[Contains essays by leading philosophers and scientists on emergence. Many different perspectives, but all interesting, thought- and discussion-worthy!]
So what does this mean for the question of the definition and origin of life?
For one, it renders the search for a single magical molecule completely meaningless, since it will not help in resolving the origin of life.
Instead, a new framework is established, whereby we need to search for non-living components (i.e. the building blocks) and see how they can interact together. Once we have that information, we can speculate on the origins of a complete system. It is this system that we call life.
This is ideal from not only a philosophical standpoint, but also a practical and methodological one. This program allows speculation to be restricted to only the last step – the emergence of the system. The first two steps can be examined with experiments and lab work, meaning that origin of life research fulfils the criteria of being scientific, instead of being filled with “just-so” stories.
Keeping with the historical theme, I identified three milestones in origin of life research.
The first is this excerpt from a letter from Charles Darwin to his favourite pen pal Joseph D. Hooker. It was published posthumously and garnered attention quickly and its reputation is now cemented – it’s the famous “warm little pond” letter. As a sidenote, this is not representative of Darwin’s thoughts on the origin of life, but merely a reaction to origin of life theories floating around at the time.
These theories can be lumped into 3 categories:
Divine intervention: i.e. creation myths.
Spontaneous generation: The idea that life can spontaneously arise. Although disproven by Louis Pasteur in the 1860s in the same experiments that led to the establishment of the germ theory of disease, spontaneous generation remained popular, and this letter was partly a reaction to Sir Richard Owen’s claim of having seen it with his own eyes (it was actually just meiobenthic worms creeping out of the sand, nothing more).
Panspermia: A theory that persists until today in both serious and silly fashions. This is the idea that life was seeded from outer space by meteors. The silly way to think of this is that bacteria or other unicellular organisms were brought here complete; a plausible scenario is that the chemical building blocks of life were transported by meteors.
What Charles Darwin is endorsing here is none of those. Instead, he is talking about abiogenesis: that the chemical building blocks of life (amino acids, etc.) can be formed by natural, chemical means.
This is the only logical way to think about the origin of our abiotic components. It also incorporates the idea of panspermia: the chemicals, wherever they came from, must also have formed by abiogenesis.
But abiogenesis, at Darwin’s time, was still a hypothesis. Urea could be synthesised, as could a couple of other vital biological molecules, but these were not thought of in terms of origin-of-life research. There was no real laboratory test of abiogenesis yet.
Recommended Reading: Peretó, J., Bada, J. L. & Lazcano, A. 2009. Charles Darwin and the Origin of Life. Origins of Life and Evolution of the Biosphere 39, 395-406. [On Darwin’s thoughts about the origin of life.]
The next milestone comes courtesy of Alexander Oparin, a brilliant Russian chemist who, in 1924, published this book (title supposedly translates to “The Origin of Life” or something similar).
His hypothesis is outlined in the picture. I consider this a milestone because while it is speculation, his scenarios are plausible and grounded in chemistry. They can easily be tested in the lab.
In 1936 (1938 in English), he greatly expanded his ideas and released a new book called The Origin of Life. In this new one, he synthesised and reviewed all previous work done in relevant organic, inorganic and geochemistry, as well as work done on membranes and self-assembling chemicals.
The result is an outstanding achievement with a lot of creative, but realistic, ideas and hypotheses. This is a book that anyone interested in the origin of life should read. Many of his ideas are now wrong and outdated. But the thinking behind them is spot-on and underlies how we currently go about the origin of life research, as we’ll see later.
The third, and by far most significant, milestone is the Urey-Miller experiment. First, some history: Harold Urey was a professor at the University of Chicago in the 1950s, where he held a lecture series on the origin of life. Stanley Miller attended it and was very impressed, particularly when Urey mentioned the lack of abiogenesis experiments. A year later, Miller asked to do a Ph.D. under Urey’s supervision, outlining this experiment. After some lukewarm resistance by Urey, Miller was accepted.
His experiment was deceptively simple: a flask of boiling water sending steam to a container with methane, ammonia, hydrogen and carbon monoxide (what was thought back then to be the composition of the early atmosphere). An electrical spark – simulating lightning – discharged into this mixture, and the reaction products were collected.
A week later, Miller took liquid samples and the black tarish residue that had formed and tested their chemical compositions. What he found was one of the groundbreaking discoveries of modern science: they had amino acids in them. Amino acids are the building blocks of proteins.
Miller had shown that abiogenesis is possible.
The Urey-Miller experiment was a methodological spark of genius, but in the details, it is slightly flawed. The mixture supposed to simulate the early Earth’s atmosphere is now known to be wrong. However, this does not invalidate the premise one bit. When repeated with an accurate gas mixture, we get even more amino acids than what Miller got (see picture).
Diagram: Parker, E. T., Cleaves, H. J., Dworkin, J. P., Glavin, D. P., Callahan, M., Aubrey, A., Lazcano A. & Bada, J. L. 2011. Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. PNAS 108, 5526-5531.
