'Obelisks': Entirely New Class of Life Has Been Found in The Human Digestive System t.co/gn7gTd6QFw
— ScienceAlert (@ScienceAlert) January 29, 2024
Obelisks’: Entirely New Class of Life Has Been Found in The Human Digestive System
NATURE
29 January 2024
Peering into the jungle of microbes that live within us, researchers have stumbled across what seem to be an entire new class of virus-like objects.
“It’s insane,” says University of North Carolina cell biologist Mark Peifer, who was not involved in the study, told Elizabeth Pennisi at Science Magazine. “The more we look, the more crazy things we see.”
These mysterious bits of genetic material have no detectable sequences or even structural similarities known to any other biological agents.
So Stanford University biologist Ivan Zheludev and colleagues argue their strange discovery may not be viruses at all, but instead an entirely new group of entities that may help bridge the ancient gap between the simplest genetic molecules and more complex viruses.
“Obelisks comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes,” the researchers write in a preprint paper.
Named after the highly-symmetrical, rod-like structures formed by its twisted lengths of RNA, the Obelisks’ genetic sequences are only around 1,000 characters (nucleotides) in size. In fact, this brevity is likely one of the reasons we’ve failed to notice them previously.
…just as scientists are exploring the surface of planets in the search for life, we’re learning staggering new things much closer to home about the human body.
In fact, experts have discovered that there’s an entire lifeform that we’re only just learning about which lives inside humans.
New research has found virus-like genetic materials, called Obelisks, hitherto unnoticed by the scientific community.
According to the authors of new research, including Stanford University biologist Ivan Zheludev, the makeup of the material doesn’t bear similarities with any other biological agents, which has led them to believe that Obelisks could provide a link between simple genetic molecules and viruses.
The research was uploaded to bioRxiv. Writing in the paper, the authors said: “Obelisks comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes.”
The fact they’ve gone undetected for so long could be due to their tiny size. Obelisks’ genetic sequences are only around 1,000 characters in total, which even on a microscopic scale is pretty small.
The study analysed 5.4 million datasets of genetic sequences and one set of research in the study also found that Obelisks turned up in half of the patients’ oral samples. The authors also suggest that Obelisks could be present in different parts of the human body.
The human microbiome just gained a new dimension: scientists have discovered tiny bits of RNA — even smaller than viruses — that colonize the bacteria inside human guts and mouths1. Too minimalistic to be considered a standard life form, these scraps of genetic material are among the smallest known elements to transfer information that can be read by a cell, and the sequences they encode are new to science.
“That’s, like, wildly weird,” says cell and developmental biologist Mark Peifer from the University of North Carolina at Chapel Hill, who was not involved in the work. The research rekindled his sense of the joy that scientific discovery can bring, he says. “The world is just full of new things. And once you start to look, you find them.”
The work was posted on the preprint server bioRxiv on 21 January and has yet to be peer reviewed.
New neighbours
‘Obelisks’, as preprint co-author Ivan Zheludev at Stanford University in California and his colleagues are calling the newly discovered elements, are flattened circles of RNA. The authors’ analysis suggests that these circles are folded into rod-like structures.
Such flattened circles have been seen before in the form of ‘viroids’, structures made of RNA that are similar to viruses, but much smaller. They were first discovered in the 1970s when some were found to cause diseases in plants. Soon scientists discovered a similar element that can cause hepatitis in humans. More recently, a flurry of studies have reported viroid-like elements in a range of animals2,3 and fungi4, and a 2023 study5 provided the first hint that they might also be present in bacteria.
www.nature.com/articles/d41586-024-00266-7#:~:text='Obelisks‘,%20as%20preprint%20co,folded%20into%20rod-like%20structures.
Interestingly though, scientists discovered that, regardless of the total number of cells, if they are grouped according to their function, the proportions for each individual remain the same.
The researchers explained in their findings: “These patterns are suggestive of a whole-organism trade-off between cell size and count and imply the existence of cell-size homeostasis across cell types.”
Scientists believe there is a natural balancing act at play between different cell types with new cells being produced to maintain the balance.
The body produces fewer larger cells (such as muscle fibres) and more smaller cells (like blood cells). It is hoped that future studies will be able to uncover exactly how this happens and how bodies seem to naturally regulate cells.
www.indy100.com/science-tech/mathematical-pattern-human-body-cells-2665717644
In a paper published earlier this month, physicist Melvin Vopson, of the University of Portsmouth, offered scientific evidence for a philosophical theory known as the simulation hypothesis.
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This, in a nutshell, posits that the entire universe and our objective reality are just super-advanced virtual reality illusions.
Elon Musk is among the well-known fans of the theory, which – as Dr Vopson notes in his paper – has been “gaining traction in scientific circles as well as in the entertainment industry”.
The university lecturer also pointed out that recent developments in a branch of science known as information physics “appear to support this possibility”.
www.indy100.com/science-tech/simulation-theory-evidence-proven-2667107019
A new study has revealed that Artificial Intelligence systems are able to resist sophisticated safety methods designed to keep them in check.
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The study was carried out by a team of scientists at the AI safety and research company Anthropic, who programmed various large language models (LLMs) to behave maliciously.
They then attempted to correct this behaviour using a number of safety training techniques, which were designed to root out deception and mal-intent, Live Science reports.
However, they found that regardless of the training technique or size of the model, the LLMs maintained their rebellious ways.
Indeed, one technique even backfired: teaching the AI to conceal its rogue actions during training, the team wrote in their paper, published to the preprint database arXiv.
“Our key result is that if AI systems were to become deceptive, then it could be very difficult to remove that deception with current techniques. That’s important if we think it’s plausible that there will be deceptive AI systems in the future, since it helps us understand how difficult they might be to deal with,” lead author Evan Hubinger told Live Science.
www.indy100.com/science-tech/rogue-ai-safety-study
Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data.
“Obelisks” share several properties: (i) apparently circular RNA ∼1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the “Oblins”.
We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in ∼7% of analysed stool metatranscriptomes (29/440) and in ∼50% of analysed oral metatranscriptomes (17/32).
Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case.
Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.
www.biorxiv.org/content/10.1101/2024.01.20.576352v1.full
Really wild and cool discovery for virus nerds: an entirely new class of viroids found by Stanford's Andrew Fire and colleagues, in a search of human oral microbiomes. They encode a new class of proteins as well: t.co/0DVvRhlGcO
— Steven Salzberg 💙💛 (@StevenSalzberg1) January 26, 2024
The world is full of amazing things. Hiding in the human microbiome is a crazy new class of "viroids", small virus-like parasites–perhaps the first not found in a eukaryotes. 1/3t.co/fpJX8MVsKY pic.twitter.com/O5BEZEXqvh
— Mark Peifer (@peiferlabunc) January 21, 2024
h/t Digital mix guy Spock