Dr. Jamie McGowan, a postdoctoral scientist at the Earlham Institute, was studying the genome of a protist collected from freshwater. The goal was practical. Researchers wanted to test a DNA sequencing pipeline that could work with extremely small amounts of DNA, including DNA from a single cell.

Instead, the team found an unexpected genetic outlier. The organism, identified as Oligohymenophorea sp. PL0344, turned out to be a previously unknown species with a rare change in how it reads DNA instructions and builds proteins. The PLOS Genetics study reported that two codons normally associated with gene stopping signals had been reassigned to different amino acids, a combination the researchers described as previously unreported.

“It’s sheer luck we chose this protist to test our sequencing pipeline, and it just shows what’s out there, highlighting just how little we know about the genetics of protists.”

A Tiny Organism With a Big Genetic Surprise

Protists are difficult to define neatly because they are so diverse. Many are microscopic, single celled organisms, including amoebas, algae, and diatoms. Others are much larger and multicellular, such as kelp, slime molds, and red algae.

“The definition of a protist is loose — essentially it is any eukaryotic organism which is not an animal, plant, or fungus,” said Dr. McGowan. “This is obviously very general, and that’s because protists are an extremely variable group.

“Some are more closely related to animals, some more closely related to plants. There are hunters and prey, parasites and hosts, swimmers and sitters, and there are those with varied diets while others photosynthesize. Basically, we can make very few generalizations.”

Oligohymenophorea sp. PL0344 belongs to a group called ciliates. These swimming protists can be seen under a microscope and are found in many watery environments. Ciliates have become especially interesting to geneticists because they are known hotspots for genetic code changes, including changes involving stop codons.

When Genetic Stop Signs Change Meaning

In most living things, three stop codons tell the cell where a gene ends: TAA, TAG, and TGA. These work like punctuation marks in the genetic instructions, signaling that protein construction should stop.

The genetic code is usually described as nearly universal because most organisms use the same basic rules. Variations do occur, but they are rare. In the small number of known genetic code variants, TAA and TAG usually change together and usually end up meaning the same thing. That pattern suggested the two codons were evolutionarily linked.

“In almost every other case we know of, TAA and TAG change in tandem,” explained Dr. McGowan. “When they aren’t stop codons, they each specify the same amino acid.”

This organism did something different. In Oligohymenophorea sp. PL0344, only TGA appears to function as a stop codon. The other two signals have been repurposed. TAA specifies lysine, while TAG specifies glutamic acid. The researchers also found more TGA codons than expected, which may help compensate for the loss of the other two stop signals. The PLOS Genetics paper reported that the remaining UGA stop codon is enriched just after coding regions, suggesting it may help prevent harmful readthrough when translation continues too far.

“This is extremely unusual,” Dr. McGowan said. “We’re not aware of any other case where these stop codons are linked to two different amino acids. It breaks some of the rules we thought we knew about gene translation — these two codons were thought to be coupled.

“Scientists attempt to engineer new genetic codes — but they are also out there in nature. There are fascinating things we can find, if we look for them.

“Or, in this case, when we are not looking for them.”

How Cells Read DNA Instructions

DNA can be thought of as a set of instructions, but the instructions must be copied and interpreted before they have an effect. First, a gene is transcribed into RNA. That RNA copy is then translated into amino acids, which are linked together to form proteins and other functional molecules.

Translation begins at the DNA start codon (ATG) and normally ends at a stop codon (normally TAA, TAG, or TGA). In this ciliate, that familiar ending system has been rearranged. The discovery shows that even one of biology’s most conserved systems can be more flexible than expected.

The team’s genome and transcriptome analysis also identified suppressor tRNA genes that match the reassigned codons, supporting the conclusion that the organism truly reads these former stop signals as amino acids. In the study, UAA was found to code for lysine and UAG for glutamic acid.

Later Work Shows Ciliates Are Genetic Rule Breakers

Follow up work has strengthened the idea that ciliates are unusually rich sources of genetic code surprises. In a 2024 PLOS Genetics study, researchers reported multiple independent reassignments of the UAG stop codon in phyllopharyngean ciliates. Some uncultivated ciliates from the TARA Oceans dataset appear to use UAG to encode leucine, while Hartmannula sinica and Trochilia petrani were found to use UAG to encode glutamine.

