The Rocky Origins of Life

alkaline hydrothermal vent

In an essay in my series on Vitalism (Crossing the Line Between Death and Life, 30 May 2014), I mentioned the Miller-Urey experiment in 1953 as a breakthrough in the study of abiogenesis - the emergence of living things from non-living matter. It turns out, however, that having produced amino-acids and some other medium-sized organic molecules, nothing much else happens in these "organic soup" style experiments. Getting a soup of organic molecules to do anything interesting has proved an intractable problem and neither electrocution, bombardment with ultraviolet light, nor physical shocks help. New research has shown that Miller's estimates of the early atmosphere of the earth were probably wrong. He assumed the atmosphere of Jupiter would provide a good model for the early atmosphere of the earth: ammonia, methane and hydrogen. However, the heavy asteroid bombardment during the early epoch of the solar system, during which our moon was formed, blasted off the existing atmosphere and it was replaced with an atmosphere of mainly carbon-dioxide and nitrogen, with only traces of methane and other gases. Similar gases make up the modern day atmospheres of both Mars and Venus. Unfortunately, this mix of gases is very much less likely to get even as far as amino-acids in the Miller-Urey set up. So the idea of a naturally occurring organic soup fails on two counts: it probably never existed, and even if it had, nothing interesting happens in sterile soup (more on this below). Some comets and meteorites have a mixture of water and organic compounds similar to those produced by Miller-Urey and thus some of the building blocks of life may have come from space, but this still leaves us with the organic soup problem.

Another hypothesis of how life emerged from non-living matter has recently emerged and been promoted by British scientist, Nick Lane (amongst others), This is described in his book Life Ascending: The Ten Greatest Inventions of Evolution (2009). This hypothesis is known as the Alkaline Hydrothermal Vent Origin of Life. For the full detail of this hypothesis, see Russell et al (2013) and the "further reading". In this essay I will both paraphrase and embellish the version of the theory set out in Lane (2009).

We begin with a caveat. Even if we show that this theory is possible and plausible, it still won't tell us exactly how life began here. That is impossible to know. But if we can show that the chemical reactions that underpin life can be started in similar conditions, then we may be able to better understand life more generally. There will be general rules that govern the emergence of life and we can specify some of those rules. In addition if we can show that life emerging from chemistry is plausible it further undermines any remaining tendency to explain life through forms of Vitalism.

One thing we can already identify is the basic chemistry of life. For example all life on earth involves reducing carbon-dioxide (CO₂) to methane (CH₄) and water (H₂O). Some organisms do this directly, most do it indirectly, but this is what all organisms do at a minimum. And since this doesn't happen spontaneously in an organic soup, we need to specify the kind of conditions in which it will happen.


Signs of Life

Stromatolite
via Wikimedia

By 3400 million years ago, the signs of life on earth are unequivocal. The first life seems to have been in the form of bacteria or archaea. Taxonomists now recognise five kingdoms of living things: animal, plant, fungi, bacteria, and archaea. On the surface bacteria and archaea can be indistinguishable, but internally, chemically there are major differences (I'll say more on this later in the essay). Archaea are typically found in niches involving high temperatures, extremes of pH (both acid and alkali) or other factors that would kill most organisms. They are sometimes called extremophiles.

We can see in fossils of this early period, and perhaps earlier, the ratio of carbon isotopes that we expect to see from fossilised living things. This ratio, which sets life apart from non-living chemistry, is the basis of Carbon-14 (¹⁴C) dating. We also see fossilised structures of a form of life that we still see in shallow oceans today, i.e. the stromatolite. Archaea and bacteria continued to be the dominant forms of life for 2500 millions years before fossils of complex organisms begin to appear. Arguably they still are the dominant form of life, exploiting a vast range of ecological niches and far outweighing any other form of life in terms of biomass.

Replicators, molecules which copy themselves accurately, seem to be essential to any form of life and thus most existing theories have focussed on how such molecules might have been produced, usually in a soup of organic precursor compounds (like Miller-Urey). However, Lane refers to the various "organic soup" theories as "pernicious" because the idea deflects attention away from the underpinnings of life. As Lane says, if you take a tin of actual (sterilised) soup and leave it for a few million years it does not spawn new life, instead all the complex molecules gradually break down into simpler molecules. In other words following the dictates of thermodynamics the soup goes in the wrong direction. "Zapping" it with electricity or radiation only accelerates the degradation. The laws of thermodynamics means that a soup is far too unlikely a route to life. One can never ignore thermodynamics as they govern everything.

Thermodynamics - The Science of Desire

The physics of matter is a story of attractions and repulsions and thus, according to Lane, "it becomes virtually impossible to write about chemistry without giving in to some sort of randy anthropomorphism." (13-14) I'll do my best. Chemical reactions happen if all the participants want to participate or can be forced to. Molecules "want" to exchange elections or can be induced to overcome their shyness.

