Category: Phenomena (page 1 of 2)

Tales From the Deep Earth

Cross section of the varying layers of the Earth .  (Yuri Arcurs via Getty images)

When especially interesting new planets are discovered in the cosmos, scientists around the world begin the process of identifying their characteristics — their orbit, their mass and density,  their composition, their thermal properties and much more.  It’s all part of a drive that seems to be innate in humans to learn about the workings of the world (or worlds) around us.

This began millennia ago when our distant ancestors started to learn about the make-up and processes of Earth.   We now know enormous amounts about our planet, but I was recently introduced to a domain where our knowledge has some substantial holes.  The area of the Earth least well understood is, not surprisingly, what lies deep below us, in the mantle — the inner 2,900 kilometers (2000 miles) of the planet between the outer crust and the iron core.

The on-going exploration of this vast region — made up substances including some which cannot remain intact on the Earth’s surface — struck me as in some ways comparable to the study of exoplanets.   It’s also a realm where scientific observation is limited, but what knowledge is gained then leads through induction, deduction, modeling and exacting lab work to a gradual expansion back of our knowledge.

And in the case of some high-temperature, high-pressure minerals, this has led to a most unusual technique for identifying and naming key components of our inner planet.  Unable to reach or preserve some of the most important components of the mantle,  geochemists and other deep Earth scientists go to incoming meteorites to learn about what’s beneath (deeply beneath, that is) our feet.

With this in mind, here is a look at the discovery and recent naming of the mineral hiroseite, an unusual but quite widespread component of the very deep Earth.


ELSI director Kei Hirose has been honored for his pioneering work in identifying and describing components of the Earth’s lower mantle. In recognition of his work, a newly identified lower mantle mineral has been given the name of hiroseite. (Nerissa Escanlar)


It was two decades ago when Kei Hirose – a Japanese geochemist expert in high-pressure, deep-Earth phenomena, then at the Tokyo Institute of Technology – began researching a long-standing problem in understanding the working of the lower depths of our planet’s enormous mantle: the last 300 kilomiles above the boundary with the scalding iron core.

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On The Rugged Frontier Of The Hunt For Signs Of Life On Early Earth And Ancient Mars

The vigorously debated finding from the Isua greenstone or supercrustal belt, a 1,200-square-mile area of ancient rocks in Greenland.  Proponents say the rises, from .4 to 1.6 inches tall, are  biosignatures of bacteria and sediment mounds that made up stromatolites almost 3.8 billion years ago.  Critics say additional testing has shown they are the result of non-biological forces.  (Nature and Nutman et al.)

Seldom does one rock outcrop get so many visitors in a day, especially when that outcrop is located in rugged, frigid terrain abutting the Greenland Ice Sheet and can be reached only by helicopter.

But this has been a specimen of great importance and notoriety since it appeared from beneath the snow pack some eight years ago. That’s when it was first identified by two startled geologists as something very different from what they had seen in four decades of scouring the geologically revelatory region – the gnarled Isua supercrustal belt – for fossil signs of very early life.

Since that discovery the rock outcrop has been featured in a top journal and later throughout the world as potentially containing the earliest signature of life on Earth – the outlines of half inch to almost two inch-high stromatolite structures between 3.7 and 3.8 billion years old.

The Isua greenstone, or supracrustal belt contains some of the oldest known rocks and outcrops in the world, and is about 100 miles northeast of the capital, Nuuk.

If Earth could support the life needed to form primitive but hardly uncomplicated stromatolites that close to the initial cooling of the planet, then the emergence of life might not be so excruciatingly complex after all. Maybe if the conditions are at all conducive for life on a planet (early Mars comes quickly to mind) then life will probably appear.

Extraordinary claims in science, however, require extraordinary proof, and inevitably other scientists will want to test the claims.

Within two years of that initial ancient stromatolite splash in a Nature paper (led by veteran geologist Allen Nutman of the University of Wollongong in Australia), the same journal published a study that disputed many of the key observations and conclusions of the once-hailed ancient stromatolite discovery.  The paper concluded the outcrop had no signs of early life at all.

