Monthly Archives: January 2017

Extreme living conditions; the origin of life and other adventures

Extreme events are fascinating.  Extreme sports may give us a kind of vicarious thrill, at least until something goes awry at which point we might comment about the foolishness of the act.  Extremes in the natural world are the stuff of movies; asteroids, tsunamis, tornadoes, plagues.  Perhaps our morbid fascination with such events derives from the realization that they can be real.

Over the last 2-3 decades, science too has developed a fascination for extreme living, for creatures that happily thrive in conditions that most other life forms, including us, would find inclement.  They are extremophiles, life forms like bacteria, algae and small critters that can endure extremes of temperature, pressure (e.g. deep sea black smokers), radioactivity, darkness, low levels of oxygen, high acidity or alkalinity, and even lack of water. The variety of extreme environments in which these life forms have evolved is, from a scientific perspective, quite stunning in that it provides us with many different analogues for our quest to understand the origin of life on earth, and whether life can exist on other planets.  A few examples are noted below.


Nature’s deep-freeze; nature’s caldron

Lake Untersee, in East Antarctic, is up to 160m deep, has a perennially frozen ice cover several metres thick and beneath the ice, clear water with a pH of 10.4 and constant temperature of 4-5oC.  Modern stromatolites are growing, quite happily, on the lake bottom; these are laminated or algal mat-like structures that in this case are composed of cyanobacteria, the same kind of bacteria that flourished during the first 3 billion years of earth history.

Extreme polar deserts in the McMurdo region of Antarctica, the Dry Valleys, also are home to a variety of algae, cyanobacteria, mosses, lichens and a few microscopic invertebrates such as nematodes.  Creature comforts here include average annual temperatures ranging from -14o to -30oC (summer temperatures hover around zero), annual precipitation less than 100mm very little of which is liquid water, and katabatic winds up to 200km/hour (katabatic winds are high density air flows that move downslope under the influence of gravity).  The dry valleys have been used by NASA as testing grounds for Martian exploration.


The Andean mountains east of Atacama desert (northern Chile), include some of the driest places on earth.  Salars (salt lakes) here support diverse microbes, green algae, and small crustaceans like brine shrimp in its salars.  Unlike the Antarctic lakes, the Atacama salars, particularly those in the high mountains, have a thick crust of gypsum and halite that cover waters that are 5-10 times more saline than seawater.  Temperature extremes for the mountain salars range from about +20oC to -20oC.  This is also where Flamingos congregate to breed every summer – a spectacular sight.

At the opposite end of the temperature scale are the boiling geothermal hot pools, geysers, and mud pools.  In New Zealand, these silica-rich waters are heated by magma chambers only a few kilometres beneath the surface (this is the Taupo Volcanic Zone).  Specialized microbes are known to form at boiling temperatures (100-105oC) and are also quite prolific in waters 60-80oC.  The biota at the highest temperatures tend to be a bit sparse (I guess there are not many who really want to live there), but they can be detected from organic biomarker molecules and some of the microscopic silica structures that precipitate from hot water.  The siliceous rock that forms in these extreme environments is called geyserite (note that deposits from hot carbonate-rich waters are called travertine, a particular kind of limestone).  Professor Kathy Campbell (Auckland University) and her colleagues have written an excellent technical review of Geyserite (world-wide).  Their studies have also used DNA sequencing to identify and classify the different microbes.


Life in the distant past; life on distant planets

Questions about the beginnings of life and whether life exists anywhere else in the universe, invite all manner of responses; wonder, mystery, how, when, and from some, ridicule.  From a scientific perspective, we search for answers in many ways.  Extremophiles have assumed some importance in this regard.

Science’s fascination with extremophiles has several threads.  The metabolism of these sporty life forms provides information on how they thrive, for example in deep-freeze (they produce their own antifreeze proteins), or oxygen-deficient conditions where they derive their metabolic energy from dissolved sulphur (sulphates) and iron compounds.  Studies of extremophile enzymes are already providing technological dividends (making biofuels, gobbling up toxic mining or radioactive waste), and medical research that makes use of extremophile antibiotic, antiviral and antitumor properties.