That later study also found that UAA remains the preferred stop codon in those phyllopharyngean ciliates, while UAG has repeatedly shifted into a protein coding role. The findings point to repeated changes in the genetic code across poorly studied microbial eukaryotes and reinforce the idea that ciliates are among the strongest exceptions to the standard genetic code.

Together, these discoveries suggest that the genetic code is not as fixed as it once seemed. For most organisms, the rules remain remarkably stable. But in overlooked microbial life, especially ciliates, evolution has repeatedly found ways to edit the instructions.

Funding and Publication

The original research was published in PLOS Genetics in 2023. It was funded by the Wellcome Trust as part of the Darwin Tree of Life Project and supported by the Earlham Institute’s core funding from the Biotechnology and Biological Sciences Research Council (BBSRC), part of UKRI. The publication reported sequencing data and genome assembly resources deposited in public repositories.

Today, choosing whether to wear a hat is a personal decision. But about 400 years ago, strict social rules governed “hatiquette,” and removing a hat was expected as a sign of respect. According to a study published in The Historical Journal (Cambridge University Press), refusing to doff (“do off”) a hat could serve as a deliberate and highly visible act of protest.

One striking example comes from 1630, when an outspoken oatmeal maker was brought before England’s highest church court. After being told that some of the judges were also privy councillors, he briefly removed his hat in acknowledgment. But he quickly put it back on, declaring, ‘as you are privy councillors … I put off my hat; but as ye [bishops] are rags of the Beast, lo! — I put it on again’.

This kind of behavior became more common during the turbulent reign of Charles I. As political tensions grew, refusing to remove a hat evolved into a widely recognized gesture of defiance, especially during the English Civil War.

From Social Custom to Political Protest

Historian Bernard Capp, Emeritus Professor at the University of Warwick, explains that hat etiquette once reinforced social hierarchy. “Long before the civil wars, men and boys were expected to doff their hats, indoors or out, whenever they met a superior,” he says. “That was about respecting your place in society, but in the revolutionary 1640s and 1650s, hat-honor became a real gesture of defiance in the political sphere.”

Prominent figures used this act to make powerful statements. In 1646, the radical Leveller John Lilburne, imprisoned in Newgate, prepared to appear before the House of Lords by resolving to ‘come in with my hat upon my head, and to stop my eares when they read my Charge, in detestation’. A few years later, in 1649, Digger leaders William Everard and Gerrard Winstanley refused to remove their hats when brought before General Fairfax, insisting he was ‘but their fellow Creature’. Others, including Fifth Monarchist Wentworth Day, followed suit in later prosecutions.

This gesture crossed political lines. After losing power, royalists also used it to signal resistance. Charles I himself kept his hat on during his trial in January 1649, rejecting the authority of the court. Similarly, the earl of Peterborough’s son refused both to remove his hat and to enter a plea when tried for treason in 1658.

At times, elites used hat etiquette in reverse. Some royalist leaders, including Lord Capel, removed their hats before execution as a calculated appeal to the crowd. As Capp explains, “This was a sort of populist political gesture, essentially inviting the moral support of the crowd.”

A Father’s Unusual Punishment

Not all hat-related conflicts played out in public arenas. Professor Capp highlights a revealing domestic story involving Thomas Ellwood and his father in 1659. In an effort to control his 19-year-old son, the father confiscated all of his hats.

Ellwood later recalled: ‘I was still under a kind of Confinement, unless I would have run about the Country bare-headed, like a Mad-Man’. Because going without a hat carried social stigma, he effectively remained confined at home. His repeated association with the Quakers, who were known for refusing to remove their hats, had already caused family disputes and even physical punishment.

Ellwood’s memoir, published in 1714, shows how deeply ingrained these norms were. As Capp notes, “It makes no sense to us today. But in 1659, father and son just saw this as common sense. Thomas couldn’t leave the house without a hat — it would have brought too much shame on himself and his family.”

Why Hat-Doffing Declined

Some historians have suggested that the rise of handshaking replaced hat-doffing, but Capp disagrees. “The handshake evolved very slowly as a mode of greeting and had no bearing on hat-honor as a gesture of deference,” he says.

