We tend to view ourselves and the complex cells that build us as a distinct branch of the tree of life from the compact, seemingly featureless cells of bacteria and archaea. But we've found that our genome is actually a hybrid, a mish-mash of genes from bacteria and archaea, along with some that have evolved in our own lineage.
Scientists gradually settled on a simple explanation for this: the first complex cells were the product of a fusion between archaeal cells and bacteria, with the bacteria ultimately evolving into the mitochondria, a chemical-power-generating structure that still retains a bit of its own genome. Over time, many of the other bacterial genes were transferred to the nucleus of what was becoming what we now call a eukaryote, intermingling with the archaeal genes there.
But a new study has taken a careful look at some of the genes shared by all eukaryotes and comes to the conclusion that the reality is a little more complicated and that there were several waves of gene transfers from bacteria. The big picture of a merger between bacteria and archaea is still right, but it was only part of a picture where gene transfers among species were commonplace.
PHOENIX, Ariz. — When someone says they’re “addicted to caffeine,” it might not seem that alarming. After all, many people rely on a morning coffee or an afternoon energy drink to get through the day. But Sophia Zeng, 16, says we might need to reconsider our attitudes about one of the most common drugs in the world.
Her research hints that caffeine might impact genes involved in brain development. And it may affect kids and adults in different ways.
After noticing that she and her mother responded differently to caffeine, Sophia Zeng did a series of experiments to explore the effects of this common drug on developing brains.K.G. Carpenter
The American Academy of Pediatrics advises that kids avoid caffeine. Yet many kids and teens consume caffeine in some form every day. Sophia is one of those caffeine drinkers. She first got curious about the effects of this drug when she noticed differences in how she and her mom reacted to caffeinated tea.
Sophia’s mom is “really a tea lover,” she says. “After drinking tea, she would feel more focused.” But drinking tea didn’t always leave Sophia feeling good. “If I stopped drinking it, I’d receive headaches,” she says. To get rid of those headaches, she needed more caffeine. That got Sophia wondering: Why does caffeine make some people feel happy and helpful, while leaving others with increased stress and headaches?
Sophia’s work earned this sophomore from Tsinghua International School in Beijing, China, a spot at the 2026 Regeneron International Science & Engineering Fair, or ISEF. This is a program run by the Society for Science (which also publishes this magazine). Sophia was among 1,725 students from 65 nations or territories who competed in 2026. Participants shared nearly $7 million in prizes.
A three-stage approach
Dye-ing for caffeine
These images show a decrease in rat neuron complexity with increasing caffeine exposure. The “control” group was exposed to no caffeine. “NGF” neurons were exposed to nerve growth factor, which is expected to promote neuron growth. Other neurons were exposed to low, medium and high levels of caffeine. MAP2 is a protein on the surfaces of cells. Red fluorescent dye binds to those proteins to reveal neurons’ shapes and growth. DAPI is a fluorescent dye that highlights the nuclei of cells. Together, these colorful tags reveal that with increasing levels of caffeine, fewer neurons grow and fewer connections form between neurons. S. Zeng
The first thing Sophia did was look at past data on caffeine. She analyzed published studies with the goal of identifying new patterns. This approach is called bioinformatics.
Sophia focused on studies that had looked at how caffeine affected the brains of adult mice. Her analysis suggested that caffeine could alter which genes in a mouse’s DNA were active, or expressed.
Next, Sophia took her work to a lab. She grew rat brain cells in petri dishes for six days, then exposed the cells to different levels of caffeine. Two days later, she compared the neurons under a microscope.
To make the neurons show up clearly, Sophia used fluorescent dyes that bind to the cells. Dyes can highlight important features, such as how the cells are forming connections with one another. Those neuron-to-neuron connections are called synapses.
Dishes exposed to more caffeine contained fewer neurons, Sophia found. What’s more, those neurons showed fewer connections. Caffeine seemed to make neuronal networks simpler and scarcer.
In another set of experiments, Sophia studied young zebrafish that had been exposed to different levels of caffeine. She looked at how far the fish swam and where. More caffeinated fish swam more, she says. They also made erratic choices, spending time in regions of their tank that calm fish typically avoided. Both of these findings hinted that the fish that got more caffeine were more anxious.
But Sophia didn’t stop there. She looked at what changes in the fishes’ brains might have led to this behavior. Sophia measured the activity of four genes involved in brain development. All four were less active in the caffeine-exposed fish, she found.
Takeaways for caffeine drinkers
Interestingly, some genes in the young zebrafish were turned down, or less active, in a way not seen in the neurons from adult rats. So, caffeine may affect the brain differently at different ages, Sophia says. But together, the mouse brain data, the rat neuron experiment and the fish studies all point to the same pattern. Caffeine seems to affect gene activity in neurons. And that in turn may impair brain development and behavior.
Past caffeine exposure changed the movement patterns of zebrafish. As caffeine exposure increased, fish moved more erratically throughout the four zones of their aquarium. (The bright dots on the heatmaps show where the fish swam.) This evidence points to behavior changes and increased anxiety linked to caffeine.S. Zeng
“I feel that we really don’t talk about caffeine, even though we drink it,” Sophia says. It’s in so many everyday drinks, she adds. Between soda, tea and other beverages, young people may be consuming a lot more of it than they realize.
Sophia suggests greater skepticism about using this drug. People tend to think about caffeine as a helpful tool for focus, she notes, and dismiss potential downsides. But her findings highlight that caffeine comes with trade-offs — and those trade-offs may harm young brains more than we know.
The extinct Eurasian cave lion (Panthera spelaea) and today’s African and Asian lions (Panthera leo) belong to separate evolutionary lineages that diverged roughly 1.7 million years ago -- far earlier than previously thought, according to an analysis of 12 cave lion genomes spanning more than 100,000 years.
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