Life beyond the extremes of our own existence on earth may provide clues to its beginnings long ago.  We have successfully identified primitive forms of bacteria as far back as 3.4 billion years.  Given that the earth is about 4.6 billion years old, and that water had accumulated perhaps 300-400 million years later, it is conceivable that life forming processes were active during these very early times.  The environmental conditions then were extreme.  There was no oxygen, and therefore no protective ozone layer – UV radiation was extreme.  Surface temperatures were probably higher; water vapour and carbon dioxide in the ancient atmosphere probably provided significant greenhouse conditions. The mere existence of extremophiles today tells us that the most primitive life forms could have utilized the extreme conditions during the earliest part of earth history.

The possible development of primitive life forms elsewhere in our solar system is not a huge step in logic, although empirical verification is a pretty big hurdle.  Mars, the nearest and obvious choice for a first look, does have some of the ingredients that we think are essential for life; it has an atmosphere with carbon dioxide, albeit at much lower pressures than earth, it shows clear evidence for water in its distant past, such as river valley landscapes and minerals like calcium sulphate.  It is cold, averaging about -53oC at the surface but not so cold to exclude extremophiles.

There is even conjecture that Europa, one of Jupiter’s small moons (but not much smaller than earth), could harbor if not life forms, then some of the molecular ingredients that might lead to primitive life forms. Europa is thought to be an ice-covered moon with liquid water beneath.  The surface ice is contorted by Jupiter’s massive gravity field, resulting in the large cracks seen in the NASA Galileo mission image.  There is also some evidence for massive water plumes extending geyser-like into space.  At the equator, the temperature is about -160oC; at the poles -220oC, far too cold for even the most extreme extremophiles.  However, gravitational friction may keep the inner part of Europa’s oceans liquid in which case temperatures may by more conducive to life-forming processes.



Some of these conjectures may seem a bit far-fetched.  But it really wasn’t so long ago that people believed the earth to be 6000 years old (the famous Bishop Ussher calculation – some still do believe this), or that bacteria could not survive, let alone proliferate, in boiling water.  In science, the absurd frequently turns out to be real.

A technical overview of extremophiles (PDF) can be downloaded here



Biomarkers; forensic tools for hydrocarbon fingerprinting

I like a good detective thriller. Danish, Norwegian, Swedish and Britain’s BBC networks have produced some quality shows over the past few years.  Forensics is usually equated with ‘who dunnit?’ but science also makes use of forensic-like tools to help unravel mysteries and solve problems.  This post looks at certain chemical compounds found in hydrocarbon deposits.  The compounds are specific, complex organic molecules called biomarkers.  Biomarkers provide scientific fingerprints of oil deposits, that help scientists and oil explorationists decipher the where, when and how such deposits formed, and environmental scientists monitoring the migration and degradation of spilled oil. Continue reading


The Greenhouse Advantage

Venus and Mars.  Popular mythologies aside, neither planet has a particularly hospitable temperament.  Both are rocky planets, like earth, and both have atmospheres of carbon dioxide (about 95%) and nitrogen (about 3%).  Surface temperatures on Venus hover around 450oC; those on Mars about -53oC.  Venus is not only a tad warm, its surface atmospheric pressure is 92 times that on earth; that on Mars about 6 one thousandths of earths comfort zone.  Venus’ inclemency is the result of run-away Greenhouse processes; Mars’ is due to virtually no Greenhouse effects. Earth resides in that ‘Goldilocks zone’, being neither too hot nor too cold. Lucky us!


An energy budget

The sun heats the earth’s surface, atmosphere and oceans; earth’s internal heat contributes very little to this process.  For the climate to be stable over a reasonable length of time (decades, centuries) there must be a balance between incoming heat from the sun and outgoing heat lost to space; this heat is lost via reflection, convection and conduction.  Perturbations in this balance result in the surface either heating up or cooling down. We know that these long-term imbalances do occur because there have been glaciations and intervening periods of more clement surface conditions. Major climatic variations like these are mainly the result of (predictable) periodic perturbations in earth’s orbit and rotation, namely the Milankovitch cycles.

