Category: Our World (page 1 of 4)

Viruses, the Virosphere and Astrovirology

An electron microscopic image of the 2019 novel coronavirus grown in cells at The University of Hong Kong.  Thin-section electron micrographs of the novel coronavirus show part of an infected cell, grown in a culture, with virus particles being released from the cell’s surface. (The University of Hong Kong)

 

When the word “virus” first came into use, it was as a “poison” and “a very small disease-causing agent.”  While the presence of viruses was theorized earlier, they were not fully identified until the 1890s.

So from their earliest discovery, viruses were synonymous with disease and generally of the ghastly epidemic type of disease we now see with coronavirus.  Few words carry such a negative punch.

Without in any way  minimizing the toll of viruses on humans (and apparently all other living things,) men and women who study viruses know that this association with disease is far too restrictive and misses much of what viruses do.  It’s perhaps not something to argue while a viral pandemic is raging, but that’s when the focus on viruses is most intense.

Here, then, is a broader look at what viruses do and have done — how they inflict pandemics but also have introduced genes that have led to crucial evolutionary advances, that have increased the once-essential ability of cyanobacteria in early Earth oceans to photosynthesize and produce oxygen, and that have greatly enhanced the immunity systems of everything they touch.  They — and the virosphere they inhabit — have been an essential agent of change.

Viruses are also thought to be old enough to have played a role — maybe a crucial role — in the origin of life, when RNA-like replicators outside cells may have been common and not just the domain of viruses.  This is why there is a school of thought that the study of viruses is an essential part of astrobiology and the search for the origins of life.  The field is called astrovirology.

Viruses are ubiquitous — infecting every living thing on Earth.

Virologists like to give this eye-popping sense of scale:  based on measurements of viruses in a liter of sea water, they calculate the number of viruses in the oceans of Earth to be 10 31.  That is 10 with 31 zeros after it.  If those viruses could be lined up, the scientists have calculated, they would stretch across the Milky Way 100 times.

“The vast majority of viruses don’t care about humans and have nothing to do with them,” said Rika Anderson,  who studies viruses around hydrothermal vents and teaches at Carleton College in Minnesota. … Read more

Theorized Northern Ocean of Mars; now long gone.  (NASA)

Change is the one constant in our world– moving in ways tiny and enormous,  constructive and destructive.

We’re living now in a time when a rampaging pandemic circles the globe and when the climate is changing in so many worrisome and potentially devastating ways.

With these ominous  changes as a backdrop, it is perhaps useful to spend a moment with change as it happens in a natural world without humans.  And just how complete that change can be:

For years now, planetary scientists have debated whether Mars once had a large ocean across its northern hemisphere.

There certainly isn’t one now — the north of Mars is parched, frigid and largely featureless.  The hemisphere was largely covered over in a later epoch by a deep bed of lava, hiding signs of its past.

The northern lowlands of Mars, as photographed by the Viking 2 lander. The spacecraft landed in the Utopia Planitia section of northern Mars in 1976. (NASA/JPL)

Because our sun sent out significantly less warmth at the time of early Mars (4.2-3.5  billion years ago,) climate modelers have long struggled to come up with an explanation for how the planet — on average, 137 million miles further out than Earth — could have been anything but profoundly colder than today. And if that world was so unrelentingly frigid, how could there be a surface ocean of liquid water?

But discoveries in the 21st century have strongly supported the long-ago presence of water on a Mars in the form of river valleys, lakes and a water cycle to feed them.  The work done by the Curiosity rover and Mars-orbiting satellites has made this abundantly clear.

An ocean in the northern lowlands is one proposal made to explain how the water cycle was fed.

And now, In a new paper in Journal of Geophysical Research: Planets,  scientists from Japan and the United States have presented modelling and analysis describing how and why Mars had to have a large ocean early in its history to produce the geological landscape that is being found.

