“Weird Life”: The Story of the Cell
“The synthesis of life, should it ever occur, will not be the sensational discovery which we usually associate with the idea. If we accept the theory of evolution, then the first dawn of the synthesis of life must consist in the production of forms intermediate between the inorganic and the organic world, forms which possess only some of the rudimentary attributes of life, to which other attributes will be slowly added in the course of development by the evolutionary action of the environment.” - Stephane Leduc, 1911
In July 2007, a group of scientists associated with the American Research Council issued a report about something they termed “weird life.” Weird life, they said, could be life in a form that we have never seen before - an organism may not depend on water, for example, or it may have a completely different, non-nucleic-acid based system of heredity and still be alive. Their definition of weird life was vague, and not by accident: One of the primary challenges in the discussion of life, both on earth and elsewhere in the universe, is that life itself is a very difficult thing to parameterise. As David Greer, a professor of physics at New York University, says, “There is no mathematically rigorous definition of life.” Our determination of life is based entirely on our own human experience, and thus its working definition is less a set of functional rules for classification and more a set of somewhat ambiguous statements designed to organise the unknown. The precise problem with trying to organise the unknown, of course, is that nothing is known about it; but without a reconcilable definition of life - or “weird life”, as the case may be - we don’t even know where to start looking.
The key, I think, to this almost certainly inaccurate (and definitely not mathematically rigorous) but working definition is to explore how life came about in the first place. This serves two purposes: First, the definition of life could arguably be based on the most basic conditions necessary for it to occur, and second, life in its most rudimentary forms are more likely to be homogenous across biological systems (however more complex or different from our own) than the large-scale plants and animals we traditionally associate with life. In addition, the makeshift definition should be written as a set of provable postulates, and should be sufficiently inclusive to potentially apply to all forms of aptly labeled “weird life” without being overly promiscuous, so to speak.
The Primordial Soup’s Gone Off
Ever since Stanley Miller’s infamous experiment in 1953, the long-time leading hypothesis into the origin of life was his theory, built around the reducing atmospheric gases of early earth and electric charge passing through them in the form of lightning. Miller’s experiment, which has been replicated, successfully showed that shooting a spark through reducing gases in a laboratory beaker produces biomolecules - in Miller’s case, approximately 10 amino acids and several nucleic acid precursors, although others who have repeated the experiment have had rather more success. The experiment illustrates clearly that life could have begun this way.
Of course, the origin of life is still a black box; in reality any number of plausible hypotheses could be correct. However, for me there are several unaddressed issues in Miller’s experiment that make me skeptical that it is the whole story behind the evolution of us. The primary issue is simply time; the earth is only 4.5 billion years old, and the oldest microfossils of early cell-like structures that have been found date back 3.5 billion years. While a billion years seems like - well, a billion years to us, it’s actually quite quick on an evolutionary timescale. To me, this means that life didn’t simply come down to a lucky lightning strike - it indicates that there was a driving force behind its development that pushed it forward faster.
In 1993, a different theory for the origin of life - termed the hydrothermal vent idea - came into prevalence. It suggested that instead of a collection of atoms in the early ocean, life came out of deep-sea hydrothermal vents. There is much compelling evidence for this idea; two of the most compelling bits, I think, are the existence of an energy disequilibrium and the interconnected micropores found on the vents’ surface.
The ocean, even on the early earth, was a fairly stagnant place in terms of energy gradients; lightning strikes could perhaps have caused them sporadically, but in different locations and to varying degrees with very little continuity. Hydrothermal vents, on the other hand, are rich in energy disequilibrium, boasting temperature, pH, and redox gradients.
