A nice survey of research into the origin of life

The theory of natural selection provides a way of understanding how life, starting from one or a few microorganisms, has evolved over time to give us the immense variety and complexity we see all around us now. But it does not, at least directly, tell us how the very first thing that we can call a living organism came about. Natalie Elliot provides a nice survey into what current research says about the origin of life and she says that this research has also resulted in significant changes in what we mean by ‘life’.

She starts out by reviewing what happens as we trace our ancestors back in time.

Somewhere at the end of the line lies life’s oldest ancestor. This ancestor has acquired a name: LUCA, the last universal common ancestor. It also has a hypothetical nature and place in the biological order of things: LUCA is a microorganism or group of microorganisms from which all life on Earth descends. Though scientists, such as the molecular biologist William Martin of Heinrich Heine University in Dusseldorf, and his team, have been able to infer some part of LUCA’s genetic profile, they don’t have a complete portrait. They also can’t see beyond LUCA: LUCA isn’t necessarily the first life, and scientists can’t see what other life forms could have cropped up before it. Ultimately, LUCA is the living system that scientists identify to say that, at least once, somewhere, spontaneously, life got its start on Earth.

Unfortunately, this road stops there and we cannot see beyond, that she likens to the event horizon of a black hole. We then need to think in a new way about how things that we don’t normally think of as living could organize themselves differently to become the self-replicating entities that we now see as life.

Darwinian natural selection has helped researchers develop hypotheses for thinking about the process by which chemicals organise themselves into living forms. Natural selection, the process that shapes evolution, tells us that, as populations reproduce and change, those species best adapted to their environment survive. Many researchers think that natural selection can also explain the process by which inanimate matter begins to organise itself into living forms. If new species emerge by natural selection, then there might be prebiotic chemical precursors that become capable of evolution – perhaps evolution marks the beginning of life.

The most well known model for how this replication might happen is of course the DNA spiral but she says that it only takes us so far.

Watson and Crick’s discovery was, of course, profoundly significant for evolutionary biology in general, and for molecular biology in particular. But what was its significance for origins-of-life research?

With a mechanism for replication, scientists began to explore the idea that early life, if not the first life, began with the onset of replication. There was one problem, however: DNA couldn’t be the first self-replicator – it couldn’t have emerged spontaneously through the chemicals of early Earth. Once it’s formed, DNA carries the information required for making proteins which do much of the functional work of life, from structuring cells to transmitting signals between organs. DNA also relies on specific kinds of proteins called enzymes in order to catalyse reactions that allow it to copy itself. But proteins weren’t present on early Earth, and they require DNA for their production. If neither DNA nor self-replicating proteins came first, what molecules began the process of replication?

More recently, attention has shifted to the RNA molecules which previously were formerly seen as having a secondary role in the replication process.That search explores whether the appearance of proteins might have signaled the beginning.

In the 1960s, scientists began to consider that one candidate for this process might be ribonucleic acid, or RNA. In living organisms, RNA helps DNA convert its information to the functional products made possible by proteins.

In recent years, RNA world has therefore met with some rival theories about Earth’s first replicators. In 2017, for example, the scientists Elizaveta Guseva, Ken A Dill and Ronald N Zuckermann proposed a theory that protein-like molecules might have been the first replicators.

The physicist England sees things another way. For him, life isn’t a surprising thing at all: it follows naturally from the laws of physics. In his hypothesis, called ‘dissipation-driven adaptation’, the laws of the Universe generate the ordered structure we call life. His theory addresses Schrodinger’s challenge to explain why life doesn’t follow the path of matter in closed systems toward greater entropy, and why it instead becomes more ordered and complex over time. As England explains in a lecture in 2014, and in his forthcoming book, in non-equilibrium systems with a powerful source of energy, such as the Sun, matter necessarily forms structures that help dissipate energy. For living things, one of the most efficient ways to organise in order to dissipate energy is to reproduce. In accordance with England’s theory, life forms increase in complexity not only because they are subject to Darwinian evolution, but also, more fundamentally, because they must improve at dissipating energy.

Hanging over all this research is the question of exactly what we mean by ‘life’ and has led to suggestions that that definition too has to be broadened.

As the evolutionary frame for origins-of-life research has expanded and frayed, so too has the definition of life. Once scientists start thinking about prebiotic chemicals spontaneously organising, the boundaries between living and nonliving begin to blur. For some researchers, such as the evolutionary biologist David Krakauer, challenges to the definition of life are welcome. According to Krakauer, the focus on the replication of forms that we call living things prevents us from thinking biologically about the fascinating array of emergent systems before us – things we wouldn’t say are alive.

