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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."
These alien-like creatures are virtually invisible in the deep sea.
- A team of marine biologists used nets to catch 16 species of deep-sea fish that have evolved the ability to be virtually invisible to prey and predators.
- "Ultra-black" skin seems to be an evolutionary adaptation that helps fish camouflage themselves in the deep sea, which is illuminated by bioluminescent organisms.
- There are likely more, and potentially much darker, ultra-black fish lurking deep in the ocean.
The Pacific blackdragon
Credit: Karen Osborn/Smithsonian<p>When researchers first saw the deep-sea species, it wasn't immediately obvious that their skin was ultra-black. Then, marine biologist Karen Osborn, a co-author on the new paper, noticed something strange about the photos she took of the fish.</p><p style="margin-left: 20px;">"I had tried to take pictures of deep-sea fish before and got nothing but these really horrible pictures, where you can't see any detail," Osborn told <em><a href="https://www.wired.com/story/meet-the-ultra-black-vantafish/" target="_blank">Wired</a></em>. "How is it that I can shine two strobe lights at them and all that light just disappears?"</p><p>After examining samples of fish skin under the microscope, the researchers discovered that the fish skin contains a layer of organelles called melanosomes, which contain melanin, the same pigment that gives color to human skin and hair. This layer of melanosomes absorbs most of the light that hits them.</p>
A crested bigscale
Credit: Karen Osborn/Smithsonian<p style="margin-left: 20px;">"But what isn't absorbed side-scatters into the layer, and it's absorbed by the neighboring pigments that are all packed right up close to it," Osborn told <em>Wired</em>. "And so what they've done is create this super-efficient, very-little-material system where they can basically build a light trap with just the pigment particles and nothing else."</p><p>The result? Strange and terrifying deep-sea species, like the crested bigscale, fangtooth, and Pacific blackdragon, all of which appear in the deep sea as barely more than faint silhouettes.</p>
David Csepp, NMFS/AKFSC/ABL<p>But interestingly, this unique disappearing trick wasn't passed on to these species by a common ancestor. Rather, they each developed it independently. As such, the different species use their ultra-blackness for different purposes. For example, the threadfin dragonfish only has ultra-black skin during its adolescent years, when it's rather defenseless, as <em>Wired</em> <a href="https://www.wired.com/story/meet-the-ultra-black-vantafish/" target="_blank">notes</a>.</p><p>Other fish—like the <a href="http://onebugaday.blogspot.com/2016/06/a-new-anglerfish-oneirodes-amaokai.html" target="_blank">oneirodes species</a>, which use bioluminescent lures to bait prey—probably evolved ultra-black skin to avoid reflecting the light their own bodies produce. Meanwhile, species like <em>C. acclinidens</em> only have ultra-black skin around their gut, possibly to hide light of bioluminescent fish they've eaten.</p><p>Given that these newly described species are just ones that this team found off the coast of California, there are likely many more, and possibly much darker, ultra-black fish swimming in the deep ocean. </p>
Using machine-learning technology, the genealogy company My Heritage enables users to animate static images of their relatives.
- Deep Nostalgia uses machine learning to animate static images.
- The AI can animate images by "looking" at a single facial image, and the animations include movements such as blinking, smiling and head tilting.
- As deepfake technology becomes increasingly sophisticated, some are concerned about how bad actors might abuse the technology to manipulate the pubic.
My Heritage/Deep Nostalgia<p>But that's not to say the animations are perfect. As with most deep-fake technology, there's still an uncanny air to the images, with some of the facial movements appearing slightly unnatural. What's more, Deep Nostalgia is only able to create deepfakes of one person's face from the neck up, so you couldn't use it to animate group photos, or photos of people doing any sort of physical activity.</p>
My Heritage/Deep Nostalgia<p>But for a free deep-fake service, Deep Nostalgia is pretty impressive, especially considering you can use it to create deepfakes of <em>any </em>face, human or not. </p>
How long should one wait until an idea like string theory, seductive as it may be, is deemed unrealistic?
- How far should we defend an idea in the face of contrarian evidence?
- Who decides when it's time to abandon an idea and deem it wrong?
- Science carries within it its seeds from ancient Greece, including certain prejudices of how reality should or shouldn't be.
Plato used the allegory of the cave to explain that what humans see and experience is not the true reality.
Credit: Gothika via Wikimedia Commons CC 4.0<p>When scientists and mathematicians use the term <em>Platonic worldview</em>, that's what they mean in general: The unbound capacity of reason to unlock the secrets of creation, one by one. Einstein, for one, was a believer, preaching the fundamental reasonableness of nature; no weird unexplainable stuff, like a god that plays dice—his tongue-in-cheek critique of the belief that the unpredictability of the quantum world was truly fundamental to nature and not just a shortcoming of our current understanding. Despite his strong belief in such underlying order, Einstein recognized the imperfection of human knowledge: "What I see of Nature is a magnificent structure that we can comprehend only very imperfectly, and that must fill a thinking person with a feeling of humility." (Quoted by Dukas and Hoffmann in <em>Albert Einstein, The Human Side: Glimpses from His Archives</em> (1979), 39.)</p> <p>Einstein embodies the tension between these two clashing worldviews, a tension that is still very much with us today: On the one hand, the Platonic ideology that the fundamental stuff of reality is logical and understandable to the human mind, and, on the other, the acknowledgment that our reasoning has limitations, that our tools have limitations and thus that to reach some sort of final or complete understanding of the material world is nothing but an impossible, <a href="https://www.amazon.com/dp/B01K2JTGIA?tag=bigthink00-20&linkCode=ogi&th=1&psc=1" target="_blank" rel="noopener noreferrer">semi-religious dream</a>.</p>