Saturday, September 13, 2014

The Origin of Life

Some papers on the earliest steps from geology to biology.

One of the great questions, second only to the origin of the universe (multiverse) and perhaps the nature of thought in the brain, is how life got started on Earth. (Leaving aside, of course, the even more daunting question of peace in the Middle East.) Of the three, the mind is well on its way to definitive solution, and the origin of the universe is rather unlikely to ever be solved, or at least there is no prospect that I can see, despite enormous advances in cosmology. The origin of life occupies a middle ground, so far off in time that certainty may be impossible, but bounded enough by our knowledge of the ambient conditions and their rich aftermath that detailed and plausible theories can be, and have been, advanced.

The papers reviewed here are not new, (dating from from 1997 and 2003), but provide background for my post two weeks ago about the divergence of Archaea and Bacteria, and constitute what I think remains the leading hypothesis for the origin of life (elaborated in more recent papers 1, 2, 3). (Other recent origin of life refs 1, 2, 3, 4, 5.) This hypothesis situates the scene of action at thermal vents at the ocean floor, where highly reduced and alkaline geological fluids percolate up into an ocean that was, at that time, far less oxidizing than today, but still, due to the prevalence of CO2, several logs more oxidizing and acidic than the geochemical fluid.

As still seen today, this fluid deposits rich chimneys of iron sulfide wherever it emerges, in a porous matrix that could host untold chemical complexity. And there are / were a full spectrum of more moderate vents, with lower temperatures and less harsh chemistries. These locations attract theorists of the origin of life because they provide a great deal of potential energy, in a form that life still uses: the electro-chemical gradient in the form of acid / base (protons) and oxidation / reduction (electrons).

They also provide the key elements (sulfur, iron, nickel, tungsten) that are needed, and the kinds of enclosed, yet semipermeable, spaces that would be needed to accumulate the compounds needed as proto-cells. So the 1997 paper by Russell and Hall delves into the kind of proto-metabolism that the energy gradients and structures at these locations might have provided. The Earth was saturated with CO2 at the time, as free oxygen had not yet been photosynthesized into existence.

But let's take a step back and ask what is needed for life. The basics are a membrane or some other compartment to keep inside and outside apart, an energy source, a metabolic system to harness that energy to create the molecules on the inside, like complex carbon molecules of our form of life, and a genetic replication system that controls the metabolism and other characters, so that they can be selected via Darwinian evolution.

Not all of these things have to happen at the same time, and the goal for figuring out how geology generates life is to locate conditions where as many of the earliest requirements are present for free in the geological environment, and deduce what had to happen at which stage thereafter. A great deal has been made of the RNA world (references 1, 2, 3, 4, 5, 6, 7, 8, 9, 10) as a near-certainty in the progression from proto-life to the last common ancestor of all life. Our ribosome, for one thing, carries its clear signature. But this is a very late stage in the origin of life. The RNA world presupposes metabolism, a cell structure, and a replication system, even while it gives rise to a translation system that sets forth on the protein- and DNA-centric course we are on today.

So, energy is a must. Nothing can happen without it, but it can take many forms, from lighting discharges to sunlight, to chemical gradients from stable geological sources. As discussed in the previous post, chemical gradients remain the bread and butter of cellular energy, and are the most likely original form, leading to the hypothesis that undersea hydrothermal vents are an excellent candidate setting for consistent gradients of pH and redox, among other chemicals, approximating our current chemiosmotic metabolism.

Overview of Russell & Martin theory, with CO2 reduction occurring in mineral "bubbles" at the hydrothermal / oceanic interface.

Prior to biological, lipid-based membranes, such vents also supply porous rocks and somewhat sealed bubbles of rock that could serve as chambers or "cells" for pre-biotic chemistry. And lastly, they provide the actual enzymatic chemicals that remain at the core of our coupled redox metabolism- condensed iron and sulfur complexes that conduct electrons between proteins and across membranes while pumping protons in the opposite direction or reducing carbon compounds.

Example of a contemporary iron-sulfur  (Plus nickel) cluster that forms the heart of many enzymes that reduce (or oxidize) carbon compounds, in this case carbon dioxide to carbon monoxide, given water and a proton acceptor such as ferredoxin, another iron-sulfur protein.

What was the most elementary metabolism? Somehow, carbon compounds must have been reduced from the high level of CO2 and CO on early Earth to the sugars and polymers that form the basis of life, such as ATP, NAD, ribose, and the various metabolic intermediates of the Krebs cycle (which we use to break down food to CO2). The authors present a reverse Krebs cycle as the founding metabolism, where carbon compounds are built up (i.e. reduced) using electrons as well as catalytic surfaces furnished by Fe-S minerals mediating between external acid to internal alkaline conditions.

