Sunday, July 14, 2013

Dear Abby’s Advisor Agony Advice


We briefly interrupt our redox-tastic summer to prevent the first installment of a new feature: a brand-new agony column for those who supervise scientists.

As a side-benefit of having my name, I have received countless letters that start:
“Dear Abby, I have a problem. Ha-ha-ha.” 
Or emails: Dear Abby, I have a problem :-) (or j/k).

But every once in a while, I get some real ones. For example:

Advisor Abby,
My students come to my office, and just start crying. Since I remember that you cried all the time when you were a student, you might have some perspective. What should I do?
Sincerely, Big Famous Professor

Dear BFP,
Some people are leakier than others. Don’t make a bit deal of it. Ask student if they prefer to wait until they’ve stopped crying to have a conversation, or if they can simultaneously cry and converse. Do keep a box of soft tissues handy, though.

***
Advisor Abby,
My students don’t write up their papers. What can I do to make them?
Yours, Struggling Associate Professor Who Needs More Pubs to Come Up for Full

Dear SAP,
You can’t make anyone do anything. But you can give lots of support, provide coffee and treats, institute a quarterly manuscript-exchange day, and remind your research group to write in small, bite-sized pieces every day.

***
Advisor Abby,
Students just aren’t as good as they used to be.
Signed, Professor Out-of-Touch

Dear POT,
Your job is to bring out the best in other people. Please concentrate on that.

***
Dear Readers—I would love your input on a request for advice that I recently received from a colleague, written below.

Advisor Abby,
In my 20 years as an experimental scientist, I have developed a nose for a good experiment—what might be interesting, what isn’t, what is worth the risk, what is likely to be a waste of time, etc. I realize that my judgment is not always infallible, and sometimes there is ambiguity. But in this case it is very clear what is the interesting and important next step in the project, and a junior scientist working with me is strongly motivated to do the much less interesting experiment.
As an advisor I like to give my students and especially postdocs as much latitude as possible to frame their science and design their own experiments. When the experiments are routine and don’t cost that much in terms of equipment and/or people’s time, then the stakes are low and it’s ok for a student or postdoc to travel a while down a path that I suspect will yield less fruit.  But when the stakes are high—say only 24 hours of experimental time have been granted on a costly instrument—then I feel more strongly that my judgment is heeded.
            How do I show the junior scientist why the experiment they want to do is the less interesting experiment, but while still allowing them to save face?
Signed,
Definitely Right, but Also Trying to Be Kind.
 ***

If you're an advisor  or other scientific supervisor, and you have some experience with this type of situation, please let DRAT know how you approach these situations.

If you're a student and/or postdoc or are supervised by another, please let DRAT know how *you* would want your adivisor to interact with you in this situation.

Friday, July 12, 2013

Earth Electrochemistry: Basic Definitions and Guiding Principles





Broad Definition: Electrochemistry is chemistry, but where electrically-charged particles are mobile.

Narrower definition: electrochemistry is a chemical reaction in which the electrochemical step (the moving of an electron or hole) is the rate-limiting step. This way, the chemical reaction can be driven forwards or backwards by supplying a source of sink of electrons. This is very useful, on so many levels.

Here are the four guiding principles for all of electrochemistry.

1.     Chemical Thermodynamics. Electrochemistry is simply thermodynamics, but the electron is counted as a chemical species: add the electrochemical potential to all of the chemical potentials. If you can do thermodynamics, you can do electrochemistry too.

2.     Charge Neutrality. Adding the chemical potential of an electron adds another constraint—charge balance. Charge neutrality must be conserved, so for every electron liberated, it must be consumed by another reaction. No extra electrons nor deficits allowed! Therefore, electrochemical reactions are *always* coupled oxidation and reduction= “redox” reactions. If you’re sitting in a seminar in which the words “redox” or “oxygen fugacity” have just floated by, pay attention, and simply follow the electrons. It’s the geochemistry equivalent of mass/energy/momentum balance.

3.     Mass Balance. As in thermodynamics, mass balance plays an important role. The charge taken up by the sum of all oxidation reactions has to equal the charge taken up by the reduction reactions. For simplicity in Earth science contexts, we’ll do our best to assume that only one oxidation reaction and one reduction reaction dominates. Remember by rule 2 charge neutrality—that a set of oxidation and reduction reactions must dominate together! The challenge in application will be to determine which set of reactions dominates setting the local equilibrium for the local system, and which sub-systems are forced to respond. Chemically—who leads and who follows? But even asking this simple question can get complicated. Hopefully for most systems of interest, only one set of redox reactions dominates setting the environment, and everything else simply responds. As always, my general philosophy is to start simple and only get complicated if I am forced to do so by reality.

4.     Kinetics. Electrochemical thermodynamics tells us whether or not a redox reaction is energetically favored, and addresses whether a reaction has the ability to proceed. But kinetics tells us how quickly it will happen—and therefore whether or not the reaction will actually really occur in a real system. Again in the interest of binary simplicity in Earth science contexts I like to think of kinetics as either very fast (kinetic limitations unimportant: hey we have geologic time!) or zero (very slow—as in diffusion-limited solid state reactions even over geologic time.)

Given these four considerations—each is worth at least one undergrad and one grad level course all by itself—we are set up to do all Earth electrochemistry. The rest is just data and examples.

