chemiosmosis and the origin of life

Learned a new word today: chemiosmosis.

Before Mitchell, everyone assumed that cells got their energy using straightforward chemistry. The universal energy currency of life is a molecule called ATP. Split it and energy is released. ATP powers most of the energy-demanding processes in cells, from building proteins to making muscles move. ATP, in turn, was thought to be generated from food by a series of standard chemical reactions. Mitchell thought otherwise. Life, he argued, is powered not by the kind of chemistry that goes on in a test tube but by a kind of electricity.

The energy from food, he said, is used to pump positively charged hydrogen ions, or protons, through a membrane. As protons accumulate on one side, an electrochemical gradient builds up across the membrane. Given the chance, the protons will flow back across, releasing energy that can be harnessed to assemble ATP molecules. In energy terms, the process is analogous to filling a raised tank with buckets of water, then using the water to drive a waterwheel.

Mitchell dubbed his theory chemiosmosis, and it is not surprising that biologists found it hard to accept. Why would life generate energy in such a complicated and roundabout way, when simple chemical reactions would suffice? It just didn't make sense.

More, much more, at the link about how chemiosmosis might be the key to understanding the origin of life on earth.

Or read the snapshot version: from hydrothermal vents to full-fledged cells in ten increasingly plausible steps.

in the stardust of a comet

Boosting theories that life on Earth was seeded from interstellar bodies, the amino acid glycine has been isolated in comet leavings.

Previously, researchers have found amino acids in space rocks that fell to Earth as meteorites, and tentative evidence for the compounds has been detected in interstellar space. Now, an amino acid called glycine has been definitively traced to an icy comet for the first time.

"It's not necessarily surprising, but it's very satisfying to find it there because it hasn't been observed before," says Jamie Elsila of NASA's Goddard Space Flight Center, lead author of the new study. "It's been looked for [on comets] spectroscopically with telescopes but the content seems so low you can't see it that way."

It's fantastic to finally see the results of research that began in 1998 with the launching of NASA's Stardust mission. Read more about NASA's astrobiology efforts here. Read more about Elsila here.

the earliest critters

Scientists may have discovered traces of the eldest ancestors of contemporary animals: spongy goo fossilized in stone.

The previous oldest animal fossils date from "only" 650 million years ago, although "molecular clocks" based on rates of genetic divergence indicate that animals should have originated about 850 million years ago. The new findings may therefore help solve the problem of the 250 million-year-gap.

Palaeontologists have looked long and hard for traces left by the first multi-celled organisms, fully aware that the soft-bodies might have left very few fossils.

The breakthrough came when Elizabeth Turner, of Laurentian University in Sudbury, Ontario, spotted odd patterns in the rocks of 850-million-year-old limestone reefs in the Mackenzie Mountains of Canada's Northwestern territory, and has spent the last 15 years, with Fritz Neuweiler of University Laval in Quebec, trying to deduce their origin.

Now Turner and Neuweiler, along with David Burdige of Old Dominion University in Virginia, have shown that the patterns match the distinctive textures found in reefs built by sponges.

As all science goes, these findings are tentative, subject to further theorizing. And, as always, read the whole thing.

Miller-Urey experiment resuscitated, with new results

Read the article or watch the video. Exciting news in origin-of-life research, for sure.


Update: PZ has more.

the microbe ate uranium (byproducts)

Another breakthrough in origin-of-life research: a gold bug, but not outta Poe.

Chivian's analysis shows that D. audaxviator gets its energy from the radioactive decay of uranium in the surrounding rocks. It has genes to extract carbon from dissolved carbon dioxide and other genes to fix nitrogen, which comes from the surrounding rocks. Both carbon and nitrogen are essential building blocks for life as we know it, and are used in the building blocks of proteins, amino acids. D. audaxviator has genes to produce all the amino acids it needs.

D. audaxviator can also protect itself from environmental hazards by forming endospores – tough shells that protect its DNA and RNA from drying out, toxic chemicals and from starvation. It has a flagellum to help it navigate.

