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5 non-coding RNAs stepping out of DNA's shadow

Tina Hesman Saey
Science News
Wed, 10 Apr 2019 14:10 UTC
RNA molecules health roles
© James Provost
These molecules play crucial roles in human health and disease
These molecules play crucial roles in human health and disease

DNA is the glamour molecule of the genetics world. Its instructions are credited with defining appearance, personality and health. And the proteins that result from DNA's directives get credit for doing most of the work in our cells. RNA, if mentioned at all, is considered a mere messenger, a go-between - easy to ignore. Until now.

RNAs, composed of strings of genetic letters called nucleotides, are best known for ferrying instructions from the genes in our DNA to ribosomes, the machines in cells that build proteins. But in the last decade or so, researchers have realized just how much more RNAs can do - how much they control, even. In particular, scientists are finding RNAs that influence health and disease yet have nothing to do with being messengers.

The sheer number and variety of noncoding RNAs, those that don't ferry protein-building instructions, give some clues to their importance. So far, researchers have cataloged more than 25,000 genes with instructions for noncoding RNAs in the human genome, or genetic instruction book (SN: 10/13/18, p. 5). That's more than the estimated 21,000 or so genes that code for proteins.
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Water

Scientists discover an edible mushroom that eats plastic and could potentially clean landfills

Elias Marat
The Mind Unleashed
Tue, 02 Apr 2019 00:00 UTC
plastic eating mushroom
Whether we like it or not, our society has become completely reliant on plastic. From food preservation to water transportation, computer technology to healthcare and medicine, plastic can be found in nearly every facet of the human experience.

But as we well know, plastic is a double-edged sword, with massive amounts of plastic waste not only piling up in landfills, but floating in the most remote depths of our oceans and water supplies. And despite our knowledge of plastic's harmful effects on the environment, we've become so reliant on plastic that there seems to be no end in sight. In fact, plastic production is growing on a yearly basis - and posing a potentially mortal threat to us all.

However, a newly-discovered type of mushroom could not only play a crucial role in slashing plastic pollution, but could have myriad other uses in addressing the environmental crises the planet faces.

Discovered in 2012 by Yale University students, Pestalotiopsis microspora is a rare species of mushroom from the Amazon rainforest that's capable of subsisting on a diet of pure plastic, or more accurately, the main ingredient in plastic - polyurethane - before converting the human-made ingredient into purely organic matter.

Comment: Hardly a month goes by that someone doesn't discover an excellent application for some form of mushroom!

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Info

New state of matter: Elements can be solid and liquid at same time


University of Edinburgh
Tue, 09 Apr 2019 20:28 UTC
Potassium
© Aleksander/Fotolia
Scientists have discovered a new state of physical matter in which atoms can exist as both solid and liquid simultaneously.

Until now, the atoms in physical material were understood to exist typically in one of three states - solid, liquid or gas.

Researchers have found, however, that some elements can, when subjected to extreme conditions, take on the properties of both solid and liquid states.

Novel structure

Applying high pressures and temperatures to potassium - a simple metal - creates a state in which most of the element's atoms form a solid lattice structure, the findings show.

However, the structure also contains a second set of potassium atoms that are in a fluid arrangement.

Under the right conditions, over half a dozen elements - including sodium and bismuth - are thought to be capable of existing in the newly discovered state, researchers say.

Until now, it was unclear if the unusual structures represented a distinct state of matter, or existed as transition stages between two distinct states.
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X

Poverty's mark on our genes

Thomas McDade
Northwestern University
Thu, 04 Apr 2019 00:00 UTC
DNA strand
© ken/Fotolia
A new Northwestern University study challenges prevailing understandings of genes as immutable features of biology that are fixed at conception.

Previous research has shown that socioeconomic status (SES) is a powerful determinant of human health and disease, and social inequality is a ubiquitous stressor for human populations globally. Lower educational attainment and/or income predict increased risk for heart disease, diabetes, many cancers and infectious diseases, for example. Furthermore, lower SES is associated with physiological processes that contribute to the development of disease, including chronic inflammation, insulin resistance and cortisol dysregulation.

In this study, researchers found evidence that poverty can become embedded across wide swaths of the genome. They discovered that lower socioeconomic status is associated with levels of DNA methylation (DNAm) -- a key epigenetic mark that has the potential to shape gene expression -- at more than 2,500 sites, across more than 1,500 genes.