The molecules in food want very much to react with oxygen, but don't do so spontaneously, fortunately or we'd all go up in flames! Even reactions that result in a net release of energy often require some "activation energy" to overcome their "shyness" or initial reluctance to react. Another way of looking at the chemistry of life is that it boils down to the juxtaposition of two molecules, hydrogen and oxygen, out of equilibrium. They react with a discharge of energy, leaving warm water. And this is the problem with the organic soup theory - nothing wants to react, so nothing happens. There is no disequilibrium that might drive the necessary reactions. Disequilibrium is a key to life. 

Some origin of life theories focus on RNA, the single-stranded counterpart of DNA, which under certain conditions can self-replicate (normally in a cell RNA replication is dependent on large protein complexes called ribosomes). The idea that a very complex molecule like RNA might have come about without a thermodynamic disequilibrium driving the reactions is not credible. Thus although self-replicating RNA is plausible, there must be more to it. RNA is composed of nucleotides which combine an amino-acid, a sugar (ribose) and a phosphate group. As monomers (ATP), dimers (NADH), and polymers (RNA, DNA), nucleotides play several vital roles in living cells. Although we get amino acids from the Urey-Miller experiment, nucleotides are very much more difficult to make. Nucleotides do not just form spontaneously. One cannot just throw amino acids, ribose, and phosphate into a bucket and expect nucleotides to form. In fact it is worse than this because the conditions required for the synthesis of ribose and amino-acids are very different and they could not happen in the same bucket. They must be synthesised separately and then brought together. But then the reaction will not take place in the presence of water. Nor do nucleotides easily polymerise in the absence of a catalyst to form RNA or DNA. Although aspects of RNA based explanations of the origin of life remain plausible, RNA is certainly not the first step in the direction of life. Many conditions had to exist in order for RNA to be synthesised. If life did not evolve in a chemical soup, where did it come from?

An important clue was the discovery of vents on the sea-floor close to the great ocean ridges where the tectonic plates are forced apart by up-welling magma. These vents, known as "black smokers", spew out hot (300-400°C), acidic water, laden with chemicals, particularly metal and hydrogen sulphides (which account for the dark colour). They support a variety of lifeforms at densities rivalling rain forests. Bacteria use hydrogen sulphide (H₂S) to power their metabolism. Effectively they detach the hydrogen from H₂S and attach it to carbon dioxide to form organic matter and elemental sulphur (and this is one of the most direct processes for reacting H₂ with CO₂). This conversion requires energy and it comes from the juxtaposition of two worlds in dynamic disequilibrium, i.e. from cold sea water and the hot vent water. The bacteria that sustain this world live at the margins where the two meet and mix. Then some animals graze on the bacteria and a food chain is established. Or else the bacteria live in symbiotic relationships inside the animals. Tube-worms for example host such bacteria which feed them and because of this do not have a digestive system.

These hot vents became a candidate for the origin of life since the disequilibrium solved the thermodynamic problem. Possible mechanisms for life emerging at these hot vent sites were proposed by German chemist and patent attorney, Günter Wächtershäuser. These involved chemistry taking place on surfaces of iron-pyrites. Unfortunately conditions on the early earth make this route unlikely. Oxygen is still central to the metabolism of the vent archaea and bacteria. They still react hydrogen and oxygen, if only indirectly. There is also the concentration problem, that is, bringing enough of the reactants together in open water to make a self-sustaining reaction. For life to come about organic molecules must dissolve in water and somehow react to form polymers like RNA. But this is extremely unlikely if they are not contained (by a membrane) and concentrated.

Alkaline Vents

Serpentenized olivine

A second kind of hydrothermal vent was predicted Mike Russell, now working at NASA's Jet Propulsion Lab. Russell had conjectured that these other vents would be an even better candidate for the origin of life. Alkaline vents are not volcanic, but rely on the reaction between a type of rock called olivine and sea water. Such rock undergoes a process known as serpentinization after a common form of this rock, serpentine, which is green and thought to resemble the scales of a snake. In serpentinization, water becomes incorporated into the structure of the rock which expands and fractures. The volume of water incorporated in this way is believed to equal the volume of the all the oceans. But the water and rock also chemically react, producing highly (chemically) reduced compounds such as hydrogen, methane and hydrogen sulphide and a high pH value, i.e. the water in serpentinized rock is strongly alkaline. The reaction is also exothermic, i.e. heat producing, and so drives the convection that powers the alkaline vents. The reaction can be represented in simplified form as:

olivine + H₂O → serpentinite + H₂ + heat

or

2Fe²⁺ + 2H₂O → 2Fe³⁺ + 2OH^- + H₂

Alkaline vent Structure 

Note that hydrogen and methane were key ingredients in the Miller-Urey experiments in the 1950s. Having been first predicted by Russell in the 1980s, living vents were discovered in 2000 during a submarine expedition to the mid-Atlantic. The vents form spectacular coral-like structures (right) that can be 60m in height.

