Friday, September 9, 2016

Hello? Earth Calling . . . PART 6

For Hello? Earth Calling . . . PART 1 CLICK HERE
For Hello? Earth Calling . . . PART 2 CLICK HERE
For Hello? Earth Calling . . . PART 3 CLICK HERE
For Hello? Earth Calling . . . PART 4 CLICK HERE
For Hello? Earth Calling . . . PART 5 CLICK HERE 

(This is the final post in this series.)

What's Next in Exoplanet Hunting?

We might never be able to set foot on an exoplanet ourselves but don't let that get you down. While sci-fi fantasy is always tantalizing, our scientific reality is evolving so fast that I think we can soon reach the real answer to our most basic question, "Are we alone?" We might soon be able to "see" an exoplanet directly, and learn much about it. NASA's James Webb Telescope (see below) is set to launch in 2018.

Illustration of the James Webb Space Telescope, as of 2009. Launch date is expected to be 2018. Credit NASA
Its main mission is to study the formation of distant stars and galaxies but it is also designed to directly observe exoplanets and study their atmospheres for biosignatures of life. It will be super-stable with optical components that distort the image less than a nanometer, about the size of a few atoms. It will be equipped with a honeycomb-like multi-piece mirror that is about four times larger than Hubble's mirror (Hubble Telescope is shown below).

Hubble Space Telescope departing from the space shuttle Atlantis in 1990. It is still in operation. Credit NASA
James Webb telescope will observe in near-infrared and no doubt it will deliver good exoplanet data. But its development began in 2002, and since then exoplanet astronomy has literally exploded. New technologies specific to viewing exoplanets is what we will need very soon. The history of exoplanet exploration, though short, is interesting. It started out with much speculation and many false discoveries. The first exoplanet (gamma Cephei b) was detected in 1988 by Canadian astronomers Bruce Campbell, G.A.H Walker and Stephenson Yang at the University of Victoria. This planet, a huge gas giant 1.6 times larger than Jupiter, was at the limit of detection then so the discoverers and other astronomers remained skeptical of it for years (solid confirmation of it didn't come until 2002). Some astronomers consider this team to be the true pioneers of exoplanet exploration but if you look you will notice that it is downplayed even on Wikipedia (and fair enough - they did retract their discovery). The story of their discovery, well told in this Globe and Mail article, is an interesting one full of self-doubt and heartbreak. I think it is evidence that we Canadians need to toot our own horn a bit more.

After that other confirmations of exoplanets trickled in. As astronomers began to turn their attention to exoplanets, indirect detection methods improved, and the floodgates opened. Now garnering much interest from many scientific fields and excitement from everyone around the world, scientists and engineers are already at work on ambitious next-generation space telescopes such as (NASA's) HabEx. These telescopes will be devoted to direct exoplanet imaging. They aim to achieve an optical stability in the picometer range, less than the diameter of an atom. They also plan to use even larger mirrors and observe across the visual, near-infrared and ultraviolet spectra, which will offer even more detailed exoplanet surface/atmospheric data. It might take up to 30 years before one of these telescopes is a reality, however. A mission needs to be finalized and the technology required has to be developed first.

HabEx (Habitable Exoplanet Imaging Mission) would allow us to directly observe exoplanets within about a 30 light-year radius from Earth. Another NASA mission just initiated and in concept stage is the Large Ultraviolet/Optical/Infrared(Luvoir) Surveyor, which is an even more ambitious telescope with a larger mirror. Either mission will provide groundbreaking new data by directly imaging exoplanets with incredible precision across different spectra for the first time. Direct imaging, through the James Webb telescope coming soon, and then hopefully to be followed up with one of these next-generation telescopes, is the only way to really know if a planet is potentially habitable. The light absorbed by its atmosphere must be thoroughly analyzed to know what it is composed of, what the climate and weather are like, whether the surface is protected from radiation and temperature extremes, and whether liquid water is likely to be present. Besides determining whether a planet is potentially habitable, these missions have the ultimate goal of discovering chemical evidence for extraterrestrial life.

Still in conceptual stage, HabEx will be a large space telescope that will focus first on planets that are the right distance from their stars to have liquid surface water. I suspect Proxima b will be at the top of the list. The ability to directly image this tiny faint distant planet in superb detail will be amazing.

Even with this most advanced technology, astronomers won't be able to see a round defined planet image. Instead they will see an image that is less than one pixel. That might not sound impressive but the information in that pixel is astounding. That tiny dot can be analyzed as an absorption spectrum across various wavelengths in the visible, near-infrared and UV spectra. This EM radiation is starlight that passes through the exoplanet's atmosphere twice. It is absorbed by the atmosphere and then reflected from the planet back out into space and to the telescope. The absorption bands in the spectra will tell the astronomers which elements are present in the exoplanet's atmosphere and possibly on its surface as well. Those signatures will give clues to the planet's surface temperature and pressure, overall habitability, and even signs of life that might be present if atmospheric oxygen, ozone or methane is found.

