Blogging David Goodsell’s “The Machinery of Life” (Chapter 1)

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. Below is my response to chapter 1.

———-

Chapter 1

In this first chapter, Goodsell is trying to help us acquire our bearings in an otherwise completely unfamiliar setting, zooming out with the big picture before zooming down into the details of the microscopic world, and so he writes the following (1):

All life on Earth is composed of cells, which are themselves composed of molecules.

Thus, for example, a single Escherichia coli bacterium consists of three key nanoscale-based elements (1):

  • “[A] multilayered cell wall”;
  • “[C]orkscrew-shaped flagella” that “are turned by motors in the cell wall, propelling the cell through its environment”; and
  • “[t]he interior of the cell”, which is filled with “molecular machines for building and repairing molecules, for harnessing different sources of energy, and for sensing and protecting against environmental dangers.”

Notice what Goodsell is emphasizing here, for he is foreshadowing where the rest of his book will be taking us: we’re going to learn about cellular “skin”; cellular movement; nanomachine building and repair (based on DNA blueprints); energy harnessing and storage; environment sensing; and cellular defense (and offense).

Or, to put it another way, a cell, if it is to live, needs the ability to do the following things: 

  • diagnose its situation (environment sensing);
  • preserve its integrity against the surrounding environment by making machines, taking up arms, and putting up defences;
  • move;
  • gather and store the energy to move.

The cellular world, in other words, is a Shakespearean sea of troubles. And this idea fits rather nicely with Goodsell’s fight-against-entropy definition of what life is, which he takes from Erwin Schrödinger (29):

In 1944, the physicist Erwin Schrödinger presented a very simple definition of life that has withstood the test of time. He identified one property that all life shares: living things avoid decay into equilibrium.   

But the weapons of nanoscale warfare are not what we humans experience at our vastly larger material scale, though they have analogies to it. In chapter 2, Goodsell will tell us that, even as our human-scale world of “familiar machines” is “built of metal, wood, plastic, and ceramic,” a cell’s “nanoscale machinery . . . is built of protein, nucleic acid, lipid, and polysaccharide” (10). Thus, a cell’s walls are made of lipids; its DNA of nucleic acid; its molecular machines of protein; and its energy storehouses of polysaccharides.

My own analogy (not Goodsell’s) is the following:

  • Because they are flexible and protective, but can also let things pass in and out of them, lipids are akin to sheets of spongy mesh.
  • Because the four chemically similar nucleotides—the adenine (A) thymine (T) cytocine (C) and guanine (G) of DNA—have to be stable and durable to protect the information that they collectively encode, nucleic acids are akin to a piggy bank ceramic (breakable in a pinch, but also capable of protecting “the money”; the family coins; the family jewels);
  • because the 20 different amino acids are so readily made into such a stunning and vast variety of forms and machines, proteins are akin to plastic Lego blocks; and
  • because they are sugary-gluey when wet, polysaccharides can be thought of as wood. In fact, polysaccharides really are the molecules that make up the cellulose in wood. (And thus they are the molecules that underlie paper and plant starch as well). According to Goodsell, much of your house, if it is not made of bricks, is made of polysaccharides (24).

So, there it is: a cell at the nano-scale is something like spongy mesh, ceramic, legos, and energy-combustable wood fashioned together by software-like code instructions into a blobby golem, moving, eating, and farting. Something to frighten your children with. 

But we’re not in chapter 2 yet. I’m getting ahead of myself.

In the next post, I’ll blog on some more details from chapter 1. In the video below, the process of a leukocyte cell fighting inflammation or infection is described. In response to signals, the cell rolls, activates, adheres, stops, and migrates to the right inflammation or infection spot in between endothelial cells in a process called “leukocyte extravasation.” Mind blowing. Each part of this extraordinary performance involves the production and orchestration of protein machines. 

About Santi Tafarella

I teach writing and literature at Antelope Valley College in California.
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1 Response to Blogging David Goodsell’s “The Machinery of Life” (Chapter 1)

  1. Pingback: Blogging David Goodsell’s “The Machinery of Life” (Evolution, Scale, and the Counter-Intuitive Nano-Realm) | Prometheus Unbound

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