Biocurious is a weblog about biology, quantified.

The Machinery of Life

by PhilipJ on 2 November 2009

The recent redesign here at Biocurious resulted in a return to our roots, so to speak, with Escherichia coli once again adorning the banner at the top of every page. This image is from David Goodsell‘s newly released second edition of The Machinery of Life, a book for the biocurious if there ever was one.

The Machinery of Life is a short (167 pages) and accessible introduction to life at the molecular scale. A more readable approach than found in a textbook, we are led through the various kinds of molecules you will find in biological systems (nucleic acids, proteins, lipids, and sugars), how these molecules are created, how energy is harnessed to power living things, and how living things protect themselves at the molecular scale. Along with clear explanations, images of molecules for which David Goodsell has become famous are used to illuminate concepts from the text. A favourite of mine is reproduced below (Fig. 2.2), which shows how enolase, an enzyme composed of two subunits which is involved in glycolysis, is held together by hydrogen bonds (the blue-red lines).

molecular complementarity

After introducing the molecules and their roles, we get a tour of cellular interiors, starting with the simple and relatively unstructured bacteria, specifically E. coli, the workhorse of molecular biology. E. coli shows us how crowded cellular interiors really are, and how such biological processes as protein synthesis, nucleic acid repair, and cellular locomotion via flagella occur. A particularly beautiful example of the crowded bacterial cellular milieu can be seen in Fig. 4.3, where the density of water and other small molecules (shown in green, pink, red, and yellow) surrounding proteins and nucleic acids (in blue and purple, respectively) is shown with particular clarity.

water and small molecules

The book then turns to the study of human cells and the way our cells interact to form components of our bodies. This is largely an introduction to the different compartments found within eukaryotic cells (in contrast with the unstructured bacterial cellular interiors), and the cooperation, or at very least interaction, between cells that gives rise to muscles, the role of blood in the body, clotting (perhaps the 3rd edition will reference Andre’s PhD work), and the nervous system. The image detailing a nerve synapse (Fig. 6.10) is truly remarkable for those of us not used to the complexity of living things.

nerve synapse

The latter third of the book then features various aspects of personal health, such as cancer, aging, viral infections, antibiotics, etc. This section is particularly apt to read now, given the current worldwide panic over H1N1 influenza. My own PhD molecule of interest, rhodopsin, also makes an appearance. It is at the end of the book where you can also find the relevant data for PDB entries which were used to generate all the figures containing molecular structures, as well as a list of additional references to continue the study of life at the molecular scale.

We’ve long been fans of David’s work here at Biocurious, and I was not let down with The Machinery of Life. In addition to the clear presentation of ideas, the physical quality of paper and binding are excellent, exactly as I was hoping for a book filled with such wonderful imagery. The price for such a book was also a welcome surprise (maybe I’m too used to academic prices!), at about $25 in Canada.

If you do pick up the book, click here for a small list of errata, or you can browse through reduced-size versions of all the figures, sans figure captions. For those you’ll need to buy the book, which is in my opinion well worth it.

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Required readings

by PhilipJ on 9 March 2008

Doing science isn’t just about running experiments and analyzing data, even though it can feel that way sometimes. Fortunately (in some cases), we also have to give talks at other universities and conferences, write papers for journals, apply for grants, etc. These tasks require entirely different skills than theory or labwork do, though we get little formal education on these matters. To get these skills, it is a necessity to read books outside of our normal expertise, and it’s often not clear, given how little extra time graduate students usually find they have, which books to invest said time in.

I’ve got my own favourites that have proven valuable, but it’d be great to hear what everyone else has read and found useful too.

First and foremost, effectively displaying data is a must. The most wonderful experimental result in the world can be made incomprehensible by a poorly thought out graph, either because of quantitative issues or overuse of chartjunk. Edward Tufte’s four books have been extremely useful in thinking about how to visualise complex information in an efficient way. You will think twice about how to present your results after reading his books (the first of the four, The Visual Displaying of Quantitative Information being the most immediately relevant), and they help with scientific figures as well. There are also pointers on more effective use of PowerPoint and similar programs.

Stylistic guidelines for writing abound, but the short and sweet (and inexpensive!) Strunk & White is as good as they get, and I’ve never felt the need to read any others. It’s short enough that rereading it periodically isn’t difficult, and considering how poor we are at writing, everyone should get a copy.

Finally, outside of Kuhn’s The Structure of Scientific Revolutions, I’ve read precious little philosophy of science. I’m of two minds as to the importance of the philosophy of science to the actual day to day work we do, but I’m sure there are interesting ideas I’ve missed out all the same.

Now over to you: what are your must-reads outside of science?

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Avoid Boring People

by PhilipJ on 18 October 2007

James Watson has written another memoir, this time entitled Avoid Boring People: Lessons from a Life in Science, which this Times article says “contains an inflammatory epilogue with eye-popping theories that will, undoubtedly, leave ethicists choking with disbelief”. I’m less excited about his thoughts on the intelligence of people from Africa or how to get a date, and more excited by his insight into how to be a successful scientist. That being said, the article does contain a lot on Watson’s day to day life, and I enjoyed reading all of it.

This section outlines something we all know, but don’t necessarily emphasize enough:

For Watson, the ability to socialise is a key skill, one he believes can help propel you far beyond your peers. “Gossip is a fact of life also among scientists. And if you are out of the loop of what’s new, you are working with one hand tied behind your back.”

Socialising is certainly an important aspect of any successful career in science (and out, for that matter), but it isn’t always easy to do at huge meetings like the March Meeting of the APS, where there are literally thousands of people in attendance. The smaller conferences I’ve attended (with 50-100 people) have been a great way to meet others, in my own field and out. Part of it is the (usually) more relaxed atmosphere, where it doesn’t matter if sessions run a little late, and everyone isn’t as rushed, often leading to longer time for questions after talks, which I’ve found are the best way to start talking to someone—everyone likes it when you’re interested in their science! On the opposite side, the audience is necessarily quite a bit smaller. Does anyone have any advice on how to make the most out of your conference trips, particularly the large national conferences where almost everyone (boring and interesting alike) can be found?

Update — for another take on the book itself, see this week’s Nature review by Huntington F. Willard, here (subscription required).

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