this point it is typeset.

2. I solicit reviews on social media and by emailing select experts.  There is a commenting section on PeerJ PrePrints where these reviews can be added.  I got some suggestions by email but no one added comments for this particular paper.

From what I can tell the idea is much the same on F1000Research

3. I revise my manuscript and put a new version on PeerJ PrePrints with another plea for comments/reviews.  Then I submit to PeerJ.  PeerJ finds 2 reviewers for me, typesets the manuscript (after minor corrections in this case), publishes the reviews, provides a comment section for further review, and gets it indexes, for \$298 (in this case). Again, there is a comment sections where people can continue to review the manuscript and also the reviewers comments, which I choose to make public.

So, from where I stand I pay F1000Research \$1000 extra for guaranteed and immediate typesetting of a manuscript which may not get reviewed, while I pay PeerJ \$300 for guaranteed reviews of a manuscript which may not get typeset (if it is rejected). 

I couldn’t care less about the typesetting. When I deposit my preprint I consider my work published - and I can do that for free. The remaining steps are taken mainly to be able to add it on my CV under “Peer Reviewed Publication” with additional indexing as a nice bonus.  

As Gowers has shown, if you remove the typesetting this can done for \$10/paper.

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Sunday, September 20, 2015

Surface tension and the non-polar solvation entropy

I made a stupid sign mistake in one of my video lectures and have spent part of the weekend sorting things out in my mind.  So here is a note to self before while it is still fresh in my mind.

The non-polar free energy of solvation can be written as
$$\Delta G_{\text{np-solv}} = \gamma_{\text{np}} SASA$$
where where $SASA$ is the solvent accessible surface area.  The argument is that one of the main contributions to $\Delta G_{\text{np-solv}}$ is the energy required to make the molecular cavity in the solvent, which, for macroscopic objects, is a function of the surface tension of the liquid $\gamma$ and the surface area of the cavity.
$$\Delta G_{\text{np-solv}} \propto \gamma SASA$$
$\gamma$ is positive for water so $\Delta G_{\text{np-solv}}$ is positive in water.

So far, so good.  But this simple picture fails when considering the solvation entropy
$$ \Delta S_{\text{np-solv}} = - \left( \frac{\partial \gamma_{\text{np}}}{\partial T} \right) SASA$$
For water the bulk surface tension decreases with increasing temperature as you would expect, which suggests that $ \Delta S_{\text{np-solv}}$ is positive when in fact it is observed to be negative.

So if $ \gamma_{\text{np}}$ has anything to do with $\gamma$ this would imply that the surface tension associated with molecular-sized cavities increase with temperature.  It is not clear why that would be so and this, in part, has led Graziano to argue that, effectively, $ \gamma_{\text{np}}$ has nothing to do with $ \gamma$ but is a strictly empirical parameter.

A little more detail that ultimately doesn't shed any more light
$ \gamma_{\text{np}}$ is also positive but not equal to $\gamma$. One reason is that $\Delta G_{\text{np-solv}}$ also contains contributions from repulsion and dispersion interactions with the solute.  However, if one computes $\Delta G_{\text{np-solv}}$ from hard sphere simulations the corresponding $ \gamma_{\text{np}}$ values still does not match the $\gamma$ value for bulk water.

Tolman has argued that the surface tension depends on the curvature of the surface and suggested the following approximation
$$\gamma (R) = \gamma \left( 1 - \frac{2\delta}{R} \right)  $$
where $R$ is the cavity radius and $\delta$ is a parameter called the Tolman length.  When $R < 2\delta$
$$ \frac{\partial \gamma (R)}{\partial T} =  \left( \frac{\partial \gamma}{\partial T} \right) \left( 1 - \frac{2\delta}{R} \right)$$
will indeed be positive, but only when $\Delta G_{\text{np-solv}}$ is negative.  What is observed is positive $\Delta G_{\text{np-solv}}$ and  $\Delta S_{\text{np-solv}}$.

Ashbaugh has pointed out that a  temperature-dependent $\delta$ solves this problem but Graziano fired back that since there is no analytical form for $\delta$, $\frac{\partial \delta}{\partial T}$ is just another temperature dependent parameter, and you might as well use $\frac{\partial \gamma_{\text{np}}}{\partial T}$ as a parameter (I am paraphrasing here).

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Saturday, September 19, 2015

ProCS15 paper: reviews are in

2015.10.2 update: Our rebuttal can be found here.  The paper is now accepted.