Lead author Ramses Ramirez, a planetary scientist with the Earth-Life Science Institute in Tokyo, said it was not possible to determine how long the ocean persisted, but their team concluded that it had to be present  in that early period around 4 billion to 3.5 billion years ago.  That is roughly when what are now known to be river valleys were cut in the planet’s southern highlands.… Read more

What, Exactly, Is A Virus?

An illustration of the coronavirus. (Centers of Disease Control)

By now, the coronavirus is an all too familiar menace to most of the peoples of the world.  How it is spread,  the symptoms of the disease,  the absolute necessity of taking precautions against it — most people know something about the coronavirus pandemic.

But the question of what a virus actually is, what are its characteristics and where do they come from,  this seem to be far less well understood by the public.

So here is a primer on this often so destructive agent and its provenance — a look into the complicated, sometimes deadly and yes, fascinating world of viruses.

Viruses are microscopic pathogens that have genetic material (DNA or RNA molecules that encode the structure of the proteins by which the virus acts), that have a  a protein coat (which surrounds and protects the genetic material), and in some cases they have an outside envelope of lipids.

Most virus species have virions — the name given to a virus when it is not inside a host cell. They are too small to be seen with an optical microscope because they are one hundredth the size of most bacteria.

Transmission electron microscope image shows SARS-CoV-2, the virus that causes COVID-19, isolated from a patient in the U.S. Virus particles are emerging from the surface of cells cultured in the lab. The spikes on the outer edge of the virus particles give coronaviruses their name, crown-like. (NIAID-RML)

Unlike bacteria, viruses are generally not considered to be “alive.”

Although viruses do have genomes, they need to take over the machinery of other living cells to follow their own genome instructions.  This is why viruses cannot reproduce by themselves — as opposed to non-viral parasites  that can reproduce outside of a host cell.

Viruses are also too small and simple to collect and use energy, i.e., perform metabolism.   So they just take energy from the cells they infect, and use it only when they make copies of themselves.  They don’t need any energy at all when they are outside of a cell.

And viruses have no way to control their internal environment,  and so they do not maintain their own homeostasis as living creatures do.

These limitations are what lead many scientists to describe viruses as “almost alive,” which is a complicated state of existence indeed.

 

Infectious particles of an avian influenza virus emerge from a cell. 

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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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Using Climate Science on Earth to Understand Planets Beyond Earth

Climate expert Tony Del Genio has just retired after 41 years-plus at NASA’s Goddard Institute of Space Studies (GISS) in New York City. Here Del Genio is attending a Cubs game at Wrigley Field with (from the lower right) Dawn Gelino, Shawn Domogal-Goldman, Aaron Gronstal and Mary Voytek. All are part of the NASA NExSS initiative. (Dawn Gelino)

Anthony Del Genio started out his career expecting to become first an engineer and then a geophysicist.  He was in graduate school at UCLA and had been prepared by previous mentors to enter the geophysics field.  But a 1973 department-wide test focused on seismology, rather than fields that he understood better, and his days as a geophysicist were suddenly over.  Fortunately,  one of his professors saw that he had done very well in the planetary atmospheres and geophysical fluid dynamics sections of the exams, and suggested a change in focus.

That turned out to be a good thing for Del Genio, for the field of climate modeling, and for NASA. Because for the next four decades-plus, Del Genio has been an important figure in the field of climate science — first modeling cloud behavior and climate dynamics on Earth with ever more sophisticated atmospheric general circulation models (GCMs), and then beginning to do the same on planets beyond Earth.

His entry into the world of Venus, Saturn, Titan and distant exoplanets beyond is how I met Tony in 2015. At the same time that Many Worlds began as a column, Del Genio was named one of the founding leaders of the Nexus for Exoplanet System Science (NExSS) — the pioneering, interdisciplinary NASA initiative to bring together scientists working in the field of planetary habitability.  (NExSS also supports this column.)

