Category: English

Source: The Conversation – USA (2) – By Robert I. Harris, Assistant Professor of Economics, Georgia Institute of Technology

With gasoline prices still high – averaging over US$4.50 a gallon in mid-May 2026 – President Donald Trump said he wanted Congress to suspend the federal gas tax, which is 18.4 cents a gallon for gasoline and 24.3 cents a gallon for diesel. A bill has been introduced in the Senate, and one is expected to follow in the House, according to Politico, but their fate is unclear.

States also charge their own taxes, ranging from 70.9 cents a gallon for gas in California to 8.95 cents in Alaska. Indiana, Georgia and Utah have suspended their gas taxes for at least some of 2026, and other states are considering similar measures.

As an energy economist, I have seen how suspending those taxes does reduce prices, but not as much as politicians – or drivers – might hope. Research on past gas tax holidays has found that consumers get about 79% of the reduction in gas taxes. That means oil companies and fuel retailers keep about one-fifth of the tax cut for themselves rather than passing that savings to the public.

Suspending the federal gas tax, which would require Congress to pass a law, wouldn’t help consumers much anyway. Even if oil companies passed on the whole savings to consumers, national average gas and diesel prices would drop only about 4%. The percentage reduction in high-cost states such as California would be even smaller.

Gas taxes are just one part of what drives gas prices. Overall, the price of a retail gallon of gas is the sum of four things: the cost of crude oil, refining, distribution and marketing, and taxes.

In nationwide figures from January 2026, crude oil accounted for about 51% of the pump price, refining roughly 20%, distribution and marketing about 11% and taxes about 18%. That mix shifts with conditions: When crude oil prices spike, that can drive more than 60% of the price; when the price drops, taxes and logistics are larger shares of the cost.

Crude oil is the biggest ingredient

Because the price of crude oil is the largest element, most of the price at the pump is derived from the global oil market.

Usually, big swings in crude prices come mainly from shifts in global demand and expectations – not from supply disruptions, according to widely cited research in 2009 by the economist Lutz Kilian.

But what is happening in early 2026 with the war in Iran is one of the exceptions: a classic supply shock. Severe disruptions to shipping through the Strait of Hormuz and attacks on Middle East oil infrastructure have taken millions of barrels a day off the global market.

Most drivers generally can’t quickly reduce how much they drive or how much gas they use when prices rise, so gasoline demand doesn’t change much in the short run. That means a jump in crude costs tends to result in people paying more rather than driving less.

Refining, regulations and the California puzzle

Refining turns crude into gasoline at industrial scale. The U.S. doesn’t have a single gasoline market, though. Roughly a quarter of U.S. gasoline is a cleaner-burning blend of petroleum-derived chemicals called “reformulated gasoline,” which is required in urban areas across 17 states and the District of Columbia to reduce smog.

California uses an even stricter formulation that few out-of-state refineries make. California is also geographically isolated: No pipelines bring gasoline in from other U.S. refining regions.

California’s gasoline prices have long run above the national average, explained in part by higher state taxes and stricter environmental rules. But since a refinery fire in Torrance, California, in 2015 reduced production capacity, the state’s prices have been about 20 to 30 cents a gallon higher than what those factors would indicate.

Energy economist and University of California, Berkeley, professor Severin Borenstein has called this the “mystery gasoline surcharge” and attributes it to the fact that there isn’t as much competition between refineries or gas stations in California as in other states. California’s own Division of Petroleum Market Oversight says the surcharge cost the state’s drivers about $59 billion from 2015 to 2024. It’s not exactly clear who is getting that money, but it could be gas stations themselves or refineries, through complex contracts with gas stations.

Getting the gas into your car

The distribution and marketing category covers the costs of everything involved in getting the gasoline from the refinery gate to your tank.

Gasoline moves by pipeline, ship, rail and truck to wholesale terminals, and then by local delivery truck to service stations.

At the retailer’s end, the key factors are station rent and labor, the cost to buy gasoline in bulk to be able to sell it, credit card fees of as much as 6 to 10 cents a gallon at current prices, and franchise fees paid to the national brand, such as Sunoco or ExxonMobil, for permission to put their branding on the gas station.