"One question that has arisen when considering the capacity of other planets to support life is whether organisms can exist independently, without access even to the Sun," says Chivian. "The answer is yes and here's the proof. It's philosophically exciting to know that everything necessary for life can be packed into a single genome."

It's quite probable that the bacterium is over 3 million years old. If it can survive there, who knows what might be living elsewhere.

tweaking the constants

A while back, I linked to an article that, I figured, seriously undermined the Anthropic Principle's logic. Further monkeying with crucial constants reveals that, indeed, it's flawed to presume that we should test for "cosmic fine tuning" by changing only one variable at a time. [sub. req.]

[U of Michigan, Ann Arbor's Fred] Adams started with a simple definition of a star: a massive body held together by its own gravity that is stable, long-lived and generates energy through nuclear processes. Just three constants are involved in the formation of such stars. One is the gravitational constant. The second is alpha, the fine structure constant that determines the strength of interactions between radiation and matter. The third is a composite of constants that determines the reaction rates of nuclear processes.

Adams then cooked up a batch of virtual universes, computing a wide range of values for the three constants, each universe possessing laws of physics unlike our own. The results:

About a quarter of the resulting universes turned out to be populated by energy-generating stars. "You can change alpha or the gravitational constant by a factor of 100 and stars still form," Adams says, suggesting that stars can exist in universes in which at least some fundamental constants are wildly different than in our universe.

The possibility of life-supporting black holes, about as wild as you can get, cosmologically speaking, arose in Adams' simulations. CalTech's Sean Carroll comments:

"I don't know what it would look like or how it would work, but black holes radiate, just like stars do. Why couldn't you have life arise in the 'atmosphere' of a gently radiating black hole?"

Crazy stuff.

Those still clinging to the Anthropic Principle had better dig those fingernails in pretty tight.

today's origin-of-life links

From NewScientist:
A list of some of the hardiest organisms that inhabit inhospitable environments.

A new discovery along those lines: life buried far, far under the rubble of an ancient meteorite impact.

Added: Martian soil: good for turnips?

From PZ Myers:
Learning about life's common ancestor by examining Amphioxus.

From AstroBio.net:
Life's early history on Earth is tough to track down, due to several billion years of volcanic, oceanic, tectonic, and atmospheric changes. So, why not look for Earth ejecta on the moon?

the rise and fall of microbes

Rise: Bacterial co-evolution has might have made you what you are today:

"If animals from an omnivorous background have moved into a more herbivorous lifestyle they have absolutely needed bacterial partners and microbes to allow that to happen," Gordon says.

David Relman, a microbiologist at Stanford University in California agrees that microbes could have played an important part in mammalian evolutionary history.

"It's possible that our microbial makeup has guided and played a major role in defining who we are and what we do, but it could also be the flip side," he says. Gut microbe populations could passively respond to changes in host physiology and diet.

To answer that question, researchers need a better grasp on the factors that determine an animal's gut flora – including genes and diet. To make things even more complex, other studies have shown that gut microbe populations change over the course of months and years.

"It's a daunting set of potential variables, only some of which you can control," Relman says.

Should make for interesting research. In similar news, "If cells could vote, people would be a minority in their own body." We've mentioned this before, but it's worth repeating: you are a superorganism.

Fall:

Life has been found 1.6 kilometres beneath the sea floor, at temperatures reaching 100 °C.

The discovery marks the deepest living cells ever to be found beneath the sea floor. Bacteria have been found deeper underneath the continents, but there they are rare. In comparison, the rocks beneath the sea appear to be teeming with life.

John Parkes, a geobiologist at the University of Cardiff, UK, hopes his team's discovery might one day help find life on other planets. He says it might even redefine what we understand as life, and, bizarrely, what we understand by "age".

Parkes has been hunting for deep life for over 20 years. Recently, he and his colleagues examined samples of a mud core extracted from between 860 metres and 1626 metres beneath the sea floor off the coast of Newfoundland.