The reviews of the ProCS15 paper we submitted on August 25 arrived last evening. 25 days to first decision. The verdict was "minor revisions". The editor was Freddie Salsbury, Jr (who also handled our very first PeerJ paper) and both reviewers chose sign their reviews.  Another very pleasant publishing experience with PeerJ.

Editor's comments
Both reviewers have some minor corrects to make and the second reviewer raises a point of skepticism about QM-based vs empirical estimators. A discussion addressing this would likely be of benefit to the field.

Reviewer Comments
Reviewer 1 (Xiao He)
Basic reporting
No Comments
Experimental design
No comments
Validity of the findings
No comments
Comments for the author
This manuscript is of great importance and I totally support its publication in PeerJ. The authors present an excellent and accurate chemical shift prediction program (ProCS15) based on millions of DFT calculations on simplified models. ProCS15 has extended the capability of previous ProCS program, which predicts the backbone amide proton chemical shift, to fast estimation of chemical shifts of backbone and C beta atoms in large proteins. The accuracies of chemical shifts on two proteins (namely, Ubiquitin and GB3) predicted by ProCS15 are very close to the results from fragment-based DFT calculations by Zhu et al., and Exner and co-workers. Nevertheless, the computational cost of ProCS15 is within a second. This program will be widely used in the NMR community. I only have a few minor points.

1) In the Introduction section, “RMSD observed for QM-based chemical shift predictions may, at least in part, be due to relatively small errors in the protein structures used for the predictions, and not a deficiency in the underlying method.” I agree with the first half of the statement, however, the limitation of current density functionals also contributes to the discrepancy between experiment and DFT calculations, especially for the 15N chemical shift prediction.

2) The first AF-QM/MM work is highly recommended to be cited in the paper,
He X., Wang B. and Merz K.M., Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach. J. Phys. Chem. B 113, 10380 (2009)
Reviewer 2 (Dawei Li)
Basic reporting
No comments.
Experimental design
No comments
Validity of the findings
No comments
Comments for the author
This work is a direct extension of the author’s previous work on quantum based protein chemical shift calculation. The performance is comparable to other quantum based predictors but is worse than current empirical predictors. Because of this, I am still skeptical about all quantum-based predictors. Without solid cross-validation, it is very hard to argue that quantum predictors can capture subtle effect better than empirical predictors. It is true they respond more sensitively to minor structural change, but not necessary in a correct way. On the other hand, it is very useful for the whole community to have more selections that is different from previous ones. (Note that predictions from most empirical predictors are highly correlated, i.e., it won’t provide more information by switching from one to another empirical predictor.) In this context, this work should be published.

It is nice that the prediction performance can be improved a lot if applied to more realistic NMR-derived ensembles. This is expected because the experimental chemical shift of a given nucleus reflects the Boltzmann-weighted average of the 'instantaneous' chemical shifts of a large number of conformational substates that interconvert on the millisecond timescale or faster. This behavior has been discussed many times in the literature. All Ubiquitin NMR structures cited in this work are generated specifically to be a more realistic presentation of protein ensemble in solutions, except 1D3Z. 1D3Z is a traditional NMR structure model, where NMR conformer “bundle” should not be confused with a dynamic ensemble representation of the protein. In these types of NMR models, the spread of atomic positions merely provides information about the uncertainties of the atomic positions with respect to the average structure and has no direct physical meaning. The author may need to provide more comments on this in their last section titled “Comparison to experimental chemical shifts using NMR-derived ensembles”.

Saturday, September 5, 2015

Why I chose to become a subject editor for the RIO Journal

I agreed to become a subject editor on a new journal called The Research Ideas and Outcomes (RIO) Journal. When Scientific Reports asked be I declined. Here's some of the reasons why I said yes to RIO Journal, in rapidly descending order of importance.

1. The world needs a low-cost alternative to PLoS ONE*
Many people say things like "I couldn't afford to publish all my papers OA at $1350/paper" and so they publish none as OA. While PLoS ONE offers a no-questions-asked full or partial fee-waiver most people feel funny about asking for it (not me though). PeerJ and PeerJ Computer Science offer very cost effective alternatives to PLoS ONE for bio- and computer science-related papers.  For example, on average a PeerJ paper costs me about $200-300. But what about other areas? I was assured that the cost of publishing in RIO Journal would be comparable to PeerJ.  Should this prove not to be the case (the pricing is still a bit up in the air) then I'll resign as subject editor.

