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Mystery virus found with mostly unknown DNA
The origin and phylogeny of the Yaravirus are not yet clear.
- A virus has been found whose DNA is 90% absolutely unfamiliar.
- Scientists have no real idea what it developed from, or how.
- Viruses used to be thought of as simple, jumbles of things — not so much any more.
In Lake Pampulha in the Brazilian city of Belo Horizonte, scientists found an amoeba virus unlike anything seen before. Named after Yara, the mother of waters in Brazilian mythology, 90 percent of the Yaravirus's genome is comprised of genes never before described. Sifting through the publicly available database of 8,535 metagenomes produced nothing like it, and only 6 of its genes seem to be distantly related to known homologs.
While "most of the known viruses of amoeba have been seen to share many features that eventually prompted authors to classify them into common evolutionary groups," according to the researchers in a preprint paper, Yaravirus is "a new lineage of amoebal virus with a puzzling origin and phylogeny."
Not so simple after all
Giant viruses compared in size to to other common viruses and bacteria
Image source: Meletios Verras/Shutterstock
The recent discovery of "giant viruses" — a group to which Yaravirus doesn't belong — has revealed that the organisms are capable of things previously thought beyond their reach.
To begin with, the giant variety is roughly 10 times larger than, say, the influenza virus. With that size comes complexity, too — the flu virus has 11 genes, while a giant virus can have as many as 2,500. And that complexity has turned thinking about viruses on its head.
Conventional wisdom had been that viruses were relatively disorganized agglomerations of stray genetic material incapable of reproduction, and thus dependent on host cells for sustenance. It was previously believed that hijacking their host's metabolisms was the only way that they could survive, and that they were so incredibly simple that they weren't universally considered to be "alive."
Giant viruses, which derive their name from their oversized protein shell or capsid, have genomes complex enough to engage in the synthesis of proteins. They are also capable of DNA repair, replications, transcription, and translation, which has changed the way scientists think about these supposedly simple organisms.
For the scientists who found the Yaravirus, virologists Bernard La Scola from Aix-Marseille University in France and Jônatas S. Abrahão from Brazil's Federal University of Minas Gerais, the discovery is just the latest enigmatic virus they've discovered. Last year, they found a pair of giant viruses (two other viral outliers) which they named as two flavors of Tupanvirus: Tupanvirus soda lake and Tupanvirus deep ocean, each after the extreme aquatic environments in which they were found. They belong to the Mimiviridae virus family, shown above.
Lake Pampulha, where Yaravirus was found
Image source: Teófilo Baltor
Yaravirus represents the latest surprise in viruses, but it's not a giant virus —it's comprised of small particles about 80 nm in size. It's simply that its genome is so novel.
The paper notes, "Using standard protocols, our very first genetic analysis was unable to find any recognizable sequences of capsid or other classical viral genes in Yaravirus [our emphasis]." This leaves authors LaScola and Abrahão no option but to guess what it is. They suggest that it's likely to be the first found example of some unknown amoeba virus group, or perhaps a much-degraded version of some unknown giant virus. They can only conclude, "The amount of unknown proteins composing the Yaravirus particles reflects the variability existing in the viral world and how much potential of new viral genomes are still to be discovered."
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Construction of the $500 billion dollar tech city-state of the future is moving ahead.
- The futuristic megacity Neom is being built in Saudi Arabia.
- The city will be fully automated, leading in health, education and quality of life.
- It will feature an artificial moon, cloud seeding, robotic gladiators and flying taxis.
The Red Sea area where Neom will be built:
Saudi Arabia Plans Futuristic City, "Neom" (Full Promotional Video)<span style="display:block;position:relative;padding-top:56.25%;" class="rm-shortcode" data-rm-shortcode-id="c646d528d230c1bf66c75422bc4ccf6f"><iframe type="lazy-iframe" data-runner-src="https://www.youtube.com/embed/N53DzL3_BHA?rel=0" width="100%" height="auto" frameborder="0" scrolling="no" style="position:absolute;top:0;left:0;width:100%;height:100%;"></iframe></span>
Frequent shopping for single items adds to our carbon footprint.
- A new study shows e-commerce sites like Amazon leave larger greenhouse gas footprints than retail stores.
- Ordering online from retail stores has an even smaller footprint than going to the store yourself.
- Greening efforts by major e-commerce sites won't curb wasteful consumer habits. Consolidating online orders can make a difference.
A pile of recycled cardboard sits on the ground at Recology's Recycle Central on January 4, 2018 in San Francisco, California.
Photo by Justin Sullivan/Getty Images<p>A large part of the reason is speed. In a competitive market, pure players use the equation, <em>speed + convenience</em>, to drive adoption. This is especially relevant to the "last mile" GHG footprint: the distance between the distribution center and the consumer.</p><p>Interestingly, the smallest GHG footprint occurs when you order directly from a physical store—even smaller than going there yourself. Pure players, such as Amazon, are the greatest offenders. Variables like geographic location matter; the team looked at shopping in the UK, the US, China, and the Netherlands. </p><p>Sadegh Shahmohammadi, a PhD student at the Netherlands' Radboud University and corresponding author of the paper, <a href="https://www.cnn.com/2020/02/26/tech/greenhouse-gas-emissions-retail/index.html" target="_blank">says</a> the above "pattern holds true in countries where people mostly drive. It really depends on the country and consumer behavior there."</p><p>The researchers write that this year-and-a-half long study pushes back on previous research that claims online shopping to be better in terms of GHG footprints.</p><p style="margin-left: 20px;">"They have, however, compared the GHG emissions per shopping event and did not consider the link between the retail channels and the basket size, which leads to a different conclusion than that of the current study."</p><p>Online retail is where convenience trumps environment: people tend to order one item at a time when shopping on pure player sites, whereas they stock up on multiple items when visiting a store. Consumers will sometimes order a number of separate items over the course of a week rather than making one trip to purchase everything they need. </p><p>While greening efforts by online retailers are important, until a shift in consumer attitude changes, the current carbon footprint will be a hard obstacle to overcome. Amazon is trying to have it both ways—carbon-free and convenience addicted—and the math isn't adding up. If you need to order things, do it online, but try to consolidate your purchases as much as possible.</p><p>--</p><p><em>Stay in touch with Derek on <a href="http://www.twitter.com/derekberes" target="_blank">Twitter</a>, <a href="https://www.facebook.com/DerekBeresdotcom" target="_blank">Facebook</a> and <a href="https://derekberes.substack.com/" target="_blank">Substack</a>. His next book is</em> "<em>Hero's Dose: The Case For Psychedelics in Ritual and Therapy."</em></p>
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