Del Genio is a hard-driving scientist, but also has a self-deprecating and big-picture, poetic side.  This came across at our first diner breakfast together on Manhattan’s Upper West Side (where GISS is located), and was highlighted in a piece that Del Genio just wrote for a new series initiated by the American Geophysical Union (AGU),  Perspectives of Earth and Space Scientists.   In that series, scientists are asked to look back on their careers and write about their science and journeys.  Del Genio’s perspective is the first in this series, and I will reprint most of its bottom half because I found it so informative and interesting.

But first, a quote from Del Genio’s piece that sets the stage:  “The beauty of science, if we are patient, is that nature reveals its secrets little by little, slowly enough to keep us pressing forward for more but fast enough for us not to despair.”… Read more

On the Ground in Greenland, at the Disputed Ancient Stromatolite Site

Enlarge to full screen on lower right. A pioneering three-dimensional, virtual reality look at a Greenland outcrop earlier described as containing 3.7-billion- year-old stromatolite fossils, which would be the oldest remnant of life on Earth. The video capture, including the drone-assisted overview of the site, is part of a much larger virtual reality effort to document the setting undertaken late in August. As the video focuses in on the scientifically controversial outcrop, cuts are visible in the smooth surfaces that were made by two teams studying the rocks in great detail to determine whether the reported stromatolite fossils are actually present. (Parker Abercrombie, NASA/JPL and Ian Burch, Queensland University of Technology.)

 

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, which contains some of the oldest known rocks and outcrops in the world, 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. … Read more

Exploring Early Earth by Using DNA As A Fossil

Betül Kaçar is an assistant professor at the University of Arizona, and a pioneer in the field of paleogenomics — using genetic material to dive back deep into the ancestry of important compounds. (University of Arizona)

Paleontology has for centuries worked to understand the distant past by digging up fossilized remains and analyzing how and why they fit into the evolutionary picture.  The results have been impressive.

But they have been limited.  The evolutionary picture painted relies largely on the discovery of once hard-bodied organisms, with a smattering of iconic finds of soft-bodied creatures.

In recent years, however, a new approach to understanding the biological evolution of life has evolved under the umbrella discipline of paleogenomics.  The emerging field explores ancient life and ancient Earth by focusing on genetic material from ancient organisms preserved in today’s organisms.

These genes can be studied on their own or can be synthetically placed into today’s living organisms to see if, and how, they change behavior.

The goals are ambitious:  To help understand both the early evolution and even the origins of life, as well as to provide a base of knowledge about likely characteristics of potential life on other planets or moons.

“What we do is treat DNA as a fossil, a vehicle to travel back in time,” said Betül Kaçar, an assistant professor at the University of Arizona with more than a decade of experience in the field, often sponsored by the NASA Astrobiology Program and the John Templeton Foundation.  “We build on modern biology, the existing genes, and use what we know from them to construct a molecular tree of life and come up with the ancestral genes of currently existing proteins.”

And then they ask the question of whether and how the expression of those genes — all important biomolecules generally involved in allowing a cell to operate smoothly — has changed over the eons.  It’s a variation on one the basic questions of evolution:  If the film of life were replayed from very early days, would it come out the same?

Cyanobacteria, which was responsible for the build-up of oxygen in the Earth’s atmosphere and the subsequent Great Oxidation Event about 2.5 billion years ago.  Kaçar studies and replaces key enzymes in the cyanobacteria in her effort to learn how those ancestral proteins may have behaved when compared to the same molecules today.

The possibility of such research — of taking what is existing today and reconstructing ancient sequences from it — was first proposed by Emile Zuckerkandl, a biologist known for his work in the 1960s with Linus Pauling on the hypothesis of the “molecular clock.”… Read more

A Unique Science Expedition to Greenland

Greenland from above, where the ice sheet is melting to form lakes and to expose rocks not visible for millennia. @Susan Oliver

It is my very good fortune to report that I have just arrived in Greenland for quite a scientific adventure.
 