So why are energy gradients so important? Because for cells, harnessing energy as ion gradients is about as universal as the genetic code. A new paper recently published in Cell postulates that tiny micropores found on the surface of deep-sea vents - conveniently approximately the diameter of a cell - could have been the starting point of life on earth. In modern cells, about 75% of a cell’s ATP budget - or biological energy - goes into making proteins; conversely, ATP is replenished by proteins that harness chemiosmotic gradients. The paper postulates that the energy disequilibrium provided by hydrothermal vents - specifically, that sustained disequilibrium at a submarine hydrothermal vent interfacing with ocean water - generates conditions that thermodynamically favour the formation of life’s building blocks, particularly amino acids, in the presence of hydrogen gas, carbon dioxide, and ammonium. If a leaky membrane built of lipid precursors accumulated near a vent, the budding system would have a ready-made metabolism by exploiting the pre-existing chemiosmotic gradient. Once enough precursors accumulated, and the “metabolism tap” was shut off due to the newly formed “membrane“‘s impermeability, natural selection would strongly favour cells with simple antiporters that could continue to exploit the ion gradient.
Defining Life from Vents
If, for the sake of argument, the thermal vent hypothesis is found to be the way things actually were, what then? What about life? Defining life by the characteristics of the first cell does not appeal to me; this leads to a definition of characteristics that are shared because they originate from a common ancestor, and not because they are actually fundamental to life. However, the hydrothermal vent hypothesis does, I think, enhance our understanding of what is needed for life, at least on this planet, and based upon the need for a biochemical gradient for protein production and the necessity of a lineage to exploit progress made in the previous generation, I would define life as:
- A physical compartment across the walls of which energy can be generated and utilised for biochemical reactions, and;
- one that possesses a material of heredity that may be passed to the next generation.
It’s not a particularly restrictive definition, nor is it likely broadly accurate. However, the fact remains that there are many definitions of life; few widely agreed upon, and certainly none reasonably consented to in their entirety without special cases. Considering what was necessary for the first cell to form is as valid a method of organising the unknown as any other, and perhaps, one day, we’ll be able to find a distinctly new organism somewhere in the universe, one that shifts our entire paradigm on biochemistry, heredity, and what it means to fundamentally be alive. Until then, I think, formal and constructive definitions will elude us, and “weird life” will continue to be - well, weird.
An Afterthought: The Interesting Case of Protocells
In his TedX talk, Martin Hanczyc outlined a very similar definition of life to the one I derived from the assumed origin of life inside thermal vents. It can be reasonably summarised in three words:
- Body;
- Metabolism;
- Heredity.
He works extensively with oil and water systems, designing in vitro protocells. He also works with tar systems to simulate the stuff of the early universe, like those in the images at the top of this post; his protocells are comprised of single-digit numbers of chemicals, and yet are able to locate food, respond to one another within an environment, and even divide and hybridise into wholly new organisms with new functional characteristics.
So are these protocells alive? Martin Hanczyc believes that nothing can be considered “alive” in a black-and-white way; rather, these protocells fall somewhere in the range of an intermediate between the inorganic and organic world, and while they possess some attributes necessary for life they simply fall on a continuum along with humankind and this desk. A video of his TedX talk, in which he explains further, can be found here.
Due to its length and their quantity, references in this post are cited using links where they are most relevant. Most of the information used comes from a new paper in Cell on the Origin of Membrane Bioenergetics (Martin and Lane, 2012), and Martin Hancycz’s TedX talk. For another take on Martin Hancycz’s work, see this post here.
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DNA: Celebrate the unknowns | Philip Ball
On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level, suggests Philip Ball.
This week’s diamond jubilee of the discovery of DNA’s molecular structure rightly celebrates how Francis Crick, James Watson and their collaborators launched the ‘genomic age’ by revealing how hereditary information is encoded in the double helix. Yet the conventional narrative — in which their 1953 Nature paper led inexorably to the Human Genome Project and the dawn of personalized medicine — is as misleading as the popular narrative of gene function itself, in which the DNA sequence is translated into proteins and ultimately into an organism’s observable characteristics, or phenotype.
Sixty years on, the very definition of ‘gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level.
