A Blog by Ed Yong

Life’s Rocky Start

Life is about barriers and compartments. Your body encloses your innards and keeps them separate from the outside world. Each of your cells is also a tightly packaged set of proteins and other essential molecules, bounded by a membrane. All living things are like this and for obvious reasons: Without a membrane, the contents of their cells would rapidly leak away, and become one with their environment. Life cannot exist without barriers and compartments, without some separation between an individual and everything else.

This point seems incredibly obvious, but it has a long history of being ignored.

For example, many discussions about the origin of life involve a mention of “primordial soups”. In these puddles of water, it is said, radiation and lightning fused simple molecules into complex ones. Eventually, this produced the biological chemicals that we rely on today, such as DNA and proteins. It’s a nice image, and one bolstered by Stanley Miller’s classic 1958 experiment, where he electrified a mix of water and simple gases and produced amino acids—the building blocks of proteins.

But the soup hypothesis cannot possibly be right. First, where are the compartments? How do molecules in a diffuse soup find each other with enough regularity to engage in chemical reactions? And when they do bump into each other, why would they react? Complex molecules won’t arise from simple ones on their own. They need a huge supply of energy and a constant one at that. Occasional lightning strikes aren’t going to cut it.

30-foot-high chimney in the Lost City field. By Mitch Elend, University of Washington/WHOI

For several years, a small group of scientists have championed a different scenario for the origin of life, which takes it from soupy puddles to the deep ocean. There, hot fluids bubble up from beneath the earth through rocky hydrothermal vents.

One such set of vents can be found at the bottom of the mid-Atlantic Ocean. Rather beautifully, it’s called the Lost City. It’s a field of ghostly white chimneys, made of calcium carbonate (limestone). Hot alkaline fluid, rich in methane and hydrogen, bubbles up through them. There is plenty of life here—snails, shellfish, worms, and microbes galore. And perhaps it’s in places like this that life started in the first place.

All the conditions are right, and a long way from inert soup. The vents are rich with the right basic chemicals, like methane and hydrogen. Their hot churning water provides a constant supply of energy. And they have ready-made compartments—labyrinths of small pores in the chimney’s rocks.

According to people like Mike Russell, and subsequently Bill Martin and Nick Lane, the vent provided a constant supply of fresh basic chemicals, and the necessary heat and energy to combine them into more complex organic ones. These included nucleic acids (the building blocks of DNA) and amino acids (the building blocks of proteins. The rocky pores acted as “proto-cells” that concentrated these molecules and prevented them from diffusing away. Encased in these compartments, they could react with one another, and evolve.

If this hypothesis is right, that’s the point when life emerged. Rather than the fully-formed, free-living cells we know today, the last common ancestor of all living things (known as LUCA) was a hollow piece of rock.

It’s a captivating idea, although there are still many details to flesh out. These scientists are slowly doing that, taking inspiration from the chemistry in the vents, and the biochemistry of the microbes that live there.

Lane and Martin have just published a new paper in the journal Cell that fleshes out more details of the idea, and outlines a critical step: If the first life was an immobile rocky proto-cell, how did it escape from the vents and start an independent existence?

I’ve covered their ideas for Nature News, so head over there to find out the latest chapter in this exciting origin story.

More on the origin of life:


7 thoughts on “Life’s Rocky Start

  1. to react with other cells, they would need contact and permiability. not something usually found in stone. how about some kind of chemical foam, maybe from partially dried amino acids, like seafoam.

  2. Interesting post Ed, and best wishes with your blog here at National Geographic. Also, good comments above by Bill and amphioxi pointing to the need for dynamic interactions among the hypothetical primordial entities.

    The effort by Lane and Martin to circumvent the ‘RNA world hypothesis’ in elaborating on the on the Origin of Life by embracing a ‘cell-like world model’ is to be applauded. Indeed, for reasons well rationalized, the transition from chemical to biological evolution occurred in a compartmentalized environment. To support the enormous number of dynamic interactions among these compartments, which were necessary for complex chemical evolution, these compartments allowed inter-compartmental exchanges and, very importantly, this process occurred in a self-sustained mode.

    Based on these principles, it is likely that these dynamic compartments, which were probably bound by a lipid-based membrane and were associated with the surface or with the pores of inorganic formations or conglomerates in an aqueous environment, followed a fusion/fission “life cycle” similar to that of the LUCA lineage: after assembly, thee grew by fusing with each other and reproduced by splitting into smaller compartments that continued the fusion/fission cycle – a cycle that initially was supported by thermal, mechanical, or osmotic energy.

    These self-sustaining compartments, which can be called cell-like compartments (CCs), developed in association with a surface or solution based auto- or hetero-trophic metabolism. It took these CCs several hundreds of millions years of providing an enclosed environment and fusion/fission based exchanges necessary for the population mode of evolution (i.e., collective evolution) of basic metabolism and of a coupled replication, transcription and translation system to evolve into the first genuine cells, the LUCA lineage (for more on this model on the Origin of Life see: http://hdl.handle.net/10101/npre.2009.3888.1).

  3. @ Bandea:

    The RNA world hypothesis is both alive and doing much better than Lane&Martin’s ideas, I think (and see below). But you can say they need each other.

