Prebiotic Chemistry

    The Miller-Urey Experiment Doesn't Generate Any RNA


Paleogenetics looks for commonalities across the branches of life. Some of the most ancient molecules, which occur across all forms of life, have vestigal peices of RNA attatched. These molecules are even important to human nutrition - some of them are in the multivitamin pill you take every day. In each case, the RNA part that's attached doesn't participate in its chemistry, but the fact that RNA parts are conserved throughout species tells us that they were probably around at the time of the Last Universal Common Ancestor (LUCA). This is where the record stops, where paleogenetics hits a dead end. All of the evidence that we have points to a form of life with RNA but no proteins. 

Prebiotic Chemistry starts from the other direction. An experiment starts with the chemicals and conditions present on the early Earth before life emerged (hence, Prebiotic). The most famous prebiotic Chemistry experiment was caried out by Miller and Urey at the University of Chicago and published in 1953. They mixed only simple molecules, and added heat and electrical sparks to simulate lightning. What came out were amino acids (which, as discussed before, are the building blocks of proteins). At the time, this experiment was very influential, convincing many that the molecules of life are an inevitable result of planetary formation.

However, the Miller-Urey experiment generated its amino acids in extremely low yield. Mostly it generated quite a bit of tar, a substance that is fine for paving roads but cannot form life. When the Miller-Urey experiment generated amino acids, it was before the discovery of catalytic RNA and the postulation of the RNA world. It is also worth noting that the Miller-Urey experiment generated no RNA-containing components. 

   What Defines Prebiotic?

(From Powner et al. 2009)

The conditions on Earth before life emerged more than 4 billion years ago are difficult to know conclusively. Thus, any pre-biotic laboratory synthesis which requires extensive human intervention should be viewed with some skepticism.

The scheme employed by Powner et al. (2009) is an example of what Steven Benner calls a "Relay Synthesis". It still starts with pre-biotic chemicals like cyanide and acetaldehyde, but then anything created, in no matter what yield, may be assumed to be present prebiotically and then purchased in pure form from chemical suppliers. Each chemical step must be closely watched and taken off the heat before turning into tar. Then, each reaction takes place in a scrupulously clean glass flask. Once again, these conditions bear little resemblance to the complex mixtures present on the early Earth. 

There is no disagreement on the results of these experiments. Each synthetic step actually works, but many reputable scientists question the validity of calling such a synthetic experiment prebiotic. The difficulties in this type of research and the extremely high chance of failure or controversy leads scientists to brand them 'Old Man Chemistry', or research only undertaken by chemists in the twilight of their careers when failure won't result in being denied tenure. 

Borate prevents sugar from turning into tar


As learned before, RNA is made from three components. The phosphate is present in many inorganic minerals so that isn't a problem from a prebiotic perspective. Bases are found on carbonaceous meteorites, so we know those were plausible in a prebiotic world. The difficulty is generating the sugar backbone. The ribose is the problem. 

Kim, H.-J. et al. Synthesis of Carbohydrates in Mineral-Guided Prebiotic Cycles. J. Am. Chem. Soc. 133, 9457–9468 (2011).

The problem with prebiotic synthesis of sugars is not generating product. The problem is the conditions that lead to the formation of sugars will inevitably lead to tar if not resisted in some other way. This can be demonstrated easily at home: put a tablespoon of sugar in a pan and put a glass jar on top. Put the pan on the stove and turn on the heat. In moments, the sugar will begin to react. It will first turn into a brown caramel, but eventually into a tar (a black solid with hardly any water solubility). In the inside of the jar, you'll observe condensation, droplets of water which have been released from the sugar in the course of the reaction. 

The Benner group discovered that borate, a simple chemical present in some minerals, was able to stabilize the types of sugars we observe in life today. Thus, it prevented the further reaction of these sugars to form insoluble tars. The rections that Benner describes are simple, and the use of borate and other minerals highlights the fact that the early Earth was not as clean as a freshly washed roundbottom flask. 

This synthesis also generated (in high yield) some even simpler sugars, such as threose. Threose has recently been shown to form a DNA-like structure called TNA (threoxyribonucleic acid) that is also capable of replication and therefore Darwinian evolution.