The real challenge for this technology will not be trying to capture the planet's faint image. The Hubble Space Telescope can capture images even fainter. The problem is that planets are always right next to very bright stars. As astronomer Scott Gaudi explains, there is a common analogy used to explain how much brighter stars are than their planets: its like trying to see a firefly against a searchlight, except the firefly is a thousand times fainter. The James Webb telescope will be outfitted with coronagraphs attached to it. The coronagraph is an established technology that has been used since the 1930's to block out the Sun's central disk so that we can view its coronasphere. A coronagraph works but not perfectly. HAbEx will go one step further by using two technologies. It will have a star shade as well, which is unfurled in front of the telescope and which must be perfectly matched to the star and the telescope. Watch this NASA/JPL video of how this giant sun-flower shaped shade will unfurl in space.

This star shade will be a new technology. Coronagraphs will be used while the telescope scans for suitable planets and the star shade could be unfurled for much better starlight blockage and more in-depth imaging once a candidate is found. HabEx (or the Luvoir Surveyor) could be online within a few decades. When it is, we will have not just a growing list of established exoplanets to mull over but we will obtain unique descriptions of them as well, something to really pique our imaginations! It will be very interesting to be able to directly image Proxima b, for example, and see what kind of atmosphere, if any, this rocky planet has. The question of whether it has liquid surface water might be answered as well. Meanwhile, there is a tantalizing chance that we might not have to wait decades to know this answer. Astronomers speculate that there is a 1.5 % chance that Proxima b transits in front of its star from Earth's perspective. If it does, we might have more information about it even sooner. Astronomers might be able to discern some data about its atmosphere by comparing chemical analysis of the absorption spectrum of Proxima Centauri during transit and when the planet is away from the star.

If and when HabEx, or a similar telescope, offers promising data that doesn't rule out carbon-based life on Proxima b or another nearby Earth-like planet, I suspect projects like StarChip will follow, sending a probe there to investigate further. All of this is still decades away but it is tantalizingly feasible, and we should then have our best chance yet to find solid evidence for extraterrestrial life in our universe.

Wednesday, September 7, 2016

Hello? Earth Calling . . . PART 5

For Hello? Earth Calling . . . PART 1 CLICK HERE
For Hello? Earth Calling . . . PART 2 CLICK HERE
For Hello? Earth Calling . . . PART 3 CLICK HERE
For Hello? Earth Calling . . . PART 4 CLICK HERE

The Appearance of The First Cell

It is not too far of a theoretical jump from the protein/RNA co-evolution explored in the previous article to a circular self-replicating single-stranded RNA sequence a few hundred nucleotides long. This is, in essence, a viroid in our modern ecosystem. But it is not a cell and according to most experts it is not alive. Life makes its indisputable appearance when the first cells appear on Earth. Biochemical activity is now confined and protected from the outside elements by a membrane and/or cell wall. The first simple cells would have evolved in a world where viroids (open genetic material) and virus-like entities (genetic material enclosed in a protein coat) exchanged genetic material between themselves and between the first simple cells to evolve, such as archaea and bacteria. This process is called lateral gene transfer and it could account for the acquisition of new biochemical pathways in microbes. The opportunity to acquire various new defensive chemical arsenals might also have allowed these first simple cells to survive the rapidly changing harsh conditions prevalent on our young planet at the time.

The first simple cell membrane might have been a simple bilayer phospholipid vesicle, a hollow spherical shell structure. Chemical pathways responsible for the pre-biotic formation of phospholipids are fairly well understood. When phospholipids (which have hydrophobic or water-hating tails) are placed in water they spontaneously form vesicles where the tails face inward. The gradual evolution of a more complex cell membrane (equipped with channels and cell pumps) and, for some cells, an even more protective cell wall would follow. As archaea and bacteria make their first appearance, Benal's third stage of evolution toward life - from complex biomolecules, like proteins and RNA, to cells - would be achieved. Modern archaea micro-organisms such as the simple unicellular organisms that live around hydrothermal vents and provide part of the food chain base there, might resemble what the first forms of life on Earth looked like. Archaea have the simplest life plan on this planet. They look like bacteria but they are biochemically very different. The chemistry of their bilayer phospholipid membranes is unique. It contains ether bonds that are more chemically resistant and heat-stable than those in either bacterial or eukaryotic cells. Eukaryotic cells are the kind of cells that make us up – with the exception of the extensive microbial flora in our guts, which consist of bacteria, fungi and archaea. Our relationship with unicellular life is even more intimate and intermingled than hosting microbes in our guts. Extensive evidence suggests that genetic vestiges of ancient unicellular microbes are present in each and every eukaryotic cell in our bodies as well. Our cells contain a complex mosaic of genetic material that was obtained by genetic exchanges between ancient eukaryotic micro-organisms, bacteria and archaea. In addition to lateral gene transfer, ancient cells also likely went one step further by simply engulfing other cells and eventually utilizing their unique cellular machinery as organelles. This evolutionary process, called endosymbiosis, may be responsible for the appearance of the first (organelle-containing) eukaryotic micro-organism. Symbiogenesis is the theory that various organelles inside our eukaryotic cells originated from symbiotic (cooperative) relationships between different strains of ancient archaea and bacteria.  There is strong evidence that mitochondria, the "powerhouses" of our cells where ATP is produced, are of bacterial origin. Those ancient bacteria were likely engulfed and incorporated into a eukaryotic predecessor.