Wednesday, July 10, 2013

An Interesting Planet is an Electrochemically Active Planet


What makes Earth Interesting?

And as we are increasingly able to look at other planets within our own solar system, and at solar systems around other stars—what makes a planet interesting?  And by interesting, I mean “ability to support life.” And by life I mean….link toNASA Astrobiology webpages as a starting point.

What steps do we need to take to develop an “interesting-ometer”—a remote sensor of a planetary’s interesting behavior?  How do we even start asking the questions necessary to create such a device?

I suggest electrochemical disequilibrium as a starting point.   “Interesting” in a planetary context means “out of electrochemical equilibrium”.  It may not be the only measure of interestingness. It may not even pan out as the root cause of our planet’s interestingness (so a planet that has life that is purely photochemical with no electrochemistry can also be called interesting by my first definition, but it might fail the test for electrochemical disequilibrium.)

But this starting point is useful. It allows us to frame questions and do this in ways that can be measured and quantified, by combining theory, lab experiments, and observations of the Earth in planets.

Electrochemistry is important in other ways too—we extract most of our energy from reactions that involve electron transfer; and even with the electron transfer step is not rate limiting (as in combustion of fossil fuels). It was electron transfer processes that generated the fossil fuels in the first case. Specifically the electron transfer processes associated with life.

So, even if we fail in our quest to define a planet’s “interestingness” as electrochemical disequilbrium we will have spent our time studying an interesting, important, and relevant process. And we will be less likely to be taken in by the next crop of bogus scientific quacks who come up with false electrochemical solutions to our worldwide energy problems.

Monday, July 8, 2013

Summer Blog: The Electrochemical Earth



As my colleague @lizzieday recently put it, Earth science is “redox-tastic".

Thinking of Earth as a battery is the in-thing these days. There have been so many exciting advances in looking at our Earth systems as redox systems over the last years, with several high profile papers published in the last several weeks and months, looking at oxygen fugacity in the solid earth system, with implications for the co-evolution of life and Earth, and coupled with the carbon, sulfur, iron, and oxygen cycles throughout the Earth, and throughout Earth history.

So the goal of my summer sabbatical blog is to explore the questions—is earth a battery? Which Earth systems can be examined as a battery (or fuel cell), and which cannot? What values must be quantified in order to call an Earth system a battery? Voltage drop? Current? Power? What is the connection between redox, oxygen fugacity, and electrochemistry?

My goal is not necessarily to provide specific answers, but to properly frame how I think the questions can be posed usefully, so that ideas can be quantified and tested. And to point towards the necessary quantities that must be measured in order to have answers.

My qualifications? I’ve been studying electrochemistry and surface science since my undergraduate materials science days in the mid 80s. I have been running electrochemistry experiments for over 20 years. I have a masters degree in corrosion engineering. I’ve been thinking about earth redox since I started studying geophysics in the mid 90s. I have done electrochemistry experiments at high pressure and low, in aqueous, silicate, and sulfide liquids and also solid electrolytes. I discovered isotope fractionation during electroplating in the early 2000’s. Then I predicted it theoretically, based on an extension of Marcus theory to incorporate stable isotope behavior. 

One of my research goals—long term—is to frame the need for developing a high pressure table of standard reduction potentials, to measure this table, and then show ways to use the table to understand electrochemical cycling in the Earth.

So this summer, in parallel to my working on my scientific papers and proposals, I plan to use my blog to help frame my ideas and develop my thoughts in an informal way. Comments of course are always encouraged, welcome etc.  It’s a grand experiment in coupling informal scientific writing in parallel with the formal scientific writing. I’m curious to see how it unfolds….

Tuesday, July 2, 2013

Science and the City


For a child of the 70s from Poughkeepsie, New York City represented the farthest reaches of my imagined future. (California was another planet, and where the Brady Bunch lived.) Finally, this summer I am able to spend some time living my long-term fantasy of working, writing, and walking in New York City. Since early childhood monthly trips to visit my great grandma near the Yankee Stadium, I have always found the city intoxicating. I love exploring the streets, stores, museums, spaces, people—everything the city has to offer—and it generates a restless eagerness in me—a strong urge to soak it all in, but also to contribute my own voice to the collective.

It is a similar feeling I get at the annual fall meeting of the American Geophysical Union. Every year, my research group and I put our research on display, and we also spend much time exploring others’ research. Of course it feels overwhelming. Our 4 or 5 abstracts are puny compared against the other 20,000. But that’s completely the wrong way to look at it. We are a single storefront, but we help make up the city of science.

Science is like a city, with established and up-and-coming neighborhoods, less-populated areas, barely-explored side-streets, dead-ends, and long maze-like paths leading to beautiful gardens. Individual PIs or lab groups are like storefronts/museums/performance centers each with something to offer plus their own style and personality: some are welcoming, others not-so-much; some provide huge places to explore; others fill a very specific niche. Some are good for one visit, others you return to over and over.

This is the start of my sabbatical. I will be spending the next few weeks exploring one of my favorite real cities and also the city of science, while working on my own contributions. I am especially looking to find ways to decrease the isolation of scientists by developing new ways to connect. In the city we explore by foot, cab, subway, in a three dimensional space. Science is infinitely-dimensional, so there should be more and better ways to interconnect. What are they?