Most gas station operators net only a few cents per gallon on fuel itself – which is why many gas stations are really convenience stores with pumps out front. Borenstein and some of his collaborators have also documented that retail gas prices rise quickly when wholesale costs climb but fall slowly when wholesale costs drop.

The question of gas tax holidays

Gas tax holidays reduce funding for what the taxes are designed to pay for, typically roads and bridges. That pushes road and bridge upkeep costs onto future drivers and general taxpayers.

There is an additional problem, too: Taxes on gasoline are supposed to charge drivers for some of the costs their driving imposes on everyone else – carbon emissions, local air pollution, congestion and crashes. But Borenstein has found that U.S. fuel tax levels are already far below the true cost to society. Removing the tax on drivers effectively raises the costs for everyone else.

The Jones Act: A small number that adds up

The 1920 Jones Act is a federal law that requires cargo moving between U.S. ports to travel on vessels built and registered in the U.S., owned by U.S. citizens, and crewed primarily by U.S. citizens and permanent residents. Of the world’s 7,500 oil tankers, only 54 meet this requirement. Only 43 of these can transport refined fuels such as gasoline.

So, despite significant refining capacity on the Gulf Coast, some U.S. gasoline is exported overseas even as the Northeast imports fuel, in part reflecting the relatively high cost of moving fuel between U.S. ports.

Economists Ryan Kellogg and Rich Sweeney estimate that the law raises East Coast gasoline prices by about a penny and a half per gallon on average, costing drivers roughly $770 million a year. In light of the war’s effect on gas prices, the Trump administration has temporarily suspended the Jones Act requirements – an action more commonly taken when hurricanes knock out Gulf Coast refineries and pipeline networks.

What moves the number

The result of all these factors is that the price that drivers see at the pump mostly reflects the global price of crude, plus a stack of domestic costs, only some of which are inefficient.

Tax holidays give a partial, short-lived rebate. Jones Act waivers trim pennies, though permanent repeal may cause more fundamental changes, such as reduced rail and truck transport of all goods, which could lower costs, emissions and infrastructure damage associated with cargo transportation. Harmonizing fuel blends across states and seasons may lower prices somewhat, but likely at the expense of increased emissions.

Ultimately, the best protection against oil price shocks is a more efficient gas-burning vehicle, or one that doesn’t burn gasoline at all. In the meantime, the best I can offer as an economist is clarity about what that $4.50 actually buys.

This article includes material previously published on May 1, 2026.

Robert I. Harris does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

– ref. Suspending federal gas tax wouldn’t save drivers as much as they might hope – here’s what goes into the price of a gallon of gas – https://theconversation.com/suspending-federal-gas-tax-wouldnt-save-drivers-as-much-as-they-might-hope-heres-what-goes-into-the-price-of-a-gallon-of-gas-282702

Source: The Conversation – USA (2) – By Sara M. Melo Merino, Postdoctoral Fellow in Marine Science, Smithsonian Institution

Living by the sea in the tropics means being exposed to some of nature’s most powerful forces. Hurricanes can bring storm surges, flooding and destructive waves that threaten homes, infrastructure and livelihoods.

For many communities, coral reefs are a natural first line of defense against these storms. The reefs’ rugged structures break the incoming waves, reducing the waves’ energy by as much as 97%. Globally, reefs prevent about US$4 billion a year in storm damage. Without them, studies suggest, the damage would double.

Yet, these vital ecosystems are under increasing pressure. Rising ocean temperatures, pollution and coastal development are driving the loss of reef-building corals – the species that create the physical structure of coral reefs and underpin their ability to protect coastlines and provide habitat for marine life.

Protecting key coral reefs from these human-caused stresses could help the reefs continue to reduce future storm damage.

But which reefs should be prioritized?

We study coral reefs and marine environments. In a new research paper, we examined the likely impact that future warming will have on reefs across the Caribbean over the coming decades, including which reefs are most likely to persist under rising temperatures. Then we looked at which reefs were likely providing the greatest protective benefits for coastlines based on their functional characteristics.

The results show that about half of all the reefs with the greatest potential to continue to protect coastlines as the oceans warm are currently unprotected from human harms.