So with these milestones behind us, where are we now? We have a good idea of what the early atmosphere was composed of, and we can synthesise all sorts of biologically-significant compounds de novo in simulations of abiogenesis.
What we have not been able to do yet is synthesise a cell. This is something of a critical threshold that needs to be passed. As outlined earlier, life is a system. Simply having organic molecules swimming around doesn’t equal life. In a cell, these molecules are concentrated together so they can interact.
This is where Oparin’s brilliance shines through. He realised that the key to the cell is the membrane enveloping it. His work on self-assembly of lipids layed the foundations for our thoughts on the origin of cells.
As a note, from this point, we must delve into more speculation – at some point, we simply have to step back and say that we don’t, and can’t, know. That is the point at which we will stop.
Just as we need to know the composition of the atmosphere to accurately test abiogenesis, we also need to have a good idea of where the first cells might have originated. This may seem to be an impossible problem, but phylogenetics comes to the rescue.
The diagram above, adapted from the seminal work of Carl Woese, shows the classification of all organisms. They are split into the Bacteria, Archaea and Eucarya.
Using phylogenetics, we can puzzle out what features these three groups (taxa) share. These are then assumed to have been present in the hypothetical last common ancestor – in this case, LUCA, the last universal common ancestor of cellular life forms.We can then partially reconstruct the biology of the common ancestor.
When this is done for the three cellular domains, we find that the ancestral trait that sticks out is hyperthermophily, i.e. LUCA probably lived in places with extremely high temperatures (with respect to biology). This is why it is thought that life originated at hydrothermal vents: high temperatures, abundant chemicals and a very dynamic geochemical system, with elements and minerals constantly being replenished and depleted naturally.
In this constantly-changing environment, life first arose. But how? The most compelling idea is that of Günter Wächtershäuser, a German chemist and patent lawyer, who outlined his ideas in several papers from the 1980s onwards.
They revolve around the idea that metabolism – not genetics – came first. His favoured mechanism is through pyrite formation. Pyrite (fool’s gold), when formed, releases hydrogen, ammonia (a very important biological compound and precursor), and reduces many organic compounds (which would be present near hydrothermal vents). Additionally, a lot of energy is released in this process.
This can count as the first metabolic system. The constant source of new ‘nutrients’ and the release of energy means that this is a positive feedback loop.
Among the products of the organic reductions would be lipids. By virtue of their chemistry and physics, lipids self-assemble on their own. All modern cell membranes can be simplified as just lipid bilayers. These can form naturally as proto-cell membranes near the hydrothermal vent, and they would contain and concentrate the energy and metabolites from the pyrite formation, allowing the metabolism to be more efficient.
Another class of compounds that tend to self-assemble are nucleic acids. Through abiogenesis, their building blocks (nucleotides) can form, and they will assemble into a proto-RNA-like structure. We specify RNA because it has a peculiar property of self-catalysing its own replication.
This all would have happened concurrently with the origin of the proto-cell membranes. Until now though, we still don’t have “life” – it is only when these two systems, the genetic and the metabolic, fuse that we can have the first true cellular organism.
This fusion is best imagined as an endosymbiosis or some similar cooperative accident/effort.
This is the point at which we stop. Going further is not hard to think up of,but any scenarios will just be baseless speculation. They can be backed by chemistry at some point in the future, I have no doubt about that. But we’re not there yet, so it would be unfair of me to put in any false ideas here.
Picture Source: Brasier, M., McLoughlin, N., Green, O. & Wacey, D. 2006. A fresh look at the fossil evidence for Archaean cellular life. Philosophical Transactions of the Royal Society B 361, 887-902.
So let’s jump right ahead to the tangible evidence. Life has formed and it left a fossil record, both molecular and body. Of the latter, the Apex Chert microfossils are the most famous.
In 1993 (and earlier), William Schopf published the pictures of structures he found in thin sections from the Apex Chert, a 3.5 Ga outcrop from Western Australia. They look a lot like cyanobacteria, especially with those drawings next to them. The findings, while of course criticised, were generally accepted.
In 2002, Martin Brasier published a paper in which he provided an explanation for how these structures could form, without invoking the need for bacteria or biology. Did William Schopf (left) see real microfossils or whether he was engaging in pareidolia (suggested by Brasier, kung-fu master, right).
Schopf’s 1993 paper: Schopf, J. W. 1993. Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life. Science 260, 640-646.
Brasier’s critique: Brasier, M. D., Green, O. R., Jephcoat, A. P., Kleppe, A. K., van Kranendonk, M. J., Lindsay, J. F., Steele, A. & Grassineau, N. V. 2002. Questioning the evidence for Earth’s oldest fossils. Nature 416, 76-81.
The controversy is now over, as the latest research shows that these are nothing more than naturally-formed iron-filled cavities. They are not holes left by bacteria that were then filled with iron either. There is nothing out of the ordinary to see here.
