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    Billion-year-old grease hints at long history of complex cells / ArsTechnica · Friday, 9 June, 2023 - 20:25 · 1 minute

Image of a complex, multi-ringed molecule.

Enlarge / All steroids past and present share the complex ringed structure but differ in terms of the atoms attached to those rings. (credit: KATERYNA KON/SCIENCE PHOTO LIBRARY )

All of the organisms we can see around us—the plants, animals, and fungi—are eukaryotes composed of complex cells. Their cells have many internal structures enclosed in membranes, which keep things like energy production separated from genetic material, and so on. Even the single-celled organisms on this branch of the tree of life often have membrane-covered structures that they move and rearrange for feeding.

Some of that membrane flexibility comes courtesy of steroids. In multicellular eukaryotes, steroids perform various functions; among other things, they’re used as signaling molecules, like estrogen and testosterone. But all eukaryotes insert various steroids into their membranes, increasing their fluidity and altering their curvature. So the evolution of an elaborate steroid metabolism may have been critical to enabling complex life.

Now, researchers have traced the origin of eukaryotic steroids almost a billion years further back in time. The results suggest that many branches of the eukaryotic family tree once made early versions of steroids. But our branch evolved the ability to produce more elaborate ones—which may have helped us outcompete our relatives.

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    Jellyfish and flies use the same hormone when they’ve had enough to eat / ArsTechnica · Thursday, 6 April, 2023 - 18:26 · 1 minute

Image of a jellyfish near the surface of the ocean.

Enlarge / A Moon jellyfish. (credit: Dan Kitwood / Getty Images )

The sensation of hunger seems pretty simple on the surface, but behind the scenes, it involves complicated networks of sending and signaling, with multiple hormones that influence whether we decide to have another serving or not. The ability to know when to stop eating appears to be widespread among animals, suggesting that it might have deep evolutionary roots.

A new study suggests that at least one part of the system goes back to nearly the origin of animals. Researchers have identified a hormone that jellyfish use to determine when they're full and stop eating. And they found that it's capable of eliciting the same response in fruit flies, suggesting the system may have been operating in the ancestor of these two very distantly related animals. That ancestor would have lived prior to the Cambrian.

Feeding the fish (or jellyfish)

Given they lack any obvious equivalents to a mouth, it might seem like it would be tough to determine whether a jellyfish is even eating, much less hungry. But a team of Japanese researchers showed that the jellyfish species Cladonema pacificum has a bunch of stereotypical behaviors while feeding, including that their tentacles latch onto prey and that they then withdraw the tentacle into the bell so that the prey can be digested. And, if you keep feeding the jellyfish brine shrimp, eventually this process will slow, indicating that the animal is sensing it is well fed. (There's a movie available of the jellyfish feeding.)

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    Large language models also work for protein structures / ArsTechnica · Thursday, 16 March, 2023 - 19:01 · 1 minute

Artist's rendering of a collection of protein structures floating in space


The success of ChatGPT and its competitors is based on what's termed emergent behaviors. These systems, called large language models (LLMs), weren't trained to output natural-sounding language (or effective malware ); they were simply tasked with tracking the statistics of word usage. But, given a large enough training set of language samples and a sufficiently complex neural network, their training resulted in an internal representation that "understood" English usage and a large compendium of facts. Their complex behavior emerged from a far simpler training.

A team at Meta has now reasoned that this sort of emergent understanding shouldn't be limited to languages. So it has trained an LLM on the statistics of the appearance of amino acids within proteins and used the system's internal representation of what it learned to extract information about the structure of those proteins. The result is not quite as good as the best competing AI systems for predicting protein structures, but it's considerably faster and still getting better.

LLMs: Not just for language

The first thing you need to know to understand this work is that, while the term "language" in the name "LLM" refers to their original development for language processing tasks, they can potentially be used for a variety of purposes. So, while language processing is a common use case for LLMs, these models have other capabilities as well. In fact, the term "Large" is far more informative, in that all LLMs have a large number of nodes—the "neurons" in a neural network—and an even larger number of values that describe the weights of the connections among those nodes. While they were first developed to process language, they can potentially be used for a variety of tasks.

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    These researchers watched dead fish rot for 70 days—for science / ArsTechnica · Tuesday, 9 August, 2022 - 22:44 · 1 minute

These researchers watched dead fish rot for 70 days—for science

Enlarge (credit: Aurich Lawson/T. Clements et al.)

Sometimes science can be a messy endeavor—not to mention "disgusting and smelly." That's how British researchers described their experiments monitoring dead sea bass carcasses as they rotted over the course of 70 days. In the process, they gained some fascinating insights into how (and why) the soft tissues of internal organs can be selectively preserved in the fossil record, according to a new paper published in the journal Palaeontology.

Most fossils are bone, shells, teeth, and other forms of "hard" tissue, but occasionally rare fossils are discovered that preserve soft tissues like skin, muscles, organs, or even the occasional eyeball. This can tell scientists much about aspects of the biology, ecology, and evolution of such ancient organisms that skeletons alone can't convey. For instance, earlier this year, researchers created a highly detailed 3D model of a 365-million-year-old ammonite fossil from the Jurassic period by combining advanced imaging techniques, revealing internal muscles that had never been previously observed.

"One of the best ways that soft tissue can turn into rock is when they are replaced by a mineral called calcium phosphate (sometimes called apatite)," said co-author Thomas Clements of the University of Birmingham. "Scientists have been studying calcium phosphate for decades trying to understand how this process happens—but one question we just don’t understand is why some internal organs seem more likely to be preserved than others."

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    DeepMind AI handles protein folding, which humbled previous software / ArsTechnica · Monday, 30 November, 2020 - 22:10 · 1 minute

Proteins rapidly form complicated structures which had proven difficult to predict.