The water coming from these vents is warm (70-80°C), highly alkaline (ph 9-11) and filled with chemicals produced by serpentinization, particularly hydrogen. By contrast, in the early oceans, the water would have been cool, slightly acid (pH ~5.5), and much richer in CO2 and iron than the present day ocean. As the hot, chemical rich water mixes with the cold sea-water some of the chemicals precipitate out to form porous limestone structures, filled with tiny chambers roughly the size of an organic cell. The compartments could provide a natural means of concentrating organic molecules. While modern vents tend to lack iron, the composition of the ocean 4 billion years ago would have meant that the early vents did have iron and other metal compounds (particularly nickel, magnesium, and molybdenum) with catalytic properties embedded in their walls. Mike Russell has argued that the iron/sulphur minerals in these structures resembled enzymes that some modern living cells, especially archaea, use to catalyse chemical reactions. The flow through these early vent structures replenished basic reactants, carried off by-products, and prevented catalyst surfaces from becoming fouled, while also allowing for organic molecules to concentrate. The thin walls of the chambers provided membranes, one of the essential features of living things, with very different conditions of temperature and especially pH on either side, thus creating exactly the kind disequilibrium required to power living things.

Disequilibria

The vents provide two kinds of disequilibria that can act as drivers of chemical processes. These are quite technical and I'll try to simplify.

1. highly reduced electron donors
2. pH imbalance or proton gradient

Electron Donors

1. Bubbling up from the vent are gases like hydrogen and methane produced by the reaction of water with mantle minerals like olivine. In the presence of iron and molybdenum catalysts in the walls of the vent structures, these come into contact with CO₂ and nitrogen oxides dissolved in the water. When hydrogen reacts chemically it readily gives away its single electron to another molecule to create a hydrogen ion or proton. In chemical terms this giving away of an electron is called "reduction". Oxygen is the prototypical acceptor of electrons and thus this side of the reaction is called "oxidation". When iron is oxidised to rust, what is happening is that oxygen in the air is accepting electrons from (i.e. is reduced by) metallic iron (Fe) which is converted into ferrous (Fe²⁺). Red rust can be further oxidised to black ferric (Fe³⁺) iron. Atoms will tolerate a net positive or negative charge if they can obtain a more stable arrangement of electrons (this is a consequence of the quantum mechanics of electrons). Serpentinization involves water oxidising ferrous iron in olivine to ferric iron, with water being reduced to hydrogen gas and hydroxide ions.

H₂ and CO₂ react with a little difficulty. Although the overall reaction is exothermic, meaning that it is thermodynamically favoured, some initial energy is required to get the reaction going and a catalyst to help it along. The catalyst in the archaea that do this reaction directly is a complex of iron, nickel and sulphur atoms, which are very like the kind of minerals deposited at vent sites. "This suggests that the primordial cells simply incorporated a ready-made catalyst" (Lane 28). The activation energy seems to come from the vents themselves, which we can tell from the presence of acetyl thioesters. These molecules are the result of CO₂ first reacting with free-radicals of sulphur in the vent water, and these free-radicals provide some of the energy. We will return to this observation below.

The combination results in reactions that produce methanol (CH₃OH), methanal (CH₂O), and ultimately ethanoic acid (CH₃COOH) aka acetic acid). Such molecules can accumulate and concentrate in the cells and this allows for more complex molecules to form and polymerise in tiny versions of the Miller-Urey experimental apparatus. This gives us a more dynamic version of the organic soup. The constant flow of water from the vent solves another problem associated with surface catalysts: fouling. As reactions happen on a surface the products of the reaction build up and prevent new reactants getting to the surface. To have a sustainable reaction at a surface one must combine concentration (enough to bring molecules together) with a flow that carries away products and replenishes reactants. The pores of the vent structures seem to provide for both.


Proton Gradient

2. A feature of all living things is the creation of a proton gradient across a membrane. By this we mean that one side of the membrane has a surplus of protons (in other words an acid pH) and the membrane allows them to diffuse to the other side where there is a deficit (an alkaline pH). Since protons are positively charged this is also amounts to an electrical potential (i.e. a voltage) across the membrane.

In our mitochondria for example, this gradient is achieved by a process called electron chain transport involving four complexes of proteins that pump protons across the membrane to create a pH or proton gradient. These protons then diffuse back into the cell by a process called chemiosmosis, via another protein complex called ATP-Synthase, and in doing so power the creation of adenosine triphosphate 

triphosphate - ribose - amino-acid (adenosine)

At first sight ATP-Synthase appears so miraculous that, like the eye, it is often pointed to as evidence of intelligent design. It is difficult to imagine how something so complex could have evolved from simple steps by chance, though its evolutionary path is in fact known to some extent. ATP synthase is a complex nano-machine. A rotary engine in the cell-membrane is made up of a protein complex (with three subunits) and driven by proton diffusion or chemiosmosis; the engine uses a protein-based crank-shaft to deliver mechanical energy to a separate complex of proteins (with three subunits) inside the cell; the deformation and relaxation of this second complex catalyses the synthesis of ATP from ADP and a phosphate ion. Several good animations are available showing how ATP-Synthase works, for example this YouTube video.