It's possible that some of the freshly-discovered prokaryotes could be several million years old--their metabolism is so slow, that they live almost in a sort of permanent hibernation. Parkes figures that the mass of these undersea prokaryotes could equal that of all other life on earth.

organic molecules on a faraway planet

One more step toward discovering an extraterrestrial origin of life, NewScientist reports:

Organic molecules – in the form of methane – have been detected on a planet outside our solar system for the first time. The giant planet lies too close to its parent star for the methane to signal life, but the detection offers hope that astronomers will one day be able to analyse the atmospheres of Earth-like worlds.

Astronomers Mark Swain and Gautam Vasisht of Caltech in Pasadena, US, and Giovanna Tinetti of University College London, UK, used the Hubble Space Telescope to observe the giant planet HD 189733b, which is slightly more massive than Jupiter and lies 63 light years from Earth.

Because the planet crosses the face of its parent star as seen from Earth, some starlight is periodically filtered through the planet's atmosphere, where different chemicals absorb particular wavelengths.

The observations confirm an earlier tentative detection of water vapour and reveal the presence of methane gas.

Certified organic molecules, on the other hand, remain elusive, and rather pricey.

closer and closer to the earliest life

More exciting origin-of-life research, focusing on adenine:

Many ex­pe­ri­ments have shown it: sim­ple mo­le­cules can com­bine chem­ic­ally—out­side of liv­ing things—to form the build­ing blocks of DNA, the key com­po­nent of life. But just how this com­bina­t­ion oc­curs is un­known. Sci­en­tists want to find out, since that might ex­plain how DNA orig­i­nat­ed.

Now, chem­ists have pro­posed what they call the first de­tailed, fea­si­ble ac­count of how one of DNA’s ma­jor build­ing blocks could have aris­en on an ear­ly, life­less Earth. The nec­es­sary in­gre­di­ents: five cy­a­nide molecules, they said.

The answers are tentative and raise further questions--but that's science.

100,000 years on ice, and no freezer burn

Microbes are hardy little creatures, NewScientist reports:

Microbes can survive trapped inside ice crystals, under 3 kilometres of snow, for more than 100,000 years, a new study suggests. The study bolsters the case that life may exist on distant, icy worlds in our own solar system.

Living bacteria have been found in ice cores sampled at depths of 4 kilometres in Antarctica, though some scientists have argued that those microbes were contaminants from the drilling and testing of the samples in labs. And in 2005, researchers revived a bacterium that sat dormant in a frozen pond in Alaska for 32,000 years (see Ice age bacteria brought back to life).

Now, physicist Buford Price and graduate student Robert Rohde, both at University of California in Berkeley, US, have found a mechanism to explain how microbes could survive such extreme conditions.

They say a tiny film of liquid water forms spontaneously around the microbe. Oxygen, hydrogen, methane and many other gases will then diffuse to this film from air bubbles nearby, providing the microbe with sufficient food to survive.

Thus, virtually any microbe can remain alive in solid ice, resisting temperatures down to -55° Celsius and pressures of 300 atmospheres.

Under such harsh conditions, the microbes would not be able to grow and reproduce, but they would still be able to repair any molecular damage, keeping themselves viable for more than a thousand centuries, the team says. "It is not life as we generally think about it," says Rohde. "[They] are just sitting there surviving, hoping that the ice will melt."

And waiting for the next great HBO series to replace The Sopranos.

simulating DNA-like helixes made of dust

Those looking for life in space might have to once again expand the horizons of their search--this time to include plasma-devouring dust helixes.

Like DNA, the dust spirals can store information. They do so in the scaffolding of their bodies, as they have two stable states – one with a large diameter and the other with a small one – so a spiral could carry a series of wide and narrow sections.

The specific order of these sections can be copied from one dust spiral to another, like a genetic code. The researchers aren't sure how it happens, but they think each narrow section of spiral creates a permanent vortex of moving dust outside it. So if another spiral drifts alongside it, that vortex pinches the same length into its narrow state.

The spirals even feed, in a sense, as they need fresh plasma to survive and grow, suggesting they may compete with one another for food. Since they are also capable of passing on their genetic code, then perhaps they could evolve into more complex structures.

