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Biology

Newly Discovered Microbes Dubbed ‘Loki’ Might Be the Missing Link in Complex Cell Evolution

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Hydrothermal vents in Loki’s Castle, a harsh environment where microorganisms dubbed ‘Loki’ were found. These creatures are thought to be the ‘missing link’ between simple single-celled organisms known as prokaryotes and more complex life forms called eukaryotes.

For centuries, anthropologists have been looking for the fabled ‘missing link’ in the evolution of humans, a distant ancestor of ours which illustrates the split between our lineage and the one our ape cousins belong to. Lucy, who lived about 3.2 million years ago in Africa and is now classified as a species of Australopithecus, is perhaps the most famous missing link in the evolution of humankind. Other spectacular transitional creatures include Tiktaalik, a link between fish and land-dwelling animals, and Archaeopteryx, a dinosaur-bird hybrid.

Recently, a research team led by scientists from Uppsala University in Sweden has found a possible missing link which is arguably much more important, because it marks the transition between the simplest single-celled microorganisms called prokaryotes, and the more complex eukaryotes, which are the ancestors of all higher life forms. Biologists have dubbed these creatures LokiarchaeotaLoki, for short.

Here’s a bit of context, to understand the significance of the finding. Prokaryotes are the oldest life forms on our planet, thought to have appeared about 3.5 billion years ago. They are relatively simple and extremely sturdy microorganisms, which explains how they managed to survive in the hellish conditions at the time they appeared, and why they still thrive today. They lack a nucleus, as well as other organelles – hence their name, which roughly translates to before nucleus. Prokaryotes are divided into two large groups, called Archaea and Bacteria.

Eukaryotes (good nucleus), on the other hand, developed much later, about 1.5 to 2 billion years after prokaryotes. They are significantly more complex, comprising a nucleus and a series of organelles. Everything we think of as complex life, from fish, to cats, to people, is a eukaryote.

Until recently, how prokaryotes evolved into eukaryotes was largely a mystery. The fact that Archaea were shown to be closely related to the more complex creatures was also quite puzzling. Here is where Loki comes in.

These ancient microbes were named after the place where they were found: a hydrothermal vent system along the Mid-Atlantic Ridge between Greenland and Norway called Loki’s Castle, located more than 2,300 meters below the surface. The scientists who discovered them have recently published a paper in the journal Nature which shows that many eukaryotic features were already present in archaeons, suggesting that Loki might be an intermediate between the simple microbes and eukaryotes. According to these findings, Loki share many genes with the latter group, indicating that cellular complexity had already emerged in Archaea by the time the first eukaryotes evolved.

Though the picture of what the earliest life forms looked like and how they evolved is still pretty sketchy (after all, we’re talking about microscopic creature which lived billions of years ago), it’s discoveries like this one which help scientists complete the puzzle, one piece at a time.

Who doesn’t enjoy listening to a good story. Personally I love reading about the people who inspire me and what it took for them to achieve their success. As I am a bit of a self confessed tech geek I think there is no better way to discover these stories than by reading every day some articles or the newspaper . My bookcases are filled with good tech biographies, they remind me that anyone can be a success. So even if you come from an underprivileged part of society or you aren’t the smartest person in the room we all have a chance to reach the top. The same message shines in my beliefs. All it takes to succeed is a good idea, a little risk and a lot of hard work and any geek can become a success. VENI VIDI VICI .

Biology

The First 3D-Printed Vegan Salmon Is In Stores

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Revo Foods’ “THE FILET – Inspired By Salmon” salmon fillet may be the first 3D-printed food to hit store shelves. said that firm CEO Robin Simsa remarked, “With the milestone of industrial-scale 3D food printing, we are entering a creative food revolution, an era where food is being crafted exactly according to customer needs.”

Mycoprotein from filamentous fungi is used to make the salmon alternative and other meat substitutes. Vitamins and omega-3 fatty acids are in the product, like in animals. Is high in protein, at 9.5 grams per 100 grams, although less than conventional salmon.

Revo Foods and Mycorena developed 3D-printable mycoprotein. Years of research have led to laser-cooked cheesecakes and stacked lab-grown meats.

One reason for this push is because printed food alternatives may make food production more sustainable, which worries the fishing sector. Overfishing reduces fish populations in 34% of worldwide fish stocks.

Over 25% of worldwide greenhouse gas emissions come from food production, with 31% from livestock and fish farms and 18% from supply chain components including processing and shipping. According to Revo Foods’ website, vegan salmon fillet production consumes 77 to 86% less carbon dioxide and 95% less freshwater than conventional salmon harvesting and processing.

The salmon alternative’s sales potential is unknown. In order to succeed, Revo Foods believes that such goods must “recreate an authentic taste that appeals to the flexitarian market.”

The commercial distribution of 3D-printed food could change food production.

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Artificial Intelligence

Open-source Microsoft Novel protein-generating AI EvoDiff

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All diseases are based on proteins, natural molecules that perform vital cellular functions. Characterizing proteins can reveal disease mechanisms and ways to slow or reverse them, while creating proteins can lead to new drug classes.

The lab’s protein design process is computationally and human resource-intensive. It involves creating a protein structure that could perform a specific function in the body and then finding a protein sequence that could “fold” into that structure. To function, proteins must fold correctly into three-dimensional shapes.

Not everything has to be complicated.