Basic energy scheme where a chemical gradient is used by iron-sulfur compounds to do enzymatic work, such as hydrogenating (reducing) CO2.

"It is the interfacing of the alkaline hot springs with the acid ocean that brings about the precipitation of an iron monosulphide (mackinawite) membrane. Electrons could have been transferred across such a membrane. Also the hydrogenating potential of the mackinawite could have been enhanced by the presence of nickel (Kouvo et al. 1963; Vaughan 1969; Morse & Arakaki 1993)." 
"Iron monosulphides such as mackinawite can contain up to 20% nickel (or cobalt and copper), probably tetrahedrally bonded between the sulphur-sulphur layers (Vaughan 1970). The FeS membrane considered here may have only adsorbed a few per cent of nickel, enough to force the cleavage of the hydrothermal hydrogen at the nickel site with the production of a transient hydride. The left-over proton would be neutralized with hydroxide in the protocytoplasm. The electrons could be transported through the membrane along the iron layer situated along (001), conducting
toward the final electron acceptor such as Fe(III) on the outside of the membrane. The atomic hydrogen could then hydrogenate the CO2 molecules bound on adjacent iron sites."

"In particular, Shock (1992, 1996) has carefully calculated the metastabilities of carboxylates, ketones and alcohols as inorganic carbonate in seawater mixes with hydrothermal solutions, with their fugacities buffered by both quartz–magnetite–fayalite (QFM) and the more oxidized pyrite–pyrrhotite–magnetite (PPM) mineral suites. The fugacity of carbon dioxide is taken as 10 bars, the presumed atmospheric pressure in the Hadean (Walker 1985; Kasting et al. 1993). ... Shock (1996) demonstrated that the possible synthesis of organic molecules between 50 and 250degC is sensitive to the fugacity of the hydrothermal solution, which must be buffered by QFM for all inorganic carbon to be converted to organic molecules. This is still a conservative choice, since 4.2 billion years ago the redox state of the mantle was probably two or three log fO2 units below that of the quartz–fayalite–magnetite buffer (Arculus & Delano 1980). Remarkably, Shock (1996) demonstrated that at temperatures below about 150degC, the longer chained polymers (dodecanoate is the longest chain considered so far) will theoretically be most represented of all the organic molecules, and that they could be generated at no energy cost."
An imagined reverse TCA or Krebs cycle, where carbon compounds are grown from humble beginnings using the free energy of the redox and pH gradients at the vent structures. What would guide the soup in any direction or to any particular compounds (including chirality) is not clear.

Given the right conditions, things might have proceeded quite rapidly ... millions of years would not be needed.
"The far-from-equilibrium conditions in which these geo- chemical processes and mechanisms operated would have been widespread for a limited period of Earth history, and would have provided ample opportunity for such a unique sequence of events leading to the minimal cell, the common ancestor of all life on this planet. Although coupled to a long-lived hydrothermal system, the actual gestation period for organic synthesis and the self-assembly of organic protocells capable of fledging and replication from within the iron monosulphide hatcheries would have to have been rapid, and may have taken weeks or months, rather than the millions of years normally assumed for the emergence of life."

The second paper takes the story onward through subsequent steps of probiotic evolution, where the metabolism becomes more ramified with phosphate (on ATP) as another energy currency, and  nascent protein and RNA enzymes develop out of the organic soup. And finally the mineral membranes are supplemented and replaced by organic ones, given some ion channels and membrane-bound enzymes to carry out metabolism. This sets the stage for escape as free-living organisms.

Cartoon of the general model of Russell and Martin, with organic pro to-metabolism generating carbon compounds which then undergo chemical evolution towards the RNA world, and eventually to organic membranes and cell walls that allow complete escape from the mineral womb at the hydrothermal vent setting.

I can hardly convey the entire theory, and at an outline level it seems reasonable. But what was the force or principle that made the carbon compounds become more complex and self-organize into an RNA world with enzymes and coding / reproduction schemes? That remains a major question (but see the collection of RNA world references cited above). Energy alone, even when channeled in some approximation of the later major microbial metabolism to a profusion of organic molecules, does not, on the face of it, direct complexity or productive competition between mineral bubbles. (The authors have a later paper that claims that conditions "forced" life to emerge, but its details are not available, and the argument seems geochemical, not biological, so it does not seem to address the competitive issue.) We can refer to the anthropic principle to say that whatever led to us must have survived somehow, but that is a far weaker theory than one that drives events based on the chemistry of the time. So I think these concepts are a strong start to a theory of the origin of life, but as yet far from the whole thing.

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