Friday, July 10, 2015

The Machinery of Life

In the very first section of the 5th edition of Intermediate Physics for Medicine and Biology (Sec. 1.1), Russ Hobbie and I discuss “Distances and Sizes”.
“In biology and medicine, we study objects that span a wide range of sizes: from giant redwood trees to individual molecules. Therefore, we begin with a brief discussion of length scales.”
At the end of this section, we conclude
“To examine the relative sizes of objects in more detail, see Morrison et al. (1994) or Goodsell (2009).”
I have talked about the book Powers of Ten by Morrison et al. previously in this blog. I have also mentioned David Goodsell’s book The Machinery of Life several times, but until today I have never devoted an entire blog entry to it.

In the 4th edition of IPMB, Russ and I cited the first edition of The Machinery of Life (1998), and that is the edition that sits on my bookshelf. When preparing the 5th edition, we updated our references, so we now cite the second edition of Goodsell's book (2009). Is there much difference between the two? Yes! Like when Dorothy left Kansas to enter Oz, the first edition is all black and white but the second edition is in glorious color. And what a difference color makes in a book that is first and foremost visual. The second edition of The Machinery of Life is stunningly beautiful. It is not just a colorized version of the first edition; it is a whole new book. Goodsell writes in the preface
“I created the illustrations in this book to help bridge this gulf and allow us to see the molecular structure of cells, if not directly, then in an artistic rendition. I have included two types of illustrations with this goal in mind: watercolor paintings which magnify a small portion of a living cell by one million times, showing the arrangement of molecules inside, and computer-generated pictures, which show the atomic details of individual molecules. In this second edition of The Machinery of Life, these illustrations are presented in full color, and they incorporate many of the exciting scientific advances of the 15 years since the first edition.

As with the first edition, I have used several themes to tie the pictures together. One is that of scale. Most of us do not have a good concept of the relative sizes of water molecules, proteins, ribosomes, bacteria, and people. To assist with this understanding, I have drawn the illustrations at a few consistent magnifications. The views showing the interiors of living cells, as in the Frontispiece and scattered through the last half of the book, are all drawn at one million times magnification. Because of this consistent scale, you can flip between pages in these chapters and compare the sizes of DNA, lipid membranes, nuclear pores, and all of the other molecular machinery of living cells. The computer-generated figures of individual molecules are also drawn at a few consistent scales to allow easy comparison.

I have also drawn the illustrations using a consistent style, again to allow easy comparison. A space-filling representation that shows each atom as a sphere is used for all the illustrations of molecules. The shapes of the molecules in the cellular pictures are simplified versions of these space-filling pictures, capturing the overall form of the molecule without showing the location of every atom. The colors, of course, are completely arbitrary since most of these molecules are colorless. I have chosen them to highlight the functional features of the molecules and cellular environments.”
I have often wondered how much molecular biology a biological or medical physicist needs to know. I suppose it depends on their research specialty, but in general I believe a physicist who has read and understood The Machinery of Life has most of what you need to begin working at the interface of physics and biology: An understanding of the relative scale of biological objects, an overview of the different types of biological molecules and their structures and functions, and a visual sense of how these molecules fit together to form a cell. To the physicist wanting an introduction to biology on the molecular scale, I recommend starting with The Machinery of Life. That’s why it was included in my ideal bookshelf.

Goodsell fans might enjoy visiting his website: There you can download a beautiful poster of different proteins, all of course drawn to scale. There are many other illustrations and publications. Enjoy!

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