ATP is a universal energy currency in all living cells. It is how energy is stored and moved around the to where it is needed. ATP is a nucleotide, the basic unit, or monomer from which polymers like RNA and DNA are produced. The right-hand group is adenine, an amino-acid, and the middle part is ribose, a saccharide or sugar. And on the left is the phosphate. Compare to the units of DNA or RNA (below):

RNA Nucleotide. Wikimedia

ATP adds two more phosphate groups, the last of which is detachable to make adenosine diphosphate with the release of energy. The reaction that powers life thus looks like this.

ATP ↔ ADP + PO₄^2- + energy

The pH difference between the two bodies of water, kept separate by the membranes of the vent structure creates a voltage across the membrane that can drive a similar kind of reaction, the transformation of orthophosphate into pyrophosphate:

Note how the left-hand side of ATP is very like the pyrophosphate molecule. Russell thinks that pyrophosphate might be the precursor of ATP, that it could do the same job of providing energy to power other reactions, though less efficiently.


Scaling Up.

So in these vents we have the following essential ingredients for chemistry related to life (especially if we consider them as they might have been 4 billion years ago).

• CO₂ and nitrogen-oxides (in seawater) + H₂ (in vent water) reacting to form organic molecules
• Iron-sulphur and other metallic ion complexes that can act as catalysts
• A mechanism for concentration and replenishment
• A porous membrane formed from calcium carbonate with distinct environments on either side.
• A proton gradient
• Potentially, a pyrophosphate based energy transfer mechanism to provide activation energy for "shy" molecules.

Thus the vents provided natural reactors for sustaining chemical reactions that produce organic molecules in a far more dynamic environment than that envisaged in organic soup theories. They also provide the range of environments necessary to create the conditions for replicators like RNA. However the kind of chemical reactions that might take place in such environments are relatively simple compared with even a bacterial cell, let alone a eukaryote cell. How did we get from there to here? In attempting to answer this question Lane switches from a bottom-up to a top-down perspective.

One of the clues to how life might have proceeded can be found in the common elements of metabolism shared by almost all living cells. By comparing all living things we can reconstruct the common elements shared by all life. In this vein, a paper published in Science on 25 March 2016 (Hutchison et al 2016) has attempted to reduce the genome of a bacteria to just those genes essential for it to live. The resulting partly-synthetic organism has just 473 genes. The function of 149 of them has yet to be determined. Lane discusses the last universal common ancestor of all current forms of life, known by the acronym, LUCA. In order to identify what features LUCA might have possessed scientists compared the two oldest forms of life: archaea and bacteria. Archaea appear very similar to bacteria, but there are important differences in metabolism and biochemistry. Features in which bacteria and archaea differ include,

• Chemical structure of cell membranes structure
• Methods of lipid synthesis
• Methods of glycolysis (conversion of sugars to pyruvate)
• DNA replication
• Respiration pathways

Features which bacteria and archaea share include:

• DNA
• Ribosome (proteins which transcribe DNA into RNA)
• RNA to protein translation
• Krebs cycle
• ATP synthesis

The features that archaea and bacteria have in common are those likely to have been found in LUCA and those features where they differ were unlikely to be features of LUCA. Note that cell membrane structures are not included in the list of shared features. Archaea and bacteria appear to have separately (and in parallel) evolved lipid-based cell-membranes and methods for synthesising lipids. This is consistent with life having evolved as metabolic pathways in a physical substrate and then later having found ways to create membranes, with bacteria and archaea developing independently. In retrospect, the alkaline vent hypothesis predicts multiple parallel solutions to such problems as cell-membranes and some metabolic pathways.

The Krebs Cycle (aka Citric Acid Cycle) is shared by all forms of life. Lane refers to it as "the metabolic core of the cell". It is central to how we take the complex molecules in food and break them down into hydrogen and carbon-dioxide and in the process produce ATP to power other cell processes.

The cycle can also go backwards. In which case it consumes ATP and produces complex organic molecules, which can be used to build the components of a cell. This backwards Krebs Cycle is not common in life generally, but it is common in the archaea that live in hydrothermal vents. Crucially, given appropriate concentrations of the necessary ingredients including ATP, the chemical reactions of the backwards cycle will happen spontaneously. It is what is sometimes called "bucket chemistry", from the idea that one pours reagents into a bucket and the reactions just happen. And as the products of one step of the process build up in concentration they will automatically start to undergo the next step. No genes are required to mediate this process. It is exactly the kind of reaction that could have got started in the pours of vent structures, perhaps powered initially by pyrophosphate rather than ATP. Once this process got going, side reactions would have been almost inevitable producing amino-acids and nucleotides (the units of the DNA or RNA polymer).