Tough Intrepid Archaea

Archaea are especially interesting from a life origin point of view because they are the most likely candidates to handle the extreme conditions on our young planet. Tough ether membrane bonds explain why many archaea are extremophiles, able to live in environments far too harsh for other organisms. Most archaea also possess a unique protein cell wall, which makes them even tougher and which further differentiates them from bacteria. Archaea possess genes and metabolic pathways that closely resemble those of eukaryotes (again suggesting that eukaryotes borrowed these useful traits from archaea) but, unlike eukaryotes and like bacteria, archaea don't have any internal structure such as organelles. A single circular strand of DNA and a few independent DNA pieces called plasmids float inside an amorphous cytoplasm. DNA transfer between cells is common and viruses can infect them as well. These sources of new DNA promote rapid evolution in times of hardship, and make ancient symbiotic relationships easy to visualize. The wide variety of chemical reactions that take place inside these tiny cells is really what sets them apart and this is what ultimately made them so wildly successful, allowing them to inhabit virtually every possible location on Earth and is what allowed this life domain to exist longer than any known living organism. This chemical variety also enables archaea to utilize many different sources of energy. This makes them a prime candidate to look for on other planets and moons where a carbon-based biochemistry could also evolve.

Archaea's unique biochemistry suggests that these organisms evolved independently from bacteria, even though they share the same basic genetic structure – a single circular strand of DNA and possibly plasmids as well. The shared structure of circular DNA means that the origin of DNA probably predates the separation of archaea and bacteria into two significantly different evolutionary domains. Chemical fossils of archaea's unique lipids were found in some of Earth's oldest known sedimentary rock in Greenland, which is dated to 3.8 billion years old. This supports increasing evidence that archaea was Earth's first living organism. Archaea might also be responsible for 4.1 billion year old carbon isotope chemical fossils indicating a life process, mentioned in a previous article in this series. However, this is evidence only for carbon-based life, not for any specific life domain.

Archaea, Bacteria and Eukaryotes: A Rich Tapestry of Earth Biochemistry

While archaea stands out as being the best candidate for surviving deep underground when Earth's surface was far too hot and violent for life, aggregates of both modern archaea and modern bacteria behave in additional ways that make them both ultimate survivors. They can transfer genes laterally among one another and they can undergo recombination (gene mixing) at rates far higher than more complex eukaryotic unicellular organisms can. One can guess, with so much genetic variation available, that these organisms could adapt remarkably well and quickly to the dramatically ever-changing conditions on early Earth, especially on the surface. As conditions moderated over millions of years, variants that could utilize the Sun's ultraviolet light for energy evolved, leading eventually to the first simple photosynthetic biochemical pathways, probably in cyanobacteria. Oxygen, the waste gas of photosynthesis, oxidized iron in rock and was absorbed by organic material. Eventually, it built up in the atmosphere. Toxic to anaerobes (which includes many archaea and bacteria), atmospheric oxygenation not only kicked off one of Earth's most significant extinction events, it reacted with atmospheric methane, a potent greenhouse gas, triggering the longest global glaciation period in Earth's history. Despite the catastrophe, life persisted and aerobic organisms (those that require oxygen to live) evolved. Oxygen made it energetically possible for complex multicellular highly mobile organisms such as us to evolve. The electrochemical transport chain of cellular espiration in our cells uses oxygen to metabolize molecules such as high-energy sugars, a process which yields more energy than fermentation or anaerobic respiration. The downside of oxygen-based metabolism is the oxidative stress placed on cells. Oxygen is a very reactive molecule so peroxides and free radicals, which damage proteins and DNA, build up in cells. Cells have evolved various defense mechanisms to eliminate the destructive molecules and DNA and proteins are constantly repaired, at some metabolic cost (this is one reason why we age and die).

Obtaining Energy: Survivors Versus Specialists

Earth's biosphere boasts three different methods for carbon-based organisms to obtain energy (cellular respiration), a key and universal requirement of life: anaerobic respiration, fermentation and aerobic respiration. Each has its own advantages and disadvantages, and all three are required for complex organisms like us to survive. Many unicellular fungi (yeasts) and bacteria utilize the simple process of fermentation to obtain energy. There is no complex electrochemical gradient involved. The simplest reactions turn sugars into alcohols. The production of bread, beer, wine and cheese all require fermentation. Ruminants such as cattle, goats and deer have evolved long guts full of bacteria optimized to ferment the otherwise indigestible cellulose in grasses, bark and twigs.

