Mysterium Tremendum

The origin and evolution of the Universe is surely the age old problem that for millennia has fascinated thinking persons. That life could arise and develop to the point of thinking, reasoning creatures is an aspect of the larger problem that has caused special fascination. This means that the Universe has reached the stage where it contemplates itself. It also means it is able to fashion machines that can leave this Earth and land on the Moon, and then return, all the while carrying a few of these living, thinking creatures. How splendidly amazing this circumstance is!


In the following paragraphs, I will focus on that aspect of the broader problem we call life. Specifically, I will focus on the origin and evolution of molecular genetics, i.e. the genetic code and its associated protein biosynthesis machinery. This topic is especially interesting because mankind has learned a very great deal about it during the last hundred years and because certain conceptual issues remain unresolved in spite of this great progress. These issues constitute what I mean by the Mysterium Tremendum. My purpose will be to enunciate as clearly as possible what the unresolved issues are. To do this, a review of what is already known is necessary. This review will cover many different features of the problem because so much depends upon the context for the discussion. I hope to be able to eventually point the reader down the correct path to a potentially final resolution, although, for now, that resolution will surely remain out of grasp.


This account requires a special structure that the modern age of electronic word processing makes possible. While the main text will be presented sequentially, many side issues are presented as needed and where needed in clickable excursions [links]. The reader can choose to take those excursions as he/she sees fit. Often the content of an excursion will be used in the main text, so the excursions are not really optional.

Short Cuts


Elements of life

Polymer biosynthesis

Lipids, membranes and chemiosmosis

Energy metabolism



The full text of the article is presented in several parts listed in the Table of Contents below.


Table of Contents for Full Article

Part 1
Mysterium Tremendum
The Elements of Life
The Physico-Chemical Context for Life

Part 2
Harnessing Energy

Part 3
Monomer to Polymer Transition

Part 4
The Conceptual Issues

Part 5

Part 6
Dialogue continued

Part 7
Peptidyl transferase

Part 8
aaRS dialogue

Part 9
Practicing Molecular Algebra

Part 10
Evolution of the Genetic Code

Part 11
ur-tRNA and ur-aaRS

Part 12


Self-assembly, aggregation, and complex formation

Self-assembly of proteins, lipids, and other molecules is a spontaneous process inside cells. The prefix, "self-," is somewhat misleading. This is because visualization of the process shows a manifest decrease in translational entropy of the components that are coming together. As such this would be a violation of the second law of thermodynamics. At constant temperature and pressure, it is the Gibbs free energy that governs spontaneity, not the entropy. Nevertheless, the apparent decrease in entropy leads to an apparent increase in Gibbs free energy, a violation of the second law for systems at constant pressure and temperature. The explanation of why no violation is in fact occurring is given by analysis of the contributions of water molecules to the process. Upon self-assembly, aggregation and complex formation, displaced water molecules contribute a big increase in overall translational entropy that more than pays for the increase in Gibbs free energy of the self-assembling constituents. Only if the water molecules are visualized and accounted for during the process can the apparent violation of the second law be avoided. This fact is elaborated [here].





Last updated July 21, 2009.







© 2007-2014 Ron F. Fox