Monday, January 20, 2020

Ancient Australian Crystals Unlock History of Earth's First Magnetic Field


By Rafi Letzter - Staff Writer

It was a lot more powerful than anyone believed.

An image shows one of the tiny zircon crystals
found in Australia on a US dime. Even smaller 
particles within the zircon encode data about the 
state of the Earth's magnetic field at the time the crystal formed.
(Image: © University of Rochester / John Tarduno)


Tiny Crystals in Australia are helping scientists unlock the ancient history of our planet's first magnetic field, which disappeared hundreds of millions of years ago. And the crystals show that this field was a lot more powerful than anyone believed. That, in turn, could help answer a question about why life emerged on Earth.

Those tiny, old crystals are locked in rocks that date to well over half a billion years ago. At the time, tiny magnetic particles floated in the molten rock. But as that rock cooled, the particles, which aligned to the magnetic field orientation at the time, locked into place. And those particles still sit in a pose suggesting that they were influenced by a much more powerful magnetic field than scientists had assumed, a new study reveals.

Earth's magnetic field is generated by the planet's solid iron inner core spinning in a liquid-iron outer core. Extending far beyond our atmosphere, this field protects the planet from dangerous particles blasting through space, such as solar wind and cosmic rays. But because its visible effects on the planet's surface are so minimal, studying the field's long history is difficult. However, this history is important for understanding the future of our own planet and other planets in the universe. We know our planet has had a strong magnetic shield for a long time, because it kept its surface water and sprouted life. Otherwise, cosmic radiation would have blasted both life and water off the surface long ago. In that scenario, Earth would look a lot like Mars, where the old magnetic field collapsed as the planet cooled and its core stopped spinning, according to a statement from the researchers.

Earth has had a magnetic core for 4.2 billion years, according to the new study. But until 565 million years ago, long before the dinosaurs arrived and a bit before complex life emerged in the Cambrian explosion, that magnetic core worked completely differently. At that point, there was no inner core. But magnesium oxide, which had dissolved into the all-liquid core during the same giant impact that created Earth's moon, was slowly moving out of the core and into the mantle. That movement of magnesium generated movement in the liquid core that created Earth's early magnetic field.

When the magnesium oxide ran out, the field almost collapsed, researchers believe. But the solid inner core formed at around the same time and saved life on Earth.

Conventional wisdom held that the field produced by the old, magnesium-oxide magnet was a lot weaker than the one we have now. But studying those ancient ancient zircon crystals, which formed when the old magnetic field still suffused the planet, indicates that this was wrong.

"This research is telling us something about the formation of a habitable planet," John Tarduno, an Earth scientist at the University of Rochester and author of the new paper, said in the statement. "One of the questions we want to answer is why Earth evolved as it did, and this gives us even more evidence that the magnetic shielding was recorded very early on the planet."

The paper was published today (Jan. 20) in the journal Proceedings of the National Academy of Sciences.

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Are Birds Dinosaurs?

By Mindy Weisberger - Senior Writer

Modern birds can trace their origins to theropods, a branch of mostly meat-eaters on the dinosaur family tree.

In some birds, like this cassowary, the resemblance to extinct
 theropod dinosaurs is easy to see. (Image: © Shutterstock)

What do sparros, geese and owls have in common with a velociraptor or the mighty Tyrannosaurus rex? All can trace their origins to a bipedal, mostly meat-eating group of dinosaurs called theropods ("beast-footed") that first appeared around 231 million years ago, during the late Triassic Period.

The earliest birds shared much in common with their theropod relatives, including feathers and egg-laying. However, certain traits – such as sustained, powered flight – distinguished ancient birds from other theropods, and eventually came to define modern-bird lineage (even though not all modern birds fly).

Today, all non-avian dinosaurs are long extinct. But are birds still considered to be true dinosaurs?
In a word: Yes.

"Birds are living dinosaurs, just as we are mammals," said Julia Clarke, a paleontologist studying the evolution of flight and a professor with the Department of Geological Sciences at the University of Texas at Austin.

In spite of the physical differences that distinguish all mammals from other species, every animal in that group — living and extinct — can trace certain anatomical characteristics to a common ancestor. And the same is true for birds, Clarke told Live Science.

