Let’s take a closer look at an origin-of-life paper published by Koonin et al. in the Proceedings of the National Academy of Sciences (PNAS). Here at ENV, Casey Luskin has already noted the article and Nature‘s take on it. The language of the paper is appropriately speculative because, as the authors admit, there is no geological evidence for their hypothesis. The article is extremely detailed in some parts while, in other respects, being disappointingly short on details.
The PNAS article stands out in one respect. Rather than focus on one small problem relevant to the origin of life (e.g. nucleotide concentration, energy sources), the authors attempt to situate their theory in the overall context of current origin-of-life research. Thus the paper includes 145 references. Unfortunately, the authors stop short before reaching the all-important step of saying how exactly life arose from non-life. They do suggest a couple of items that must have been in place for this transition to occur, but only because we already know they are vital for the function of a cell.
Early Earth Bombardment
The first paragraph of the paper offers a caveat, acknowledging the difficulties in finding geological traces of the first life forms. Studies have indicated that the earliest life may be older than the oldest known rocks, which are dated at 4 billion years old. However, the Earth may have gone through a period of heavy bombardment by comets or asteroids around 3.8 or 3.9 billion years ago. Whether there was a short period of heavy bombardment or a longer period of intermittent bombardment is a debated in the scientific community. (See here for a summary of the debate.)
The PNAS article assumes a “late heavy bombardment” period that scoured away any geological evidence of the primordial environment or early life:

Because of the heavy impact bombardment, the Earth surface underwent major changes approximately 3.8 to 3.9 Gigayears (Gyr) ago, so that only a few rock samples are older than 4.0 Gyr. Diverse recent data indicate that life might be older than the oldest known rocks. If life originated in the Hadean, finding any geological traces of the first life forms is unlikely.

Although they don’t say so explicitly, the authors are probably assuming that while the late heavy bombardment was devastating to the point of destroying any geological traces of the first life forms, some life forms must have survived in order to evolve. They provide no basis for making this assumption.
Chemistry Conservation Principle
The author’s argument hinges on the idea that cellular chemistry is an indicator of what the early Earth environment was like. Specifically, they call this the chemistry conservation principle, which assumes “the chemical traits of organisms are more conservative than the changing environment and hence retain information about ancient environmental conditions.” As an example, the authors cite the chemically reduced state of the cellular cytoplasm. In a reduced environment, no oxygen is present. The authors assume, therefore, that the early Earth included no oxygen in its atmosphere until some later point in history. Apparently by the time the atmosphere had oxygen in it, the biochemical pathways within the cell had become fixed.
Although they don’t state this explicitly either, for evolution to occur the authors must be assuming that while cellular biochemistry became fixed early on, other aspects of the cell were only loosely “fixed.” That way, mutational changes and adaptation to the environment could occur. It is unclear how, exactly, the authors know when something was fixed due to the primordial environmental surroundings of the cell, and when the cell had developed these features later in evolutionary history.
While the authors do consider similarities to the last universal common ancestor as part of their argument, this does not clarify how they distinguish between a fixed feature of the cell that resembles the primordial environment and a later adaptation that might have occurred before extensive branching in the evolutionary tree.
Inland Geothermal Fields
Using geochemical analysis, the authors contend that life could have emerged from “inland geothermal fields within ponds of condensed and cooled geothermal vapor.” This harkens back to Darwin’s speculation that life could have begun in a “warm little pond.” They see the disparity between ion concentration within cells and the ion concentration in modern-day seawater as evidence for a non-marine environment.
For example, cells have a high ratio of potassium-to-sodium, while marine environments do not. Therefore, cells likely did not originate in seawater, but rather in some kind of environment with a similar potassium-to-sodium ratio:

Under the chemistry conservation principle, the striking different between the intracellular inorganic chemistry and the composition of sea water suggests that the first cellular organisms dwelled in specific habitats that were enriched for the elements that are prevalent in modern cells.

A highly intricate pumping system in the cell membrane regulates the cell’s ionic gradient. The authors believe that because these systems are highly complex, they must be the product of many years of evolution and could not have existed in the first protocells. The ion preferences of the cell, however, seem traceable further back in evolutionary history because ion preferences are more universally seen in various cells. The authors, therefore, believe that the ion concentration of the early cells was in equilibrium with the environment:

Hence, the membranes of first cells probably could occlude biological polymers and even facilitate their transmembrane translocation but could not prevent (almost) free exchange of small molecules and ions with the environment. Furthermore, before the emergence of diverse membrane translocators, the exchange of small molecules via leaky membranes should have been of vital importance for the first, cells, which also implies that their interior was equilibrated with the surroundings, at least with respect to small molecules and ions.

Cells have an inordinate amount of potassium and inorganic phosphate, therefore the primordial environment must have had higher concentrations of these compounds along with particular transition metals. The authors provide extensive explanations for why cells could not have formed under normal marine conditions and conclude:

Thus, among the well characterized environments on Earth, only emissions from vapor-dominated zones of inland geothermal systems simultaneously show potassium-to-sodium ratios much greater than one, a high content of transition metals, and substantial levels of phosphorous compounds.

In sum, the authors’ argument hinges on two points:

1. The early Earth had a reducing environment (no oxygen was present).
2. The chemical environment within the cell is indicative of the surrounding early Earth environment in which the cell was formed. This is called the “conservation of chemistry principle.”

Studies have shown and continue to show that the early Earth atmosphere likely DID include oxygen. (See here for ENV’s report on a recent study affirming this.) If the interior of the cell has a reducing environment, but the early Earth likely had an oxidizing environment, then the second point, the conservation of chemistry principle, is open to serious question. Indeed, the entire basis of the paper is on very shaky ground.
While the authors go into great detail with descriptions of their theoretical geothermal vents, they still do not provide information on how inorganic molecules transition from non-life to life. To say the least, that’s an important sticking point in origin-of-life scenarios.
Furthermore, as detailed as this paper is, it is all speculation. There is no evidence that the authors have accurately described the environment in which the first cells formed. Finally, as with many origin-of-life scenarios, their descriptions of the particular ways that biomolecules interacted in the partitioned geothermal vents is too specific and too complex to have occurred by chance, particularly given the brief window of time, geologically speaking, in which these molecules had to form.
Photo credit: �li J�n, Flickr.