We mentioned acetyl thioesters above. These turn out to be very important, because when they react with CO₂ they produce molecules called pyruvates. When our cells take up simple sugars these are broken down by enzymes into pyruvates. These then enter the Krebs Cycle where they are transformed into other molecules to form many building blocks for complex chemistry. So the naturally occurring acetyl thioesters could have produced the pyruvates necessary to set off the backwards Krebs cycle to produce complex organic molecules.

"In other words, a few simple reactions, all thermodynamically favourable, and several catalysed by enzymes with mineral-like clusters at their core... take us straight into the metabolic heart of life, the Krebs cycles, without any more ado." (28)

We now hit the limits of the progress of science. Experiments designed to test how accurate this hypothesis is have been proposed. Lane speculates that peptides and small proteins and RNA are likely products. Some experiments have been performed and generally they seem to throw up problems with the model. So the field is still in the phases of repeatedly testing and redesigning to find the right parameters. However, there is reason to be optimistic that refining the model should produce a self-sustaining series of chemical reactions analogous to the first living systems, and that contain metabolic pathways which hold the key to all life: the proton gradient, a phosphate based energy transfer, and the Krebs cycle. Lane concludes that LUCA, the common ancestor of all life was most likely,

"...not a free-living cell but a rocky labyrinth of mineral cells, lined with catalytic walls composed of iron, sulphur and nickel, and energised by natural proton gradients. The first life was a porous rock..."

The conditions required for all this to happen are unusual, but happen to be exactly the conditions that prevailed on the earth 4 billion years ago. Once the conditions were in place, life was more or less inevitable and probably came about quite quickly.

Of course this story is still quite hypothetical. Some parts of the alkaline vent hypothesis are better attested than others. As far as I can tell the experimental results are still ambiguous, though promising. Other models for origins of life do exist and are being explored. See for example, Keller et. al. (2016), though this group also see a vital role for iron compound catalysis. The more we understand the biochemistry of life, the better we understand what the conditions must have been for the beginning of life. Major advances in understanding that biochemistry are still being made. Elucidating the basic structure of ATP Synthase won Paul Boyer and John E. Walker a Nobel Prize in 1997, less than 20 years ago. This is ongoing work, most of the sources cited in this essay are less than five years old (at the time of writing). 

Conclusions

A sceptical Buddhist reader, if they even got this far, may say, so what? What has any of this got to do with Buddhism? By my own admission, I don't usually countenance the idea that science supports the standard kinds of medieval worldview held by Buddhists. In fact here I am doing the opposite. By showing the plausibility, even the thermodynamic inevitability, of biochemistry emerging from geochemistry, I want to try to eliminate the last vestiges of Vitalism. No supernatural element need be added to the organic soup to make it come alive, merely some form of chemical disequilibrium across a permeable barrier (in our case a proton gradient across porous calcium carbonate). There is no equivalent of the Lord breathing life into Adam or Dr Frankenstein pumping electricity into the monster to shock it into life. Certainly energy must be available, but this is simply energy in the normal sense used by scientists, not some supernatural vital spark. Life proceeding in this manner is no less mysterious, but it is entirely natural. There is no need to introduce any supernatural element. The picture above might not be correct in every detail, but it identifies the basic elements that must be in place for life to be thermodynamically feasible: ie. H₂ and CO₂ in an environment of disequilibrium separated by a porous membrane, with catalysts present, and a replenishing flow that is balanced out by possibility for concentration of ingredients.

If we accept these ideas, and granted many will not or will find them too speculative, then life requires nothing extra in order to be passed on from one being to another. In the simplest terms, cells divide and the daughter cells go on to become other individuals. What is passed on in modern living cells is a copy of the mother-cell's genes, some of her metabolic equipment, and a section of her enclosing membrane. Nothing supernatural occurs during this process. What occurs is certainly incredibly, almost unimaginably complex and at best incompletely understood. But the broad outlines of it are clear.

I have previously argued that any afterlife is by necessity vitalistic and dualistic. The afterlife exists primarily to fulfil the longing for continued existence and as a mechanism for sustaining the Myth of a Just World. Vitalism and Dualism are the price we pay for fulfilling these longings. If the manner in which we lived is important to an afterlife theory, then that theory demands that information about how lived must survive our physical death in some coherent form. This information is then used to determine our post-mortem fate. Thermodynamics precludes the possibility of this information being preserved because, in our living bodies, the information is encoded in arrangements of atoms. Those atoms become disordered almost as soon as life ends. Nor is there a credible way of transmitting this information from one being to another, even if they were in physical contact. The many Buddhist attempts to explain this information transfer, e.g. a mind-made body (manomaya kāya) or gandharva, do not meet modern standards for theories that make accurate, testable predictions. At best they are myths, at worst they are post hoc rationalisations of something we want to believe despite the evidence.

