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Mon, 06 Dec 2021
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Evolution and the biopolymer problem

Structure of RNA

The structure of the RNA for the large ribosomal subunit in E. Coli. (About 3000 nucleotides.) The ribosome also has a small RNA sub unit (~1500 nt) and about 50 proteins. A happy accident?
We address the following hypothesis: If purely natural processes produced the first living organism, such processes must have conveniently strung together perfect sequences of monomers (i.e., the basic building blocks of life: amino acids, nucleotides, lipids, and sugars) to form the essential biopolymers of life: RNA, DNA, proteins, and glycans. Thankfully, we know enough about natural processes to provide a definitive answer to this hypothesis.

We start by assuming that nature could form the monomers out of simpler molecules, select them out of a morass of other harmful and undesired molecules, concentrate them in one location, and accomplish this faster than the natural degradation of the monomers. (An earlier Long Story Short episode on the origin of life clearly refuted these assumptions.) A natural process to form biopolymers must then overcome several additional barriers.


Strange things happening in Earth's atmosphere over the North pole - NASA launches rocket to investigate

Cusp around Earth
© Andøya Space Center/Trond Abrahamsen
North of Norway over the Norwegian and Greenland Seas, a magnetic bubble known as the cusp surrounds Earth and dips inward. Some air in the cusp is unusually dense, and the CREX-2 mission aims to understand why.
Strange things happen in Earth's atmosphere at high latitudes. Around local noon, when the Sun is at its highest point, a funnel-shaped gap in our planet's magnetic field passes overhead. Earth's magnetic field shields us from the solar wind, the stream of charged particles spewing off the Sun. The gap in that field, called the polar cusp, allows the solar wind a direct line of access to Earth's atmosphere.

Radio and GPS signals behave strangely when they travel through this part of the sky. In the last 20 years, scientists and spacecraft operators noticed something else unusual as spacecraft pass through this region: They slow down.

"At around 250 miles above Earth, spacecraft feel more drag, sort of like they've hit a speed bump," said Mark Conde, a physicist at the University of Alaska Fairbanks and the principal investigator for NASA's Cusp Region Experiment-2, or CREX-2, sounding rocket mission. That's because the air in the cusp is noticeably denser than air elsewhere in the spacecrafts' orbits around Earth. But no one knows why, or how. By understanding the forces at play in the cusp, scientists hope to better anticipate changes in spacecraft trajectories.

The CREX-2 payload was successfully launched at 3:25 a.m. EST on December 1, 2021, from the Andøya Space Center in Norway. The four-stage Oriole IV sounding rocket carried the payload to an apogee of 392 miles. Preliminary reports are that the flight was successful and the ampules carrying the vapors performed as planned. Good data was received including data from the vapor imaging team.


China's lunar rover spots cube-shaped 'mystery hut' on far side of the moon

It's likely a large boulder excavated by an ancient lunar impact.
Cube Shaped Lunar Object
© CNSA/Our Space
An image from China's Yutu 2 showing a cube-shaped object on the horizon on the far side of the moon.
China's Yutu 2 rover has spotted a mystery object on the horizon while working its way across Von Kármán crater on the far side of the moon.

Yutu 2 spotted a cube-shaped object on the horizon to the north and roughly 260 feet (80 meters) away in November during the mission's 36th lunar day, according to a Yutu 2 diary published by Our Space, a Chinese language science outreach channel affiliated with the China National Space Administration (CNSA).

Our Space referred to the object as a "mystery hut" (神秘小屋/shenmi xiaowu), but this a placeholder name rather than an accurate description.

Team scientists have expressed a strong interest in the object and Yutu 2 is now expected to spend the next 2-3 lunar days (2-3 Earth months) traversing lunar regolith and avoiding craters to get a closer look, so updates can be expected.

A likely explanation for the shape would be a large boulder which has been excavated by an impact event.


New form of biological self-replication or overexcited hype?