(*note that this implies PLoS ONE-like review criteria and use of the CC-BY license)

2. I like the idea of getting "publishing-credit" for my research proposals and other research output
Roughly speaking for every proposal I write, I write one paper less. With the current ~10% success rate I now write more proposals and, hence, fewer papers. I would like to change that because my productivity is judged in large part by my production of peer reviewed papers, and RIO Journal looks like the way to do this.

There are plenty of places where you can share your proposals (I have used figshare which even gives you a DOI) but if I can get them peer reviewed (what RIO Journal calls "validated") at RIO Journal then I can list them on my publication list and get "credit".  If RIO Journal can deliver this for $200-300 count me in.

3. All the other stuff
A. The manuscript is visible upon submission, i.e. you "automatically post your pre-print".
B. The reviews are made public and are assigned DOIs
C. Commenting is possible
D. The people behind the journal are doing this to improve science rather than making money

All these things are very nice but I am not willing to pay extra for it.

This work is licensed under a Creative Commons Attribution 4.0

Sunday, August 23, 2015

Thermodynamics for Biochemists: a YouTube textbook

As you may know I don't use textbooks in my courses anymore.  Instead I make my own video lectures and make the corresponding slides accessible.  Inspired by Engineering Mathematics: YouTube Workbook I have now organized the slides from one of my courses into a "YouTube textbook".

It's mostly in Danish but a few subsections are in English.  I am working on a fully English version where the bottleneck is re-recording the videos.  You can see the progress here.

This work is licensed under a Creative Commons Attribution 4.0

Tuesday, August 18, 2015

Writing an informed teaching statement for a university faculty position

In the US new open faculty positions are starting to be announced and ChemBark and Chemjobber are curating a list for chemistry this year.  Most of these positions will require a teaching statement. When I wrote my teaching statement back in 1996 I really didn't know what to write. You find a textbook, make some lecture notes, show up 3 hours a week and write on the blackboard, and assign some problems in the book. How do you fluff that up so it fills a page?

The main point of this blog post is that in 2015 the traditional lecture model is just one of many teaching styles you can choose and you should make an informed decision, i.e. even if you choose to lecture you now really have to argue why you choose that.  What follows is a very, very brief overview (CliffsNotes) that is mainly intended to introduce you to terms that you have not have heard of but that you really need to know in order to make an informed decision.

Alternatives to the lecture approach
The main argument against the lecture model is that students only real learn by actively doing, do the the most general umbrella term for these new approaches is active learning. One fairly popular variant of active learning is project based learning which can be combined with inquiry-based learning.  These approaches can be hard to implement for large-enrollment courses. Another, increasingly popular, variant of active learning is the flipped classroom approach. The flipped classroom is often equated with blended-learning and video lectures, but the flipped classroom approach can also be based on a textbook.

There are several variants of the flipped classroom that differ on how the "lecture" time is used.  The most basic implementation of flipped classroom is simply to use the lecture time as help sessions for homework. The flipped classroom approach can also be combined with inquiry based learning using the POGIL approach.  Perhaps the most popular variant of the flipped classroom approach is the peer instruction or "clicker" approach, which scales very nicely to very large courses.

Another interesting new idea in education (that can also be used with the standard lecture model) is specification grading which is part of a relatively new movement within higher education called competency-based learning.

Finally, here are two recent peer-reviewed studies that document improvements in learning compared to the traditional lecture approach: Active learning increases student performance in science, engineering, and mathematics and Improved Learning in a Large-Enrollment Physics Class

Some pedagogical terms and concepts
Here are some  pedagogical terms and concepts that should inform your teaching no matter which style you choose.
Cognitive load - you can learn up to 7 new things at a time
Spaced learning - it doesn’t stick until you’ve seen it 3-4 times over a period of time
Formative assessment - you learn by answering questions if you get immediate feedback
Just in case vs just in time teaching - “You’ll need to know this later” is not a good motivator

Video Lectures and Web clickers
Though not strictly required, many teachers who use the flipped classroom approach make video lectures. This can be done relatively cheaply and easily using screencasting software such as Camtasia or Screenflow together with Powerpoint. One can also make pencasts (handwritten video lectures) using, for example, iPad apps such as Explain Everything or the Livescribe pen but such pencasts often appear too slow when watched online.

Traditional clickers are increasingly being replaced by "web-clickers" such as Socrative or Poll Everywhere on smartphones and laptops

More information
Active learning: tools and tips
My flipped classroom: what I did and how I did it
Why Not Try A Scientific Approach To Science Education?
Psychological insights for improved physics teaching
Carl Wieman Science Education Initiative - Resources
Confessions of a converted lecturer (Youtube) (abbreviated version)

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