These frames make us pay attention to life in different ways. When we recognise the universal ways that matter organises and replicates; when we entertain the possibility that the transmission of information across computational and cultural systems can mark the emergence of life; when we turn to the biosphere as a living system, we begin to look for life in places that often seem inanimate. We look for signs of life in the outer planets or in the interstices of rocks and ice; or we see life replicating in the iterative tapestries of culture. We look for ways that life surprises us. It almost seems as though life emerges precisely when our ideas about it begin to conform to the phenomenon that we are attempting to conceive.

This is a fascinating area of research. The origin of life was at one time considered one of the last great mysteries that might be forever inexplicable. It thus provided hope for religious people who fought the notion that science was making the idea of a deity unnecessary. Along with the origin of the universe, the origin of life was the ultimate ‘God of the gaps’, the explanation they gave for what they thought (or more likely hoped) science would never explain. Of course this ‘explanation’ just consisted of ‘making stuff up’.

But both those questions are no longer mysteries for which we throw up our hands in bafflement, not knowing where to even start. They have transitioned to becoming puzzles that scientists are working on and that is a major step towards finding a solution.

(Jesus and Mo)


  1. Reginald Selkirk says

    His theory addresses Schrodinger’s challenge to explain why life doesn’t follow the path of matter in closed systems toward greater entropy, and why it instead becomes more ordered and complex over time.

    This is an exmaple of answering the wrong question. Living things themselves may have become more ordered over time, but they did it by increasing the entropy of their environments. We eat. We breathe. We poop.

  2. Reginald Selkirk says

    Did you notice this at the bottom:

    This Essay was made possible through the support of a grant to Aeon from the John Templeton Foundation.

    The Templeton Foundation’s relationship with science is tenuous. Perhaps this explains why the essay swerves into mysticism near the end.

    The failure to mention ribosomes is peculiar.
    In the 1960s, it was known that RNA could encode information just as DNA does, but that RNA is more chemically active, and thus might be able to catalyze chemical reactions as protein does. As the article mentions, the first known examples of RNA enzymes were discovered in the early 1980s.
    But ribosomes have been a subject of scientific study for a long time. They are the ‘factories’ where proteins get assembled from amino acids at the direction of the information stored in mRNAs; known in biology as ‘translation’. It was known that ribosomes are large and complex, consisting of a few score pieces of RNA and protein. When the first X-ray crystallographic structures of ribosomes came out around the turn of the century, it became clear that the catalytic core of the ribosome was constructed of RNA, not protein. Ribosome is an RNA enzyme. Here was another example of an RNA enzyme, and it was not something obscure and esoteric, it was right at the heart of life-as-we-know-it. The structures of ribosomes convinced a lot of molecular biologists that the RNA World Theory was essentially correct.

  3. anat says

    The article doesn’t pay enough attention to the ‘metabolism first’ views on origin of life, such as proposed by Stuart Kaufman and others. In these scenarios the first things that replicated weren’t specific molecules but systems including multiple catalytic molecules that as a set promoted the formation of one another (autocatalytic sets).

  4. Rob Grigjanis says

    Reginald Selkirk @1:

    This is an exmaple of answering the wrong question

    I think you’re misunderstanding the question. Yes, the presence of life actually increases the entropy of the system life+environment (more than it would increase without life, in general). The question is why there are subsystems (organisms) which decrease entropy locally.

  5. Ridana says

    Once scientists start thinking about prebiotic chemicals spontaneously organising, the boundaries between living and nonliving begin to blur.

    I think it was in another entry in this blog (?) that Hank Green commented, “When you look very, very closely, every sharp line turns out to be blurry.” Though he was commenting on a different topic altogether, that struck me as words to live by. 🙂

  6. Reginald Selkirk says

    Rob Grigjanis #4: I am not misunderstanding the question. I am pointing out that, if that is the question being asked, the writer should make that very very clear, rather than provide fuel for 2LOT Creationists, who are strongly motivated to misunderstand the question.

  7. says

    I want to post about this very thing and something is still holding me back. Some fear I haven’t figured out. I’m chipping away at it.

    I’ve drawn the pathways that synthesize purines (A G) and pyrimidines C U/T until I can do it from memory. Including places where the three domains of life do things differently. Including reaction intermeadiates. There are so many things to write about like the way ribose has a different relationship with purines and pyrimidines. Purines are built onto ribose and pyrimidines are built and then bound to ribose.
    The amino acid glycine is used in purine biosynthesis, the amino acid aspartate is used in pyrimidine biosynthesis. The entire time the intermeadiates are ribonucleitides, not deoxyribonucleitides.