But that is very speculative, says Morfill, explaining that the simulation is far too simple to include such complex processes as evolution. "It has a lot of the hallmarks for how we define life at present, but we have not simulated life," Morfill told New Scientist. "To us, they're just a special form of plasma crystal."

Scientists plan to search for real-life analogues within planetary rings.

anions in space

Another advance in astrobiology:

In less than a year, re­search­ers say they have found the first three mol­e­cules in space with neg­a­tive elec­tri­cal charge. Such mol­e­cules have an ex­cess of elec­trons, neg­a­tively-charged sub­a­tom­ic par­t­i­cles.

"This dis­cov­ery con­tin­ues to add to the di­vers­ity and com­plex­ity that is al­ready seen in the chem­is­try of in­ter­stel­lar space," said An­tho­ny J. Remi­jan of the Char­lottes­ville, Va.-based Na­tional Ra­di­o As­tron­o­my Ob­serv­a­to­ry.

"It al­so adds to the num­ber of paths avail­a­ble for mak­ing the com­plex or­gan­ic mol­e­cules," the in­gre­di­ents of life, he added. Such sub­stances are thought to have formed in the same gi­ant clouds that give rise to stars and plan­ets.

Oc­tate­traynyl an­ions, the most recent type discovered, are the largest yet.

get your molecules from a dying star

Another amazing discovery from the world of astrobiology:

"Where we thought molecules could never form, we're finding them. Where we thought molecules could never survive, they're surviving," says Lucy Ziurys, an astronomer at the University of Arizona in Tucson, US.

Using the 10-metre radio dish atop Mount Graham in Arizona, Ziurys and her team searched the extended envelope of gas around VY Canis Majoris, a red hypergiant star estimated to be 25 times the Sun's mass and nearly half a million times the Sun's brightness.

There they found the telltale radio emissions of various compounds, including hydrogen cyanide (HCN), silicon monoxide (SiO), sodium chloride (NaCl) and a molecule, PN, in which a phosphorus atom and a nitrogen atom are bound together....

Because VY Canis Majoris is an oxygen-rich star, it was not expected to harbour so many interesting molecules. Oxygen atoms easily outnumber carbon atoms around such stars and would be expected to take up the available carbon by forming carbon monoxide (CO).

The discovery of molecules such as HCN and a carbon sulphur compound (CS) around VY Canis Majoris suggests that chemical composition can vary greatly within a circumstellar envelope. It also implies that the chemistry that leads to life may be more widespread in the universe and more robust than previous studies have suggested.

In related news:

Achim Tappe of the Harvard-Smithsonian Center for Astrophysics, Cambridge, Mass., used Spitzer's infrared spectrograph instrument to detect abundant amounts of polycyclic aromatic hydrocarbons along the ridge of supernova remnant N132D. The remnant is located 163,000 light-years away in a neighboring galaxy called, the Large Magellanic Cloud.

"The fact that we see polycyclic aromatic hydrocarbons surviving this explosion illustrates their resilience," says Tappe.

These intriguing molecules are comprised of carbon and hydrogen atoms, and have been spotted inside comets, around star-forming regions and planet-forming disks. Since all life on Earth is carbon based, astronomers suspect that some of Earth's original carbon might have come from these molecules - possibly from comets that smacked into the young planet.

Astronomers say there is some evidence that a massive star exploded near our solar system as it was just beginning to form almost 5 billion years ago. If so, the polycyclic aromatic hydrocarbons that survived that blast might have helped seed life on our planet.

The one thing Jurassic Park got right: life will find a way.

life without water?

The Anthropic Principle takes another whack. [sub. req.]

As a cradle for life's basic biochemistry, water is without a doubt an amazing molecule, but not everyone believes it is unique. "Whether water is necessary for life is, I think, very dubious," says Christopher McKay, a planetary scientist at NASA Ames Research Center in Moffett Field, California. Astrobiologist Dirk Schulze-Makuch at Washington State University in Pullman agrees. He thinks that Earth life's reliance on water is coincidental. "Life on Earth learned to work with water because it's the only liquid that is really abundant. I don't think there's anything magic about it," he says. On a warmer planet, oceans of sulphuric acid might do the job, or on a cooler planet, oceans of methanol, ammonia, or even methane.

