Was life inevitable? New paper pieces together metabolism's beginnings

Dec 13, 2012

(Phys.org)—Describing how living organisms emerged from Earth's abiotic chemistry has remained a conundrum for scientists, in part because any credible explanation for such a complex process must draw from fields spanning the reaches of science.

A new synthesis by two Santa Fe Institute researchers offers a coherent picture of how , and thus all life, arose. The study, published December 12, 2012, in the journal , offers new insights into how the complex chemistry of metabolism cobbled itself together, the likelihood of life emerging and evolving as it did on Earth, and the chances of finding life elsewhere.

"We're trying to bring knowledge across disciplines into a unified whole that fits the essentials of metabolism development," says co-author Eric Smith, a Santa Fe Institute External Professor.

Creating life from scratch requires two abilities: fixing and making more of yourself. The first, essentially hitching together to make living matter, is a remarkably difficult feat. (CO2), of which Earth has plenty, is a stable molecule; the bonds are tough to break, and a chemical system can only turn carbon into biologically useful compounds by way of some wildly unstable in-between stages.

As hard as it is to do, fixing carbon is necessary for life. A 's ability to bond stably with up to four atoms makes it phenomenally versatile, and its abundance makes it suitable as a backbone for trillions of compounds. Once an organized chemical system can harness and manipulate carbon, it can expand and innovate in countless ways.

In other words, is the centerpiece of metabolism – the basic process by which cells take in chemicals from their environments and build them into products they need to live. It's also the link between the geochemistry of Earth and the biochemistry of life.

In a paper earlier this year, Smith and Santa Fe Institute Omidyar Fellow Rogier Braakman mapped the most primitive forms of carbon fixation onto major, early branching points in the tree of life (PLoS Computational Biology, April 18, 2012). Now, the two researchers have drawn from geochemistry, biochemistry, evolution, and ecology to detail the likeliest means by which molecules lurched their way from rocks to cells.

Their 62-page "Logic of Metabolism" paper presents a new, coherent picture of how this complex system fits together.

What started as wonky geochemical mechanisms were sequentially replaced and fortified by biological ones, the authors believe. "Think of life like an onion emerging in layers, where each layer functions as a feedback mechanism that stabilizes and improves the ability to fix carbon," says Braakman.

Carbon fixing and other chemical sub-processes that together constitute metabolism each comprise dozens of steps; some are quick and easy turnkey reactions with simple molecules, others require highly specific chemical helpers, or catalysts.

The parts of metabolism that guide carbon fixation through its unstable intermediate stages fall into the latter category, requiring help. But these seemingly unlikely reactions are remarkably consistent across all living systems. In fact, says Braakman, their ubiquity and the difficulty with which they are forged make them the chemical constraints within which all living systems operate – in a sense, the scaffolding for the tree of life.

It's these dependable regularities of hierarchy and modularity, amid the panoply of reactions comprising metabolism, that stabilize the system and enable its complexity.

Braakman and Smith describe specific features of metabolism and sub-divide helper metabolites by their functions. For example, vitamin B9, a complex molecule in the 'cofactor' class, facilitates the (otherwise unstable) incorporation of one-carbon compounds into metabolism.

In mapping the chemical pathways to life's emergence, the researchers touch on a more existential question: How likely was it for life to have developed at all? Extraordinarily so, says Braakman. "Metabolism appears to be an 'attractor state' within organic chemistry, where it was likely to be selected regardless of earlier stages of chemical evolution" in the chaotic, high-energy conditions of prebiotic Earth, he says.

Can it happen elsewhere? Possibly, even probably, he says. Rocky planets usually have cores chemically similar to ours, so if a planet is volcanically (and perhaps tectonically) active and has an ocean, it will probably have hydrothermal vents that spew chemicals, creating the potential conditions for life, Braakman says. In fact, the physics of star and planet formation make the chances of such conditions pretty reasonable.

Smith cautions, however, that we still have much to learn about the chemical and physical conditions that might lead to life-like organization, but he hopes their paper will at least "lead to experimental questions that focus more directly on the key functions that link metabolism to ."

Explore further: Scientists find clues to cancer drug failure

More information: Read the paper in Physical Biology (December 12, 2012): iopscience.iop.org/1478-3975/10/1/011001/article

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1 / 5 (4) Dec 13, 2012
My understanding is that the reason why life exists on Earth is fairly easy to explain (although the exact process by which it happens is complicated).
In the simplest terms, the inexorable increase in entropy forces local systems to attempt to exist in the lowest energy state which is practical.

In Earth's atmosphere this plays out with the unstable, high energy molecules in the atmosphere slowly breaking down into numerous stable products, like CO2. In most cases these stable molecules contain a fairly low amount of chemical energy (satisfying longterm entropic requirements), but CO2 contains quite a bit. But the real kicker is that CO2 is very hard to break down, due to the fact that (by an large) only multi-stage reactions can break it down.