Instead, several factors likely contributed to the shift. Social manners gradually became less formal. Wigs also became more popular, reducing the importance of hats. In crowded cities, constantly removing one’s hat may have simply become impractical. As Capp puts it, “Conventions gradually change over generations and are usually multicausal.”

Hats as Protection and Social Necessity

Even after political tensions eased in the 18th century, hats remained highly valued. Court records from the Old Bailey reveal that people often prioritized their hats over money during robberies.

In 1718, William Seabrook was attacked by thieves on Finchley Common and lost about £15. When they took his hat, he pleaded for its return, and the robbers eventually tossed it back. According to the record, ‘they also took away his Hat, upon which he begg’d of them not to take away his Hat and make him go home bare-headed; then they threw down his Hat in the Road and left it’.

Capp suggests there may have been an informal understanding between robbers and victims. “There seems to have been an unwritten convention that if victims meekly surrendered their valuables, they deserved at least a small favor,” he says.

Health concerns also played a role. Many men wore wigs over shaved heads, making them more vulnerable to cold weather. Medical advice at the time stressed the importance of keeping the head warm, warning that going outside without a hat could lead to illness.

A 1733 case illustrates this clearly. After being robbed at gunpoint, Francis Peters handed over his valuables but protested when the thief ‘snatch’t off my Hat and Wig,’ arguing that ‘it was very unusual for Men of his Profession to take such Things, and that it being very cold it might indanger my Health’. The thief ignored him, though he later apologized when confronted in prison.

The Social Meaning of Being Bareheaded

In 18th-century England, appearing without a hat carried serious social consequences. It was often associated with extreme poverty or mental instability. As a result, people were deeply concerned about being seen bareheaded, especially in legal settings.

Capp notes, “Even in London’s seedy underworld, a hat felt essential.” When Thomas Ruby was tried for burglary in 1741, he ‘begged very hard’ to have his hat returned, explaining ‘for he had none to wear’.

The significance of hats went beyond practicality. As Capp concludes, “What you wear says something about how you see yourself and the world. And the hat is so eloquent because it’s so versatile — you can position it in so many ways, take it off, wave it around, and attach messages to it.”

Today, the same underground network that once fueled industry could help power a cleaner future. Through a partnership with the University of Victoria-led Accelerating Community Energy Transformation (ACET) initiative, Cumberland is exploring how its abandoned mine shafts and tunnels can support a new source of energy.

At the center of this effort is the Cumberland District Energy project. Researchers are studying how water trapped in the old mine system can be used to generate geothermal energy capable of heating and cooling buildings throughout the town.

Mayor Vickey Brown believes the project could help reshape Cumberland’s identity. Already known for outdoor recreation like mountain biking and hiking, the village could also become a model for clean energy innovation.

“This is a way to highlight the history of Cumberland and bring it into a sustainable-future, clean-energy ethos,” she says. “It’s something that old Cumberland can be proud of, because we’re using the waste of that old resource to transition to cleaner energy.”

How Underground Mine Water Could Heat and Cool Buildings

The concept relies on a simple but powerful idea. Water sitting deep inside abandoned mines tends to stay cooler than the air during summer and warmer during winter. According to ACET project lead Zachary Gould, this steady temperature difference can be harnessed using heat pumps.

These systems would draw on the underground water to regulate indoor temperatures, offering heating in colder months and cooling during warmer periods. The approach could deliver energy at relatively low cost while producing very little carbon.

“[The Cumberland District Energy project] is technically a very large ground-source heat exchanger,” explains Emily Smejkal of the Cascade Institute, who focuses on geothermal energy.

Because the tunnels extend beneath much of the town, this system could potentially serve a wide area. Mapping efforts by geologists have already revealed the scale of the underground network, helping researchers estimate how much energy it might provide.

Initial plans are focusing on key areas, including a proposed civic redevelopment site with a community center, municipal buildings, and affordable housing, as well as an industrial zone near Comox Lake.

“It’s been a big motivation to think about this energy system in the context of how we can reduce the costs of critical infrastructure and provide critical amenities for community members,” says Gould.

