The Archean (3.8-2.5 bybp) Period and the Hydrothermal Vent Origin of Life
Webpage for original source is HERE (READ ME for review)
Hydrothermal vents (black smokers) support a variety of archaea. The discovery
of the archaea in extreme environments suggests that life evolved under hellish
conditions. Hydrothermal vent movies are
here, here, and
here.
VERY Good one here

Major events that may have occurred at hydrothermal vents. Initially, the first cells are thought to have been a component of the geothermal system (i.e., actually part of the rock without cell membranes). The first pathways developed in these "organisms".
The initial information molecule is thought to be RNA for a variety of reasons. RNA is the genetic material for many viruses (although DNA is far more common).
RNA viruses appear to affect members of most kingdoms (with the notable exception of arthropods).
These viruses come in two flavors: "Sense" viruses have the coded information that can be immediately translated into a protein sequence. RNA viruses of the "Antisense" type must be transcribed into the sense form before proteins can be assembled. Some viruses have double-stranded RNA (both sense and antisense) or even ambisense (single-stranded RNA with both sense and antisense forms in the same genome). Among humans, RNA viruses cause a variety of diseases including SARS, Flu, and Hepatitis C. RNA viruses are particularly interesting since they can mutate so quickly (in most cases the is no check on mutations since there isn't a complimentary strand).
Although some textbooks still discuss only three types of RNA (ribosomal RNA, transfer RNA and messenger RNA), many other non-coding RNA (ncRNA) species have been isolated. Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. However, almost all means of gene identification assume that genes encode proteins, so even in the era of complete genome sequences, ncRNA genes have been effectively invisible. Recently, several different systematic screens have identified a surprisingly large number of new ncRNA genes. Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.
As the geothermal-coupled protocells differentiated into free, individual cells the first of the archaea evolved (probably iron sulfide metabolizing thermophiles). This seed later serves as the progenitors of the eubacteria (true bacteria) and eucarya (eucaryotic cells). One current theory is that there may not be a single LUCA (Last Universal Common Ancestor). Instead, the first ancestor may have evolved through a symbiotic relationship among several protocells and/or gene swapping among a community of genes. More on that is here. The original paper is here.
More on RNA World here and here

The unusual chemistry of the hydrothermal vent provides a convenient electromotive force. Since many basic metabolic processes ultimately depend on electron pumps, this is a reasonable and testable place to start (see the electron transport chain, for example). Reduction of iron provides a mechanism for a 770 mV potential while differences in pH between the vent and water serves as a proton source. Heat and chemicals from the vent can produce all sorts of goodies that can be processed in a Stanley-Miller reaction to produce more complex organic molecules.

Green rust [Fe2+Fe3+(OH)6]Cl and makinawite (FeS)
produced by the geochemical reactions at the vent can serve as
election channels
for the electromotive forces outlined in the previous diagram.


Natural and artificial pyrite membranes that can form at hydrothermal vents. These structures provide both a method of compartmentalization and a conductive layer for electron transport.

Detail of ion movement at FeS membranes as must have occurred ca 3800 mybp. Other than the photolysis of water by UV radiation, all of the remaining reactions occur at natural hydrothermal vents or in laboratory simulations.

This diagram depicts a mackinawite membrane serving as an electron transport mechanism between the environment external to the vent (left side) and the internal vent chemistry (right side of image). The resistively of the membrane can be adjusted by doping it with nickel or cobalt atoms. Thus, some areas of the iron sulfide membrane can have higher conductivity than others thereby setting the stage for different biochemical pathways along the membrane.


Amino acids can also be generated at the vent by relying on reactions that have been observed in the Miller spark-gap experiment. Paradoxically, the poison cyanide is required for the production of amino acids (Strecker synthesis). The resulting amino acids can be assembled into proteins. Did lefty molecules seed life?

RNA associated with an FeS membrane can code for protein synthesis. Initially, the proteins served as membrane components, not an enzymatic function. RNA would have served as both the information storage molecule and the catalyst for various metabolic activities required for a primitive self-replicating system. Jump to the RNA world!



Mackinawite-protein membrane based on the synthesis proposed in the previous diagram. Proteins would naturally associate with the metallic structure because of their close association during synthesis. The individual at the right is Flat Rat and is not shown to scale.

Production of organic compounds at the vent could provide internal compounds for the protocell. RNA and peptides would coevolve by the mechanisms already discussed.

This diagram depicts metal membranes based on the conductive properties of the FeS membranes. These structures are found in a primitive hyperthermophilic archaeon (Methanothermus fervidus). Structures such as these in a living archaeon support the assumption that metal membranes served as the initial cell compartmentalization mechanisms while simultaneously providing a transport mechanism to power a primitive protometabolism. More information on the genetic sequencing of the genes responsible for this structure can be downloaded HERE
(A)
(B)
(C)
(D)
Mechanisms for compartmentalization of protocells. (A) Metallic cell based on Mackinawite-protein membrane. (B) Proteinoid microspheres. Proteinoids have several attractive properties. They are readily formed (heat nearly any combination of amino acids), the membranes can support an electrical potential difference, they can grow and divide, are subject to selection (based on the type and concentration of amino acids in the initial brew), and they are about the size of bacteria. (C) Coacervates form spontaneously in certain organic solutions, are composed of lipids, and have osmotic properties. (D) Micelle. Composed of phospholipids (a major component of cell membranes) are easily formed, grow and divide, and have osmotic properties that allow preferential "ingestion" of certain molecules. More on micelles is here. More on protocells is here.

What have we explained?

Yet another time line!c