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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

Tales From the Deep Earth

January 19, 2020 / Marc Kaufman / 0 Comments

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.

Using Climate Science on Earth to Understand Planets Beyond Earth

January 2, 2020 / Marc Kaufman / 1 Comment

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

September 10, 2019 / Marc Kaufman / 1 Comment

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

Exploring Early Earth by Using DNA As A Fossil

September 3, 2019 / Marc Kaufman / 0 Comments

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

August 25, 2019 / Marc Kaufman / 0 Comments

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.

If Bacteria Could Talk

July 29, 2019 / Marc Kaufman / 0 Comments

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.

Starting Life on Another Planet

May 17, 2019 / Elizabeth Tasker / 0 Comments

Inside the planet simulator at McMaster University — A look inside the planet simulator in the Origins of Life laboratory at McMaster University. Within this chamber, the origins of life can be explored on different worlds (McMaster University).

Have you ever wondered if you could kick-start life on another planet? In the Origins of Life laboratory at McMaster University in Canada, there is a machine that allows you to try this very task.

Exactly how life began on the Earth remains heavily debated, but one of the most famous ideas was proposed by Charles Darwin in a letter to a friend in 1871:

“But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts…” Darwin began.

In contrast to the vast ocean, a pond would allow simple organic molecules to be concentrated and increase the probability of reactions that would form chains of longer molecules such as RNA; a single-stranded version of DNA that is thought to have been used for genetic information by the earliest forms of life.

It is highly likely that such warm little ponds would have the necessary ingredients to build such complex molecules. Experiments performed by Stanley Miller and Harold Urey in the 1950s demonstrated that water containing just the basic molecules of methane, ammonia and hydrogen would react to form a wide range of simple organics. Meteorites have also been found to contain similar molecules, proposing an alternative way of populating pools of water on the early Earth.

These ponds should therefore contain plenty of simple organics such as nucleotides, which stack together to form RNA. However, this stacking step turns out to be tricky.

“Anywhere where you have stagnant water and take sample, you will find organic molecules,” explains Maikel Rheinstädter, associate director of McMaster’s Origins Institute. “But you only find the building blocks, not the longer chains. Obviously, something is missing.”

In pond water, molecules are free to move around and potentially meet to initiate a reaction. The problem is that nucleotides carry a negative charge which repels the molecules from one another. While their motion is unconstrained, the nucleotides will therefore not approach close enough to react and form a longer molecule.

The solution is to dry out the pond.

As winter turned to summer on our young planet, shallow pools would have evaporated to leave the molecules suspended in the water lying on the muddy clay bottom.… Read more

A New and Revelatory Window Into Evolution on Earth

March 22, 2019 / Marc Kaufman / 0 Comments

A Leanchoilia fossil from at the Qingjiang site in China. A very early arthropod found with sharply defined appendages is an arthropod and one of the prime examples of early Cambrian life (D Fu et al., Science 363:1338 (2019)

Virtually every definition of the word “life” includes the capability to undergo Darwinian evolution as a necessary characteristic. This is true of life on Earth and of thinking about what would constitute life beyond Earth. If it can’t change, the thinking goes, then it cannot be truly alive.

In addition, evolutionary selection and change occurs within the context of broad planetary systems — the chemical makeup of the atmosphere, the climactic conditions, the geochemistry and more. If an environment is changing, then the lifeforms that can best adapt to the new conditions are the ones that will survive and prosper.

So evolution is very much part of the landscape that Many Worlds explores — the search for life beyond Earth and effort to understand how life emerged on Earth. Evolution happens in the context of broad conditions on Earth (and perhaps elsewhere), and finding potential life elsewhere involves understanding the conditions on distant planets and determining if they are compatible with life.

This all came to mind as I read about the discovery of a remarkable collection of fossils alongside a river in China, fossils of soft-bodied creatures that lived a half billion years ago in the later phase of what is termed the the Cambrian explosion. They are of being compared already with the iconic “Burgess Shale” fossil find in Canada of decades ago, and may well shed equally revelatory light on a crucial time in the evolution of life on Earth.

Artist rendering of Qingjiang life showing characteristics of different early Cambrian taxonomical groups. More than 50 percent had never been identified before. (ZH Yao and DJ Fu)

The new discovery is reported in the journal Science in a paper authored by Dongjing Fu and a team largely from the Northwest University in Xi’an. The paper reports on a zoo of Cambrian-era creatures, with more than half of them never identified before in the rock record.

The animals are soft-bodied — making it all the more remarkable that they were preserved — and some bear little resemblance to anything that followed. Like the Burgess Shale fossils, the Qingjiang discovery is of an entire ecosystem that largely disappeared as more fit (and predatory) animals emerged.… Read more

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

March 4, 2019 / Marc Kaufman / 0 Comments

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

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