In other words, poverty leaves a mark on nearly 10 percent of the genes in the genome.
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Igloo

Why Behe is right about polar bears: Part 3 - Unacknowledged discrepancies, inconsistent standards


Evolution News
Tue, 09 Apr 2019 15:19 UTC
polar bear
© Eva Blue via Unsplash
In their second objection to Michael Behe's case in Darwin Devolves, Nathan Lents and Arthur Hunt argue that Behe exaggerates the number of positively selected genes in polar bears that are estimated to have suffered at least one damaging mutation. Or to be more precise, they think Behe's lower limit is overstated, while agreeing with his upper limit. Let's evaluate their claims. Here's what they write:
Now it's getting harder to excuse Behe's exaggeration. Specifically, using one specific predictive algorithm, the authors found that only 7 of the 17 genes with the strongest signatures for positive selection are unequivocally predicted to possess at least one "damaging" mutation. Even Behe's "about half" is just 41%, which means that the lower limit on Behe's estimation is also wrong. It's not 65-83%, it's 41-83%. The range is so wide because computational predictions invariably involve uncertainty.
It's worth noting that they accept the PolyPhen-2 program used by Liu et al. (2014), recognizing it as capable of finding that a protein's function was probably damaged by a mutation. This contradicts objections made by other critics of Behe, answered here in the preceding post.

A Matter of Methodology

Now, everyone knows statistics are easily manipulated. What matters is whether the methodology behind the statistics is sound. Presumably, the closer your method is to that used by authorities published in peer-reviewed papers, the better. Much like we saw in considering the previous objection, Lents and Hunt in their own treatment of Darwin Devolves come up with different numbers from Behe only by using a different methodology than the one used by the paper itself. When you follow the methodology employed by Liu et al., you get numbers like what Behe provides in his book.

Comment: Previous instalments:

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Galaxy

NASA images show how solar wind heats up Jupiter's atmosphere faster and deeper than previously thought


NASA
Mon, 08 Apr 2019 10:16 UTC
Jupiter
© NAOJ and NASA/JPL-Caltech
Scientists used red, blue and yellow to infuse this infrared image of Jupiters atmosphere, which was recorded by the Subaru Telescope on the summit of Mauna Kea, Hawaii on Jan. 12, 2017.
New Earth-based telescope observations show that auroras at Jupiter's poles are heating the planet's atmosphere to a greater depth than previously thought - and that it is a rapid response to the solar wind.

"The solar wind impact at Jupiter is an extreme example of space weather," said James Sinclair of NASA's Jet Propulsion Laboratory in Pasadena, California, who led new research published April 8 in Nature Astronomy. "We're seeing the solar wind having an effect deeper than is normally seen."

Auroras at Earth's poles (known as the aurora borealis at the North Pole and aurora australis at the South Pole) occur when the energetic particles blown out from the Sun (the solar wind) interact with and heat up the gases in the upper atmosphere. The same thing happens at Jupiter, but the new observations show the heating goes two or three times deeper down into its atmosphere than on Earth, into the lower level of Jupiter's upper atmosphere, or stratosphere.

Comment: Evidently the planets within our solar system are intimately connected to our star in ways we've yet to fully comprehend: Also check out SOTT radio's: Behind the Headlines: The Electric Universe - An interview with Wallace Thornhill

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Bizarro Earth

California's 'earthquake pause' is unprecedented

Stephanie Pappas
Live Science
Fri, 05 Apr 2019 15:10 UTC
San Andreas Fault
© Shutterstock
The San Andreas Fault runs through the Carrizo Plain in California.
It's a little too quiet in California, seismically speaking.

The state is experiencing a century-long lull in large, ground-rupturing earthquakes, temblors that actually offset the earth at the surface. The 7.9-magnitude Great San Francisco Earthquake of 1906 was a ground-rupturing quake; photographs taken in its aftermath show roads and fences with new bends and twists.

Now, new research finds that this 100-year earthquake gap is very unlikely to be a statistical fluke. Instead, something geological is probably causing the peaceful period.