Fermentation also functions as a "plan B" in the metabolism of some of our mammalian tissues. For example, our muscle cells turn to fermentation when they are not getting enough oxygen to function, as during a long strenuous workout when glucose stored in the muscle cells is used up. Fermentation produces lactic acid as a cellular waste product and that makes our muscles feel sore and stiff afterward. Our bodies are specialized for optimal performance over a narrow range of conditions, such as temperature, food, and the right mixture of gases to breathe. This energy efficiency has allowed our large curious energy-draining brains to evolve. Microbes such as archaea trade efficiency for survivability under great and unpredictable environmental stresses. For example, bacteria and archaea survived for millions of years tucked away in areas devoid of oxygen while Earth's surface remained frozen solid. These organisms, though tough and versatile, have a much less efficient electrochemical gradient than oxygen-using aerobes. In the anaerobic electrochemical transport chain, less oxidizing substances such as sulphates, nitrates and sulphur are used instead of oxygen. Less oxidation = less available metabolic energy. On a very stable planetary environment complex organisms like us could excel but in unstable conditions, microbes will likely win the life game. These differences on Earth offer clues to what kinds of life we could expect to detect on various exoplanets based on their geology and climate.

Unique Geological History = Unique Planetary Biosphere

Simple unicellular organisms, though not winners in the energy game, are winners at long-term survival. Dwelling in soil and under water, they make life for multicellular organisms such as us possible. They are key drivers of the carbon and nitrogen cycles, and they break down dead organic matter and remove heavy metals from solution in water. Life evolved under a great variety of environmental pressures, creating a great range of biochemical adaptations. This rich variety is what our complex modern biosphere is based upon. How likely is it that such a variety of unicellular life evolved under harsh and rapidly changing conditions on another world? A planet's unique biochemical variety might depend on the changing conditions in which it evolved geologically. Is a wide variety of unicellular life necessary for more complex multicellular life, intelligent technology-bearing life like us, to evolve? How many worlds have life that is restricted to a simple palette of a few different but tough unicellular plans?

Unicellular Life Might Be Plentiful In the Universe

Although knowledge about our evolutionary progression from pre-life chemistry to simple unicellular life is not yet seamless, research in many areas is beginning to fit enough pieces on the table to glimpse what life's beginnings might look like. Any of the three carbon-based biochemical energy pathways described above (and more) could evolve on other worlds if a variety of organic molecules are present along with liquid water and available energy. By looking closely at the evolution of archaea and bacteria on Earth, we get the sense that at least simple unicellular carbon-based life could evolve even in very different and very hostile environments.

The origin of proteins, RNA and DNA explored in the previous article in this series does not mean that other completely unique kinds of biochemistry couldn't develop into possibly very complex living organisms on other planets. It only means that Earth's general biochemistry is the one that won out over time here. Exotic biochemistries might exist on exoplanets, perhaps under temperature or pressure extremes not encountered on Earth, utilizing biological solvents other than water and deriving energy from a star unlike the Sun. However, based on what we know about Earth's history, archaea-like carbon-based life, and life evolved from archaea-like ancestors seems to be a good bet, at least on planets with liquid water. One can argue that an archaea-like last universal ancestor evolved into our unique complex multicellular life as a response to Earth's unique geological evolution. Who knows how a similar unicellular ancestor might evolve on an exoplanet where geological evolution veered off in another direction?

We've explored the past - how life came about on our once young and very violent planet. Next we will look at what the future holds. Scientists are working on sophisticated technologies that will get us a closer and more intimate look at the exoplanets we are discovering on almost a daily basis.

Tuesday, September 6, 2016

Hello? Earth Calling . . . PART 4

For Hello? Earth Calling . . . PART 1 CLICK HERE
For Hello? Earth Calling . . . PART 2 CLICK HERE
For Hello? Earth Calling . . . PART 3 CLICK HERE

How did Life Arise On Earth?

No one knows exactly how life arose from non-living matter on Earth, but many researchers focus on the kinds of chemical reactions that could have given rise to the first living system. This is the field of abiogenesis. It is a multidisciplinary study that relies heavily on geology, chemistry and biology.

It is now well known that the starting material for life on Earth consisted of complex organic molecules. These are molecules that contain carbon, and they are not just found on Earth. They are present throughout our solar system and even in interstellar space. There, many complex molecules are formed on the surfaces and inside the water ice mantles of dust grains in the star-forming cores of giant gas clouds. Simple molecules like hydrogen and carbon monoxide are excited under gravitational pressure as they are bombarded with ultraviolet (UV) radiation. In this environment they break apart into reactive radicals. These charged molecular fragments reform over and over, gradually building new increasingly complex molecules. A tantalizing recent discovery was the detection of iso-propyl cyanide in a star-forming cloud 27,000 light years from Earth. Iso-propyl cyanide (C4H7N; shown below left as a simplified molecular diagram) is a fairly complex organic molecule composed of nitrogen, carbon and hydrogen and, like proteins, it has a branched carbon backbone.

