Blogging David Goodsell’s “The Machinery of Life” (Evolution, Scale, and the Counter-Intuitive Nano-Realm)

David Goodsell is a molecular biologist at The Scripps Research Institute in California, and he has written a hippie-beautiful introductory text to molecular biology, The Machinery of Life (2nd edition, Springer 2010), which Scientific American calls “an impressive and original book.”

I call it “hippie-beautiful” because the watercolors that illustrate life’s molecular machines were painted by the author and have the faint echo of 1960s poster art.

And I’m a hippie-sympathetic California English teacher.

I blogged on the Preface here and part of chapter 1 here. Below is my response to Goodsell’s reflections on evolution, scale, and the counter-intuitive nano-realm (also in chapter 1).

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Evolution, Scale, and the Counter-Intuitive Nano-Realm

In chapter 1, David Goodsell is orienting us to the broad picture of cellular life, which includes our evolutionary history. It’s in chapter 1 that Goodsell tells us that some of the machinery of multicellular life has been conserved from ancient single-cell innovations. No need, in other words, to reinvent the wheel (or the rotary flagellum). Thus, Goodsell writes the following (3):

Many molecular machines are virtually identical in all living cells. This is particularly true for molecules that play an essential role in the processes of life, such as the enzyme glyceraldehyde-3-phosphate dehydrogenase, which is vital for the metabolism of sugar in all three organisms [Escherichia coli bacteria, spinach, and humans].

With regard to contemporary life’s descent from a common ancestor, Goodsell also notes the following (2):

[W]hen you look in the microscope, you will find that all living organisms are composed of cells, and that the cells in a tree look amazingly similar to the cells in your own hand.

Perhaps the most remarkable observation from biology is that even bacteria share this family history with us. . . . [A] single cell [bacterium] uses much the same machinery as your own cells. . . . Every living thing on Earth uses a similar set of molecules to eat, to breathe, to move, and to reproduce. Because of this, trees and frogs and botulism bacteria all require water and food, they all will die if they get too hot or too cold, and they can reproduce and make new trees and frogs and botulism bacteria if the conditions are just right.

In addition to evolution, a second orienting issue is addressed in chapter 1: the matter of scale. To help us get our heads around just how tiny a single cell is, Goodsell tells us that a human cell is (3):

. . . roughly 1000 times smaller than the last joint in your finger. A 1000-fold difference in size is not difficult to visualize: a grain of rice is about 1000 times smaller in length than the room you are sitting in. Imagine your room filled with grains of rice. That will give you an idea of the billion or so cells that make up your fingertip.

Goodsell then asks us to imagine yet another 1000 times reduction, which brings us to the nano-realm (3-4):

Another 1000 times reduction takes us to the world of molecules. Molecules are so small that they are smaller than the wavelength of light, so there is no way to “see” them directly with a light microscope. . . . An average protein, taken from any cell, contains about 5000 atoms and is about one-thousandth the length of a typical cell, or about one-millionth the width of your fingertip. Again, to get an idea of these sizes, think of a room filled with rice grains. This will give an idea of the size of the proteins that are packed into each of your cells.

Does this mean that things are so small in the molecular realm that we should visualize them in quantum terms (as opposed to Newtonian terms)? Goodsell says that, for the most part, quantum thinking is not necessary to understand molecular biology (5):

One basic thing remains the same at our size and at molecular size: the solidity of matter. At the scale of molecules, we do not need to worry too much about the odd things that happen with quantum mechanics: to a first approximation, molecules have a definite size and shape, and it is perfectly fine to imagine them bumping into each other and fitting together if the shapes match. If we look closely, their edges may be a bit fuzzy, but for most purposes, we can think of them as physical objects like tables and chairs.

Some things are, however, quite dramatically counter-intuitive. Gravity, for example, is a negligible consideration at the level of the molecule (as an analogy, think of the mosquito taking its ease atop pond water). And things are always crowded and agonistically jostling in the molecular world. No rest for the wicked (5):

The motions and the interactions of biological molecules are completely dominated by the surrounding water molecules. . . . Inside the cell [a] protein is battered from all sides by water molecules. It bounces back and forth, always at great speed, but takes a long time to get anywhere.

Goodsell’s analogy is of an airline terminal (6):

You enter an airline terminal and want to reach a ticket window on the far side of the room. . . . If the room is empty, you dash across in a matter of seconds. But imagine instead that the room is crowded full of other people trying to get to their respective windows. With all the pushing and shoving, it now takes you 15 minutes to cross the room! In this time, you may be pushed all over the room, perhaps even back to your starting point a few times.

This is life in the cell’s “big city.” But molecular movement, though hindered by crowding and jostling, is still mind-blowingly fast. Goodsell asks us to imagine two molecules—an enzyme and a sugar molecule—placed at opposite ends of a cell. How long do you suppose it will take for them to meet? Here’s the answer (6):

They will bump around and wander through the whole cell, encountering many molecules along the way. On average, though, it will only take about a second for those two molecules to bump into each other at least once. This is truly remarkable: this means that any molecule in a typical bacterial cell, during its chaotic journey through the cell, will encounter almost every other molecule in a matter of seconds.

The molecular world teems and my human mind reels.

Below is a video rendering of blood flow at the molecular level based on a David Goodsell painting. The next time you see blood, it’s a different way to think about it (as a quirky tumbling of protein machines).

About Santi Tafarella

I teach writing and literature at Antelope Valley College in California.
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