"We're unusually quiet," said study co-author Glenn Biasi, a geophysicist at the U.S. Geological Survey (USGS) in Pasadena, California. "The biggest faults and the faults carrying most of the slip have not ponied up."
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Cassiopaea

NASA's new aurora experiment colors the sky in Norway


Live Science
Sat, 06 Apr 2019 12:00 UTC
aurora experiment
© Frank Olsen via Facebook
Auroras are spectacular light shows, but a recent display in the skies over northern Norway was out of this world - sort of.

On Friday (April 5), clusters of purple, blue and yellow lights appeared in the country's night sky; as the ghostly shapes hovered, their eerie glow and unusual formation invited speculation about visiting alien spacecraft.

But extraterrestrials weren't behind the demonstration. It was NASA, launching a new rocket system from Norway to study the flow of winds in Earth's upper atmosphere, representatives of the agency's Wallops Flight Facility in Wallops, Virginia, tweeted that day.

Following the appearance of an aurora that night, NASA created another spectacular light show with chemical compounds, expelled by the Auroral Zone Upwelling Rocket Experiment (AZURE). This is the first of eight rocket missions to launch from Norwegian bases in Andøya and Svalbard. The missions will analyze the interactions of Earth's magnetic field lines and particles from space that bombard our planet, according to a NASA statement.

Comment: There couldn't be a more important time to study our changing atmosphere:

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Network

Scientists discover exotic new patterns of synchronization

Natalie Wolchover
Quanta Magazine
Thu, 04 Apr 2019 12:00 UTC
fireflies
© Spencer Black Blackvisual.com
In a world seemingly filled with chaos, physicists have discovered new forms of synchronization and are learning how to predict and control them.

This time-lapse photo of blue ghost fireflies during mating season was taken in the woods near Brevard.
When the incoherent claps of a crowd suddenly become a pulse, as everyone starts clapping in unison, who decided? Not you; not anyone. Crickets sing in synchrony; metronomes placed side by side sway into lockstep; some fireflies blink together in the dark. All across the United States, the power grid operates at 60 hertz, its innumerable tributaries of alternating current synchronizing of their own accord. Indeed, we live because of synchronization. Neurons in our brains fire in synchronous patterns to operate our bodies and minds, and pacemaker cells in our hearts sync up to generate the beat.

Objects with rhythms naturally synchronize. Yet the phenomenon went entirely undocumented until 1665, when the Dutch physicist and inventor Christiaan Huygens spent a few days sick in bed. A pair of new pendulum clocks - a kind of timekeeping device that Huygens invented - hung side by side on the wall. Huygens noticed that the pendulums swung exactly in unison, always lurching toward each other and then away. Perhaps pressure from the air was synchronizing their swings? He conducted various experiments. Standing a table upright between the clocks had no effect on their synchronization, for instance. But when he rehung the clocks far apart or at right angles to each other, they soon fell out of phase. Huygens eventually inferred that the clocks' "sympathy," as he called it, resulted from the kicks that their swings gave each other through the wall.

Comment: See also: And check out SOTT radio's:

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Snowflake

Why Behe is right about polar bears: Part 2 - The APOB gene and damaging mutations


Evolution News
Mon, 08 Apr 2019 18:31 UTC
polar bear
© Jacqueline Godany via Unsplash.
There is an old joke that goes like this:
Question: When does "damaging" not mean "damaging"?

Answer: When a peer-reviewed paper in a top scientific journal says over 40 times that mutations are predicted to be "damaging," but then an ID guy comes along and cites the paper to suggest the mutations are probably damaging.
Actually that's not an old joke, but maybe someday it will be. Anyway, it perfectly describes what is going on right now with critics of Michael Behe and his argument about mutations in polar bear genes.

In Darwin Devolves, Behe cites a paper in the journal Cell, Liu et al. (2014). He does so as evidence that the adaptive mutations in the polar bear gene APOB were "very likely to be damaging - that is, likely to degrade or destroy the function of the protein" (pp. 16-17). Two ID critics, biologists Nathan Lents and Arthur Hunt, object that Behe is wrong because only "some" but "[d]efinitely not all of them or even most of" the mutations in the gene were probably damaging. They go even further and claim that "the authors [of Liu et al. (2014)] do not expect the polar bear APOB to be broken or damaged" and "There is no evidence for Behe's claim that APOB is degraded or diminished in polar bears."

Comment: See part 1 here:

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