“But it’s not just an energy system,” he adds. “It’s an opportunity to look at resource extraction in a new way in a village that was built on extractive principles. This project could turn those ruins of extraction, so to speak, into an opportunity and a shared community asset.”

A Coal Mining Legacy That Shaped the Community

Coal mining defined Cumberland for generations. Beginning in 1888 and continuing until the late 1960s, about 16 million tonnes of coal were extracted from the Comox Valley, according to historian Dawn Copeman. Ships departing from Union Bay carried the coal to markets as far as Japan, helping fuel global industries.

The resource powered steamships, heated homes, and supported metal production through coking processes. But the industry also came with significant costs. Working conditions were dangerous, many miners were injured or killed, and the burning of coal contributed to climate change.

Repurposing these abandoned mines for clean energy does not erase that history, Copeman says. Instead, it offers a way to use it constructively.

She notes that a proposed coal mining project near Union Bay in 2011 faced strong opposition. In contrast, the current geothermal effort has been received more positively.

“Being able to use something that’s already there for heating, I think it’s positive,” she says.

From Geological Curiosity to Clean Energy Plan

The idea for using the mines as a geothermal resource began with local geologists discussing methane issues associated with old mining sites. Those conversations gradually expanded into exploring whether the same underground spaces could support other energy uses.

Cory MacNeill, a geologist from Cumberland, explains that while deep geothermal drilling was not practical in the area, the existing mine water offered a more accessible solution. It could help offset seasonal temperature swings without the need for extreme depths.

Similar projects already exist in places like Nanaimo, British Columbia, and Springhill, Nova Scotia, showing that the concept can work in former mining communities.

“It’s about reimagining these old resources and relics of industry,” MacNeill says. “It’s really powerful to look at all of this mining and look at ways that we can benefit from it from a more environmental standpoint.”

Turning Old Infrastructure Into a Sustainable Future

Mayor Brown connected the idea to real-world action after attending an ACET webinar aimed at municipalities.

“They said, ‘We’re looking for projects to work with municipalities.’ And I thought, ‘I have a project.'”

Two blocks of municipal land, including the village office, council chambers, public works facilities, and a recreation center, sit directly above a former mine site. Brown saw an opportunity to test whether geothermal energy could support redevelopment plans in that area.

As a small community of about 4,800 people, Cumberland does not have the internal engineering resources to fully evaluate such a project. ACET’s expertise has been essential in assessing feasibility and building a business case.

“We need their academic expertise and their capacity to help us do those business cases, and also do the [geothermal] exploration side of it,” Brown says.

If an initial pilot proves successful, the potential extends far beyond the first site. The network of tunnels beneath the town could support broader energy use.

Lower-cost heating and cooling could also make the area more attractive to businesses that rely heavily on temperature control, such as greenhouses and food processing facilities. That, in turn, could bring jobs, strengthen the tax base, and improve quality of life.

“We haven’t always worked very well with natural systems,” Brown says. “But I think this is a model of using the tools and resources you have in place to look after the needs of your community. And I think that’s far more resilient than the way we’ve done it in the past.”

The team’s solution, called “Mollifier Layers,” improves how AI handles these problems by refining the math behind the process instead of simply increasing computing power. The approach could have wide-ranging applications, from decoding genetic activity to improving weather predictions.

“Solving an inverse problem is like looking at ripples in a pond and working backward to figure out where the pebble fell,” says Vivek Shenoy, Eduardo D. Glandt President’s Distinguished Professor in Materials Science and Engineering (MSE) and senior author of a study published in Transactions on Machine Learning Research (TMLR), which will be presented at the Conference on Neural Information Processing Systems (NeurIPS 2026). “You can see the effects clearly, but the real challenge is inferring the hidden cause.”

Instead of relying on more powerful hardware, the researchers focused on improving the underlying mathematics. “Modern AI often advances by scaling up computation,” says Vinayak Vinayak, a doctoral candidate in MSE and co-first author of the study. “But some scientific challenges require better mathematics, not just more compute.”

Why Inverse PDEs Matter in Science

Differential equations are the backbone of scientific modeling. They describe how systems change over time, whether it is population growth, heat flow, or chemical reactions.