The Caribbean’s hidden coastal defenders

The value of coral reefs is evident along the Mexican Caribbean coast, where tourism is a major economic driver and the main source of income for local communities. The tourism industry there can generate up to $15 billion in a single year. Much of that value depends directly or indirectly on healthy coral reefs.

Losing the reefs would not only affect fish that rely on coral structures for habitat, and the livelihoods of people who depend on them, it would also cost millions of dollars in increased storm damage. An estimated 105,800 people, along with buildings and other infrastructure worth $858 million, are located in coastal areas protected by reefs in the Mexican Caribbean alone.

The role of reefs becomes especially clear during extreme events.

In 2005, Hurricane Wilma, a Category 5 storm, struck the coast of Quintana Roo in the Yucatán Peninsula, Mexico. Near the small town of Puerto Morelos, the coral reefs broke the waves, helping lower the wave height that had reached nearly 36 feet (11 meters) offshore to less than 6 feet (2 meters) near the coast. The reefs near Puerto Morelos are part of a protected national park where public access to the reefs is heavily regulated.

Not all reefs protect the coast equally

However, not all reefs provide the same level of protection for coastlines. Our research shows that the differences depend on the reef engineers – the coral species that built the reef.

Reefs dominated by large, complex and rigid corals, such as thickets of elkhorn corals, create rough, elevated structures that can break and slow incoming waves, providing the greatest protection. In contrast, reefs made up of smaller or flatter species offer less resistance.

Knowing which reefs deliver the greatest structural protection can help countries and communities prioritize protecting them from human pressures, such as pollution and ship traffic.

We found that of the highest-priority reefs – based both on functionality and how well they are expected to survive rising water temperatures by midcentury – only 54% were protected. In the Caribbean’s western, southwestern and Florida ecoregions, priority reefs were most likely to be in formal marine protected areas, while the Greater Antilles and Bahamas had several unprotected reefs.

The Bahamas, Puerto Rico, Turks and Caicos, and Cuba have many high-value reefs that remain unprotected, meaning there are opportunities to increase protection on these important reefs. The reefs that we identified as important for conservation based on their physical functionality have also been reported to support high levels of biological diversity.

While a large percentage of coral reefs off Belize, Honduras and Puerto Rico are protected, we found that several reefs with the greatest potential for protecting coastlines were not within marine protected areas.

Why does this matter in a warming world?

Ocean warming is driving more severe and frequent coral bleaching events. When water temperatures rise too high, corals expel zooxanthellae – the algae that live in their tissues, provide them with energy and give corals their color. If heat stress is too intense or prolonged, many corals won’t recover.

As corals die, the reef structures they built break down and lose complexity over time. The coastal defenses they provide disappear.

At the same time, high-intensity hurricanes are becoming more frequent.

This creates a dangerous combination: stronger storms hitting coastlines that are less protected.

Protecting coral reefs is essential, not only for the sake of marine biodiversity, but for safeguarding coastal communities, their economies and the millions of people who live there.

Sara M. Melo Merino received a scholarship from Secretaría de Ciencia, Humanidades, Tecnología e Innovación
(Secihti No. 246257).

Lorenzo Alvarez-Filip and Steven Canty do not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and have disclosed no relevant affiliations beyond their academic appointment.

– ref. Many of the Caribbean’s most important reefs are going unprotected – https://theconversation.com/many-of-the-caribbeans-most-important-reefs-are-going-unprotected-281490

Source: The Conversation – USA – By Ji Y. Son, Professor of Psychology, California State University, Los Angeles

The nonprofit ARC Prize Foundation on May 1, 2026, released the results of a new benchmark: a test of an AI system’s ability to solve a game. The results were striking – humans scored 100%, while the most advanced AI systems scored under 1%.

At first glance, this may be surprising to users of AI who are impressed by its polished essays, codebases and multistep projects generated in seconds. How can these brilliant AI systems struggle with these simple Tetris-shape puzzles?

That confusion points to a risk: AI is becoming integrated into everyday life faster than people can make sense of it.

We are cognitive psychologists who study how to teach difficult concepts. To recognize the limits and risks of today’s AI agent systems, it’s important for people to grasp that the systems can both accomplish superhuman feats and make mistakes few humans would. To that end, we propose a new way to think about AIs: as button-pushing explorers.

