Week 3: Gaining Insights from LUCA on Why our Code is Flawed Pt. 1

Some of the topics that have been repeatedly mentioned are: The History of Evolutionary Thought, "tree -thinking",  mutation as the origin of variation, natural selection (mentioned most frequently), artificial selection (especially when tied to the age of genomics). Although we have not discussed this in lecture yet, the first four chapters in Life Ascending are structured around the invention of life itself: LUCA. These chapters collaboratively approach questions such as: 

What are we ascending from? and What mechanisms gave rise to our origins?

LUCA, our last universal common ancestor is thought to be an archaean microorganism that optimized the extreme environments of the hydrothermal vents. In chapter 1, the environment LUCA optimized was described in detail. In chapter 2, the physical processes of LUCA were further explained by the catalytic properties of RNA. In the chemical gradient, basal structures such as pyruvate began to form and were early letters in the genetic code. Interestingly, LUCA is thought to resemble the modern retrovirus HIV. Because it is thought that RNA arose before DNA, it makes sense that an organism with a tiny genome made up of RNA would be good early candidate for LUCA.

As we look further into LUCA’s physical and environmental origins, we begin to question how these origins relate (indirectly or directly) to the origins of the genetic code itself. Each codon has three letters that code for a specific mechanism within the organism. The first letter of the codon is tied to simple precursors such as pyruvate mentioned previously as being catalyzed in the vents discussed in chapter 1 (Lane 47). The second letter also has a specific purpose: to determine where on the scale of solubility the amino acid falls. We can see the strong deterministic relationship between the first and second letters. But what about the third letter? This is where degeneracy comes into play.The third position in the codon is information-free: it doesn’t matter which base is present. This degeneracy leads me into my fascination with the role of flexibility and random chance present in the code. I will elaborate on this fascination further in my next post.