Lifeboat Foundation: Safeguarding Humanity
Toggle light / dark theme

Blog

Category: biological – Page 5

Evaluating BindCraft for Generative Design of HighAffinity Peptides Biology

Interesting paper evaluating BindCraft (a generative AI tool for making small proteins) for peptide generation. BindCraft was found to work well for generating peptides to bind certain protein targets, while it failed completely for other protein targets. The protein targets for which experimental peptide hits were discovered were the ones with more structural data available, likely reflecting BindCraft’s training data.

This website uses a security service to protect against malicious bots. This page is displayed while the website verifies you are not a bot.

Scientists discover learning and memory formation in model membranes

“Science is a conversation,” said John Katsaras, neutron scattering scientist at ORNL’s Spallation Neutron Source, a Department of Energy Office of Science user facility. “Many years ago, Pat [Collier] and I wanted to see what would happen when we combined our scientific interests. He wanted to explore soft matter systems for neuromorphic computing [computing systems designed to mimic how the brain processes information], and I’ve studied the structure and dynamics of lipid membranes over the past 40 years. We are now applying decades of our soft matter experience to a problem neither one of us would have imagined pursuing five years ago.”

Soft matter includes materials that readily change shape, such as membranes, gels and polymers. Although biological membranes vary in complexity, they all share a common foundation: a lipid bilayer, or double layer of molecules. Each lipid contains a hydrophilic (water-attracting) head and a hydrophobic (water-repelling) tail.

To study membrane properties under electrical stimulation, Katsaras and Collier used water droplets suspended in oil, known as a droplet interface bilayer. These early experiments showed unexpected electrical data, prompting them to shift their attention to membranes surrounding neurons, where many memory and learning processes occur.

X-ray analysis reveals the inner life of leaves while advancing engineering efforts to reduce ‘crop sweat’

In the Midwestern summer, humans and plants have to breathe through the heat and humidity. Researchers hope that a retooled crop plant—one with an improved ventilation system within its leaves—could thrive while avoiding drought stress by reducing “crop sweat.” Thanks to next-generation imaging technology powered by Argonne National Laboratory’s particle collider beamline, a team of scientists now has precise schematics of the leaf’s interior and can refine approaches to breeding hardier crop plants.

The research, published in Plant Physiology, was led by postdoctoral researcher James Fischer in the laboratory of plant biology and crop sciences professor Andrew Leakey at the University of Illinois Urbana-Champaign. Their work represents the first detailed look at how the pores on the leaf surfaces of sorghum, a highly productive and resilient grass crop, connect to the air pathways, photosynthetic centers and veins beneath.

“There are connections between each component of the leaf… t’s a highly organized system,” Fischer said. “We are really defining the leaf beyond just carbon dioxide goes in, water comes out.”

New Monte Carlo method accelerates simulations of densely entangled polymer melts

Long polymer chains are everywhere: in synthetic materials, soft matter, biological systems such as chromosomes, and mathematical models of filaments and knots. When many such chains are densely packed, they form what physicists call a polymer melt. In this crowded environment, each chain is constrained by the others around it. These entanglements are central to the behavior of polymeric materials, but they also make the systems extremely difficult to simulate. As chain length increases, the time needed to obtain a new independent configuration grows very rapidly. For very large systems, conventional simulations can therefore become computationally prohibitive.

For more than 70 years, scientists have used many “tricks” to speed up this process, including so-called Monte Carlo methods with ingenious moves designed to accelerate the evolution of the system. These methods helped, but the basic problem remained: In a dense melt, changes still had to propagate through a highly tangled system, slowing down the simulation.

Scientists Discover a 3.7-Billion-Year-Old Secret of Early Life

Ancient microbes appear to have used molybdenum as far back as 3.7 billion years ago, despite the metal being scarce in Earth’s early oceans.

Scientists funded by NASA have found that organisms living on Earth more than 3 billion years ago were already using molybdenum, even though the metal was extremely rare in the environment at that time. The research, in Nature Communications, is the first study to show that ancient life depended on molybdenum this early in Earth’s history.

Today, molybdenum plays a key role inside cells by helping important biochemical reactions happen faster. It forms part of essential enzymes that drive several major biological processes in living organisms. These reactions matter not only for individual forms of life, but also for planet-scale biogeochemical cycles, including the nitrogen cycle. Without molybdenum, the same reactions could still occur naturally, but far too slowly to support life.

Throwing Like a Girl: Is Biology Allowed to Explain Anything?

Fausto-Sterling is not an incidental figure in modern debates about sex. Her famous 1993 essay The Five Sexes helped popularize the idea that the familiar male-female binary is biologically inadequate. She proposed additional “sexes” based on intersex conditions and argued more broadly that sex should be understood as a continuum.

Those arguments became enormously influential. In our view, they also created lasting confusion by encouraging people to mistake variation in sexual development for evidence that biological sex itself is not binary. But when it comes to sexual reproduction, the distinction is straightforward: females are organized around producing ova and males around producing sperm. There is no third gamete type or reproductive role, and intersex conditions do not create one.

One of us has examined these arguments in an essay for Skeptic. Other evolutionary biologists, including Colin Wright, have also offered detailed treatments of the issue.

Early Evolution of Life: Publication in Science Advances

Because an organism isn’t truly “alive” in the biological sense until it can survive as an autonomous, free-living cell, the researchers reached a radical conclusion.

How and where did the first forms of life arise? These are the main questions driving research at the Institute of Molecular Evolution at Heinrich Heine University Düsseldorf (HHU). In a new publication in Science Advances, an international team led by Düsseldorf biologists uncovers pioneering insights into the network of chemical reactions that the very first cells used to make the building blocks of life and which sources of energy they used to drive those reactions. They retraced the origin of enzymes during life’s earliest divergence into bacteria and archaea, and found evidence for two independent origins of life for free-living cells.

Rethinking how we name and classify our human ancestors following recent evolutionary discoveries

Recent advances in our understanding of human evolution challenge the way we currently name and classify our ancestors, according to new research from Monash University. The study, published in the American Journal of Biological Anthropology, argues that we need a rethink and proposes reclassifying all species of humans and our closely related fossil relatives that have lived in the past 4–5 million years as part of the genus Homo.

Curved surfaces reshape active materials, localizing vibrations near defects

Many materials, both living and engineered, are powered from within. Scientists have thoroughly investigated how such ‘active’ materials operate, but so far, mostly in circumstances where the curvature of the environment does not play a role. In research published in Physical Review Letters this week, a team of physicists proposes a framework to describe how active materials operate in the presence of curvature. The framework explains striking biological observations and may lead to geometry as a design parameter for new materials.

Examples of active materials include tissues made of moving cells and mechanical metamaterials that use embedded motors or actuators. A major difference between such active materials and ordinary materials lies in the way they deform. Push an ordinary material, and it will deform where the force acts. Active materials, on the other hand, can generate further forces that redirect deformations, leading to all kinds of unexpected, but often quite useful, behavior.

A striking example comes from observations in biological experiments, where starfish embryos were found to self-organize into crystal-like structures on a water surface. In this example, an extra factor comes into play: The water surface in the test tubes used in the experiments is not flat but slightly curved—just like the surface of water in an ordinary drinking glass that curves upward where the water touches the glass. One consequence of the curvature is that the starfish embryos don’t fit on the surface in a completely regular pattern: Instead, the pattern has occasional irregularities or defects.

/* */