Mental models for AI

We teach college students, a group rapidly incorporating AI tools into their daily routines. That gives us regular opportunities to ask what they think is going on with AI. The answers vary widely. One student said that someone at OpenAI or Anthropic is reading and approving every response the system generates. Another, more succinctly, said, “It’s magic.”

These responses illustrate two tempting ways of making sense of AI. At one extreme, AI is treated as an inscrutable black box – a powerful but ultimately mysterious force. At another, people explain it using the same assumptions they use to understand other humans: that its outputs reflect reasoning or judgment.

The worry is that these misinterpretations don’t go away as users gain more experience interacting with AI, and they might get reinforced. When AI performs well, its output can feel like evidence of understanding or confirmation that it really is something like magic. That apparent success makes it harder to question what the system is actually doing. Biases can seem logical or inevitable; harmful behavior can look like a deliberate choice or even fate, as if it could not have gone any other way.

Saying that AI models are shaped by patterns in data, training processes and system design is true, but that’s too abstract to tell people when to trust the systems’ outputs or when they might fail. To help people avoid misplaced trust in AI, AI literacy efforts will need to include some mechanistic understanding of what produces their behavior – explanations that are perhaps not perfectly accurate but useful. Statistician George Box once wrote, “All models are wrong, but some are useful.”

Researchers have come up with several mental models for large language models. One is “stochastic parrot,” which shows that the models use statistical methods – stochastic refers to probabilities – to mimic responses with no understanding of meaning. Another is “bag of words,” which emphasizes that the models are collections of words – for example, all English words found on the internet – with a mechanism for giving you the best set of words based on your prompt.

These ways of thinking about large language models were never meant to be complete accounts of the systems. But the metaphors serve an important cognitive purpose: They push back against the idea that fluent language is necessarily caused by humanlike understanding.

But as the AI systems people use are increasingly powerful agents capable of stringing together actions on their own, it’s important for people to have a different kind of mental model: one that explains how they act. One place to find such a model is in earlier research on AI systems that learned to play Atari 2600 games. These systems didn’t understand the games the way humans do, but they still managed to rack up a lot of points.

The simple loop: Act, observe, adjust

Imagine a neural network, a relatively simple kind of AI model, placed into a video game it has never seen before. It does not “understand” the game like a human would. It has no idea whether it’s shooting space invaders or navigating an ancient pyramid. It doesn’t know the goals or rules.

Instead, it learns to play through a simple loop: Take an action – move left, jump, shoot – observe what changes, and then adjust. If an action leads to a good outcome, such as gaining points, it adjusts to become more likely to take similar actions in similar situations. If it leads to a bad outcome, such as losing a life, it adjusts in the opposite direction.

Even this simple mechanism can produce surprisingly capable behavior. Over time, by repeating this loop, the neural networks learned to play a wide range of Atari games – but not all games.

There is one game that famously stumped these early neural networks: Montezuma’s Revenge. To make progress, a player must carry out a long sequence of actions – climbing ladders, avoiding obstacles, retrieving keys – before receiving any reward at all. Unlike simpler games, most actions offer very little immediate feedback. The game required something like goal-directed, long-term planning.

Early neural networks would try a few actions, receive no reward and fail to make further progress through Montezuma’s underground pyramid. From the system’s perspective, all actions looked equally useless. But researchers made a breakthrough by changing the feedback signal. Instead of rewarding only success, they also rewarded the system for doing something new. The rewards were for visiting parts of the game it had not seen before or trying actions it had not previously taken. This tweak encouraged exploration.

With that change, performance improved dramatically. The neural network began navigating obstacles, taking multiple steps toward goals and adapting when things went wrong. From the outside, this kind of behavior can look like planning or problem-solving. But what looks like planning was not caused by sophisticated planning abilities. The underlying mechanism is still the same simple loop: act, observe, adjust.

This kind of system isn’t a stochastic parrot or a bag of words. It’s closer to a button-pushing explorer: something that doesn’t understand the world in a human sense but moves forward by pushing buttons, seeing what happens and adjusting what it does next.

From video games to modern AI agents

Today’s AI systems can do far more than play games like Montezuma’s Revenge. They can coordinate tools, write and run code, and carry out multistep projects. The range of possible actions is much larger, and the environments in which they operate are increasingly complex.