Microsoft introduced EvoDiff, a general-purpose framework that generates “high-fidelity,” “diverse” proteins from protein sequences, this week. Unlike other protein-generating frameworks, EvoDiff doesn’t need target protein structure, eliminating the most laborious step.

Microsoft senior researcher Kevin Yang says EvoDiff, which is open source, could be used to create enzymes for new therapeutics, drug delivery, and industrial chemical reactions.

Yang, one of EvoDiff’s co-creators, told n an email interview that the platform will advance protein engineering beyond structure-function to sequence-first design. EvoDiff shows that ‘protein sequence is all you need’ to controllably design new proteins.

A 640-million-parameter model trained on data from all protein species and functional classes underpins EvoDiff. “Parameters” are the parts of an AI model learned from training data that define its skill at a problem, in this case protein generation. The model was trained using OpenFold sequence alignment data and UniRef50, a subset of UniProt, the UniProt consortium’s protein sequence and functional information database.

Modern image-generating models like Stable Diffusion and DALL-E 2 are diffusion models like EvoDiff. EvoDiff slowly subtracts noise from a protein made almost entirely of noise to move it closer to a protein sequence.

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Beyond image generation, diffusion models are being used to design novel proteins like EvoDiff, create music, and synthesize speech.

“If there’s one thing to take away [from EvoDiff], I think it’s this idea that we can — and should — do protein generation over sequence because of the generality, scale, and modularity we can achieve,” Microsoft senior researcher Ava Amini, another co-contributor, said via email. “Our diffusion framework lets us do that and control how we design these proteins to meet functional goals.”

EvoDiff can create new proteins and fill protein design “gaps,” as Amini noted. A protein amino acid sequence that meets criteria can be generated by the model from a part that binds to another protein.

EvoDiff can synthesize “disordered proteins” that don’t fold into a three-dimensional structure because it designs proteins in “sequence space” rather than structure. Disordered proteins enhance or decrease protein activity in biology and disease, like normal proteins.

EvoDiff research isn’t peer-reviewed yet. Microsoft data scientist Sarah Alamdari says the framework needs “a lot more scaling work” before it can be used commercially.

“This is just a 640-million-parameter model, and we may see improved generation quality if we scale up to billions,” Alamdari emailed. WeAI emonstrated some coarse-grained strategies, but to achieve even finer control, we would want to condition EvoDiff on text, chemical information, or other ways to specify the desired function.”

Next, the EvoDiff team will test the model’s lab-generated proteins for viability. Those who are will start work on the next framework.

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Biology

Chinese Dinosaur Might Have Been as Iridescent as a Hummingbird

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Earlier this month, I wrote an article on a toy line of scientifically accurate Velociraptor action figures with plumage inspired by modern birds. I mused how impressive it would be if prehistoric raptors had been covered by feather patterns not unlike those in the toy line. Little did I know that two weeks later, researchers would reveal that some theropods had iridescent feathers that outshine David Silva’s velocifigures.

The Caihong juji, Mandarin for “rainbow with a big crest” (or just Caihong for short), was a “paravian theropod,” a clade commonly known for its winged forelimbs (even though many weren’t capable of flight) and enlarged sickle foot claws. In 2014, a farmer in the Qinlong County in the Hebei Province of Northeastern China gave a nearly complete Caihong fossil, feathers included, to The Paleontological Museum of Liaoning. Finding a complete skeleton is rare in paleontology and proved very helpful to the researchers. However, you might wonder just how scientists were able to determine the iridescent nature of the Caihong’s plumage. Two words: fossilized melanosomes.

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Melanosomes are organelles that create, store, and transport melanin, which determines the pigments/colors of animal hair, fur, skin, scales, and feathers. Upon examining the Caihong’s head, crest, and tail feathers with an electron microscope, scientists discovered platelet-shaped structures similar in shape to the melanosomes that give hummingbirds their iridescent coloring. The rest of the body feathers had melanosome structures similar to those in the grey and black feathers of penguins, which would have made for an odd sight: a duck-sized dinosaur with body feathers as drab as a raven’s and head and neck feathers more colorful than a peacock’s.

The inferred feather coloration of the Caihong is not its only unusual feature, though. The dinosaur had longer arm and leg feathers than its relatives, and its tail feathers created a “tail surface area” that was larger than the famous proto-bird the Archaeopteryx.  Furthermore, the Caihong had bony crests, which while common among most dinosaurs, are almost unheard of among paravian theropods. But, more importantly, it had proportionally long forearms, which is a feature of flight-capable theropods, even though scientists believe the Caihong didn’t fly. While this dinosaur apparently has the earliest examples of proportionally long forearms in the theropod fossil records, it still falls in line with the belief that the evolution of flight-capable feathers outpaced the evolution of flight-capable skeletons. The melanosomes, however, are the more intriguing discovery, since they are the earliest examples of “organized platlet-shaped nanostructures…in dinosaurian feathers.”

While paleontologists are confident the Caihong’s platelet structures are melanosomes, the researchers understand that their discovery is based partially on inference and could potentially be incorrect. If the structures aren’t melanosomes, well, that invalidates this entire article. But that’s what paleontology is all about: examining the evidence, creating inferences supported by that evidence, and changing those inferences when new information becomes available. Still, the concept of dinosaurs with iridescent feathers is pretty cool. If you want to learn more about the Caihong juji, you can read the original article on Nature.

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