Model of a self-replicating xenobot
© Evolution News
Model of a self-replicating xenobot
Scientists at the University of Vermont, Tufts University, and the Wyss Institute for Biologically Inspired Engineering at Harvard University claim to have created the first self-replicating xenobot. Xenobots are artificially interconnected biological tissues whose arrangements are determined by some algorithm. An announcement at the Wyss Institute website lauds the researchers for having "discovered an entirely new form of biological reproduction" and for applying their discovery to "create the first-ever, self-replicating living robots." CNN science writer Katie Hunt described the research in equally glowing terms in her article "World's first living robots can now reproduce, scientists say":
The xenobots are very early technology — think of a 1940s computer — and don't yet have any practical applications. However, this combination of molecular biology and artificial intelligence could potentially be used in a host of tasks in the body and the environment, according to the researchers. This may include things like collecting microplastics in the oceans, inspecting root systems and regenerative medicine.
Achieving true self-replication would be a historical accomplishment, but are these descriptions accurate or more appropriately categorized as hype.

Microscope 1

'Pac-Man' blobs become world's first self-replicating biological robots

pacman xenobots self replicating artificial life
© Douglas Blackiston and Sam Kriegman
An artificial-intelligence-generated Pac-Man shaped parent xenobot scoops up a sphere of stem cells.
These bio-bots are made from frog cells.

Tiny groups of cells shaped like Pac-Man are the world's first self-replicating biological robots.

The tiny bots are made from the skin cells of frogs, but they don't reproduce by mitosis or meiosis or any of the other ways cells divide and replicate in normal circumstances. Instead, they build more of themselves from raw materials — free-floating frog skin cells — creating multiple generations of nearly identical organisms.

In action, the bots (dubbed "xenobots" by their inventors), even look like Pac-Man. They move in wild corkscrews and spirals, their open "mouths" scooping the free-floating skin cells into piles. The cells tend to adhere, or stick together, once put in contact with one another, so these piles gradually meld into new, spiraling xenobots.

Comment: Kreigman's last remarks could almost be taken as an unconscious endorsement of intelligent design.


Study suggests Sun is likely an unaccounted source of the Earth's water

The sun, solar winds and asteroid Itokawa.
© Curtin University
The sun, solar winds and asteroid Itokawa.
A University of Glasgow-led international team of researchers including those from Curtin's Space Science and Technology Centre (SSTC) found the solar wind, comprised of charged particles from the Sun largely made of hydrogen ions, created water on the surface of dust grains carried on asteroids that smashed into the Earth during the early days of the Solar System.

SSTC Director, John Curtin Distinguished Professor Phil Bland said the Earth was very water-rich compared to other rocky planets in the Solar System, with oceans covering more than 70 percent of its surface, and scientists had long puzzled over the exact source of it all.

"An existing theory is that water was carried to Earth in the final stages of its formation on C-type asteroids, however previous testing of the isotopic 'fingerprint' of these asteroids found they, on average, didn't match with the water found on Earth meaning there was at least one other unaccounted for source," Professor Bland said.

"Our research suggests the solar wind created water on the surface of tiny dust grains and this isotopically lighter water likely provided the remainder of the Earth's water.

"This new solar wind theory is based on meticulous atom-by-atom analysis of miniscule fragments of an S-type near-Earth asteroid known as Itokawa, samples of which were collected by the Japanese space probe Hayabusa and returned to Earth in 2010.


Ultra-dense exoplanet seemingly made of solid iron has been spotted by astronomers orbiting a nearby star

According to the Interactive Extra-Solar Planets Catalogue, humans have spotted some 4,878 planets in 3,604 solar systems other than our own. Termed exoplanets, only few have been found in the habitable zone around their parent star, and none have been confirmed to have life.

There are few things that are standard or typical across the universe, but the exoplanet GJ 367b still manages to stick out as an oddball in Earthling discoveries. Astronomers at the German Aerospace Center's Institute of Planetary Research, using data gathered by NASA's Transiting Exoplanet Survey Satellite (TESS), reported the find in a paper published in Science on Thursday.