But these agents are still fundamentally button-pushing explorers. The behavior can be sophisticated, but the process that produces it is not. Humans can often infer how a new environment works after just a few observations. Systems that rely on these feedback loops cannot. They need to try many actions and see what happens before they can make progress.

This helps explain both the strengths of these AI systems and some of their most concerning failures. What these agents learn depends on what is being rewarded. And in real-world systems, those reward signals are often imperfect.

AI systems that conduct negotiations aim to maximize their client’s interests, sometimes with deceptive tactics. Rental pricing software used by landlords ends up price fixing. Marketing tools generate persuasive but misleading reviews.

These systems aren’t trying to be evil or greedy. They are adjusting to the signals they are given. From the button-pushing explorer perspective, these failures are downright predictable.

Effective AI literacy means holding two ideas at once: These systems can do surprisingly complex things, and they are not doing them the way humans do. If AI is seen as humanlike or magical, its outputs feel authoritative. But if it is understood, even imperfectly, as a button-pushing explorer shaped by feedback, people are likely to ask better questions: Why is it doing this? What shaped this behavior? What might it be missing?

That’s the difference between being impressed by AI and being able to reason about it.

Ji Y. Son receives research funding from the Gates Foundation and Valhalla Foundation.

Alice Xu does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

– ref. Button-pushing explorers: How to grasp that AI agents can do amazing things while knowing nothing – https://theconversation.com/button-pushing-explorers-how-to-grasp-that-ai-agents-can-do-amazing-things-while-knowing-nothing-281498

Source: The Conversation – USA – By Christian Waugh, Professor of Psychology, Wake Forest University

Picture Gigi, having a chat with her boss, when the meeting takes a sharp turn. Gigi’s boss tells her that her work has been lacking recently and that maybe she needs to stay late a couple of evenings to make it up. Surprised by her boss’s remarks, she feels the rumblings of anxiety rising in her mind and body. Psychology research suggests that Gigi feels anxious because she interpreted her boss’s remarks as something threatening that perhaps she can’t handle.

Just as Gigi starts frantically looking online for new jobs, she spies the “employee of the month” plaque on her desk from last year. She thinks to herself that maybe she can get back to her old form. She has changed her initial view of the situation (need to run away from a threat) to a new one (let’s rise to the challenge), causing her anxiety to subside. Psychologists call this process reappraisal.

Studies show that reappraising emotional situations is a powerful way to change how you feel. When you find the silver linings in bad situations or give others and yourself the benefit of the doubt, it can help you feel better.

I’m a psychology researcher who’s interested in how people change their emotions. Gigi may feel a little less anxious in the moment, but does she truly believe that she can make up the work on time and regain her former glory? My colleagues and I set out to investigate whether it’s possible to start the process of reappraisal without going all the way through with it. Are people getting the full benefit from trying to think differently about their emotions?

Reappraisal has multiple steps

When my colleague Kateri McRae and I first started thinking about what it means to fully reappraise emotional experiences, we were struck by something we saw in the emotion regulation research. Almost all of the studies treated reappraisal as a one-step process. Researchers would ask participants to “reappraise this to make yourself feel better” and then measure the effects.

However, theories about how people regulate their emotions suggest that, like any effortful psychological process, reappraisal involves multiple steps.

When you want to change how you’re feeling, you first generate a reappraisal. You bend and stretch your mind to come up with some alternative way to look at the situation. For Gigi, seeing the employee of the month plaque helped. She could have also thought of her boss’s previous compliments or how it felt to get projects done early.

After you generate a reappraisal, it might seem like you’re done, but you’re not. That alternative interpretation is fragile and must compete with your original take that’s driving your emotion. Somehow you need to strengthen that reappraisal so it can stick.

We call this implementation – when you focus and elaborate on that reappraisal to really change your mind about the situation. For Gigi, she may continue to think about all the ways that she can be a great employee so that it lodges firmly in her mind and makes her anxiety truly disappear.