While the European and US space agencies methodically hunt for Earth-like, water-based life on Mars, evidence is emerging elsewhere to suggest that life doesn't need water. Engineers who harness enzymes in the manufacture of industrial chemicals are seeing at first-hand that these essential biological catalysts can also function in hydrocarbon fluids such as hexane, indicating water might not be as essential as we thought.

At the same time, many point out that not all of water's properties are unique. A handful of other liquids, such as hydrogen fluoride, sulphuric acid, ammonia and even hydrogen peroxide share water's ability to carry around hydrogen ions which catalyse chemical reactions that are crucial for cells to digest nutrients - and all have been proposed as liquids for life. For example, people have suggested that hydrogen peroxide-based microbes inhabit the Martian soil (see "Life on Mars after all?"), and that the clouds of Venus may harbour sulphuric acid aliens (see "Acid drinkers"). Life in non-water solvents might just be possible, at least from the standpoint of getting basic cellular machinery such as enzymes to function....

So where would be the most likely place in our solar system to look for genuinely alien biochemistries? Both McKay and Schulze-Makuch have proposed that microbes on the surface of Saturn's moon Titan might consume a gas called ethene that is produced high in the atmosphere by sunlight, and release methane as a waste product. These microbes' cells would be filled with liquid methane or ethane. Before we send a probe to Titan to test directly for life, most people think another mission will be needed to improve our understanding of the non-biological chemical reactions that happen there - so we can distinguish them from genuine signs of life. "If there's life on Titan, it's probably quite exotic, quite different from life on Earth," says Schulze-Makuch. "We would have to refine our understanding, so we know what to look for."

Suffice it to say that the non-water hypothesis is tentative, and we'll likely not see experimental results in this decade, or observational results within our lifetime. Theoretically, though, the size of the universe and the fresh list of potential requisite traits means that our current estimates of habitability need serious revision.

Scientific American takes advantage of interactive publishing

Missed this somehow: last month, Scientific American put up an advance copy of an article, asking readers to fire back with questions or comments. Stage two is now available, as Robert Shapiro appends his article with further info and sources.

I hope more science publications try this.

what came before RNA? recent origin-of-life research heads in thermodynamic directions

In a recent article in Scientific American, Robert Shapiro explains why ">the prospects for "RNA World" OOL theory are bleak. You can be sure creationist hacks are salivating over this quote:

There is no reason to presume than an indifferent nature would not combine units at random, producing an immense variety of hybrid short, terminated chains, rather than the much longer one of uniform backbone geometry needed to support replicator and catalytic functions. Probability calculations could be made, but I prefer a variation on a much-used analogy. Picture a gorilla (very long arms are needed) at an immense keyboard connected to a word processor. The keyboard contains not only the symbols used in English and European languages but also a huge excess drawn from every other known language and all of the symbol sets stored in a typical computer. The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne. With similar considerations in mind Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth "would have been a near miracle." I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above.

Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life....

If that were the conclusion, origin-of-life researchers would have reason to throw down their beakers in despair.

But the end of one hypothesis is just the beginning of another:

Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention.

Fortunately, an alternative group of theories that can employ these materials has existed for decades. The theories employ a thermodynamic rather than a genetic definition of life, under a scheme put forth by Carl Sagan in the Encyclopedia Britannica: A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive. This small-molecule approach is rooted in the ideas of the Soviet biologist Alexander Oparin, and current notable spokesmen include de Duve, Freeman Dyson of the Institute for Advanced Study, Stuart Kauffman of the Santa Fe Institute, Doron Lancet of the Weizmann Institute, Harold Morowitz of George Mason University and the independent researcher Günter Wächtershäuser. I estimate that about a third of the chemists involved in the study of the origin of life subscribe to theories based on this idea....

