Richard Borge for Quanta Magazine
Many types of discoveries can surprise and delight, but few findings are more exciting than the overturned assumption — when scientists, sometimes accidentally, stumble upon a way to flip received wisdom on its head.
For example, biologists have assumed for decades that the immune system regulates itself, without the intervention of our brains. But this year they discovered that a neural circuit in the brainstem dials the levels of inflammatory molecules up and down — a revelation made in a lab with expertise not in immunology but in the sense of taste. “Perhaps it took a change in perspective to make the discovery,” Esther Landuis wrote in Quanta.
Scientists made a number of other significant advances in our basic understanding of how life works this year. New tools — artificial intelligence, in particular — have been integrated into biology and are driving discoveries. Researchers are creatively probing the different ways that multicellularity could have evolved, including, in some cases, why it hasn’t. And they’re better understanding how tiny molecular changes manifest in evolution and everyday biology.
Fran Pulido for Quanta Magazine
Biologists Meet the AI Revolution
In 2024, hardly a week could go by without some big new paper related to Google DeepMind’s AlphaFold2: a neural network that can accurately predict the three-dimensional structure of a folded protein from the one-dimensional string of its amino acid molecules. In drug discovery, for example, biologists tested its ability to identify new drug targets and psychedelic molecules. In basic science, AlphaFold2 helped researchers examine viral evolution and discover a protein that binds a sperm to an egg during fertilization. These incremental advances indicated a sea change in the relationship between biology and computer science.
“This changes structural biology in many good ways, and not bad ways,” said Paul Adams of Lawrence Berkeley National Laboratory. “This only makes this a more exciting field to work in.”
In May, Google DeepMind released AlphaFold3, which predicts the shapes of proteins as they interact with other molecules. Then, in October, the Nobel Prize in Chemistry was awarded to John Jumper and Demis Hassabis from Google DeepMind, the creators of AlphaFold2, and David Baker from the University of Washington, who revolutionized the design of proteins using AI. (Yasemin Saplakoglu’s extended Quanta feature on the research, from June 2024, proved to be prescient: “People thought that they could become millionaires because they had the right algorithm, and some other people thought that they would immediately win the Nobel Prize,” Silvio Tosatto of the University of Padua told her.)
Robert Neubecker for Quanta Magazine
Pivotal Moments in Evolution
“How did we get here?” is one of biologists’ favorite questions. They tend to track the origins of life to a few pivotal moments in evolutionary history, and this year they made progress in understanding how life as we know it took off.
An interdisciplinary group applied the latest tricks of phylogenetics — using genes and genomes to build evolutionary trees — to trace all of modern life back to our shared ancestor. This ancient cell, or population of cells, is known as LUCA, which stands for “last universal common ancestor,” the one from which everything alive today emerged. The researchers’ innovation was a technique that assessed the probability that each of thousands of genes was present in LUCA. The work suggested that LUCA was a surprisingly complex cell that metabolized hydrogen gas and carbon dioxide, had a rudimentary immune system, and likely lived in a microbial ecosystem (from which LUCA was the sole survivor). The study also dated LUCA to some 4.2 billion years ago — earlier than researchers had thought.
Another pivotal moment — or rather, collection of moments — was the evolution of multicellularity, which occurred not once but at least 25 times, and probably more. The biologist Carl Simpson tracked the emergence of animal multicellularity to a period of Earth’s history when the planet was frozen over, known as Snowball Earth. Another study asked why bacteria and other prokaryotic cells failed to evolve into complex multicellular life. The answer could come down to an evolutionary process called genetic drift.
Bacteria have evolved simple forms of multicellularity, such as living in colonies, but archaea were never observed doing the same — until this year, when researchers found that simply squeezing archaeal cells could get them to form multicellular, tissue-like structures. And in China, scientists discovered fossils of multicellular eukaryotes dating to 1.6 billion years ago — pushing the timeline for eukaryotic multicellularity back by some 600 million years.
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Nonhuman Minds and Perception
Scientists are biased toward perceiving and understanding the world in a specific way: We see with eyes, hear with ears and think with a miraculously complex organ made of billions of cells. Other organisms also sense, perceive and respond to their environments, but it can be hard to imagine their experience. This year biologists pushed us to open our minds.