We tested this idea in a study. We showed 89 undergraduate participants images of negative situations and asked them to first just generate a reappraisal of the image that could help them feel better about it. For example, they might see a picture of a frail man in a hospital bed and tell themselves that the man is getting good treatment and will be better soon. Then, we showed them the image again and asked them to focus and elaborate in their mind on their reappraisal.

Participants felt a little better after generating a reappraisal, but they felt much better after implementing it by focusing and fleshing out the details. In a follow-up study, we showed that these emotional boosts persisted when viewing the images later.

Choosing to commit to feeling better

So we experimentally showed that people reappraise their feelings in two steps. So what? That’s probably what everyone does naturally, anyway, right?

This was the next question we sought to answer. We conducted a study with 52 undergraduate participants like the earlier one, but with a twist. This time, after participants generated a reappraisal, we gave them a choice to continue the reappraisal process by implementing it or to stop the process by distracting themselves.

Participants chose to continue reappraising their emotions only about half the time. Even though reappraisal made participants feel better about the emotional images, there were still many times when they stopped the process prematurely and did not enjoy its full benefits.

In real life

These studies showing the benefits of fully following through on emotional reappraisals are lab experiments, but they have implications for how people try to help themselves feel better in real life.

First, it’s hard to intentionally change how you think about something, and people tend to dislike continuing to do hard things. Indeed, in our choice study, people opted to give up on reappraising when they weren’t feeling its benefits early on. Knowing this human tendency might give you the best chance of continuing reappraisal even when it doesn’t feel like it’s working or is hard.

Second, people often get reappraisals from others, and it’s tempting to think that hearing a new perspective is all you need. Indeed, we have unpublished data that shows that participants feel pretty good when receiving a reappraisal from someone else about their own situation. But other people cannot change your mind for you. You must do that yourself if you want to truly feel better.

Next time you’re in an unpleasant situation like Gigi’s, don’t just cursorily think that you can rise to the challenge. Really think through the situation and let your new perspective become your only one.

Christian Waugh receives funding from National Institutes of Health.

– ref. You can change your emotions – but it’s a 2-step process that takes some effort – https://theconversation.com/you-can-change-your-emotions-but-its-a-2-step-process-that-takes-some-effort-280000

Source: The Conversation – USA – By Marc Zimmer, Professor of Chemistry, Connecticut College

Fingerprinting transformed police investigations by making it possible to place a suspect at a crime scene with physical evidence. Similarly, genome sequencing has changed how disease detectives study outbreaks by allowing them to read a pathogen’s genes as a biological record of where it came from and how it spread.

One way to think about sequencing is to imagine a virus or bacteria’s genome as a recipe book. Each gene is a recipe for making a protein. When scientists sequence a pathogen, they read the order of the genetic letters in those recipes.

Over time, small changes appear in the recipes as the pathogen mutates. By comparing those changes in samples collected from different places and times, researchers can determine which infections are related and estimate when and where the pathogen entered a population.

Scientists have used sequencing in this way to track outbreaks of COVID-19, Ebola, mpox and foodborne illnesses. This information helps public health investigators connect cases that might otherwise seem unrelated.

Still, genomic sequencing has limits. It can show that different pathogen strains are related, but it cannot fully explain why an outbreak began in one place, why it spread in a particular direction, or how human behavior shaped its course. Answering those questions requires combining genomic data with historical records, archaeological artifacts, trade records and epidemiological investigations.

I am a chemist and the author of “Diseases Without Borders: Plagues, Pandemics, and Beyond,” a book for young adults on infectious disease and the ways it has shaped human history. In my research, I’ve found that while the genome can help researchers trace the evolutionary trail of a pathogen, other fields are needed to explain the environmental conditions that allowed this trail to become an outbreak.

Ancient DNA tells only part of the story

Advances in DNA sequencing and extraction over the past decade have made it possible to recover fragments of ancient DNA from bones and teeth. Researchers can use these genomes to study a metaphorical molecular fossil record of microbial evolution.

The Black Death, one of the deadliest pandemics in history, shows both the power and the limits of sequencing.

The infectious disease behind the Black Death, plague, is caused by the bacterium Yersinia pestis. DNA recovered from the teeth of people buried more than 5,000 years ago in what is now Sweden revealed the existence of an ancestral form of Y. pestis that had not yet adapted to fleas.

