Summer Research and Reading

Last week was an in-between week. Classes and final exams were over the previous week, and I enjoyed seeing our senior class graduate and meeting their happy families. This week, many of the students are back for summer research, so the building is starting to bustle with activity again. My research lab is being renovated this summer, and on that pretext I decided not to take on summer students. (Actually I do have one student starting today who is primarily working in a different lab this summer 75% of the time. The other 25% of the time she will continue her project in my lab from the past year. She is remarkably independent and can make good progress with little supervision.)

I took advantage of the quietness last week to outline my research plan for the summer. Having the time to slowly read through my research students’ final reports from the spring semester, I decided to focus on moving one of the exploratory student projects to the point of submitting a manuscript. I outlined the scope of the suite of molecular complexes that needed to be calculated (I’m a computational chemist) and put it on my white board – now clear of last-minute questions from students prior to final exams. I’ve been adding small flourishes to the diagram as I make progress on the project. Here’s a snapshot from today.

I have two other goals: (1) learn a new piece of potentially useful software, and decide if I want to purchase licenses for the next year, and (2) devote some time to reading broadly in my field. Starting last week I divided up my day so that research on my main project takes place in the morning. The afternoon is spent reading and learning the new software, with the last hour at work on research again. If some of the earlier computations have finished, I set up a few more calculations for the machines to crunch on while I’m away from work in the evenings. I do have the occasional administrative task or meeting to attend to, but so far this plan is working out well.

Besides reading papers directly related to my research projects, my May-June reading plan will cover three books. The first is a book I actually read through quickly over winter break: Nick Lane’s The Vital Question: Energy, Evolution and the Origins of Complex Life. The goal was to take a first pass to see if there were any crucial insights I should incorporate into my current research projects. The goal this summer is to read through it again slowly and carefully, and evaluate the grand plan put forward by Lane as he pulls together different pieces supporting his hydrothermal vent redox coupling scenario. I’m familiar with the work by Lane, and also that of Mike Russell who had predicted the existence of milder temperature alkaline vents before Lost City was discovered. Lane’s book is well-written and he always has provocative and interesting ideas. (Since discovering his excellent book Oxygen over a decade ago, I’ve kept an eye out on his writings.) I hope to write a multi-part blog presenting and analyzing some of the ideas in his book in late June or early July.

In the meantime I have just started reading A Brief History of Creation by Bill Mesler and Jim Cleaves. It begins with the ideas of Anaximander (one of those Greek philosophers), then moves on to Aristotle and the idea of Spontaneous Generation. Augustine of Hippo makes a brief appearance before we skip forward to the 17^th century featuring Francesco Redi and Antonie van Leeuwenhoek. I did not know much of the history surrounding these two men, but the authors have an engaging narrative that brings them to life! Next up, in the 18^th century, is a story of rivalry between Needham and Voltaire, with appearances by the Comte de Buffon (I still can’t get over his funny sounding title). No story would be complete without a love triangle involving a girl, a brilliant one at that – and very possibly smarter and more capable than all the men featured. That’s as far as I’ve gotten but I’m looking forward to the rest of the book. Depending how it goes, I might use it in a class in place of Genesis: The Scientific Quest for Life’s Origins by Robert Hazen. (I previously used this as supplementary reading in two classes and it worked well.)

While the books by Lane and Mesler/Cleaves are aimed at a more general audience, I’m most of the way through a more academic book, The Minimal Cell. The subtitle of the book describes its contents: The Biophysics of Cell Compartment and the Origin of Cell Functionality. Like many other specialized academic books in the sciences, it is a collection of articles by different authors. One of the editors (who also contributes to the volume) is Pier Luigi Luisi, a big name in the origin-of-life field. He has brought together an eclectic collection of scientists with expertise in different areas. The result is an interesting book but also highly technical in parts, and therefore not as accessible without background information. I struggled through parts of the book and skimmed over some areas.

Interesting things I learned from this collection of articles:

·      Cell cytoplasm is super-crowded, and this has a significant impact on the thermodynamics and kinetics of chemical reactions. Having just taught second-semester Physical Chemistry, it’s a reminder how the “dilute” approximation greatly simplifies the equations. But this is clearly not the case in the cytoplasm!

·      What is the lower limit of organism size? Given the ALH84001 controversy twenty years ago, and more recent reports of nanobacteria, this is particularly relevant to demarcating the transition from chemistry to biology. I learned about gene sizes, water content, number of copies of ribosomes and other proteins needed for minimal functionality, and differences in autotroph, heterotroph and parasitic requirements. Given certain assumptions, the limit might be ~200nm in diameter assuming a sphere.

·      The behavior of water and solutes in gels and at interfaces is very interesting. I have very little background in rheology, and I found it both fascinating and baffling. Given the size of cells and their membranes, it’s crazy how they still function while being experimentally subjected to electroporation, the patch-clamp method, and inserting microelectrodes. One author described this as disrupting the membrane using lances, swords and guns.

·      Building a minimal cell from scratch to investigate how few components are needed for the cell to “do its work” complements reductionist approaches where things were taken apart to learn how they functioned. But this may have importance beyond origin-of-life questions. A carefully engineered minimal cell could be very specific and efficient in its biosynthetic task. Furthermore its fragility outside narrow laboratory conditions also reduces potential hazards of such organisms “escaping” into the outside-world.

Reading and Research – an excellent way to spend the summer! No doubt I will also be thinking about my classes (I’m excited!) and some ideas that I have been churning on how to teach chemistry in the context of magic. I expect to be blogging about those too! I am reminded how much I appreciate the rhythm of life in academia, and count myself very fortunate to get paid for something I love doing.