    A recent empirically constrained thermodynamic theory shows that RNA nucleotides must ‘crystallize’ to replicators due to an effective thermodynamic force. As opposed to earlier pathways such as L&M this will be enforced, so without stalling the pathway by accidents.
    [“Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution”, Woo et al, PLOS Comp Biol 2012]

    There is also a thermodynamics paper by England in review, that predicts that RNA is the so far only known heteromer that can pass the thermodynamics bound of replication without an adapted protein enzyme metabolism. [Statistical Physics of Self-Replication”, England, arxiv 1209.1179]

    Taken together these results are tested by observation of RNA at the root.

    But the time frame is intriguing in this context. The experimentally characterized kinetics predicts that replicator crystallisation happens within ~ 30 000 years.

    Miller modeled sea water being sterilized by passing through hydrothermal vents in ~ 10 000 years. Free chemical systems must procreate before then. Here crystalization pass muster only if the maturing sequence pool is retained by porous walls in the vents.

    At the other end it has been claimed that the maximum lifetime of hydrothermal vents, at least today, is ~ 100 000 years. RNA ‘crystallization’ clears that constraint. Bare lipid packaged sequence pools may not be able to grow and reproduce without vents, but with reproduction they can seed the next vent and continue there. (RNA has a halflife against hydrolyzation of ~ 4 years.)

    The coupling to Lane and Martin’s ideas suggests itself.

  4. @ Larsson:

    As you know, the RNA world hypothesis has dominated the thinking on the origin of life ever since it was shown that RNA molecules can serve both as carriers of genetic information and as enzymes. Apparently, this theory provides such an intuitive solution to the origin of life that basically all textbooks of Biology and Biochemistry published in the last two decades have adopted it.

    However, in the furry of enthusiasm for this theory, it has been forgotten that the RNA world starts with ready-made, self-replicating RNA molecules, which is a *no start*.

    One way of thinking about the origin of self-replicating RNA molecules is that a random population of RNA molecules was somehow synthesized and some members of this population were able to self-replicate by chance, which jump-started the RNA evolution.

    The big question, however, is how this large population of RNA molecules originated in the first place? Also, a template-based RNA self-replication process is more complicated than it is usually perceived and, as emphasized by Christian deDuve, self-replication of RNA “does not make chemical sense” (“Chemistry and selection”; http://www.ncbi.nlm.nih.gov/pubmed/17443872).

    Other evolutionists who are not satisfied with the RNA world theory are Charles Kurland and Eugen Koonin. The title of one of Kurland recent papers on the subject tells much of his perspective: “The RNA dreamtime: modern cells feature proteins that might have supported a prebiotic polypeptide world but nothing indicates that RNA world ever was” (http://www.ncbi.nlm.nih.gov/pubmed/20806270). And, dissatisfied with the current explanations on the origin of life, Koonin apparently felt that he had no choice (short of not addressing it, or allowing for the origin of life to become a religion) but to call upon the weak anthropic principle as an explanation: “The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life” (http://www.ncbi.nlm.nih.gov/pubmed/17540027).

    However, in the ‘cell-like world’ theory on the origin of life (http://precedings.nature.com/documents/3888/), RNA does take a central role in the origin of coupled replication, transcription and translation (RT&T) system, which evolved within the CCs.’ According to this model, the ancestral ribosomes originated as RNA synthesizing machineries. Later, the ancestral ribosomes evolved into template-based RNA synthesizing/replication machineries that had their own RNA genome. At this early evolutionary stage, each ribosome within the CCs had its own genome for storing the genetic information necessary for production of RNAs. Eventually, the ribosomal genome evolved into a “cellular genome,” which was an evolutionary breakthrough because it allowed the centralization of genetic information within the CCs: all ribosomes within a CC used the same genetic information and RNA products. Free from the burden of producing RNAs, the ancestral ribosomes evolved into powerful protein synthesis machineries – the modern ribosomes.

    This model is a huge departure from the current thinking and very complex; however, to my knowledge, it is the only cohesive paradigm that addresses the origin of RT&T and of the first cellular organisms: the LUCA lineage.

  5. “Cell-like containers”, acting as factories of identical molecules, might
    resemble cells in some ways, but if they cannot enlarge and then produce
    more containers, they are not producing themselves. We might imagine
    them expanding into bigger, neighboring containers, and even getting
    segregated from the smaller quarters, but how do the better growers
    get represented at the fount?

    A complete set of molecules (of whatever sort) that can mutually and
    collectively reproduce that set, contained in an extensible,
    semipermiable membrane, seems like the minimum we should consider
    alive. The Lost City might still resemble the site of life’s origin,
    but perhaps only as a place where the right sort of molecules are
    abundant. The signature event would be enclosure in the membrane.

    Spontaneously arising membranes (perhaps seeded by appropriate crystal
    structures around the mouth of of an exit pore?) would be necessary,
    because no known cell produces a membrane *de novo*: they extend and
    pinch off existing membranes. Given enough little bags full of
    potentially reproducing molecules, the one that actually grows and
    buds would soon take up all the free amino acids, as the rest
    eventually lyse. If it were to happen more than once, e.g. at
    different sites, the overabundance of the molecules produced in
    successful lineages would make mixtures of molecules freed by lysed
    cells the more likely to occur, mixing lineages.

    We have many examples of RNA arising from non-biological processes.
    Where are the membranes? We may think of the entire set of membranes
    of all cells existing in the world today as fragments pinched off of
    a single successful progenitor. To find the origins of life, find wheres
    membranes happen without it. Nucleic acids are just the membrane’s
    way of making more membrane.

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