    Purine biosynthesis intersects with biosynthesis of thiamine (vitamin b1, helps make…ribose), and biosynthesis of the amino acid histidine.

    I’ve nearly memorized the pathways of most other known molecules that use the same form of ribose as is used in purine and pyrimidine biosynthesis, 5-phospho-ribosyl-pyrophosphate (diphosphate), PRPP. They include histidine, the amino acid tryptophan, and the cofactor nicotinamide or NAD/NADP (vitamin b3, niacin).

    I’ve drawn out the protein domain architecture for each of the purine and pyrimidine biosynthetic proteins to maybe most of the existing literature by way of sites like uniprot, supfam and lately I’m using the ECOD system repeating what I did with supfam.

    I am currently identifying the protein fold superfamilies for the purine and pyrimidine biosynthetic proteins and writing down what other proteins share their parts. I’m looking for patterns among other proteins that share the domains and looking for patterns.

    I’m confronting what happens when you have to consider what genomes evolved from. Phylogeny isn’t just genetics. I have a lot of time to draw and read and think while I clean for my coworkers.

  8. friedfish2718 says

    It is most amusing that although Mr Singham copy-pasted large chunks of the AEON article, he omitted the most relevant phrase (it is in the first paragraph):
    . . . . What they have hit is the world’s most theoretically fertile dead end.
    . . . . What they have hit is the world’s most theoretically fertile DEAD END.
    I agree with Mr Singham about people commenting on articles they have not read. Mr Singham is either guilty of the same sin or he is plain dishonest.
    Mr Singham’s conclusion: “But both those questions are no longer mysteries for which we throw up our hands in bafflement, not knowing where to even start”, does not match Ms Elliot’s conclusion above”. I disagree with Ms Elliot in that the application of information theory to the question of life creation is THE WORLD’S MOST THEORETICALLY FERTILE FIELD.
    A chess grandmaster told me:”play the pieces on the board, not the person across the board.
    A commentator noticed the essay was funded by the John Templeton Foundation. So what? Read, evaluate, and judge the essay by the arguments set forth in said essay.
    Another commentator writes “… rather than provide fuel for 2LOT Creationists …”. So what? Creationists do their thing. You do your own thing. Creationists are living rent free in your mind.
    Adolf Hitler was a vegetarian and a non-smoker. So, being vegetarian is evil? So, is abstaining from smoking evil?
    Ilya Prigogine (Nobel Prize in Chemistry 1977) for his work on finding that importation and dissipation of energy into chemical systems could result in the emergence of new structures (hence dissipative structures) due to internal self reorganization. A local decrease in entropy MUST be accompanied with entropy increase outside the local system. The author, Natalie Elliot, seems to
    have a political science, not a STEM, background, so I expect her not to be precise in her writing. I find her to be quite a dilettente.
    I agree with one commentator that one should focus first on the catabolic (metabolic) pathways then secondly on the anabolic pathways. Need to get the free energy before building the life forms.
    One still has the information issue: the set of catabolic pathways cannot be haphazard, the set must be built according to a blueprint, a pretty detailed blueprint, a blueprint with an information load greater by many orders of magnitude than that contemplated by the self-reorganizing structures studied by Prigogine.
    The cartoon is silly and irrelevant. Anyone theorizing, making hypotheses, are “making stuff up”. The point is to see if the “made up stuff” matches up with reality.
    The theorist (like Mr Singham) makes things up; the experimentalist checks if the “made up stuff” is compatible with the material world.
    The theorist, without experimentation to keep it in check, is just another sci-fi writer. And sci-fi writers are well known to make things up.
    Mr Singham, do you know that the essay presents the basis of the “Intelligent Design” hypothesis?
    The “Intelligent Design” hypothesis is NOT warmed up Creationism.
    A sophisticated version of Conway’s Game of Life may give us a clue as to the minimum information load to create life.

  9. says

    @friedfish2718 9
    Theorists are also have to account for existing bodies of work. It’s not just “making things up”.

    Additionally catabolic pathways can’t be ignored. Some of them can function in reverse under different conditions and pieces of ancient metabolism may be lurking within. Coenzyme A is used in anabolism of fatty acids as well as in breakdown of many other things like amino acid skeletons. In the right environment those may have been catabolic.

    I don’t see the usefulness of intelligent design to any of this. It all looks like hierarchially nested kludges to me.

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