The total energy that earth receives from the sun is called the total radiance.  It is primarily in the form of visible and infrared light, with lesser proportions of short wave-length UV, gamma and x-ray frequencies, and longer wavelength frequencies like microwaves.  Partitioning of the incoming light is illustrated in the cartoon below. About 30% is reflected directly back to space by clouds, aerosols and the earth’s surface, especially ice sheets (referred to as the albedo); 70% is absorbed by the atmosphere, and both the solid and liquid earth.


However, to maintain an energy balance, some of this absorbed light energy must be converted and re-radiated back to space.  We witness this re-radiation in our everyday lives.  The many hues of red, blue, green, and yellow in my backyard are visible because a part of the light spectrum is reflected. If the entire spectrum is reflected, we see white; the red flowers are reflecting only light in the red part of the spectrum – the remaining light energy is absorbed. The absorbed energy is absolutely necessary for biological growth.  If no light or heat energy is reflected, we see nothing – black.





The greenhouse blanket

The Martian surface is frigid because most of the light-heat energy that gets to the planet’s surface is reflected and re-radiated back to space – Mars has no blanket.  Our own atmosphere is made up of 78% nitrogen, 21% oxygen, and very small amounts of carbon dioxide, methane, and water vapour.  Nitrogen and oxygen are almost completely transparent to sunlight in the visible and infrared part of the spectrum – they do little to help warm or cool the planet.  That task has been appointed to the greenhouse gasses; water vapour (most abundant), carbon dioxide, methane, nitrous oxide, and more recently certain industrial hydrocarbons that have chlorine and fluorine in their molecular structure.  Despite their very low concentrations in the atmosphere (water vapour is most abundant, CO2 is 0.04%, methane is even less), they are solely responsible for maintaining the kind of climatic conditions we have become accustomed to.  All except the chlorofluorocarbons occur naturally.

How does this greenhouse process work?  As an example, a carbon dioxide molecule consists of a carbon atom bonded to two oxygen atoms.  Bonding is loose enough such that infrared light energy will cause the atomic bonds to vibrate; in doing so the molecule absorbs heat.  All the greenhouse gasses operate on the same principle.  However, they also react to heat energy at different frequencies in the infrared part of the spectrum – this is illustrated below, comparing water and CO2.  Water vapour absorbs energy over certain frequencies across the light spectrum, but importantly there is a ‘window’ between about 8-15 micrometres (part of the infrared frequency range) where it does not absorb heat; heat can escape through this frequency window.

This creates for us a wonderfully fortuitous balance between some infrared heat being absorbed by water vapour and other parts of the heat energy spectrum that can escape to space.  Part of the energy balance  is also moderated by CO2 that absorbs heat in parts of the infrared spectrum that water does not.  Nitrous oxide and methane also play an important role in maintaining the balance between heat that is absorbed, and heat that is redirected to space.  It is worth reiterating that, except for water, the concentrations of these greenhouse gasses are very low and that even minor changes to these amounts will result in some degree of warming or cooling of the atmosphere.

An additional factor in the greenhouse effect is the amount of aerosol and extremely fine particulate matter in the atmosphere.  Volcanic eruptions contribute some of these although addition to the atmosphere is sporadic.  The potential cooling effect from violent eruptions is well documented (Krakatoa 1883, Pinatubo 1991).  Soot from industrial burning and clearing of forests is also present and may influence atmospheric heating.

Although oxygen has no role in greenhouse maintenance, it does interact with certain ultraviolet light frequencies to produce ozone (O3) in the upper atmosphere; this happy circumstance means that most of the harmful UV energy is filtered out by ozone before it reaches the surface.



There is an enduring image of Earth rising above the moon’s horizon, taken during the first manned lunar mission.  Small, cloud swirled, seemingly fragile.  Our atmosphere looks thin.  When you look at this image, and then consider some of the details of how the atmosphere works, the balancing acts among all the gas components, the partitioning of heat and mass from air, earth and oceans, you realize how precarious the conditions conducive to our well-being really are.  I’m not sure who said it first, but it really is all we’ve got.


A Gaggle of Goose Barnacles

You never know what new treasures will be discovered strolling along a beach after a good storm.  The beach may have changed shape; cusps, ruts and rills smoothed, some of the sand moved offshore beneath the waves, a few sand dunes cut in half.  There’s flotsam and jetsam, a few bedraggled seabirds.  And there are shells, mostly devoid of their original inhabitants.