Over the next days, a group of scientists (along with me and NASA videographer Mike Toillion) will be traveling to the site of the stromatolite that might, or might not, be the oldest remains of life on Earth.  In a 2016 Nature paper, it was described as having been fossilized about 3.7 billion years ago.
 
Another Nature paper two years later challenged the biological origins of the “fossil,” and the debate has been pretty vigorous since.

Vigorously debated putative stromatolite from the Isua Peninsula, Greenland.

We’ll be helicoptering about 100 miles northeast of the capital Nuuk to get to the Isua peninsula, where the oldest (or almost the oldest, depending on who you choose to follow) rock formations on Earth can be found. Three days and two nights on the ice, or what we hope is still ice. And then a day or more of scientific debate.

I will be writing about this and more (some folks involved the Mars 2020 mission will also be testing instruments at the site) for Many Worlds in the days and weeks ahead.

To me this is an important story not only because of the possible age of the stromatolite find.  If confirmed, it would move back the presence of identified life on Earth by 200 million years.

It is also important because of the fact that scientists with different views on this important issue have traveled thousands of miles to go to the site together and try to reach a consensus—or at least to vigorously argue their cases.  Doesn’t often happen in such high profile science.

Greenstone Belt formations on the Isua Peninsula where our team will be headed.

 
Greenland has, of course, been in the news of late for reasons ranging  worrisome purchase offers to far more worrisome warming.  Remarkable are the “moulin” — which drain the water running on the ice sheet and send it down thousands of feet to the water or land below. 
Kind of a ice black hole.

A “moulin” in Greenland that acts as a very deep drain for water melting on the ice sheet.

Now it’s in my news because, well, I’m here in Greenland, to learn, to report back, and to take in everything this spectacular place has to offer.
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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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The Interiors of Exoplanets May Well Hold the Key to Their Habitability

Scientists have had a working — and evolving — understanding of the interior of the Earth for only a century or so.  But determining whether a distant planet is truly habitable may require an understanding of its inner dynamics — which will for sure be a challenge to achieve. (Harvard-Smithsonian Center for Astrophysics)

The quest to find habitable — and perhaps inhabited — planets and moons beyond Earth focuses largely on their location in a solar system and the nature of its host star,  the eccentricity of its orbit, its size and rockiness, and the chemical composition of its atmosphere, assuming that it has one.

Astronomy, astrophysics, cosmochemistry and many other disciplines have made significant progress in characterizing at least some of the billions of exoplanets out there, although measuring the chemical makeup of atmospheres remains a immature field.

But what if these basic characteristics aren’t sufficient to answer necessary questions about whether a planet is habitable?  What if more information — and even more difficult to collect information — is needed?

That’s the position of many planetary scientists who argue that the dynamics of a planet’s interior are essential to understand its habitability.

With our existing capabilities, observing an exoplanet’s atmospheric composition will clearly be the first way to search for signatures of life elsewhere.   But four scientists at the Carnegie Institution of Science — Anat Shahar, Peter Driscoll, Alycia Weinberger, and George Cody — argued in a recent perspective article in Science that a true picture of planetary habitability must consider how a planet’s atmosphere is linked to and shaped by what’s happening in its interior.

They argue that on Earth, for instance, plate tectonics are crucial for maintaining a surface climate where life can fill every niche. And without the cycling of material between the planet’s surface and interior, the convection that drives the Earth’s magnetic field would not be possible and without a magnetic field, we would be bombarded by cosmic radiation.

What makes a planet potentially habitable and what are signs that it is not. This graphic from the Carnegie paper illustrates the differences (Shahar et al.)

 

“The perspective was our way to remind people that the only exoplanet observable right now is the atmosphere, but that the atmospheric composition is very much linked to planetary interiors and their evolution,” said lead author Shahar, who is trained in geological sciences. “If there is a hope to one day look for a biosignature, it is crucial we understand all the ways that interiors can influence the atmospheric composition so that the observations can then be better understood.”

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