That sounds to me like an extraordinarily exciting state of affairs, comparable perhaps to the disruptive discovery in cosmology in 1998 that the expansion of the Universe is accelerating rather than decelerating, as astronomers had believed since the late 1920s. Yet, while specialists debate what the latest findings mean, the rhetoric of popular discussions of DNA, genomics and evolution remains largely unchanged, and the public continues to be fed assurances that DNA is as solipsistic a blueprint as ever.
[Read more]](http://24.media.tumblr.com/9ab3ef1a55a301b505c568b3b66c0fa7/tumblr_mltd46Lm8x1qjofuoo1_1280.jpg)
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Land creatures might not have come from the sea
Cartoonists have found many clever ways to depict the conventional wisdom that complex life evolved in the sea and then crawled up onto land. But a provocative new study suggests that the procession might be drawn in the wrong direction. The earliest large life forms may have appeared on land long before the oceans filled with creatures that swam and crawled and burrowed in the mud.
This story is told from fossils that date from before an extraordinary period in Earth history, called the Cambrian explosion, about 530 million years ago. That’s when complex life suddenly burst forth and filled the seas with a panoply of life forms.
Paleontologists have found fossil evidence for a scattering of fossil animals that predate that historic moment. These mysterious organisms are called Ediacarans. Many scientists have assumed Ediacarans were predecessors of jellyfish, worms and other invertebrates. But Greg Retallack at the University of Oregon says he always had his doubts.
Retallack has been building the case that Ediacarans weren’t in fact animals, but actually more like fungi or lichens. And if that idea weren’t enough of a departure from standard theory, he now argues in a paper in the journal Nature that Ediacarans weren’t even living in the sea, as everyone has assumed. He says he has reanalyzed some Australian rock where they’re found and concluded that it’s ancient soil, not marine mud.
These early life forms were landlubbers.
“What I’m saying for the Ediacaran is that the big [life] forms were on land and life was actually quite a bit simpler in the ocean,” Retallack says.
So does that suggest life evolved on land and moved into the ocean? “Yes, in a nutshell,” he says.
Paul Knauth at Arizona State University has been pondering this same possibility. “I don’t have any problem with early evolution being primarily on land,” says Knauth, a professor in the School of Earth and Space Exploration at Arizona State University. “I think you can make a pretty good argument for that, and that it came into the sea later. It’s kind of a radical idea, but the fact is we don’t know.”
Knauth says it could help explain why the Cambrian explosion appears to be so rapid. It’s possible these many life forms gradually evolved on the land and then made a quick dash to the sea.
And, he adds, “that means that the Earth was not a barren land surface until about 500 million years ago, as a lot of people have speculated.”
The new analysis of the Ediacaran fossils is at least a hint that this could be right. But of course if you’re a scientist making an extraordinary claim, you need to back it up with extraordinary evidence.
“To me the evidence is not a slam-dunk,” says Shuhai Xiao, at Virginia Tech. He argues, among other things, that the same Ediacaran species found in what is arguably soil is also found in deposits that he says were ocean sediments.
That would imply that the same species would be able to live both on dry land and under a salty ocean. Xiao finds that unlikely. “It’s pretty hard for the same species to be able to live in both environments.”
So he is not convinced that Retallack is really looking at fossils in terrestrial soil. And so begins a sharp academic debate.
Xiao is far from alone in his skepticism. The current ideas have many defenders. Retallack seems to relish the controversy. He knows what he’s in for.
“The idea that Ediacaran fossils were marine invertebrates is so deeply entrenched, it’s in all the textbooks,” he says. When someone (namely him) comes along and says that’s not so, “it’s going to be treated like a death in the family. It’s going to go through all the phases of grief, starting with denial.”
It remains to be seen whether the story ends with acceptance of Retallack’s provocative proposal.](http://25.media.tumblr.com/5296bf30ddc315227ad58780cb9e7a15/tumblr_meyzrwmB7u1qcbrp0o1_1280.jpg)