In April, a group of biologists, cognitive scientists and philosophers signed a declaration that extends scientific support for “phenomenal consciousness” to a wider suite of animals than anyone has formally acknowledged before, including insects, crabs, octopuses, fish, reptiles and amphibians. The phenomenally conscious creature “has the capacity to experience feelings such as pain or pleasure or hunger, but not necessarily more complex mental states such as self-awareness,” Dan Falk wrote for Quanta.
Plants don’t have consciousness, per se, but sometimes they need to make calculations. Research showed that European beech trees can sense the longest day of the year. Every year like clockwork, trees across a stretch of 1,500 kilometers, from England to Italy, synchronize their reproduction in a spectacle known as masting. Ecologists analyzed over 60 years of data to show that the beeches time this event to the summer solstice and peak daylight. Another study looked at perception in the weed Arabidopsis. It turns out seedlings use air spaces between their cells to scatter light and create a gradient from bright to dim so they can follow the light as they grow.
This year, researchers also discovered that single-celled bacteria can sense the seasons changing. Their simple circadian clocks can track the shortening of days as winter approaches, allowing them to prepare for colder weather, even if that winter arrives many generations later.
Nash Weerasekera for Quanta Magazine
It’s RNA’s World. We’re Just Living in It.
Since its discovery, the molecule RNA has been considered something less than DNA: single-stranded, flimsy, a mere messenger. But research has increasingly revealed that RNA is more central to life than that. Most of the so-called noncoding portions of the genome are, in fact, transcribed into RNA molecules that play non-messenger roles in cells, such as regulating the expression of genes. A new view is emerging that many important, dynamic genome processes may play out through RNA. This concept was reinforced by the Nobel committee, which awarded the Nobel Prize in Physiology or Medicine to the researchers who discovered microRNA. These short molecules enable the kind of gene regulation that underpins complex, multicellular life.
A growing body of research also suggests that RNA is a communication tool. This year, for the first time, researchers found archaeal cells exchanging noncoding RNAs in extracellular vesicles, creating a kind of cellular texting system for sharing timely, short-lived messages. The discovery confirmed that archaeans, bacteria and eukaryotes can all exchange these RNA messages. Transmitting information beyond the cell, it turns out, may be one of RNA’s innate roles.
In one of the year’s strangest discoveries, biologists found a new form of “wildly weird” RNA — flattened circles smaller than viruses and dubbed “obelisks” — living in the bacteria that colonize our guts and mouths. No one knows yet what they do. “The world is just full of new things,” Mark Peifer of the University of North Carolina, Chapel Hill told Nature. “And once you start to look, you find them.”
Nico Roper for Quanta Magazine
Insights Into the Mind
One of the most mind-blowing discoveries of the year is about the integration of the brain and body. Most immunologists have long assumed that the immune system is self-regulating. For the first time, researchers have found a neural circuit, located in the brainstem, that adjusts the immune system. This circuit senses inflammatory molecules in the body and then dials their levels up or down to protect healthy tissues. The work represents growing interest in structures that connect the mind and body, such as the vagus nerve, which links the brain to organs to marshal emotional response, and the cerebrospinal system that bathes the spinal cord and brain in clear fluid — and this year was discovered to bathe nerves across the body, too.
This year researchers also made progress in understanding how the rapid firing of thousands of neurons — known as a “sharp wave ripple” — forms memories. When we have an experience, neurons fire in a certain order, as if they’re tapping out “a melody on the piano,” Daniel Bendor of University College London told Quanta. During rest and sleep, the hippocampus replays the sequence, but faster and potentially hundreds or thousands of times, generating electrical ripples. With rest, these sequences are more likely to be solidified into long-term memories.
On the teeny-tiny scale, neuroscientists are continuing their work to reconstruct the brain neuron by neuron. This year, Google scientists used AI tools to stitch together 5,000 images taken from 1 cubic millimeter of a human brain, or one one-millionth of the entire structure, to build an astonishing 3D map. It contains roughly 57,000 neurons and 150 million synapses, incorporating 1.4 petabytes of data. In a related case, researchers for the first time mapped the entire fruit fly brain. The size of a grain of sand, it is the largest brain to be fully mapped to date, at 140,000 neurons (compared to the 86 billion in a human brain). Next up, before we can think about mapping a full human brain, is the mouse brain, which contains about 1,000 times as many neurons as the fly’s.