Systems of the type I have described usually have been classified under the heading "metabolism first," which implies that they do not contain a mechanism for heredity. In other words, they contain no obvious molecule or structure that allows the information stored in them (their heredity) to be duplicated and passed on to their descendants. However a collection of small items holds the same information as a list that describes the items. For example, my wife gives me a shopping list for the supermarket; the collection of grocery items that I return with contains the same information as the list. Doron Lancet has given the name "compositional genome" to heredity stored in small molecules, rather than a list such as DNA or RNA.

The small molecule approach to the origin of life makes several demands upon nature (a compartment, an external energy supply, a driver reaction coupled to that supply, and the existence of a chemical network that contains that reaction). These requirements are general in nature, however, and are immensely more probable than the elaborate multi-step pathways needed to form a molecule that can function as a replicator.

Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle. The greatest amount of new data has perhaps come from Günter Wächtershäuser and his colleagues at the Technische Universität München. They have demonstrated portions of a cycle involving the combination and separation of amino acids, in the presence of metal sulfide catalysts. The energetic driving force for the transformations is supplied by the oxidation of carbon monoxide to carbon dioxide. They have not yet demonstrated the operation of a complete cycle or its ability to sustain itself and undergo further evolution. A "smoking gun" experiment displaying those three features is needed to establish the validity of the small molecule approach.

That's the difference between science and pseudoscience: science requires experimental validity. Creationists have harped for years on the low probability of life's spontaneous emergence in the universe. Meanwhile, scientists have been fashioning, testing, junking, redeveloping, and once again fashioning more and more plausible scenarios, not content to rest in comfortable ignorance.

world's smallest microbes?

The search for life outside the universe may have widened again.

Four million of a newly discovered microbe — assuming the discovery, reported yesterday in the journal Science, is confirmed — could fit into the period at the end of this sentence.

Scientists found the microbes living in a remarkably inhospitable environment, drainage water as caustic as battery acid from a mine in Northern California. The microbes, members of an ancient family of organisms known as archaea, formed a pink scum on green pools of hot mine water laden with toxic metals, including arsenic.

Life crops up where you least expect it, with the persistence of unwanted hair.

[Link via Helmut]

bacteria that feast on radiation's fruits

The search parameters for life on other planets just widened:

Uranium and other radioactive elements in the rock emit radiation that shatters water molecules, producing high-energy hydrogen gas that is able to cleave chemical bonds.

The bacteria exploit this hydrogen gas to turn sulphate (SO4) molecules from the rock into hydrogen sulphide (HS). It is the energy-trapping equivalent of photosynthesis. The energy of radiation, which makes hydrogen gas energetic enough to form these bonds, replaces the energy of the Sun.

The bacteria are probably descended from light-dependent strains, which means that certain initial conditions still apply. However, this means that planets that appear cold and dead, a billion light-years distant, may in fact teem with life.

those sinister amino acids

A couple months ago I blogged about a putative advance in the study of chirality, back when Meir Shinitzky figured that water's properties might explain why amino acids are left-handed. I wrote, "The problem isn't yet solved to everyone's satisfaction, but at least demonstrates that saying 'Science will never / can never' is often a bet against the odds."

Now, in an important new finding that builds on Shinitzky's work,

Donna Blackmond at Imperial College London and colleagues dissolved a mixture of solid L and D versions of the amino acid serine in water. They found that a small difference in the initial proportion of one version gets amplified in the resulting solution. So a 100:1 mixture of L- and D-serine produces a solution made up almost entirely of L-serine, but so does a 100:99 mixture (Nature, vol 441, p 621).

"It doesn't matter what proportions of solid amino acids you throw in, you always get exactly the same proportions in solution," says Blackmond, whose team has found a similar effect with other amino acids. She says she is surprised that no one noticed the effect before.

I'll wager a left-handed shovel that the origin of chirality will be explained to (pretty much) everybody's satisfaction within the next decade. And I, unlike certain blowhards we all know and love, keep my wagers.