Raglan (west coast New Zealand – i.e. the coast facing Tasman Sea) was a bit like that this week.  One particularly neat find on our jaunt was a largish log completely covered in Goose Barnacles.  It is usually the case that critters like these are dead by the time they wash up the beach.  But this time all were still alive.  The log was a slowly-seething mass of stalked shells, parched, and all looking for a way out of their predicament.

Goose barnacles, other than being fascinating to watch up close, have served the science of evolution.  Charles Darwin’s book about them, published in 1851, contains many of the ideas he was formulating about species variations and embryonic development, laying some of the foundations for his ‘Origin of Species’.


Lepas anatifera

Yes, that’s its zoological name.  The common name ‘Goose barnacle’ has an interesting history that from a 21stC perspective seems slightly weird.  The word derives from a 13th century usage for a seabird – the so-called Barnacle Goose, an Arctic migrant.  Gaggles breed in the Arctic then migrate to spend a balmy winter on British shores.  Coastal Brits, those that hadn’t been press-ganged into the Crusades, were never quite sure where the birds came from (they never saw the eggs).  They surmised that the actual stalked barnacle looked a bit like the actual bird, and that the birds hatched in much the same way, from the planks of ships, whereupon they would fly off to join their gaggle.

Lepas attaches with a long fleshy stalk (a peduncle) to flotsam, logs, basically anything that floats; the Raglan examples were up to 20cm long.  The stalk is part of the animal that can move the shell to take advantage of currents, light, or food.  The animals live cheek-by-jowl, as you can see in the image.  They are crustaceans like crabs and shrimp.

Barnacle guts are contained within five shelly plates.   They feed by filtering microscopic particles, plankton, and algae from seawater using delicate, feathery protrusions called cirri (hence the general classification as Cirripedes).  In the video, our Raglan examples are extending their cirri in air – perhaps they can sense the incoming tide.


Darwin’s barnacles; sources of invention

He wrote four books on these critters; two on living groups (the stalked group and the sessile-attached group), and two volumes on fossil representatives.  The first was on the stalked variety, including Lepas. A second volume on (living) barnacles that are more commonly cemented to rocks was published in 1854. His studies of these creatures provided him with insights into species variation and embryonic development.  As Martin Rudwick illustrates in his wonderful book ‘The Meaning of Fossils; Episodes in the History of Palaeontology, Darwin understood that both phenomenon would require cogent explanation to convince his audience of the central theme of his ‘Origins’; natural selection.   Thus, his studious and systematic observations of barnacles, seemingly a dry topic, provided both the data and the wherewithal for creative thinking.

Prevailing 19th century thought on species development, postulated by pioneer biologist Jean-Baptiste Lamarck (1744-1829), was that species tended to progress toward improvement and complexity.  Darwin’s recognized that regression was also an important adaptive process in evolution.  He based this challenge to the status quo on the well-known fact that free-swimming barnacle larvae have legs (like other crustaceans), and that these appendages are converted “into an intricate food-collecting device, and lost many of the functions and organs associated with a free-swimming life.” (Martin Rudwick, p233).  This feeding device is the cirri.

As is so often the case in science, the seemingly innocuous, tedious, but deliberate gathering of data can lead to startling invention and discovery. The humble Goose Barnacle has certainly done its part in shaping our ideas on the biological world. With our barnacle-covered log, we were witness to a microcosm struggling for survival; hundreds of individuals and a single community. Some days later, most are dead, scavenged by seagulls and demolished by waves. Perhaps all that’s left are a few broken, disarticulated shells.


Martin J.S. RudwickThe Meaning of Fossils; Episodes in the History of Palaeontology. Second Edition, 1976, Science History Publications, Neale Watson Academic Publications Inc, New York.

There is a nice essay by Marsha Richmond (2007) on Darwin’s barnacles, written for Darwin on Line.

You can also find lots of interesting general information and teaching resources on Darwin, including his voluminous correspondence (more than 2000 letters), on Cambridge University’s Darwin Correspondence Project