The Mud Failed to Grow

 In later years, with the development of new bio- chemical techniques and improved microscopes, the complexity of the cell was revealed. The “simple lumps” were shown to contain thousands of dif- ferent types of organic molecules, proteins, and nucleic acids, many discrete subcellular structures, specialized compartments for specialized processes, and an extremely complicated architecture. Looking back from the perspec- tive of our time, the episode of Bathybius haeckelii seems silly or downright embarrassing, but it shouldn’t. Haeckel and Huxley were behaving naturally, like Calvin: since they were unaware of the complexity of cells, they found it easy to believe that cells could originate from simple mud.

Throughout history there have been many other examples, similar to that of Haeckel, Huxley, and the cell, where a key piece of a particular scientific puzzle was beyond the understanding of the age. In science there is even a whimsical term for a machine or structure or process that does something, but the actual mechanism by which it accomplishes its task is unknown: it is called a “black box.” In Darwin’s time all of biology was a black box: not only the cell, or the eye, or digestion, or immunity, but every biological structure and function because, ultimately, no one could explain how bio- logical processes occurred.

Biology has progressed tremendously due to the model that Darwin put forth. But the black boxes Darwin accepted are now being opened, and our view of the world is again being shaken.

Take our modern understanding of proteins, for example.

Proteins

In order to understand the molecular basis of life it is necessary to understand how things called “proteins” work. Proteins are the machinery of living tissue that build the structures and carry out the chemical reactions necessary for life. For example, the first of many steps necessary for the conversion of sugar to biologically-usable forms of energy is carried out by a protein called hexo- kinase. Skin is made in large measure of a protein called collagen. When light impinges on your retina it interacts first with a protein called rhodopsin. A typical cell contains thousands and thousands of different types of proteins to perform the many tasks necessary for life, much like a carpenter’s workshop might contain many different kinds of tools for various carpentry tasks.

What do these versatile tools look like? The basic structure of proteins is quite simple: they are formed by hooking together in a chain discrete subunits called amino acids. Although the protein chain can consist of anywhere from about 50 to about 1,000 amino acid links, each position can only contain one of 20 different amino acids. In this they are much like words: words can come in various lengths but they are made up from a discrete set of 26 letters.

Now, a protein in a cell does not float around like a floppy chain; rather, it folds up into a very precise structure which can be quite different for differ- ent types of proteins. Two different amino acid sequences—two different proteins—can be folded to structures as specific and different from each other as a three-eighths inch wrench and a jigsaw. And like the household tools, if the shape of the proteins is significantly warped then they fail to do their jobs.