"They're firmly nested in that one part of the dinosaur tree," she said. "All of the species of birds we have today are descendants of one lineage of dinosaur: the theropod dinosaurs."
What makes a bird, a bird?

Modern birds have feathered tails and bodies, unfused shoulder bones, toothless beaks and forelimbs that are longer than their hind limbs. They also have a bony plate near their tails called a pygostyle. Other types of extinct theropods had one or more of these features, but only modern birds have all of them, according to Takuya Imai, an assistant professor with the Dinosaur Research Institute at Fukui Prefectural University in Fukui, Japan.

In a primitive bird from Japan called Fukuipteryx — a 120-million-year-old avian that Imai described in November 2019 and the earliest known bird with a pygostyle — the preserved structure closely resembled the pygostyle of a modern chicken, Imai previously told Live Science. In other words, some structures in modern birds can be traced back to some of their earliest ancestors.

However, primitive birds still had much in common with non-avian theropods, said Jingmai O'Connor, a paleontologist specializing in dinosaur-era birds and the transition from non-avian dinosaurs, at the Institute of Vertebrate Paleontology and Paleoanthroplogy in Beijing, China.

In fact, early birds were "very dinosaur-like" compared to modern birds, O'Connor told Live Science in an email. "Some had long, reptilian tails, teeth and claws on their hands," she said. And many theropod dinosaurs that were not birds had true feathers, "which are feathers that have a central part down the middle and branching barbs," according to Clarke.

Paleontologists distinguish between animal groups through precise measurements of subtle variations in bones and other fossilized body tissues, including "little bumps and tubercles [a rounded bulge on a bone] that are related to reorganizing different muscle groups," Clarke said. This morphological data is translated into numbers that are then processed by algorithms to pinpoint how animals are related, O'Connor explained. By using these algorithms in a system known as cladistics, experts can differentiate ancient birds from their theropod relatives.



Early birds

The earliest known bird is Archaeopteryx ("ancient wing"), which lived around 150 million years ago in what is now southern Germany. The creature weighed around 2 pounds(1 kilogram) and measured about 20 inches (50 centimeters) in length; fossil evidence shows that it sported plumage on its tail and body. The shape of its forelimbs and feathers also suggests that Archaeopteryx was capable of powered flight, a trait associated with most modern birds. However, unlike birds today, Archaeopteryx retained individual, clawlike fingers at the tips of its wings.

Fossils of birds from the early Cretaceous Period (145.5 million to 65.5 million years ago) have been found in northeastern China, such as Confuciusornis, which lived around 125 million years ago, and had a beak and long tail-feathers. Some Confuciusornis fossils, described in 2013, even included medullary bone, a spongy tissue found in female birds that are sexually mature, Live Science previously reported.

Another piece of fossil evidence links ancient birds to their modern relatives through their digestion, in the form of the earliest known bird pellet — a mass of indigestible fish bones coughed up by a Cretaceous avian in China around 120 million years ago.
Fly, robin, fly

One defining feature of birds is their ability to fly, requiring large forelimbs covered with asymmetrically-shaped feathers and roped in powerful muscles, O'Connor said.

"In the lineage evolving towards birds, most likely a lineage within the Troodontidae [a family of birdlike theropods], flight is what separates birds from their closest non-avian dinosaur (probable troodontid) kin," said O'Connor.

Then, after the evolution of flight, the small bones in birds' hands "become reduced and fused up to create this kind of stiffened structure that supports the feathers of the wing," Clarke said.

After the extinction of the non-avian dinosaurs at the end of the Cretaceous period, birds continued to evolve and diversify, developing more specialized features related to flight, such as an elongated structure in their breastbones (called a keel), and powerful pectoralis muscles to power the downstroke during flight, Clarke said.

"You see bigger and bigger pectoralis that are associated with this deep keel. And that evolved after the origin of flight and is present in living birds," she said.

Today, there are approximately 10,000 bird species worldwide. Birds might be as tiny as a hummingbird or as big as an ostrich; they might soar like an eagle or dive like a penguin. Nevertheless, they still belong to the same group of theropod dinosaurs that hatched Archaeopteryx 150 million years ago.

So, the next time you wonder what dinosaurs may have looked like when they walked the Earth, look no farther than the seagull eyeing your french fries at the beach, the crow scolding you from a fence, or the nearest pigeon pecking at crumbs on the sidewalk.