If we eliminate all forms of Vitalism and Dualism with respect to life, it makes these medieval afterlife views considerably less plausible. If nothing is required to spark matter into life, if there really is no matter/spirit duality, then the idea of something immaterial surviving death is considerably less plausible. Buddhism without the inherent matter/spirit duality, without the supernatural elements changes radically. Karma and rebirth go out the window. The focus becomes how we understand experience and how we can explain the experiences we have during the religious exercises associated with Buddhism.

Because of thermodynamics, religion is basically finished. The death throes are certainly taking a long time, but the world is slowly moving away from seeing life through a religious lens. Buddhism, as a religion in the traditional sense of being concerned with continuity, justice, disembodied spirits, and the afterlife, is finished. We have Hamlet's choice: either embrace the situation and take an active role in shaping the future; or hesitate and allow events to overrun us. But we are not Hamlet, we know how the play ends.

~~oOo~~

Bibliography

Hutchison, C. A. (2016) Design and synthesis of a minimal bacterial genome. Science, 351 (6280) DOI: 10.1126/science.aad6253

Keller, MA. et al. (2016) Conditional iron and pH-dependent activity of a non-enzymatic glycolysis and pentose phosphate pathway. Science Advances 2(1) DOI: 10.1126/sciadv.1501235

Lane, N. (2009) Life Ascending: The Ten Greatest Inventions of Evolution. W.W. Norton. [While it lasts there is a YouTube video with Nick Lane reading his own chapter on the origin of life accompanied by relevant graphics https://youtu.be/UGxAB4Weq0U]

Russell, M. J., Nitschke, W., Branscomb, E. (2013) The inevitable journey to being. Phil Trans Roy Soc Lond B. DOI: 10.1098/rstb.2012.0254

Related reading

Herschy B, et al. (2014) An origin-of-life reactor to simulate alkaline hydrothermal vents. Journal of Molecular Evolution 79: 213-227. http://www.nick-lane.net/Herschy%20et%20al%20J%20Mol%20Evol.pdf

Lane N, and Martin WF. (2012) The origin of membrane bioenergetics. Cell 151: 1406-12. http://www.nick-lane.net/Lane-Martin%20Cell%20origin%20membrane%20bioenergetics.pdf

Lane N, Allen JF, Martin W. (2010) How did LUCA make a living? Chemiosmosis in the origin of life. Bioessays 32: 271-280. http://www.molevol.de/publications/188.pdf

Sousa FL, et al. (2013). Early bioenergetic evolution. Phil Trans Roy Soc Lond B 368: 20130088. https://sites.google.com/site/shijulalns/publications

Update 26 Jul 2016
A recent study (by Bill Martin and others) in Nature Microbiology suggests that LUCA was a hydrogen metabolising thermophile. Based on analysis of the common genes in bacteria and archaea it identifies 355 genes as ancestral - i.e. belonging to LUCA.

Weiss, M. C., Sousa, F. L., Mrnjavac, N., Neukirchen, S., Roettger, M., Nelson-Sathi, S. & Martin, W. F. (2016). The physiology and habitat of the last universal common ancestor. Nature Microbiology 1, Article number: 16116. doi:10.1038/nmicrobiol.2016.116.

For a discussion of the article see

Errington, Jeff. (2016). Study tracing ancestor microorganisms suggests life started in a hydrothermal environment. PhysOrg. 26 July 2016. http://phys.org/news/2016-07-ancestor-microorganisms-life-hydrothermal-environment.html

18 Feb 2017
In Daniel C. Dennett's new book From Bacteria to Bach and Back he references a paper which shows how ribo-nucleotides can be synthesised bypassing the phase of having ribose and an amino acid, which in some cases are very difficult to stick together.

Szostak, J.W. (2009) Origins of life: Systems chemistry on early Earth. Nature. 2009 May. Available from the authors website.

Ten Precepts in Another Structure

My ordination in 2005

The Ten Precepts followed by members of the Triratna Buddhist Order are also known as the path of ten wholesome actions (dasa-kusalakamma-patha). In this essay, I look at a singular occurrence of the list that organises them differently.

In Pāḷi, the precepts are phrased so that we undertake refraining from the path of the ten unwholesome actions (dasa-akusalakamma-patha). A few months ago I surveyed all of the occurrences of precepts in the Nikāyas for a project I was working on with Dhīvan. This essay was written back then, but was on ice until we had a chance to present our findings to the College of Public Preceptors. Whilst trawling through the few dozen texts in which this list appears, I stumbled on this interesting sutta that lists the same ten actions, but instead of considering them as related to body, speech and mind, it divides them up differently. I'll begin with my translation of the relevant text:

The Discourse on Success and Failure.