Perhaps most intriguing is its carbon-nitrogen triple bond (triple lines, left), one of the most abundant bonds in biochemistry. This high-energy chemical bond participates in amino acid synthesis (amino acids bond together to form proteins). Its presence along with various other organics already detected in interstellar space suggests that life's potential building blocks are widespread in our galaxy. Computer models suggest that complex organic molecules also formed in our Sun's protoplanetary disc, a dense cloud of cosmic dust that would later form the Sun, Earth and all the other planets, moons and asteriods.

European Space Agency;Wikipedia
Like other star-forming clouds, UV photons from the forming Sun would have broken down molecular bonds in the protoplanetary dust and allowed those short simple fragments to recombine into more complex molecules. Earth, however, formed as a molten ball of material so hot that most of the chemical bonds in those complex organic molecules would have been destroyed, leaving behind much simpler molecules like hydrogen, water and carbon monoxide once again.

Tim Bertelink;Wikipedia
Once Earth cooled even slightly, in the presence of energy and water, the processes of increasingly complex organic chemistry would once again be underway. At the same time, as much as 40,000 tons of cosmic dust (which consists of both solar and interstellar molecules) rained down on the surface of Earth every year, offering its supply of complex organic building blocks.

Besides active complex organic prebiotic chemistry on Earth, other prerequisites scientists think are essential to life were present as well, including abundant water, terrestrial life's solvent. When Earth was just 500 million years old, it already contained oceans. Where the water originated remains somewhat mysterious but the picture is becoming clearer. Some researchers believed that comet impacts were a major contributor, but isotope analysis argues against this. Newer data suggests that the protoplanetary material itself, full of water-rich carbonaceous chondrites that aggregated to form Earth, contained sufficient water to form oceans. When the young Earth collided with another body and gave rise to the Moon, according to the giant impact hypothesis, the impact would have resulted in a primordial rock-water vapour atmosphere that would quickly condense into oceans.

Artist's rendering of the collision between Earth and a Mars-sized planet that formed our Moon approximately 4.5 billion years ago. Credit to NASA
There is evidence as well that those oceans could have been as hot as 230°C at first. The water condensed instead of evaporating away to be eventually lost to space because the pressure of the, then dense carbon-rich, atmosphere would have been too high to allow the water to boil.

Earth at this time would also have been constantly bombarded with asteroids, creating significant geological stress on the thin young crust and giving rise to intense volcanic activity. This violent period gave Earth all the conditions required to form life. The dense volcanic atmosphere itself also supplied abundant organic raw material, a chemical makeup that is thought to resemble gases released by volcanoes today, such as water vapour, carbon dioxide, sulphur, methane, nitrogen and hydrogen gas. With energy supplied by intense volcanic lightning and UV radiation from the Sun, chemically active organic compounds such as hydrogen cyanide, formaldehyde, acetylene and ammonia were created. These conditions have been recreated by the famous Miller-Urey experiment, which established that even many highly complex amino acids, the building blocks of proteins, can be created from simple inorganic compounds under those conditions.

General set-up of the Miller-Urey experiment. Credit to YassineMrabet;Wikipedia
These conditions were present for just 500 million years before signatures of life appeared in the (chemical) fossil record, suggesting that when conditions are right, the evolution from abiotic organic chemistry to biochemistry happens very rapidly from a geological standpoint.

As life arose, the environment on Earth would be deadly to most organisms today, including us. There was no oxygen in the atmosphere. There may have been very little or no land above water and the water itself was probably still around 100°C (boiling hot) when cellular life made its appearance. The young Sun's radiation output was also different than it is today. Even though the Sun was fainter in the visual spectrum, young Earth would have been subjected to more intense UV and X-ray radiation. Earth did not have a protective ozone layer until approximately 600 million years ago when plant life began to colonize land and release significant oxygen into the atmosphere (ozone is created when UV radiation splits oxygen (O2) molecules high up in the atmosphere, which then reform into ozone (O3)).

Life that managed to arise under these harsh conditions was also regularly bombarded by asteroid impacts. This was likely the result of gravitational instability caused by giant planets such as Jupiter and Saturn moving outward to their present orbits. A large meteor would strike the young Earth and cause all the surface water to vapourize. Computer models suggest that it would take up to 3000 years for the cloud deck to settle and rain back down into oceans. At first, life would not have a chance to develop but eventually, as asteroid impacts became fewer and less severe, large mats of unicellular extremophile-like microbes formed. Eventually, cyanobacteria colonized much of young Earth, oxygenating the oceans and atmosphere.