Debates and disputes are common in geology as the samples get older,  and especially in high profile science with important implications.  In this case, the implications of what is in the rocks reach into the solar system and the cosmos. … Read more

If Bacteria Could Talk


Hawaiian lava cave microbial mats appear to have the highest levels and diversity of genes related to quorum sensing so far.  (Stuart Donachie, University of Hawai`i at Mānoa)

Did you know that many bacteria — some of the oldest lifeforms on Earth — can talk?  Really.

And not only between the same kind of single-cell bacteria, but  back and forth with members of other species, too.

Okay, they don’t talk in words or with sounds at all.  But they definitely communicate in a meaningful and essential way, especially in the microbial mats and biofilms (microbes attached to surfaces surrounded by mucus) that constitute their microbial “cities.”

Their “words” are conveyed via chemical signaling molecules — a chemical language — going from one organism to another,  and are a means to control when genes in the bacterial DNA are turned “on” or “off.”  The messages can then be translated into behaviors to protect or enhance the larger (as in often much, much larger) group.

Called “quorum sensing,” this microbial communication was first identified several decades ago.  While the field remains more characterized by questions than definitive answers, is it clearly growing and has attracted attention in medicine, in microbiology and in more abstract computational and robotics work.

Most recently,  it has been put forward as chemically-induced behavior that can help scientists understand how bacteria living in extreme environments on Earth — and potential on Mars —  survive and even prosper.  And the key finding is that bacteria are most successful when they form communities of microbial mats and biofilms, often with different species of bacteria specializing in particular survival capabilities.

Speaking at the recent Astrobiology Science Conference in Seattle,  Rebecca Prescott, a National Science Foundation  Postdoctoral Research Fellow in Biology said this community activity may make populations of bacteria much more hardy than otherwise might be predicted.


Quorum sensing requires a community. Isolated Bacteria (and Archaea) have nobody to communicate with and so genes that are activated by quorum sensing are not turned “on.”

“To help us understand where microbial life may occur on Mars or other planets, past or present, we must understand how microbial communities evolve and function in extreme environments as a group, rather than single species,” said Prescott,

“Quorum sensing gives us a peek into the interactive world of bacteria and how cooperation may be key to survival in harsh environments,” she said.

Rebecca Prescott  is a National Science Foundation Postdoctoral Fellow in Biology (1711856) and is working with principal investigator Alan Decho of the University of South Carolina on a NASA Exobiology Program grant.

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How Creatures End Up Miles Below the Surface of Earth, and Maybe Mars Too

Poikilolaimus oxycercus is a microscopic nematode, or roundworm, found alive and well more than a mile below the surface in South Africa, where its ancestors had lived for hundreds or thousands of years. (Gaetan Borgonie)


When scientists speculate about possible life on Mars, they generally speak of microbial or other simple creatures living deep below the irradiated and desiccated surface.  While Mars long ago had a substantial period that was wetter and warmer when it also had a far more protective atmosphere,  the surface now is considered to be lethal.

But the suggestion that some potential early Martian life could have migrated into the more protected depths is often discussed as a plausible, if at this point untestable possibility.  In this scenario, some of that primitive subsurface life might even have survived the eons in their buried, and protected, environments.

This thinking has gotten some support in the past decade with the discovery of bacteria and nematodes (roundworms) found as far down as three miles below the surface of South Africa, in water dated as being many thousands or millions years old.  The lifeforms have been discovered by a team that has regularly gone down into the nation’s super-hot gold and platinum mines to search for life coming out of boreholes in the rock face of deep mine tunnels.


Borgonie setting up a water collector for a borehole at the Driefontein mine in the Witwatersrand Basin  of South Africa.  He said he stopped counting his journeys into the deep mines at 50, but that the number now is much higher. (Courtesy of Borgonie)

Now a  new paper describes not only the discovery of additional deep subsurface life, but also tries to explain how the distant ancestors of the worms and bacteria and algae might have gotten there. 

Their conclusion:  many were pulled down when fractures opened in the aftermath of earthquakes and other seismic events.  While many lifeforms were swept down, only a small percentage were able to adapt, evolve and thus survive.