(AN 3.117; i.268)

There are these three failures (vipatti) monks. What three? Failure of virtue, failure of intention, failure of views. And what, monks, is the failure of virtue. Here, monks, someone is a killer, a taker of the not given, an indulger in illicit sex, a liar, a slanderer, an abuser, a prattler. Monks, this is called a failure of virtue.

And what, monks, is a failure of intention. Here, monks, someone is a coveter and ill-willer. This is called a failure of intention.

And what, monks, is a failure of view. Here, monks, someone has wrong views, has views that are contrary, such as "there is no giving, no sacrifice, no oblation, nothing that comes from good or bad actions, no fruit or result of actions; no this world, no other world, no mother, no father; no spontaneously arisen beings; there are no seekers and priests in this world on the right path and proceeding along it, who having personally witnessed this world and the other world, would declare it [to others]." This is called a failure of views.

Because of the failure of virtue, intention or view, beings, at the break up of the body at death are reborn in a state of misery, a bad destination, a place of suffering, in hell. These are the three failures.

There are these three successes (sampadā), monks. What three? Success of virtue, success of intention, success of view. And what, monks, is the success of virtue? Here, monks, someone is one who refrains (paṭivirato) from killing, refrains from taking the not given, refrains from illicit sex; refrains from lies, slanderous speech, harsh speech, and frivolous prattle. This is called a success of virtue.

And what, monks is the success of intention? Here monks, someone is not a coveter or an ill-willer. This is called a success of intention.

And what, monks, is the success of views? Here, monks, someone has right views, views that are not contrary, such as "there is giving, sacrifice, oblation, something that comes from good or bad actions, fruit or result of actions; there is this world and the other world; there is mother and father; there are spontaneously arisen beings; there are seekers and priests in this world on the right path and proceeding along it, who having personally witnessed this world and the other world, would declare it [to others]." This is called the success of views.

Because of the success of virtue, intention or view, beings at the break up of the body at death are reborn in a good state, in the heavenly world. These are the three successes.

~o~

It's a short text and in many ways straight-forward enough. However, there are a number of features of this arrangement of the precepts that will be interesting, especially for members of the Triratna Order. Usually we think of the precepts as being grouped into those that apply to body, speech and mind (kāya, vācā, & citta). In this text the precepts are grouped according to whether they relate to virtue (sīla), to thought/intention (citta), or to view (diṭṭhi). 

In the table below we can see the precepts with the usual arrangement of the left, and this new arrangement on the right.

kāya	pāṇātipātā paṭivirato	sīla
	adinnādānā paṭivirato
	kāmesumicchācārā paṭivirato
vācā	musāvādā paṭivirato
	pisuṇāya vācāya paṭivirato
	pharusāya vācāya paṭivirato
	samphappalāpā paṭivirato
citta	anabhijjhālu	citta
	abyāpannacitto
	diṭṭhisampadā	diṭṭhi

This is a one-off arrangement. However, we do often see the first seven precepts as a separate set or combined with the śrāmanera precepts. So there must have been some sects that saw these first seven as a distinct set. This is also reflected in the different wording of the last three precepts in this setting. Whereas we have the familiar language of refraining (paṭivirata) from something, in the cittasampadā and diṭṭhisampadā the language changes.

When we chant the ten precepts we use the tradition form which involves undertaking (samādiyāmi) the training principle (sikkhapādaṃ) of abstaining (veramaṇī) from the various unwholesome actions (akusalakamma) with the action given in the ablative case (indicating "from"). Although paṭivirata and veramaṇī look very different to the untrained eye, they are in fact closely related. Both stem from the verb √ram. The first adds two prefixes, paṭi- and vi- to the past participle (rata) to give us paṭi-vi-rata. The second adds only the prefix vi- to the root which then forms a stem virama, then adds a secondary derivative suffix -anī, which in turn causes the first vowel to be lengthened and strengthened from i to e giving veramaṇī (the n is changed to retroflex ṇ by the preceding r). Where the meaning of the bare root is 'enjoy, delight in' the meaning of vi√ram is the opposite, i.e. 'refrain'.

It's also worth noting that the word sampadā comes form the verb sam√pad. This may be familiar from the verb in the Buddha's last words: vayadhammā saṅkhārā appamādena sampādetha. The verb here is often translated as 'strive' as in "with mindfulness strive on". The form here is a causative, so in fact it means 'bring about success'. I wrote about these words many years ago in my essay on the Buddha's last words.

