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Biology

Scientists Discover Jellyfish Sleep Even Though They Don’t Have Brains

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Sleeping is widely regarded as a good way to recharge your brain, but that raises a particularly perplexing question: do animals without brains sleep? The answer is, surprisingly, yes, at least when it comes to jellyfish.

Earlier today, three graduate student researchers at the California Institute of Technology (Ravi Nath of the Sternberg laboratory, Claire Bedbrook of the Gradinaru laboratory, and Michael Abrams of the Goentoro laboratory) announced they have discovered that jellyfish sleep. You probably wonder how the team was even able to quantify what would be considered sleep in animals without brains or spines, but before they started the experiment, the researchers debated, considered, and finally devised the three necessary criteria for sleep that they used in the study:

  1. The animal must exhibit a period of demonstrably reduced activity, otherwise known as “quiescence.”
  2. The animal must respond slower to stimuli during this period.
  3. The animal must show an increased desire to enter a period of quiescence when deprived of it.

These criteria were devised by examining sleep in other animals, including humans. “When humans sleep, we are inactive, we often can sleep through noises or other disturbances which we might otherwise react to if we were awake, and we’re likely to fall asleep during the day if we don’t get enough sleep,” explained Bedbrook.

The jellyfish chosen for the experiment study was the most evolutionarily primitive one on the planet: a Cassiopea jellyfish, or just simply Cassiopea. Unlike most jellyfish, Cassiopea spends most of its life lying upside down on the ocean floor like some weird, fleshy, pulsating sea plant. During the study, cameras monitored this animal 24/7, and the researchers noted the jellyfish pulsed slower at night, 39 times per minute instead of the regular 58 times per minute during the day. This slower pulse fulfilled the “period of reduced activity/quiescence” criterion, but what about the other two?

To show that the Cassiopea react slower during this period of reduced activity, the researchers placed the jellyfish on a platform in the study tank and pulled the platform out from under it when it started “sleeping.” Normally, Cassiopea would immediately swim to the bottom of the tank, but at night, the team discovered it floated listlessly in the water for up to five seconds before heading to the tank floor. This suggests the Cassiopea jellyfish isn’t readily aware of its environment when it enters a period of quiescence, which fulfilled another sleep criterion and left the final one, an increased desire to sleep when deprived of sleep.

The only way to show that animals experience an increased desire to sleep when deprived of it is to, well, deprive them of sleep, which is exactly what the team did; they “poked” the Cassiopea awake by pulsing water at them every 10 seconds for 20 minutes. Just as the researchers predicted, the jellyfish fell asleep during the day, thus fulfilling the final criterion and demonstrating even jellyfish sleep. However, the researchers considered the possibility that the period of quiescence wasn’t sleep but instead some analogous sleep-like state, so they exposed the jellyfish to compounds known to induce sleep in other animals, such as melatonin. The jellyfish reacted just as the researchers predicted, which, according to Abrams, means the mechanism determining the Cassiopea‘s sleep is “similar to those of other organisms — including humans.”

I know what you’re thinking: why is determining if jellyfish sleep so important? Well, normally when we think about sleep, we think about resting our brains to convert short-term memory into long-term memory and to rejuvenate our cognitive functions. However, jellyfish don’t have brains and thus don’t have memories and cognitive functions as we know them, which raises the question: why do jellyfish need sleep? The study might not shed any light on this particular question, but, according to Nath, “This finding opens up many more questions: Is sleep the property of neurons? And perhaps a more far-fetched question: Do plants sleep?” Only time will tell just how much we can discover about sleep, including its evolutionary origins.

All you have to do to get my attention is talk about video games, technology, anime, and/or Dungeons & Dragons - also people in spandex fighting rubber suited monsters.

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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