The is how Gaetan Borgonie, lead author of the paper in Scientific Reports, explained it to me via email:

“After the discovery of multicellular animals in the deep subsurface up to 3.8 km (2.5 miles) in South Africa everyone was baffled and asked the question how did they get that deep? This question more or less haunted us for more than a decade as we were unable to get our head around it.Read more

All About Emergence

A swarm of birds act as an emergent whole as opposed to a collection of individual birds. The workings of swarms have been fruitfully studied by artificial life scientists, who look for abstracted insights into life via computers and other techniques. (Walerian Walawski)


If there was a simple meaning of the often-used scientific term “emergence,” then 100-plus scientists wouldn’t have spent four days presenting, debating and not infrequently disagreeing about what it was.

But as last month’s organizers of the Earth-Life Science Institute’s “Comparative Emergence” symposium in Tokyo frequently reminded the participants, those debates and disputes are perfectly fine and to be expected given the very long history and fungibility of the concept.

At the same time, ELSI leaders also clearly thought that the term can have resonance and importance in many domains of science, and that’s why they wanted practitioners to be exposed more deeply to its meanings and powers.

Emergence is a concept commonly used in origins of life research, in complexity and artificial life science; less commonly in chemistry, biology, social and planetary sciences; and — originally – in philosophy. And in the 21st century, it is making a significant comeback as a way to think about many phenomena and processes in the world.

So what is “emergence?” Most simply, it describes the ubiquitous and hugely varied mechanisms by which simple components in nature (or in the virtual or philosophical world) achieve more complexity, and in the process become greater than the sum of all those original parts.

The result is generally novel, often surprising, and sometimes most puzzling – especially since emergent phenomena involve self-organization by the more complex whole.

Think of a collection of ants or bees and how they join leaderless by the many thousands to make something – a beehive, an ant colony – that is entirely different from the individual creatures.


The Eagle nebula is an intense region of star formation, an emergent phenomenon
that clearly creates something novel out of simpler parts. (European Space Observatory.)

Think of the combination of hydrogen and oxygen gases which make liquid water. Think of the folding of proteins that makes genetic information transfer possible. Think of the processes by which bits of cosmic dust clump and clump and clump millions of times over and in time become a planetesimal or perhaps a planet. Think of how the firing of the billions of neurons in your brain results in consciousness.Read more

The Northern Lights (Part Two)

Northern Lights at a latitude of about 70 degrees north, well within the Arctic Circle. These photos were taken about 30 miles from the town of Alta. (Lisa Braithwaite)

In my recent column about The Northern Lights, the Magnetic Field and Life,  I explored the science and the beauty of our planet’s aurora borealis, one of the great natural phenomenon we are most fortunate to see in the far North (and much less frequently in the not-quite-so-far North.)

I learned the hard way that an IPhone camera was really not up to the job;  indeed, the battery froze soon after leaving my pocket in the 10 degrees F cold.  So the column had few images from where I actually was — about a half hour outside of the Arctic Circle town of Alta.

But here now are some images taken by a generous visitor to the same faraway lodge, who was present the same time as myself.

Her name is Lisa Braithwaite and she is an avid amateur photographer and marketing manager for two popular sites in the English Lake District.  This was her first hunting trip for the Northern Lights, and she got lucky.  Even in the far northern Norway winter the lights come and go unpredictably — though you can increase your chances if you show up during a time when the sun is actively sending out solar flares.

She came with a Panasonic Lumix DMC-G5 camera and did a lot of research beforehand to increase her chances of capturing the drama should the lights appear.  Her ISOs ranged from 1,600 to 64,000, and her shutter speed from 5 to 15 seconds.  The aperture setting was 3.5.

In addition to showing some of her work, further on I describe a new NASA-led and international program, based in Norway, to study the still incompletely understood dynamics of what happens when very high energy particles from solar flares meet Earth’s atmosphere.

Partnering with the Japanese Aerospace Exploration Agency (JAXA,) the University of Oslo an other American universities, the two year project will send eleven rockets filled with instruments into the ionosphere to study phenomenon such as the auroral winds and the turbulence that can cause so much trouble to communications networks.

But first, here are some morre of Braithwaite’s images, most taken over a one hour period on a single night.

Arcs are a common feature of the lights, sometimes reaching across the sky.

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The Northern Lights, the Magnetic Field and Life

Northern Lights over a frozen lake in Northern Norway, inside the Arctic Circle near Alta. The displays can go on for hours, or can disappear for days or weeks. It all depends on solar flares. (

May I please invite you to join me in the presence of one of the great natural phenomena and spectacles of our world.