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First Living Robots Created by Assembling Living Cells From Frogs Into Entirely New Life-Forms
TOPICS:
By UNIVERSITY OF VERMONT JANUARY 15, 2020
Xenobots
Cells being manipulated and assembled. Credit: Douglas Blackiston, Tufts University

Tiny ‘xenobots’ assembled from cells promise advances from drug delivery to toxic waste clean-up.

A book is made of wood. But it is not a tree. The dead cells have been repurposed to serve another need.
Now a team of scientists has repurposed living cells—scraped from frog embryos—and assembled them into entirely new life-forms. These millimeter-wide “xenobots” can move toward a target, perhaps pick up a payload (like a medicine that needs to be carried to a specific place inside a patient)—and heal themselves after being cut.
“These are novel living machines,” says Joshua Bongard, a computer scientist and robotics expert at the University of Vermont who co-led the new research. “They’re neither a traditional robot nor a known species of animal. It’s a new class of artifact: a living, programmable organism.”
The new creatures were designed on a supercomputer at UVM—and then assembled and tested by biologists at Tufts University. “We can imagine many useful applications of these living robots that other machines can’t do,” says co-leader Michael Levin who directs the Center for Regenerative and Developmental Biology at Tufts, “like searching out nasty compounds or radioactive contamination, gathering microplastic in the oceans, traveling in arteries to scrape out plaque.”
The results of the new research were published on January 13, 2020, in the Proceedings of the National Academy of Sciences.
A team of scientists at the University of Vermont and Tufts University designed living robots on a UVM supercomputer. Then, at Tufts, they re-purposed living frog cells — and assembled them into entirely new life-forms. These tiny ‘xenobots’ can move on their own, circle a target and heal themselves after being cut. These novel living machines are neither a traditional robot nor a known species of animal. They’re a new class of artifact: a living, programmable organism. They could, one day, be used for tasks as varied as searching out radioactive contamination, gathering microplastic in the oceans, or traveling in human arteries to scrape out plaque.

Bespoke Living Systems

People have been manipulating organisms for human benefit since at least the dawn of agriculture, genetic editing is becoming widespread, and a few artificial organisms have been manually assembled in the past few years—copying the body forms of known animals.
But this research, for the first time ever, “designs completely biological machines from the ground up,” the team writes in their new study.
With months of processing time on the Deep Green supercomputer cluster at UVM’s Vermont Advanced Computing Core, the team—including lead author and doctoral student Sam Kriegman—used an evolutionary algorithm to create thousands of candidate designs for the new life-forms. Attempting to achieve a task assigned by the scientists—like locomotion in one direction—the computer would, over and over, reassemble a few hundred simulated cells into myriad forms and body shapes. As the programs ran—driven by basic rules about the biophysics of what single frog skin and cardiac cells can do—the more successful simulated organisms were kept and refined, while failed designs were tossed out. After a hundred independent runs of the algorithm, the most promising designs were selected for testing.
Then the team at Tufts, led by Levin and with key work by microsurgeon Douglas Blackiston—transferred the in silico designs into life. First they gathered stem cells, harvested from the embryos of African frogs, the species Xenopus laevis. (Hence the name “xenobots.”) These were separated into single cells and left to incubate. Then, using tiny forceps and an even tinier electrode, the cells were cut and joined under a microscope into a close approximation of the designs specified by the computer.
A time-lapse recording of cells being manipulated and assembled, using in silico designs to create in vivo living machines, called xenobots. These novel living robots were created by a team from Tufts University and the University of Vermont.
Assembled into body forms never seen in nature, the cells began to work together. The skin cells formed a more passive architecture, while the once-random contractions of heart muscle cells were put to work creating ordered forward motion as guided by the computer’s design, and aided by spontaneous self-organizing patterns—allowing the robots to move on their own.
These reconfigurable organisms were shown to be able move in a coherent fashion—and explore their watery environment for days or weeks, powered by embryonic energy stores. Turned over, however, they failed, like beetles flipped on their backs.
Later tests showed that groups of xenobots would move around in circles, pushing pellets into a central location—spontaneously and collectively. Others were built with a hole through the center to reduce drag. In simulated versions of these, the scientists were able to repurpose this hole as a pouch to successfully carry an object. “It’s a step toward using computer-designed organisms for intelligent drug delivery,” says Bongard, a professor in UVM’s Department of Computer Science and Complex Systems Center.