Enlarge / Proteins rapidly form complicated structures which had proven difficult to predict. (credit: Argonne National Lab )

Today, DeepMind announced that it had seemingly solved one of biology's outstanding problems: how the string of amino acids in a protein folds up into a three-dimensional shape that enables their complex functions. It's a computational challenge that has resisted the efforts of many very smart biologists for decades, despite the application of supercomputer-level hardware for these calculations. DeepMind instead trained its system using 128 specialized processors for a couple of weeks; it now returns potential structures within a couple of days.

The limitations of the system aren't yet clear—DeepMind says it's currently planning on a peer-reviewed paper, and has only made a blog post and some press releases available. But it clearly performs better than anything that's come before it, after having more than doubled the performance of the best system in just four years. Even if it's not useful in every circumstance, the advance likely means that the structure of many proteins can now be predicted from nothing more than the DNA sequence of the gene that encodes them, which would mark a major change for biology.

Between the folds

To make proteins, our cells (and those of every other organism) chemically link amino acids to form a chain. This works because every amino acid shares a backbone that can be chemically connected to form a polymer. But each of the 20 amino acids used by life has a distinct set of atoms attached to that backbone. These can be charged or neutral, acidic or basic, etc., and these properties determine how each amino acid interacts with its neighbors and the environment.

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    Chitin could be used to build tools and habitats on Mars, study finds / ArsTechnica · Tuesday, 22 September, 2020 - 22:18 · 1 minute

A figurine of an astronaut stands next to a block.

Enlarge / Scientists mixed chitin—an organic polymer found in abundance in arthropods, as well as fish scales—with a mineral that mimics the properties of Martian soil to create a viable new material for building tools and shelters on Mars. (credit: Javier G. Fernandez )

Space aficionados who dream of one day colonizing Mars must grapple with the stark reality of the planet's limited natural resources, particularly when it comes to building materials. A team of scientists from the Singapore University of Technology and Design discovered that, using simple chemistry, the organic polymer chitin —contained in the exoskeletons of insects and crustaceans—can easily be transformed into a viable building material for basic tools and habitats. This would require minimal energy and no need for transporting specialized equipment. The scientists described their experiments in a recent paper published in the journal PLOS ONE.

"The technology was originally developed to create circular ecosystems in urban environments," said co-author Javier Fernandez . "But due to its efficiency, it is also the most efficient and scalable method to produce materials in a closed artificial ecosystem in the extremely scarce environment of a lifeless planet or satellite."

As we previously reported , NASA has announced an ambitious plan to return American astronauts to the Moon and establish a permanent base there, with an eye toward eventually placing astronauts on Mars. Materials science will be crucial to the Artemis Moon Program's success, particularly when it comes to the materials needed to construct a viable lunar (or Martian) base. Concrete, for instance, requires a substantial amount of added water in order to be usable in situ , and there is a pronounced short supply of water on both the Moon and Mars. And transport costs would be prohibitively high. NASA estimates that it costs around $10,000 to transport just one pound of material into orbit.

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    Researchers find a chemical that makes locusts swarm / ArsTechnica · Wednesday, 12 August, 2020 - 21:39 · 1 minute

Image of a person fleeing from a cloud of locust.

Enlarge (credit: NOAA )

The year 2020 may be one for the record books in terms of apocalyptic tidings. In addition to the usual background of fires , floods , and earthquakes , the plague is still around . And you might have heard something about a pandemic . But what really nails down the apocalyptic vibe is the fact that the year's seen swarms of locusts causing the sorts of problems they're famous for.

In a tiny bit of good news, the same sort of research that may bail us out with therapies and a vaccine for SARS-CoV-2 could potentially help us out against future locust swarms. That's because a team of biologists based in China has now identified the chemical that calls locusts to swarm and shown that genetic engineering can eliminate the response.

A lot of evidence

There's nothing especially exciting about any single aspect of the research here. Instead, the researchers simply put together techniques from a variety of specializations and then applied them to the topic of locust swarms. Locusts are normally solitary animals, but they become immensely destructive when conditions induce them to form massive swarms that are big enough to be picked up by radar . In addition to the altered behavior, swarming locusts actually look physically different, indicating that the decision to swarm involves widespread changes to a locust's biology.

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    Researchers engineer enzyme to break down plastic bottles / ArsTechnica · Wednesday, 8 April, 2020 - 19:59 · 1 minute

Image of plastic bottles.

Enlarge (credit: Orange County NC )

Plastics have a lot of properties that have made them fixtures of modern societies. They can be molded into any shape we'd like, they're tough yet flexible, and they come in enough variations that we can tune the chemistry to suit different needs. The problem is that they're tough enough that they don't break down on their own, and incinerating them is relatively inefficient. As a result, they've collected in our environment as both bulk plastics and the seemingly omnipresent microplastic waste.

For natural materials, breaking down isn't an issue, as microbes have evolved ways of digesting them to obtain energy or useful chemicals. But many plastics have only been around for decades, and we're just now seeing organisms that have evolved enzymes to digest them. Figuring they could do one better, researchers in France have engineered an enzyme that can efficiently break down one of the most common forms of plastic. The end result of this reaction is a raw material that can be reused directly to make new plastic bottles.

An unwanted PET

The plastic in question is polyethylene terephthalate, or PET. PET has a variety of uses, including as thin films with very high tensile strength (marketed as mylar). But its most notable use is in plastic drink bottles, which are a major component of environmental plastic waste. First developed in the 1940s, the first living organism that can break down and use the carbon in PET was described in 2016 —found in sediment near a plastic recycling facility, naturally.

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