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The Origin of Life

In this post, we will go from the formation of the Earth to the origin of life and its earliest fossil record. This is an excerpt from a lecture I gave at the University of Cyprus a couple of years ago.

Diagram: Becerra, A., Delaye, L., Islas, S. & Lazcano, A. 2007. The Very Early Stages of Biological Evolution and the Nature of the Last Common Ancestor of the Three Major Cell Domains. Annual Review of Ecology, Evolution, and Systematics 38, 361-379.This is an artist’s conception of what the Earth would have looked like in the first million years after its formation 4.54 Ga. It consisted of molten rock and had no atmosphere. Due to the lack of atmosphere, it had no protection from space objects like asteroids or meteorites, leading to very frequent impacts.

The Earth at this point in time had a moon orbiting it called Theia. ~4.51 Ga, Theia crashed into the Earth. This impact had three main effects:

  • The debris from the impact formed the present-day Moon (the giant impact hypothesis for the Moon’s formation).
  • The impact was strong enough to tilt the Earth on its axis, as well as shove it off its orbit (responsible for a whole load of phenomena, from seasons to Milankovitch cycles).
  • It is thought to have been strong enough to kickstart the circulation of magma in the asthenosphere, thus leading to the start of geological processes, including plate tectonics and volcanism.

The start of proper volcanism allowed an atmosphere to form. Previously, any elements not incorporated into the crust had been ionised by space radiation or was too light to be held by the Earth’s gravitational pull. The only element that made up the first atmosphere was nitrogen. However, with volcanism, there is a constant source of heavy gases being vented and they quickly accumulated.

It is easy to figure out the composition of this second atmosphere, as volcano output is the same today as it was in the past. The composition of volcanic gases nowadays is shown in the picture. They’re mostly water (in the form of water vapour or steam). Importantly, there was still no free oxygen. These compounds, plus nitrogen, made up the early Earth’s atmosphere.

At some point, the Earth started to cool and the water vapour condensed and fell down as rain, eventually forming oceans. This happened much earlier than previously thought, as it’s now known that the Sun was ~30% less powerful back then, compared to today. We can place the earliest evidence for a crust at ~4.4 Ga and the earliest oceans at ~4.2 Ga.

Now we can look at the origin of life. It is much more productive to have a historical perspective to see the development of thought in time.

In the history of human civilisations and societies, religious and otherwise superstitious creation myths are a hallmark of any belief system. In the picture above, from left-to-right (upper row first), I included central figures of several diverse creation myths from around the world and different time periods: Xolotl (Aztec), Mother Earth (Amazonian), Viracocha (Inca), Brahma (Hindu), Nu Kua (China), Auðumbla (Norse), Papa and Rangi (Mãori). The stories and mythology behind these are wildly different, but they all have three things in common: they are fascinating reads,they seek to explain how organisms differ from inanimate matter, and they are completely unscientific.

The creation myth established in Europe, where the scientific method was developed, was one involving a single all-powerful god (variably called Yahweh, God or Allah) who created human males by breathing life into a human male-shaped lump of clay, derived the first female (Eve) from the rib of a primordial human male (Adam); all other organisms were created ex nihilo (i.e. out of nothing).

This theological narrative was directly translated by the first “scientists” – whose goal was to uncover the laws established by this one god – as meaning that organisms, especially humans, had an extra form of energy inside them (the “breath of God”).

These ideas are diverse, differing in what form this extra energy took, where it originates, how it manifests itself and its effects. We refer to them collectively as vitalism. Early proponents of vitalistic ideas are pictured above. Wikis available at time of writing: George E. Stahl, Paul J. Barthez, Albrecht von Haller, Xavier Bichat.

Vitalism was conclusively disproven by the mid-19th century due to the development of the laws of thermodynamics and their applications to physiological systems. When beginning to investigate processes like respiration and metabolism, the biologists of the time discovered that there is no extra energy inside organisms: we are the sum of our parts and whatever we eat, nothing more.

But due to its vague notions, the idea of vitalism persisted. In fact, the strain of thought is present nowadays in pseudoscientific ideas like teleology and especially as an addendum to the outdated philosophical question of mind/brain dualism. More recent proponents of vitalism-like ideas include Hans Driesch, Jacob von Uexküll and John Eccles (!). Quite embarassing, since this associates them with dreck like Deepak Chopra…

But as already mentioned, vitalism was largely ignored by biologists as of the mid-19th century. However, this left a big void in the question of how to define life, and the biologists of the time (pictured above: Herbert Spencer, Charles Darwin, Eduard Pflüger, Hugo de Vries, August Weismann, Wilhelm Roux, Ernst Haeckel, Oscar Hertwig, Julius von Wiesner, Max Verworn) turned to chemistry instead of physics. They postulated all sorts of chemicals that could serve as “life-giving molecules” in some way.

Their ideas are too different and divergent to be lumped together as “chemical vitalism”. Charles Darwin’s gemmules were merely units of inheritance, as were Hugo de Vries’s pangenes. On the other hand, Wilhelm Roux said that the blood plasma (which he termed the isoplasson) was a life-giving fluid; Ernst Haeckel narrowed that down to specific carbohydrate plastidules present in the blood plasma as being life-giving molecules.

Of course, none of these functions and molecules have been discovered.

However, this type of thinking – that there is a life-giving molecule – persists still. The quote above is not from any one source, but it could come from any popular science book, article or documentary on the origin of life.

At first glance, it seems like a good overall explanation, because it invokes natural selection and thus evolution. Evolution is, without a doubt, the main criterion for deciding if something is living or not. If it evolves, it’s alive. So clear is this principle that this is what astrobiologists seek in order to differentiate freak molecules from actual organisms (should they find anything weird in space).

But there is a critical flaw in this sentence. Its premise is that life can be defined by the presence of a single chemical (the “first strand”, a reference to an RNA-like molecule). This is no different than the life-giving molecules of the 19th century biologists.

This problem was identified as early as the beginning of the 20th century (and before), as evidenced by this translation from German of a passage from a lecture by Oscar Hertwig, where he sets up a new way of looking at the definition of life.

In this view, life is seen as a complex property arising from the interactions of thousands of components. There are so many of these that being a reductionist and only invoking physics and chemistry misses the boat and dismisses many of the unique characteristics of life.

In essence, the complexity and sheer number of interactions mean that life is on a higher hierarchical level and subject to different phenomena and processes. For an analogy, look at society and individuals: an ant colony’s functioning is not defined by the actions of one worker, it is the result of many dynamically-changing influences on tens/hundreds of workers.

In the philosophy of science, this is referred to as the concept of emergence.

Recommended Reading: Bedau, M. & Humphreys, P. 2008. Emergence: Contemporary Readings in Philosophy and Science. MIT Press.[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, although even more recent research with more high-tech imaging provides data to back up the notion that at least some of these are biogenic structures. Regardless of the status of the Apex Chert “fossils”, there were definitely organisms around at the time, the only controversy is over whether we have their body fossil record.

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 a famous case of pareidolia, read up on ALH84001, the meteorite fragment that, in 1996, was said to have bacterial remains in it. This 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.

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