Living Technologies

Many technologies are made of steel, concrete or plastic. That can make them strong or flexible. But they also can create ecological and human health problems, like the growing scourge of plastic pollution in the oceans and the toxicity of many synthetic materials and electronics. “The downside of living tissue is that it’s weak and it degrades,” say Bongard. “That’s why we use steel. But organisms have 4.5 billion years of practice at regenerating themselves and going on for decades.” And when they stop working—death—they usually fall apart harmlessly. “These xenobots are fully biodegradable,” say Bongard, “when they’re done with their job after seven days, they’re just dead skin cells.”
Joshua Bongard, University of Vermont
Robotics expert Joshua Bongard, a computer scientist at the University of Vermont, co-led new research that led to the creation of a new class of artifact: a living, programmable organism a called xenobot. Credit: Joshua Brown, UVM
Your laptop is a powerful technology. But try cutting it in half. Doesn’t work so well. In the new experiments, the scientists cut the xenobots and watched what happened. “We sliced the robot almost in half and it stitches itself back up and keeps going,” says Bongard. “And this is something you can’t do with typical machines.”

Cracking the Code

Both Levin and Bongard say the potential of what they’ve been learning about how cells communicate and connect extends deep into both computational science and our understanding of life. “The big question in biology is to understand the algorithms that determine form and function,” says Levin. “The genome encodes proteins, but transformative applications await our discovery of how that hardware enables cells to cooperate toward making functional anatomies under very different conditions.”
To make an organism develop and function, there is a lot of information sharing and cooperation—organic computation—going on in and between cells all the time, not just within neurons. These emergent and geometric properties are shaped by bioelectric, biochemical, and biomechanical processes, “that run on DNA-specified hardware,” Levin says, “and these processes are reconfigurable, enabling novel living forms.”
The scientists see the work presented in their new PNAS study—”A scalable pipeline for designing reconfigurable organisms,”—as one step in applying insights about this bioelectric code to both biology and computer science. “What actually determines the anatomy towards which cells cooperate?” Levin asks. “You look at the cells we’ve been building our xenobots with, and, genomically, they’re frogs. It’s 100% frog DNA—but these are not frogs. Then you ask, well, what else are these cells capable of building?”
“As we’ve shown, these frog cells can be coaxed to make interesting living forms that are completely different from what their default anatomy would be,” says Levin. He and the other scientists in the UVM and Tufts team—with support from DARPA’s Lifelong Learning Machines program and the National Science Foundation—believe that building the xenobots is a small step toward cracking what he calls the “morphogenetic code,” providing a deeper view of the overall way organisms are organized—and how they compute and store information based on their histories and environment.

Future Shocks

Many people worry about the implications of rapid technological change and complex biological manipulations. “That fear is not unreasonable,” Levin says. “When we start to mess around with complex systems that we don’t understand, we’re going to get unintended consequences.” A lot of complex systems, like an ant colony, begin with a simple unit—an ant—from which it would be impossible to predict the shape of their colony or how they can build bridges over water with their interlinked bodies.
“If humanity is going to survive into the future, we need to better understand how complex properties, somehow, emerge from simple rules,” says Levin. Much of science is focused on “controlling the low-level rules. We also need to understand the high-level rules,” he says. “If you wanted an anthill with two chimneys instead of one, how do you modify the ants? We’d have no idea.”
“I think it’s an absolute necessity for society going forward to get a better handle on systems where the outcome is very complex,” Levin says. “A first step towards doing that is to explore: how do living systems decide what an overall behavior should be and how do we manipulate the pieces to get the behaviors we want?”
In other words, “this study is a direct contribution to getting a handle on what people are afraid of, which is unintended consequences,” Levin says—whether in the rapid arrival of self-driving cars, changing gene drives to wipe out whole lineages of viruses, or the many other complex and autonomous systems that will increasingly shape the human experience.
“There’s all of this innate creativity in life,” says UVM’s Josh Bongard. “We want to understand that more deeply—and how we can direct and push it toward new forms.”
Reference: “A scalable pipeline for designing reconfigurable organisms” by Sam Kriegman, Douglas Blackiston, Michael Levin and Josh Bongard, 13 January 2020, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.1910837117

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