Partial differential equations extend this idea further by capturing how systems evolve across both space and time. Scientists use them to study everything from weather patterns to how heat moves through materials and even how DNA is organized inside cells.

Inverse PDEs go a step further. Rather than predicting outcomes based on known rules, they allow scientists to start with observed data and work backward to uncover the hidden forces driving those observations.

“For years, we’ve used these equations to study how chromatin, which is the folded state of DNA inside the nucleus, organizes itself inside living cells,” says Shenoy. “But we kept running into the same problem: We could see the structures and model their formation, but we could not reliably infer the epigenetic processes driving this system, namely the chemical changes that help control which genes are active. The more we tried to optimize the existing approach, the clearer it became that the mathematics itself needed to change.”

Rethinking How AI Handles Complex Math

A key concept behind these equations is differentiation, which measures how something changes. Simple derivatives show how fast something increases or decreases, while higher-order derivatives capture more intricate patterns.

Traditionally, AI systems compute these derivatives using a process called recursive automatic differentiation. This method repeatedly calculates changes as data moves through a neural network, the foundation of modern AI.

However, this approach struggles when dealing with complex systems and noisy data. It can become unstable and demand enormous computing resources.

The researchers compare it to repeatedly zooming in on a rough, jagged line. Each step amplifies imperfections, making the final result less reliable. To overcome this, the team realized they needed a way to smooth the data before analyzing it.

Mollifier Layers Offer a Smarter Solution

The answer came from a concept introduced in the 1940s by mathematician Kurt Otto Friedrichs, who described “mollifiers,” tools designed to smooth irregular or noisy functions.

By adapting this idea, the researchers created a “mollifier layer” within AI models. This layer smooths the input data before calculating changes, avoiding the instability caused by traditional methods.

“We initially assumed the issue had to do with neural network’s architecture,” says Ananyae Kumar Bhartari, a graduate of Penn Engineering’s Scientific Computing master’s program and the paper’s other co-first author. “But, after carefully adjusting the network, we eventually realized the bottleneck was recursive automatic differentiation itself.”

The results were striking. The new method reduced noise and significantly lowered the computational cost required to solve these equations.

Implementing a “mollifier layer,” which smoothed the signal before measuring it, radically diminished both the noisiness and the power consumption scaling. “That let us solve these equations more reliably, without the same computational burden,” says Bhartari.

Unlocking the Secrets of DNA Organization

One of the most promising applications of this approach lies in understanding chromatin, the complex structure of DNA and proteins inside cells.

These structures operate at an incredibly small scale, but they play a major role in determining how genes are turned on or off.

“These domains are just 100 nanometers in size,” says Shenoy, “but because accessibility determines gene expression, and gene expression governs cell identity, function, aging and disease, these domains play a critical role in biology and health.”

By estimating the rates of epigenetic reactions, which control gene activity, the new AI method could help scientists move beyond simply observing chromatin to predicting how it changes over time.

“If we can track how these reaction rates evolve during aging, cancer or development,” adds Vinayak, “this creates the potential for new therapies: If reaction rates control chromatin organization and cell fate, then altering those rates could redirect cells to desired states.”

Beyond Biology: Wide-Ranging Scientific Impact

The potential uses of mollifier layers extend far beyond genetics. Many areas of science, including materials research and fluid dynamics, involve complex equations and noisy data.

This new framework could provide a more stable and efficient way to uncover hidden parameters across a wide variety of systems.

The researchers see this as a step toward a larger goal: turning observations into deeper understanding.

“Ultimately, the goal is to move from observing complex patterns to quantitatively uncovering the rules that generate them,” says Shenoy. “If you understand the rules that govern a system, you now have the possibility of changing it.”

This study was conducted at the University of Pennsylvania School of Engineering and Applied Science and supported by National Cancer Institute (NCI) Award U54CA261694 (V.B.S.); National Science Foundation (NSF) Center for Engineering Mechanobiology (CEMB) Grant CMMI -154857 (V.B.S.); NSF Grant DMS -2347834 (V.B.S.); National Institute of Biomedical Imaging and Bioengineering (NIBIB) Awards R01EB017753 (V.B.S) and R01EB030876 (V.B.S.) and National Institute of General Medical Sciences (NIGMS) Award R01GM155943 (V.B.S).