Not only is it enthralling to witness and scientifically crucial, but it’s quite emotionally moving as well.

Why? Because what’s before me is a physical manifestation of one of the primary, but generally invisible, features of Earth that make life possible. It’s mostly seen in the far northern and far southern climes, but the force is everywhere and it protects our atmosphere and us from the parched fate of a planet like Mars.

I’m speaking, of course, of the northern lights, the Aurora Borealis, and the planet’s magnetic fields that help turn on the lights.

My vantage point is the far northern tip of Norway, inside the Arctic Circle. It’s stingingly cold in the silent woods, frozen still for the long, dark winter, and it’s always an unpredictable gift when the lights show up.

But they‘re out tonight, dancing in bright green and sometimes gold-tinged arches and spotlights and twirling pinwheels across the northerly sky. Sometimes the horizon glows green, sometimes the whole sky fills with vivid green streaks.

It can all seem quite other-worldly. But the lights, of course, are entirely the result of natural forces.


Northern Lights over north western Norway. Most of the lights are green from collisions with oxygen, but some are purple from nitrogen. © Copyright George Karbus Photography

It has been known for some time that the lights are caused by reactions between the high-energy particles of solar flares colliding in the upper regions of our atmosphere and then descending along the lines of the planet’s magnetic fields. Green lights tell of oxygen being struck at a certain altitude, red or blue of nitrogen.

But the patterns — sometimes broad, sometimes spectral, sometimes curled and sometimes columnar — are the result of the magnetic field that surrounds the planet. The energy travels along the many lines of that field, and lights them up to make our magnetic blanket visible.

Such a protective magnetic field is viewed as essential for life on a planet, be it in our solar system or beyond.

But a magnetic field does not a habitable planet make.… Read more

2.5 Billion Years of Earth History in 100 Square Feet

Scalding hot water from an underground thermal spring creates an iron-rich environment similar to what existed on Earth 2.5 billion years ago. (Nerissa Escanlar)

Along the edge of an inlet on a tiny Japanese island can be found– side by side – striking examples of conditions on Earth some 2.4 billion years ago, then 1.4 billion years ago and then the Philippine Sea of today.

First is a small channel with iron red, steaming and largely oxygen-free water – filled from below with bubbling liquid above 160 degrees F. This was Earth as it would have existed, in a general way, as oxygen was becoming more prevalent on our planet some 2.4 billion years ago. Microbes exist, but life is spare at best.

Right next to this ancient scene is region of green-red water filled with cyanobacteria – the single-cell creatures that helped bring masses of oxygen into our atmosphere and oceans.  Locals come to this natural “onsen” for traditional hot baths, but they have to make their way carefully because the rocky floor is slippery with green mats of the bacteria.

And then there is the Philippine Sea, cool but with spurts of warm water shooting up from below into the cove.

All of this within a area of maybe 100 square feet.

It is a unique hydrothermal scene, and one recently studied by two researchers from the Earth-Life Science Institute in Tokyo – evolutionary microbiologist Shawn McGlynn and ancient virus specialist Tomohiro Mochizuki.

They were taking measurements of temperature, salinity and more, as well as samples of the hot gas and of microbial life in the iron-red water. Cyanobacterial mats are collected in the greener water, along with other visible microbe worlds.

Shawn McGlynn, associate professor at the Earth Life Science Institute in Tokyo scoops some iron-rich water from a channel on Shikine-jima Island, 100 miles from Tokyo. (Nerissa Escanlar)

The scientific goals are to answer specific questions – are the bubbles the results of biology or of geochemical processes? What are the isotopic signatures of the gases? What microbes and viruses live in the super-hot sections? And can cyanobacteria and iron co-exist?

All are connected, though, within the broad scientific effort underway to ever more specifically understand conditions on Earth through the eons, and how those conditions can help answer fundamental questions of how life might have begun.