Paper: Marshall, C. P., Emry, J. R. & Marshall, A. O. 2011. Haematite pseudomicrofossils present in the 3.5-billion-year-old Apex Chert. Nature Geoscience 4, 240-243
For another famous case of pareidolia, read up on ALH84001, the meteorite fragment that, in 1996, was said to have bacterial remains in it. This also turned out to be nothing.
The oldest confirmed cyanobacterial remains are stromatolites from the 2.7 Ga Tumbiana Formation, Australia. Stromatolites are mound structures formed by cyanobacterial colonies, nowadays found only in highly saline environments. Their structure is made up of cyanobacterial colonies overlain by secreted biofilms, on which new colonies can grow.
We can confirm that the Tumbiana stromatolites are of cyanobacterial origin due to biomarkers. Cyanobacteria have unique molecules in their cell membranes, and when they get fossilised under the right conditions, these undergo changes due to heat and pressure. These changes are well-known and unique and so serve as fingerprints.
Stromatolite-like structures are nowadays unique to cyanobacteria, but this was apparently not always so. The earliest confirmed biogenic stromatolites are pictured above, from the 3.5 Ga Dresser Formation, Australia.
We know they are biogenic due to the presence of biomarkers. However, these are not cyanobacterial biomarkers, and no living representative of any organism group can deliver them. It is therefore thought that they were built up by a now-extinct form of life, probably Archaean.
These are the earliest body records of life.
However, there is isotopic evidence of biological activity as early as 3.9 Ga, and that is our current confirmed boundary for when life originated – although, realistically speaking, it probably arose somewhat earlier, but there is no point pinpointing any exact date.
So life is finally on the Earth. It trundled along uneventfully, until 2.8 billion years ago, when the atmosphere got a 10-fold increase in oxygen. This was one of the most significant events in the history of life, as oxygen opens up the way for more biological possibilities.
This event is what we will now look at.
As you can see, for the first 1.5 Ga, the oxygen level of the atmosphere was negligible, 0.1% of present atmospheric level (so <0.1% of 21 = <0.021%). Then, in a period of 200 Ma, the level rose by an order of magnitude. This is referred to as the Great Oxidation Event.
The main reason it is so important is because it indicates a rising role of life in how the geosphere functions, because free oxygen can only come about through biological activity (photosynthesis or otherwise).
Free oxygen is also used up through myriad oxidations, for example of volcanic gases, minerals and other reduced products. These would have been ubiquitous, as they had been accumulating for 1.5 Ga.
Since we know that cyanobacteria were present from at least 2.7 Ga, we know that photosynthesis did not cause the Great Oxidation Event immediately – there was a 200 Ma lag. This is best explained by saying that this backlog of reduced materials had to first get oxidised before oxygen could accumulate.
But matters are not as clear-cut. Evidence is starting to pile up, pointing to the presence of oxygenated pockets of ocean earlier than the earliest cyanobacteria. And since free oxygen is the product of biology, this means that there must have been something that caused a reversal in the situation and allowed oxygen to rise to dominance.
This event could be the break-up of a super-continent. The diagram above shows that there is a very tight correlation between continental break-up and oxygen spikes in the entire geological record. This could just be confusing correlation and causation, but there is a plausible explanation: with the break-up of continents, you also get an increase in erosion, leading to more nutrients leeching into the oceans, leading to blooms of biological activity, including of the oxygen-producing organisms.
Theory Source: Campbell, I. H. & Allen, C. M. 2008. Formation of supercontinents linked to increases in atmospheric oxygen. Nature Geoscience1, 554-558.
This, combined with the rise of photosynthesis and cyanobacteria, led to the previous anoxic ocean with small oxic regions getting reversed to an oxic, stratified ocean, with the photosynthesising organism dominating at the surface where sunlight reaches.
The oceans remained in this state for the next 2 Ga. This was not a static state though; it was more of a dynamic equilibrium.
With the accumulation of oxygen in the atmosphere, sulfides on the continents could be oxidised to sulphates, which then entered the oceans. Many oceanic microbes can convert sulphates to sulphides again (by removing iron). In the Neoproterozoic, these microbes were co-dominant with the photosynthetic cyanobacterioa: cyanobacterial activity led to more nutrients for the sulphate reducers, but they were pushed to the bottoms as they could not compete with the cyanobacteria in the photic zone (where sunlight is), leading to a structure of a high-oxygen surface giving way to anoxic and sulfidic middle and bottom layers, with the fuzzy boundary between the two constantly changing depending on climate, etc.
This state is known as the Canfield ocean, named after Donald Canfield, an authority on early Earth oxygen and the interplay between microbes and geology, who first came up with the model.
It persisted until ~700 Ma, at which point another supercontinent, Rodinia, broke apart. The effect of that is examined in the next talk.
The above is a summary of the early history of oxygen.
For more detail: Buick, R. 2008. When did oxygenic photosynthesis evolve? Philosophical Transactions of the Royal Society B 363, 2731-2743.
If more detail wanted on origin of life: Robert Hazen’s 2005 book, Genesis, is an excellent read, that also goes into how scientists study the origin of life. Fully recommended.