© NASA/JPL-Caltech
Artist’s rendering of TOI-1231 b, a Neptune-like planet about 90 light-years away from Earth.


Second exoplanet with four stars discovered
Darker than asphalt: Hubble telescope captures images of pitch-black exoplanet
'Behaving like a comet': Astronomers discover enormous exoplanet with wild, slingshot-like orbit

Blue Planet

Recycling of tectonic plates found to be a key driver of Earth's oxygen budget

Parinacota Volcano Atacama Desert  Chile
© Glenn Gaetan
Parinacota Volcano, in the Atacama Desert of Chile.
A new study co-led by a Cornell researcher has identified serpentinite -- a green rock that looks a bit like snakeskin and holds fluids in its mineral structures -- as a key driver of the oxygen recycling process, which helped create and maintain the sustaining atmosphere for life on Earth.

"This cycle is a really a big deal," said Esteban Gazel, associate professor of earth and atmospheric sciences in Cornell's College of Engineering, and co-lead author on the study. "In the end, we're talking about the budget of oxygen on the planet and how that gets balanced through processes like subduction."

Earth is constantly recycling its life-giving supply of water and oxygen as tectonic plates sink, or subduct, deep into the planet. Elements are carried down as one piece of the planet's crust slips below another, and resurface through the resulting volcanoes.

It's a critical process, but how, exactly, subduction recycles oxygen and allows it to interact with other elements has always been a topic of debate among geoscientists.

Comment: Gazel has refined and expanded the theory which was proposed in 2010

Geologist's Discoveries Resolve Debate About Oxygen In Earth's Mantle


New dinosaur species from Chile had a unique slashing tail

© Mauricio Alvarez
Segouros illustration
Fossils found in Chile are from a strange-looking dog-sized dinosaur species that had a unique slashing tail weapon, scientists reported Wednesday.

Some dinosaurs had spiked tails they could use as stabbing weapons and others had tails with clubs. The new species, described in a study in the journal Nature, has something never seen before on any animal: seven pairs of "blades" laid out sideways like a slicing weapon used by ancient Aztec warriors, said lead author Alex Vargas.

"It's a really unusual weapon," said Vargas, a University of Chile paleontologist. "Books on prehistoric animals for kids need to update and put this weird tail in there. ... It just looks crazy."

The plant-eating critter had a combination of traits from different species that initially sent paleontologists down the wrong path. The back end, including its tail weapon, seemed similar to a stegosaurus, so the researchers named it stegouros elengassen.
© Lios Perez Lopez
Stegouros illustration

Arrow Down

Breakthrough infection study compares decline in COVID vaccine effectiveness: Pfizer vs Moderna vs J&J

3 vaccines
© Unknown
Study in Science of more than 780,000 Veterans is the first to compare waning protection rates across all three vaccine types available to most Americans and to directly report death rates after breakthrough infection.

As COVID-19 breakthrough infections continue to emerge in some vaccine recipients and health authorities are developing policies around booster vaccinations, national data on COVID-19 vaccine breakthrough infections is inadequate but urgently needed. Now a study from the Public Health Institute, the Veterans Affairs Medical Center and the University of Texas Health Science Center published today in the journal Science analyzed COVID infection by vaccination status among 780,225 Veterans.

Researchers found that protection against any COVID-19 infection declined for all vaccine types, with overall vaccine protection declining from 87.9% in February to 48.1% by October 2021.
  • The decline was greatest for the Janssen (Johnson & Johnson) vaccine, with protection against infection declining from 86.4% in March to 13% in September
  • Declines for PfizerBioNTech were from 86.9% to 43.3%
  • Declines for Moderna were 89.2% to 58%.
Covid Breakthrough infections chart
© Public Health Institute
COVID Breakthrough Infections

Comment: The results and validations in this study seem to be criteria-based on partial evidence versus detailed and complete analysis. It appears some crucial factors have been dismissed or ignored.