“We really don’t know what microbiology looked like 2.5 billion or 1.5 billion years ago,” said McGlynn, “But this is a place we can go where we can try to find out.… Read more

Messy Chemistry: A New Way to Approach the Origins of Life

Astrobiologist and chemist Irena Mamajanov and prebiotic chemist Kuhan Chandru in their messy chemistry garb at the Earth-Life Science Institute (ELSI) in Tokyo. Mamajanov leads an effort at the institute to study a new “messy” path to understanding how some prebiotic chemical systems led to building blocks of life on early Earth. (Nerissa Escanlar)

More than a half century ago, Stanley Miller and Harold Urey famously put water and gases believed to make up the atmosphere of early Earth into a flask with water, sparked the mix with an electric charge, and produced amino acids and other chemical building blocks of life.

The experiment was hailed as a ground-breaking reproduction of how the essential components of life may have been formed, or at least a proof of concept that important building blocks of life could be formed from more simple components.

Little discussed by anyone outside the origins of life scientific community was that the experiment also produced a lot of a dark, sticky substance, a gooey tar that covered the beaker’s insides. It was dismissed as largely unimportant and regrettable then, and in the thousands of parallel origins of life experiments that followed.

Today, however, some intrepid researchers are looking at the tarry residue in a different light.

Tarry residue from an experiment — a common result when organic compounds are heated.

Just maybe, they argue, the tar was equally if not more important as those prized amino acids (which, after all, were hidden away in the tar until they were extracted out.) Maybe the messy tar – produced by the interaction of organic compounds and an energy source — offers a pathway forward in a field that has produced many advances but ultimately no breakthrough.

Those now studying the tar call their research “messy chemistry,” as opposed to the “clean” chemistry that focused on the acclaimed organic compounds.

There are other centers where different versions of “messy chemistry” research are under way — including George Cody’s lab at the Carnegie Institution for Sciences and Nicholas Hud’s at the Georgia Institute of Technology — but it is probably most concentrated at the Earth-Life Science Institute in Tokyo (ELSI.)

There, messy chemistry is viewed as an ignored but promising way forward, and almost a call to arms.

“In classical origin-of-life synthetic chemistry and biology you’re looking at one reaction and analyzing its maximum result. It’s A+B = C+D,” said Irena Mamajanov, an astrobiologist with a background in chemistry who is now a principal investigator ELSI and head of the overall messy chemistry project.… Read more

Nobel Laureate Jack Szostak: Exoplanets Gave The Origin of Life Field a Huge Boost

Jack Szostak, Nobel laureate and pioneering researcher in the origin-of-life field, was the featured speaker at a workshop this week at the Earth-Life Science Institute (ELSI) in Tokyo.  One goal of his Harvard lab is to answer this once seemingly impossible question:  was the origin of life on Earth essentially straight-forward and “easy,” or was it enormously “hard” and consequently rare in the universe. (Nerissa Escanlar)

Sometimes tectonic shifts in scientific disciplines occur because of discoveries and advances in the field.  But sometimes they occur for reasons entirely outside the field itself.  Such appears to be case with origins-of-life studies.

Nobel laureate Jack Szostak was recently in Tokyo to participate in a workshop at the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology on “Reconstructing the Phenomenon of Life To Retrace the Emergence of Life.”

The talks were technical and often cutting-edge, but the backstory that Szostak tells of why he and so many other top scientists are now in the origins of life field was especially intriguing and illuminating in terms of how science progresses.

Those ground-shifting discoveries did not involve traditional origin-of-life questions of chemical transformations and pathways.  They involved exoplanets.

“Because of the discovery of all those exoplanets, astronomy has been transformed along with many other fields,” Szostak said after the workshop.

“We now know there’s a large range of planetary environments out there, and that has stimulated a huge amount of interest in where else in the universe might there be life.  Is it just here?  We know for sure that lots of environments could support life and we also would like to know:  do they?

“This has stimulated much more laboratory-based work to try to address the origins question.  What’s really important is for us to know whether the transition from chemistry to biology is easy and can happen frequently and anywhere, or are there one or many difficult steps that make life potentially very rare?”

In other words, the explosion in exoplanet science has led directly to an invigorated scientific effort to better understand that road from a pre-biotic Earth to a biological Earth — with chemistry that allows compounds to replicate, to change, to surround themselves in cell walls, and to grow ever more complex.

With today’s increased pace of research, Szostak said, the chances of finding some solid answers have been growing.  In fact, he’s quite optimistic that an answer will ultimately be forthcoming to the question of how life began on Earth.… Read more

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