This causes a huge excess of CO2 to exist which *needs* to eventually be broken down to satisfy basic physics. Simple reactions don't suffice, so more complicated ones involving self-replicating molecules (ie, life) are required.
1 / 5 (3) Dec 13, 2012
Of course, that process can only happen where conditions are right for large, self-replicating molecules to exist. If they can't exist, nothing happens, and you just end up with this huge pool of potential energy (CO2) that can't be utilized or quickly broken down (like on Venus).
5 / 5 (7) Dec 13, 2012
Yikes, so much wrong in so small a space. Life seeks low entropy because it feeds on the energy flow. For example plants use the low entropy sunlight.

Co2 is not an energy source for any creature I know of. In principle you might get energy from it but not by breaking it down. That would require large amounts of energy. You might get some energy from it by combining it with calcium for example. Not very much.

Plants take the low energy co2 and make high energy carbon compounds out of it by using the sun as an energy source. Everything else feeds on that energy. Cows eat grass and then we eat the cows. In the process we return carbon to its low energy co2 state. All flesh is grass. All grass is sunlight.

1.5 / 5 (6) Dec 13, 2012
I think this shows that life is not an accident. Bring on the ignorant flaming
5 / 5 (5) Dec 13, 2012
@Mikegyver The title indicates that the research shows that life might be an inevitable fact of physics/bio-chemistry. Let's keep the ignorant flaming to a minimum. I'd like to learn something.
1.5 / 5 (2) Dec 13, 2012
And I refuse to believe that animals don't inherit their appearance traits from the environment in which they were conceived as documented in Genesis 30:37. AND NONE OF YOU ROUND OLD EARTHERS CAN MAKE ME
1 / 5 (1) Dec 13, 2012
Philosophically speaking, intelligent living conscious entities must exist to satisfy the requirement for the predisposition to that which begets creation in the first place, which is the idea that anything existing at all being so staggeringly awesome and profound, that it simply impresses itself into being from nothing. That would necessarily be a premonition, which does not require the function of time, time not existing yet before it happens, which it does, otherwise I would not be here to write this.
not rated yet Dec 13, 2012
Philosophically speaking, intelligent living conscious entities must exist to satisfy the requirement for the predisposition to that which begets creation in the first place, which is the idea that anything existing at all being so staggeringly awesome and profound, that it simply impresses itself into being from nothing. That would necessarily be a premonition, which does not require the function of time, time not existing yet before it happens, which it does, otherwise I would not be here to write this.

No, but something about "nothing" makes it an unstable state.
4.4 / 5 (5) Dec 13, 2012
And the god of the gaps ratchets another notch smaller. Listen to them creationists squeal!
5 / 5 (3) Dec 14, 2012
"Life seeks low entropy because it feeds on the energy flow."

Exactly right. Just a few months ago the first (I think) result of a thermodynamic basis for the emergence of replicators were made. This means there is a thermodynamic force that ensures a pool of RNA will lead to replicators without the possibility of stalling, akin to how a heated pot eventually boils. That force is a free energy force. ("Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution", Woo et al, PLOS Comp Biol 2012.]

It presupposes a metabolic network supplying the necessary phosphate activated RNA nucleotides, which is why Smith et al (or Kaufmann et al) metabolic network results are interesting. But we know that too will happen from free energy forcing without stalling: as a chemical network cools, enthalpic enzymes are thus selected. It is the exact likely pathways that is interesting here.
5 / 5 (2) Dec 14, 2012
Empirically speaking, we don't know if "nothing" exists. All our observations see something, and predicting standard cosmology backwards makes it much likelier there always were something. And as GaryB notes, the simpler states (no spacetime) seems to be unstable.

The most likely outcome doing this, eternal inflation spacetime, has in its most likeliest physics of tree level vacuums no explicit need for initial conditions as of yet.

It may be, physically speaking, simply be that the multiverse is because it can be and our specific universe is because we can be. And it simply could have been otherwise over the distributions of parameters, making existence a coincidence of possibilities.
5 / 5 (2) Dec 14, 2012
Re "something about "nothing" makes it an unstable state." According to Vic Stenger it is because the "chaos" of nothing is more symmetric.

Without spacetime there isn't yet the symmetry breaking that separates between space and time dimensions or more precisely, I think, weds them so space becomes causal (relativistic/Lorentzian signature) over time.

That symmetric states observably spontaneously symmetry break sooner rather than later is because they tend toward lower energy (i.e. more persistent configurations in phase space).