About 2,000 years later, the bacterium made an important evolutionary shift: It gained the ability to survive in fleas and pass back and forth between humans, rats and other mammals via flea bites. That change made the pathogen far more dangerous and helped pave the way for three great plague pandemics that followed: the Justinianic Plague from the sixth to eighth century; the Black Death and later waves from the 1300s into the 1700s; and the third pandemic from the 19th to mid-20th centuries.

But how and why did plague emerge and move through human societies with such devastating results? Genetic results alone are not enough to answer these questions.

When gravestones become genetic evidence

Geneticists needed archaeologists, paleoclimatologists and historians to complete the picture of the plague pandemics. The genome revealed the lineage. Other disciplines supplied the historical and environmental context.

Two 14th-century graveyards in what is now Kyrgyzstan provide a striking example of how historical evidence can guide genetic investigations into the origins of a pandemic.

Historian Philip Slavin noticed archival records pointing to an unusual number of gravestones from 1338 and 1339. Some of those tombstones explicitly referred to a pestilence as the cause of death.

That clue led to the next stage of the investigation, where archaeologist Maria Spyrou and her team extracted and sequenced ancient DNA from the skeletal remains of seven people buried in the graves and found genetic traces of Yersinia pestis in three of the skeletons. These strains were close precursors of the strain linked to the Black Death and ancestors of several modern Y. pestis lineages.

This major finding was still not the whole story. It could explain where the Black Death pandemic began but not how the disease spread across Asia to Europe. Researchers found a potential answer to this question in artifacts buried at the site, which included pearls from the Indian Ocean, Mediterranean coral and foreign coins. Those objects suggested that the region was connected to long-distance trade networks.

Once the gravestones, skeletal remains, written records and trade goods were considered together, a richer picture emerged. Researchers could place the pathogen in a specific time and place and connect it to the networks of human movement that may have carried plague westward.

Sequencing provided the biological clue, revealing the pathogen’s identity and ancestry. History and archaeology turned that clue into a plausible narrative.

From ancient DNA to modern outbreaks

Genomic sequencing isn’t limited to examining outbreak cold cases. It is also researchers’ tool of choice for understanding new diseases.

When the first reported COVID-19 cases emerged in 2019, researchers quickly sequenced the virus and found that it was closely related to the virus that caused the 2002 SARS outbreak. This placed the new virus within a known family of pathogens.

Later genomic sequencing helped reveal the scale of a major superspreading event: the 2020 Biogen conference in Boston.

The biotech company Biogen brought together about 175 European and American executives at a moment when COVID-19 was only beginning to spread in the United States. In Europe, COVID-19 was also escalating, with northern Italy reporting locally transmitted clusters just days before the meeting. After the meeting, many Massachusetts cases were linked to the conference.

Researchers then analyzed thousands of viral genomes from patients in Massachusetts and elsewhere. One viral genome carried a unique genetic signature traceable to a European attendee at the conference. It matched viruses circulating in Europe but also had an additional mutation that appeared to have arisen during the attendee’s travel to Boston or early in the conference.

Because that altered sequence appeared only in people with direct or indirect ties to the meeting, it served as a genetic marker for the COVID-19 strain originating at the Biogen conference. By comparing it with other viral sequences in national databases, researchers tracked the strain associated with the conference to 29 states and several other countries.

Interviews and contact tracing alone couldn’t have made that chain of infection so clear because people may not know exactly when they were exposed, especially when infections spread through brief encounters, via travel or large meetings.

When genomes join the investigation

Genome sequencing has rewritten the history of disease by giving scientists a way to read a pathogen’s own record of change.

It can link ancient graves to later pandemics and trace a modern outbreak from one conference room to cases across a continent.

But the greatest strength of genome sequencing lies in partnership. Sequencing does not replace history, archaeology or public health investigation. It gives them a new molecular partner.

Combining work from these fields produces a fuller and more accurate account of how disease moves through the world.

Marc Zimmer does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond their academic appointment.

– ref. Genome sequencing is rewriting the history of disease outbreaks – but without social context, it can tell only part of the story – https://theconversation.com/genome-sequencing-is-rewriting-the-history-of-disease-outbreaks-but-without-social-context-it-can-tell-only-part-of-the-story-279963