Microscopic colonial filaments of
cyanobacteria; Mathewjparker;Wikipedia
Until last year, the first life on Earth was thought to be cyanobacteria. Australian microfossils of strands of these unicellular organisms date back to about 3.5 billion years ago, although there is now some dispute about the identity of these fossils. 3.7 billion year old rock in Greenland more recently revealed 1-4 cm tall humps in the rock, later confirmed as fossilized communities of stromatolites. These structures are a bit like tiny apartment complexes for bacteria, especially cyanobacteria. Though which kind of microbe the stromatolites housed is unknown, they are proof that unicellular life lived as long ago as 3.7 billion years.

In even more ancient Australian rock, chemical fossils containing a specific mix of carbon isotopes unique to life were found. These chemical traces of life are dated even further back to 4.1 billion years, a period when hot pressurized oceans were still forming and Earth was decidedly violent. Because it is a chemical fossil rather than a physical fossil, the type of organism that lived then is unknown. It might be the chemical footprint of an organism similar to bacteria, archaea or even of early eukaryotic life. It could be of an ancestral life form common to all three domains before they diverged evolutionarily.

Life on Earth is divided up into three domains: Bacteria, Archaea and Eukaryota. All three may have diverged from a common ancestor, LUCA (bottom vertical line). Image credit to Eric Gaba;Wikipedia.
It could be the signature of carbon-based life that once existed and then was wiped out in the violence of a young unstable planet, to be replaced by our ancient microbial ancestors. The first Earth organisms to leave behind sufficient fossil evidence might be just one variation on a much larger theme. Several unique biochemistries could have evolved on Earth but only the ones that could adapt best to the rapidly changing conditions on early Earth survived and colonized. The general biochemistry that survives today might simply have been lucky enough to evolve in a relatively calm period between devastations or in a place that was sufficiently protected. Somehow, we know, life made its first appearance. At what point did a collection of chemical reactions become the biochemistry of a living organism?

Did Non-life Become Life In a Hydrothermal Vent?

When did the tipping point occur where non-life organic chemistry became life's biochemistry? In 1967, molecular biologist John Bernal suggested that life forms in three stages. First, biological monomers (such as amino acids) are created. This stage seems to have been achieved throughout the universe in interstellar space as well as on solid planets, moons and even on asteroids. The second stage is the origin of biological polymers, such as proteins, which consist of several amino acids linked together.

Diagram of the chemical structure of the peptide bond (in the box) between two amino acids, creating a peptide chain, which is a protein. Credit to Chemistry-grad-student;Wikipedia.
The achievement of this stage is less well understood. One big problem is that many organic chemicals produced under Miller-Urey conditions would react with amino acids that form as well, preventing them from bonding into peptide chains. Some work suggests that networks of reactions that begin with hydrogen cyanide and hydrogen sulfide (two molecules that should have been abundant on young Earth) found in shallow water irradiated by UV light could produce amino acids, as well as nucleic acids and lipids, while producing few molecules that would inhibit protein synthesis.

Another theory suggests that intense UV radiation from our young Sun may not have been responsible for kick-starting life. In fact, the earliest organisms might have required protection from it instead. Many asteroid strikes during The Late Heavy Bombardment would have involved giant asteroids far larger than the one that caused the extinction of the dinosaurs and these strikes would repeatedly sterilize Earth down to a depth of at least tens of metres, dooming any bourgeoning life forms on the surface. Meanwhile, life could have emerged around deep-sea hydrothermal vents where conditions would be much more stable.

White smokers around Champagne Vent deep in the Marianna Trench. Credit:NOAA
Deep under water, under intense pressure and heat and no sunlight, the laws of thermodynamics might have driven the synthesis of increasingly complex organic molecules and eventually lead to the first living cells. Computer simulations of geothermally heated ocean crust yield an even greater variety of amino acids and other organic molecules than any version of the Miler-Urey experiment has. The diagram below of a typical hydrothermal vent offers an idea of just how complex that chemistry can be.

This diagram of the biogeochemical cycle of a typical hydrothermal vent created by the U.S. government offers an idea of the complex chemistry at work.
Everett Shock and Mitchell Schulte suggest that there is significant thermodynamic drive to create these organic compounds as chemically unstable hydrothermal fluids are spontaneously driven toward a state of chemical equilibrium.

A similar thermodynamic disequilibrium drives the elegant process of photosynthesis, explored in a previous article. In that case, the photosynthetic production of energy-rich sugars in plants occurs down an electrochemical gradient across disc-like membranes that are located within cellular organelles called chloroplasts. A recent study done by Russell et al (2014) suggests that a similar membrane-spanning electrochemical gradient may have been a kind of prebiotic nano-engine, a precursor to the molecular motors across cell membranes and inside organelles today, which are driven by energy gradients moving toward chemical equilibrium. Examples of these very efficient motors are myosins that contract our muscles, the cilia that move mucus and dust out of our nasal passages, the tiny propeller-like flagella that propel some bacteria, protists and sperm, the proteins that condense long double strands of DNA into chromosomes, and even RNA polymerase, which transcribes new RNA from a DNA template, is a molecular motor.