Speech Precepts

Note that in the speech precepts there are some differences. Here they are written:

• pisuṇāya vācāya paṭivirato
• pharusāya vācāya paṭivirato
• samphappalāpā paṭivirato hoti

We chant these in a different order, but we also chant pisuṇavācā vermaṇī... . It turns out that our version is grammatically incorrect because vācā is a feminine noun. The thing being refrained from is always in the ablative case. With the preceding precepts the kamma is masculine and has an ablative in -ā: hence in musāvādā veramaṇī... vada 'speech' and vadā 'from speech' (which is musā 'false'). So the ablative singular of vācā is vācāya which is what we see here. Also in this text, representing a minority reading, pisuṇa and pharusa are not compounded with vācā and being adjectives take the same gender and case ending. More often one see them compounded as pisuṇavācā and pharusavācā, but the compound still takes the ablative ending, -āya, in both instances.

With samphappalāpā we have a different problem. Here the word palāpa (with initial double pp in compounds) means 'speech, prattle' and sampha means 'frivolous'. So samphappalāpa already means 'frivolous speech' and there is no need to add vācā onto it as we do. Indeed the term samphappalāpāvācā is never found in Pāli, whereas samphappalāpā is common.

Mind Precepts

While the sīla category is more or less the way we are familiar with the precepts, with some minor grammatical corrections, notice that what we think of as the mind precepts are substantially different.

• anabhijjhālu
• abyāpannacitto
• sammādiṭṭhiko

To begin with the mind precepts do not mention 'refraining' or 'abstaining'. In fact this appears to be a pervasive pattern for these precepts throughout the early Buddhist literature, both in Paḷi and Sanskrit. The Pāḷi phrasing of the citta precepts here is simply:

Idha, bhikkhave, ekacco anabhijjhālu hoti abyāpannacitto.

Here (idha), monks (bhikkhave), someone (ekacco) is (hoti) one who is not a coveter (an-abhijjhālu) and one whose mind is not ill-willed (a-byāpanna-citto).

The word abhijjhālu is an adjectival form of the more familiar abhijjhā (which is also a feminine noun with an ablative form abhijjhāya). While our precept has the word byāpada 'ill-willing' as an action noun, here we have byāpanna the past participle 'willed-ill' and it is compounded with citta meaning "mind", "thought", or "intention".

Similarly for the tenth precept covering diṭṭhi or views, rather than refraining from wrong-viewing micchādassanā veramaṇī here we have sammādiṭṭhiko 'one who has right-view'. In fact in Pāḷi the form micchādassana is not found, but is always micchādiṭṭhi (which has an ablative form micchādiṭṭhiyā).

Conclusions

Such variations remind us that familiar lists were not always set in concrete. It is OK to think about things differently and to explore other ways of presenting our ideas. This set of categories might be seen as more practical because it is more closely aligned with the way we understand practice. One adopts ethics in order to set up good conditions for meditation. In meditation one must deal with the hindrances by temporarily eliminating  the grosser forms of craving and aversions, and then attempt to transform wrong-view into right-view.

Note that in this text, the aim is a good destination (sugati) or a bad destination (duggati) rather than anything more grand. This is not unusual. Many Buddhist texts seem aimed at what we sometimes think of as "mundane" goals like a good rebirth. Sometimes people who read the suttas are loath to take such things on face value. They argue that there must be an explanation. They might say that this is a fragment of a larger text which does aim at awakening. Or they might suggest that this was a text for lay people (though it is addressed to monks). Or perhaps they will say that this is "obviously" a late text for a degenerate age. But there is no evidence for these types of conclusions. They all involve projection rather than deduction. No. This is a bona fide Buddhist text that tells us how to get a good rebirth, which was clearly an important aspect of Buddhism from the earliest times because it crops up again and again in the suttas.

The fact that such variations are preserved also highlights what seems to me to be an important point. The Pāḷi Canon is not the literature of a single homogeneous group. Everywhere we look there is variation rather than unity. There is really no evidence for a pre-sectarian phase of Buddhism. The idea of a pre-sectarian Buddhism is the result of a distorting lens through which we look at history. This lens is a metaphor drawn from the study of biology and takes the shape of a branching tree that converges to a single point as we go back in time. In this view complexity is always greater in the future and less in the past. But this is a distortion. History is always complex. Tree does not take into account very common processes of evolution, for example, the contributions that tributaries make to the mainstream, or re-convergence after branching (hybridisation or syncretisation). I've argued that a braided river system is a far better metaphor for understanding history. In this view the source of Buddhism is a watershed, not a single spring. Buddhism incorporates influences from many traditions, including Brahmanism, Jainism, Zoroastrianism, and local animistic cults. It's likely that the basic ethics of Buddhism are the ethics of the Śākya tribe, originally from Iran.

Dhīvan and I have successfully lobbied the College of Public Preceptors to have the official versions of the precepts changed to reflect these observations, so watch out for an announcement soon (probably at this year's convention).

~~oOo~~