Buuut, I feel these possible predictions are premature, seeing how eternal inflation doesn't really go for "nothing" in the first place.
1 / 5 (4) Dec 14, 2012
In some opinions the life is forming continuously at the Earth, which is difficult to imagine for me, because the living organisms are hungry and they tend to exploit all possible sources of life for itself. In AWT the clue of life origin is in simple physical systems, not just chemistry, it means between others, that the first organisms were relatively large systems (droplets of size above 1 mm scale).
5 / 5 (2) Dec 14, 2012
@ Valeria: "Aether" was rejected by observation over a century ago. There is no such thing.

Astrobiology is driven by physics and chemistry, and it turns out there need not be any specific "clues" - there are many possible pathways.

The area of astrobiology has started to look for ways to reject erroneous hypotheses, like "aether" once was. Que thermodynamics, which works with RNA but no other (known, out of a large set) molecule for replicators and how this is tested against what is known from phylogeny, i.e. the RNA world.

The size of the replicator pool is inconsequential as long as it fits in a hydrothermal vent circulation system (see the article). After replication starts, biological fitness takes over and simple cells of today's size are fittest. (Provides isolation and, at first passive, movement.)

Those need only one more component than the nucleotide pool, lipid (spontaneously assembled) membrane vesicles, available in these vents.
1.3 / 5 (3) Dec 14, 2012
Aether is just another name for complex system of space-time curvatures, which are forming observable reality and which are of emergent nature like the density fluctuations inside of dense particle gas. These space-time curvatures exists like real particles forming the matter, or like so-called virtual particles forming the vacuum. In the same way like the solitons at the water surface: some of them are formed above it, the another solitons manifest beneath the water surface and they're barely visible at it. I already explained, why the dismissal of aether model with Michelson-Morley experiment was based on fringe idea, i.e. misunderstanding of aether model in the Maxwell time. Oliver Lodge in 1904 corrected this misunderstanding with introduction of dense aether model, but he was ignored even with another aetherists (T.J.J.See).
1 / 5 (3) Dec 14, 2012
IMO the formation of life doesn't require the replicator molecules, because the surface of droplets has its memory by itself. The tiny droplets can collect surfactants from their environment with their own motion and they grow during it. The droplets which are most sufficient with it will grow with fastest speed. When they grow sufficiently, they divide mechanically into smaller ones and their evolution will continue. I do prefer the idea, that the life was formed at the phase interface of all three phases (air, water and rock) and that it occurred at the CMBR wavelength scale, which brings the highest degree of complexity into physical world - this is the dimensional scale, where the quantum mechanics balances the gravity exactly. The evolutionary selection at the chemical level has started later and it occurred at the phase interface of the droplets.
1 / 5 (1) Dec 14, 2012
No, but something about "nothing" makes it an unstable state.
Granted, nothing is a difficult concept to grasp. It was the last number invented in mathematics.

Nothing pre-exists before creation. Not time, nor matter, nor space. It is not unstable, because something has to exist before stability factors can be applied. The universe creates and that is the beginning of time, so it is not wrong to state that the universe has existed for all time.

Nothing is not something that you can walk around in, or wave your hand through, or poke with a stick. It is nothing - very complicated to imagine a place in nothing for the universe to have begun, but surely less complicated than to imagine a universe which was always there and which had no beginning, and even more difficult to imagine a being who created it all and who was around and who evolved arms and legs as necessary adaptations to an environment he had not even created yet. Do you have a more rational explanation?
5 / 5 (4) Dec 15, 2012
@ Valeria: "Aether" was the hypothesis of a pervasive medium in the vacuum. Your idea is not that, and it isn't even wrong since it is non-testable ("forming observable reality" regardless).

@baudrunner: You are confusing math ("number") for physics. And 0 wasn't the last number in math, we have complex numbers et cetera after it.

As for when you (finally!) come to physics, you are confusing it with religion. The empirical fact is that we have something, and various kinds of "nothing" must be predicted.

As I mentioned before, currently the standard cosmology provides simplest extensions were there is no need for such extraneous objects and their extraneous mechanisms.
5 / 5 (4) Dec 15, 2012
@ Valeria: Formation of biological life requires heredity, because variation and selection evolves populations that beats immortal ones (assuming they can arise in the first place - all current "immortals" has a steady influx of genes from various environmental sources). Don't confuse chemical evolution with biological, or make it backward ("life started ... selection at the chemical level has started later").

And the bottleneck for heredity is replication.

As for physics, what are you smoking? The scale of CMBR spatial wavelength is cosmological. I think you mean the wavelengths of the CMB blackbody radiation, which covers a huge range and varies over time. Do you mean the peak wavelength, but why, and why do you think such thermal radiation couples to chemical systems on a hotter Earth? Thermodynamics and chemistry has rejected such effects, heat is heat and CMB is a diminutive source.

And no, QM doesn't "balance" gravity in any meaningful sense here.
1 / 5 (1) Dec 19, 2012
For 'Life' see:

Information transfer is 'inevitable'.
The difference between the labels 'life' and 'non life' is HOW information is transferred. (Not to be confused with how information is transmitted.)

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