Russell et al's modeling shows that the synthesis of various organic molecules (alkanes, alcohols, ketones, carboxylic acids, aldehydes, etc.) is favourable (and exothermic, which means it releases energy) when 2°C seawater containing bicarbonate is mixed into 350°C fluid water (water under enough pressure to stay liquid) containing dissolved carbon dioxide and hydrogen gas. This scenario is much like the conditions around a hydrothermal vent. The initial hydrothermal fluid becomes increasingly chemically reduced. In chemistry, reduction means the acceptance of electrons. For example, when iron and oxygen react to make rust, the iron is oxidized and the oxygen is reduced – it accepts electrons from the iron atom. As the fluid becomes more and more reduced, the rate of synthesis of organic compounds increases because the reaction becomes increasingly thermodynamically driven by the increasing differences in oxidation state (as an example, Fe, Fe2+ and Fe3+ represent three increasing states of oxidation for iron as it rusts in the presence of water or moist air). They also note that Earth's oceanic crust is mostly basalt. This is the rock through which hydrothermal vent fluid travels upward. Early Earth's basalt would have had a mineral composition much different from modern basalt because it had not yet gone through billions of years of recycling through continental plate subduction. In the beginning basalt was more highly reducing because it contained more magnesium and iron, two elements with multiple oxidation states. All of this suggests that conditions around 4 billion years ago were ripe for maximizing complex organic molecule syntheses, with nearly complete conversion of inorganic carbon (in bicarbonate in the water) into a wide variety of complex organic compounds.

Additional evidence from microbiology supports the hydrotherrmal vent life origin hypothesis. The last universal common ancestor of all living organisms on Earth may have been a unicellular thermophilic (heat-loving) organism, the kind of simple unicellular life that could have evolved around hydrothermal vents. Akanuma et al., (2013), make the argument that a universally conserved enzyme in current (extant) archaea and bacteria species, called nucleoside diphosphate kinase (NDK), must be an indispensible part of modern cell metabolism. This enzyme is not only found in all simple unicellular organisms, it is also found in a very similar form inside the mitochondria and in the cytoplasm of every living cell on Earth. It is the source of both RNA and DNA (ribonucleic acid and deoxyribonucleic acid; genetic material) precursors, and every cell on Earth uses RNA, DNA or a combination of the two (like our cells do) to reproduce. Knowing this, the researchers surmised that NDK must have been inherited from a common ancestor. It is thought to be a highly conserved protein, meaning its amino acid sequence hasn't changed much over billions of years, but it has evolved somewhat. They attempted to reconstruct its ancestral protein sequence by inferring it from NDK sequences of organisms along a reverse phylogenetic tree. They did this by obtaining the gene sequence for the proteins in NDK in extant life. Then, using reliable established methods from population genetics and probability theory, they came up with a series of possible ancestral sequences for the enzyme. After this step, they spliced those genes into very serviceable E. Coli bacteria, which then accurately translated the genetic code into the ancestral proteins. Finally, they exposed these proteins to various temperatures. They discovered that these enzyme proteins are extremely stable at very high (hydrothermal vent) temperatures, and they function optimally at around a hot 85°C. Compare this temperature to our human upper limit. Wet-bulb temperatures above 35°C for six hours or longer are fatal to humans and most other mammals because our cell membranes become unstable and most of our enzymes (essential for life's functions) become denatured. We certainly die at 85°C, but the NDK in our cells, with its ancient lineage, likely keeps on working just fine. This research suggests that the ancient enzyme and therefore the organism itself that housed it, life's universal common ancestor (LUCA), was likely a thermophile. It was probably a simple bacteria-like or archaea-like microbe and it may have gotten its start in a hydrothermal vent, meaning some of our cell machinery did too.

The Possible Co-Evolution of RNA and Proteins

Benal's third stage is the evolution from molecules to cells. The drive-to-equilibrium theory and the NDK research we explored provide a possible chemical scenario where inorganic molecules evolve into increasingly complex organic molecules such as nucleotides, lipids and amino acids, paving the way toward proteins, and toward RNA and DNA synthesis. Before we get to stage 3, however, we need to examine protein synthesis a bit further. We still don't have a possible scenario for their synthesis from amino acids, even though we have established ways in which it is possible. We know that eventually proteins evolved. As shown in an earlier diagram, proteins are composed of amino acids held together by peptide bonds. The big stumbling point here is that peptide bonds do not form spontaneously. It takes a lot of energy to make that reaction favourable enough to proceed. Inside cells, this energy is supplied by an energy-storage molecule called adenosine triphosphate (ATP)  and cellular enzymes are used to lower the activation energy (kind of like an energy hurdle that must be jumped over) of the synthesis reaction. Therefore, it is unlikely that proteins such as NDK arose unless there was a lot of free energy (perhaps in the form of heat) and a catalyst of some kind came on the scene. That catalyst could have been a simpler precursor to a modern RNA molecule and it suggests a possible scenario where RNA and proteins co-evolved. RNA is a fascinating molecule. It is self-replicating and it is an enzyme. Enzymes act as catalysts for biochemical reactions. They lower the activation energy and, by doing so, they allow reactions to proceed and they increase the reaction rate. According to the RNA world theory, spontaneously self-replicating ribonucleic acid (RNA) molecules may have been the ultimate precursor to all life on Earth. Modern RNA is a cellular master of all trades. Not only does it function as genetic material (which acts as an information storage molecule for cellular reproduction), it is also an essential non-protein enzyme. In cells, it catalyzes the formation of peptide bonds between amino acids to create protein polymers. In our bodies this happens inside the ribosomes in our cells. Inside the ribosome organelle, a complex composed of several RNA molecules and proteins carry out protein synthesis. If the first simple strands of protein polymerized thanks to the enzymatic boost from simple RNA-like molecules, we need to get to the synthesis of a simple RNA-like molecule. To evolutionarily get to the first RNA, we need to propose an abiotic (non-living) RNA synthesis pathway. The catch now is that the RNA molecule itself is very complex molecule.

A hairpin loop of RNA is shown left. A single strand is folding back on itself. It can be extremely long, composed of up to hundreds of nucleobases along a ribose-phosphate backbone. Nucleobases are green and the ribose-phosphate backbone of the molecule is blue. Image credit to Vossman;Wikipedia.

Most researchers consider it unlikely that the ribonucleotides within this molecule would form non-enzymatically.  A nucleotide is a basic building block of RNA and DNA. Each nucleotide follows the same basic plan. It is composed of a nitrogenous base (a nucleobase as in above) plus a 5-carbon sugar that is either ribose (for RNA) or deoxyribose (for DNA) and at least one phosphate group (HPO42-).

The general structure of a ribonucleotide consists of a phosphate group (the left part of the diagram shown right), a ribose sugar group (the bottom right pentagonal ring) and a nucleobase (top right). The base, or nucleobase, can be adenine, guanine, cytosine or uracil in RNA. (A, G, C or U). Image credit to Binhtroung;Wikipedia.

Ribonucleotides, as you can see, are highly complex organic molecules. The biggest problem when faced with the question of how nucleotides were formed non-biologically is the sugar unit. Sugars are biological molecules common and essential to plants, animals and many unicellular organisms but the 5-carbon sugars present in genetic material are found only in very trace amounts on meteors and geologically on Earth as sugar acids. Sugars are geologically rare and they also tend to be unstable. They decompose when exposed to heat (for example, making caramel, a partial decomposition of sucrose, requires less than 160°C) so if they were synthesized non-biologically they would not survive early Earth's violent conditions for long. However in 2011, British chemist John Sutherland discovered a non-biological pathway to create pyrimidine nucleosides that bypasses free sugars altogether. These exciting results were confirmed and explored further in a subsequent series of papers. Instead of sugars, 2 and 3-carbon molecules (glycolaldehyde, glyceraldehyde cyanamide, etc.) could be used and these are all molecules that would have been much more commonly available on and in our young planet.

There is also evidence that RNA didn't need to start out as the long complex chain of ribonucleotides that most modern forms tend to be. Even quite short sequences of RNA can still be enzymatically active. Much shorter simpler RNA-like polymers have even been shown to catalyze the formation of peptide bonds. Rajamani et al (2013) showed that these polymers could be created non-biologically (abiotically) in a lipid-rich environment. Lipids are naturally occurring molecules such as waxes, fats, phospholipids and sterols.

Once short RNA-like polymers arrive on the scene, what processes would abiotically drive them toward achieving the complexity of modern RNA? This part of our story gets quite interesting. Tracey Lincoln and Gerald Joyce (2009) suggest a form of chemical evolution might be responsible. The genetic code in RNA is built as a chain of four different ribonucleotides. Each one – G, U, A and C – has a different nucleobase that makes it unique. The chemical bonds that hold these ribonucleotides together have a fairly low potential energy. This means that (unlike peptide bonds) these bonds would have formed and broken apart regularly. While this took place, some particular combinations would have catalytic properties that can lower the activation energy required for their particular sequence to be created. This means those sequences would stay together for longer periods than other random sequences. They could also grow longer and form faster before breaking down again. RNA is a self-replicating molecule and these sequences would be able to replicate more frequently, giving them a competitive edge. Some biologists consider this point to be where life started. There are no living cells yet, but evolving RNA, by using chemical bond energy to replicate its strands, fits some definitions of life. Eventually, sequences that catalyze peptide bonding would randomly be built and some of the proteins that formed as a result would be active enzymes, which in turn would assist in RNA synthesis. A positive feedback system would be set up. Even short 5-ribonucleotide strands have been shown to catalyze protein synthesis. This RNA-protein co-evolution scenario provides us with a way in which we can start to visualize how the cellular machinery of life got its start billions of years ago. Eventually that machinery became housed in a protective envelope to form the first simple cells.

Next we will explore what may have been the first living cells on Earth.